From 09313cf3b50ae21962b6336ae4542335254e62c0 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 28 Mar 2018 13:35:13 -0600
Subject: [PATCH] shift files into doc/src
---
doc/Section_commands.txt | 1266 -----------------------------
doc/compute_displace_atom.txt | 137 ----
doc/create_atoms.txt | 335 --------
doc/delete_atoms.txt | 152 ----
doc/dump.txt | 664 ---------------
doc/dump_modify.txt | 1090 -------------------------
doc/src/Section_commands.txt | 1 +
doc/src/compute_displace_atom.txt | 78 +-
doc/src/create_atoms.txt | 14 +-
doc/src/delete_atoms.txt | 12 +-
doc/src/dump.txt | 7 +-
doc/src/dump_modify.txt | 118 ++-
doc/{ => src}/reset_ids.txt | 0
13 files changed, 195 insertions(+), 3679 deletions(-)
delete mode 100644 doc/Section_commands.txt
delete mode 100644 doc/compute_displace_atom.txt
delete mode 100644 doc/create_atoms.txt
delete mode 100644 doc/delete_atoms.txt
delete mode 100644 doc/dump.txt
delete mode 100644 doc/dump_modify.txt
rename doc/{ => src}/reset_ids.txt (100%)
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
deleted file mode 100644
index 0d7e069e06..0000000000
--- a/doc/Section_commands.txt
+++ /dev/null
@@ -1,1266 +0,0 @@
-"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 :h2
-
-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,
-the command is assumed to continue on the next line. The next line is
-concatenated to the previous line by removing the "&" character and
-line break. This allows long commands to be continued across two or
-more lines. See the discussion of triple quotes in (6) for how to
-continue a command across multiple line without using "&" characters.
-
-(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".
-
-How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable.html doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them. The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command. The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-
-As a special case, 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 single or double or triple quotes. A
-long single argument enclosed in single or double quotes can span
-multiple lines if the "&" character is used, as described above. When
-the lines are concatenated together (and the "&" characters and line
-breaks removed), the text will become a single line. If you want
-multiple lines of an argument to retain their line breaks, the text
-can be enclosed in triple quotes, in which case "&" characters are not
-needed. For example:
-
-print "Volume = $v"
-print 'Volume = $v'
-if "$\{steps\} > 1000" then quit
-variable a string "red green blue &
- purple orange cyan"
-print """
-System volume = $v
-System temperature = $t
-""" :pre
-
-In each case, the single, double, or triple quotes are removed when
-the single argument they enclose is stored internally.
-
-See the "dump modify format"_dump_modify.html, "print"_print.html,
-"if"_if.html, and "python"_python.html commands for examples.
-
-A "#" or "$" character that is between quotes will not be treated as a
-comment indicator in (2) or substituted for as a variable in (3).
-
-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 single, double, or
-triple 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 :h3,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 7"_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 core LAMMPS commands, grouped by category.
-The "next section"_#cmd_5 lists all commands alphabetically. The
-next section also includes (long) lists of style options for entries
-that appear in the following categories as a single command (fix,
-compute, pair, etc). Commands that are added by user packages are not
-included in the categories here, but they are in the next section.
-
-Initialization:
-
-"newton"_newton.html,
-"package"_package.html,
-"processors"_processors.html,
-"suffix"_suffix.html,
-"units"_units.html
-
-Setup simulation box:
-
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"create_box"_create_box.html,
-"dimension"_dimension.html,
-"lattice"_lattice.html,
-"region"_region.html
-
-Setup atoms:
-
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html,
-"group"_group.html,
-"mass"_mass.html,
-"molecule"_molecule.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"replicate"_replicate.html,
-"set"_set.html,
-"velocity"_velocity.html
-
-Force fields:
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.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:
-
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"info"_info.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"partition"_partition.html,
-"reset_timestep"_reset_timestep.html,
-"run_style"_run_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html
-
-Operations within timestepping (fixes) and diagnostics (computes):
-
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"uncompute"_uncompute.html,
-"unfix"_unfix.html
-
-Output:
-
-"dump image"_dump_image.html,
-"dump movie"_dump_image.html,
-"dump"_dump.html,
-"dump_modify"_dump_modify.html,
-"restart"_restart.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"undump"_undump.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html
-
-Actions:
-
-"minimize"_minimize.html,
-"neb"_neb.html,
-"prd"_prd.html,
-"rerun"_rerun.html,
-"run"_run.html,
-"tad"_tad.html,
-"temper"_temper.html
-
-Input script control:
-
-"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,
-"python"_python.html,
-"quit"_quit.html,
-"shell"_shell.html,
-"variable"_variable.html
-
-:line
-
-3.5 Individual commands :h3,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,
-"bond_write"_bond_write.html,
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"clear"_clear.html,
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.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_image.html,
-"echo"_echo.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"group"_group.html,
-"if"_if.html,
-"info"_info.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,
-"molecule"_molecule.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,
-"python"_python.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_ids"_reset_ids.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,
-"timer"_timer.html,
-"timestep"_timestep.html,
-"uncompute"_uncompute.html,
-"undump"_undump.html,
-"unfix"_unfix.html,
-"units"_units.html,
-"variable"_variable.html,
-"velocity"_velocity.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :tb(c=6,ea=c)
-
-These are additional commands in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"dump netcdf"_dump_netcdf.html,
-"dump netcdf/mpiio"_dump_netcdf.html,
-"dump vtk"_dump_vtk.html,
-"group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html,
-"temper/grem"_temper_grem.html,
-"temper/npt"_temper_npt.html :tb(c=3,ea=c)
-
-:line
-
-Fix styles :h3
-
-See the "fix"_fix.html command for one-line descriptions of each style
-or click on the style itself for a full description. Some of the
-styles have accelerated versions, which can be used if LAMMPS is built
-with the "appropriate accelerated package"_Section_accelerate.html.
-This is indicated by additional letters in parenthesis: g = GPU, i =
-USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-
-"adapt"_fix_adapt.html,
-"addforce"_fix_addforce.html,
-"append/atoms"_fix_append_atoms.html,
-"atom/swap"_fix_atom_swap.html,
-"aveforce"_fix_aveforce.html,
-"ave/atom"_fix_ave_atom.html,
-"ave/chunk"_fix_ave_chunk.html,
-"ave/correlate"_fix_ave_correlate.html,
-"ave/histo"_fix_ave_histo.html,
-"ave/histo/weight"_fix_ave_histo.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,
-"cmap"_fix_cmap.html,
-"controller"_fix_controller.html,
-"deform (k)"_fix_deform.html,
-"deposit"_fix_deposit.html,
-"drag"_fix_drag.html,
-"dt/reset"_fix_dt_reset.html,
-"efield"_fix_efield.html,
-"ehex"_fix_ehex.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 (o)"_fix_gravity.html,
-"halt"_fix_halt.html,
-"heat"_fix_heat.html,
-"indent"_fix_indent.html,
-"latte"_fix_latte.html,
-"langevin (k)"_fix_langevin.html,
-"lineforce"_fix_lineforce.html,
-"momentum (k)"_fix_momentum.html,
-"move"_fix_move.html,
-"mscg"_fix_mscg.html,
-"msst"_fix_msst.html,
-"neb"_fix_neb.html,
-"nph (ko)"_fix_nh.html,
-"nphug (o)"_fix_nphug.html,
-"nph/asphere (o)"_fix_nph_asphere.html,
-"nph/body"_fix_nph_body.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
-"npt (kio)"_fix_nh.html,
-"npt/asphere (o)"_fix_npt_asphere.html,
-"npt/body"_fix_npt_body.html,
-"npt/sphere (o)"_fix_npt_sphere.html,
-"nve (kio)"_fix_nve.html,
-"nve/asphere (i)"_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 (o)"_fix_nve_sphere.html,
-"nve/tri"_fix_nve_tri.html,
-"nvt (iko)"_fix_nh.html,
-"nvt/asphere (o)"_fix_nvt_asphere.html,
-"nvt/body"_fix_nvt_body.html,
-"nvt/sllod (io)"_fix_nvt_sllod.html,
-"nvt/sphere (o)"_fix_nvt_sphere.html,
-"oneway"_fix_oneway.html,
-"orient/bcc"_fix_orient.html,
-"orient/fcc"_fix_orient.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 (k)"_fix_property_atom.html,
-"python/invoke"_fix_python_invoke.html,
-"python/move"_fix_python_move.html,
-"qeq/comb (o)"_fix_qeq_comb.html,
-"qeq/dynamic"_fix_qeq.html,
-"qeq/fire"_fix_qeq.html,
-"qeq/point"_fix_qeq.html,
-"qeq/shielded"_fix_qeq.html,
-"qeq/slater"_fix_qeq.html,
-"rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"recenter"_fix_recenter.html,
-"restrain"_fix_restrain.html,
-"rigid (o)"_fix_rigid.html,
-"rigid/nph (o)"_fix_rigid.html,
-"rigid/npt (o)"_fix_rigid.html,
-"rigid/nve (o)"_fix_rigid.html,
-"rigid/nvt (o)"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
-"setforce (k)"_fix_setforce.html,
-"shake"_fix_shake.html,
-"spring"_fix_spring.html,
-"spring/chunk"_fix_spring_chunk.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/csld"_fix_temp_csvr.html,
-"temp/csvr"_fix_temp_csvr.html,
-"temp/rescale"_fix_temp_rescale.html,
-"tfmc"_fix_tfmc.html,
-"thermal/conductivity"_fix_thermal_conductivity.html,
-"tmd"_fix_tmd.html,
-"ttm"_fix_ttm.html,
-"tune/kspace"_fix_tune_kspace.html,
-"vector"_fix_vector.html,
-"viscosity"_fix_viscosity.html,
-"viscous"_fix_viscous.html,
-"wall/colloid"_fix_wall.html,
-"wall/gran"_fix_wall_gran.html,
-"wall/gran/region"_fix_wall_gran_region.html,
-"wall/harmonic"_fix_wall.html,
-"wall/lj1043"_fix_wall.html,
-"wall/lj126"_fix_wall.html,
-"wall/lj93 (k)"_fix_wall.html,
-"wall/piston"_fix_wall_piston.html,
-"wall/reflect (k)"_fix_wall_reflect.html,
-"wall/region"_fix_wall_region.html,
-"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
-
-These are additional fix styles in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"adapt/fep"_fix_adapt_fep.html,
-"addtorque"_fix_addtorque.html,
-"atc"_fix_atc.html,
-"ave/correlate/long"_fix_ave_correlate_long.html,
-"colvars"_fix_colvars.html,
-"dpd/energy (k)"_fix_dpd_energy.html,
-"drude"_fix_drude.html,
-"drude/transform/direct"_fix_drude_transform.html,
-"drude/transform/reverse"_fix_drude_transform.html,
-"edpd/source"_fix_dpd_source.html,
-"eos/cv"_fix_eos_cv.html,
-"eos/table"_fix_eos_table.html,
-"eos/table/rx (k)"_fix_eos_table_rx.html,
-"filter/corotate"_fix_filter_corotate.html,
-"flow/gauss"_fix_flow_gauss.html,
-"gle"_fix_gle.html,
-"grem"_fix_grem.html,
-"imd"_fix_imd.html,
-"ipi"_fix_ipi.html,
-"langevin/drude"_fix_langevin_drude.html,
-"langevin/eff"_fix_langevin_eff.html,
-"lb/fluid"_fix_lb_fluid.html,
-"lb/momentum"_fix_lb_momentum.html,
-"lb/pc"_fix_lb_pc.html,
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
-"lb/viscous"_fix_lb_viscous.html,
-"meso"_fix_meso.html,
-"manifoldforce"_fix_manifoldforce.html,
-"meso/stationary"_fix_meso_stationary.html,
-"mvv/dpd"_fix_mvv_dpd.html,
-"mvv/edpd"_fix_mvv_dpd.html,
-"mvv/tdpd"_fix_mvv_dpd.html,
-"nve/dot"_fix_nve_dot.html,
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
-"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
-"nvk"_fix_nvk.html,
-"nvt/manifold/rattle"_fix_nvt_manifold_rattle.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,
-"npt/uef"_fix_nh_uef.html,
-"nvt/uef"_fix_nh_uef.html,
-"phonon"_fix_phonon.html,
-"pimd"_fix_pimd.html,
-"qbmsst"_fix_qbmsst.html,
-"qeq/reax (ko)"_fix_qeq_reax.html,
-"qmmm"_fix_qmmm.html,
-"qtb"_fix_qtb.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
-"reax/c/species (k)"_fix_reaxc_species.html,
-"rhok"_fix_rhok.html,
-"rx (k)"_fix_rx.html,
-"saed/vtk"_fix_saed_vtk.html,
-"shardlow (k)"_fix_shardlow.html,
-"smd"_fix_smd.html,
-"smd/adjust/dt"_fix_smd_adjust_dt.html,
-"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
-"smd/setvel"_fix_smd_setvel.html,
-"smd/wall/surface"_fix_smd_wall_surface.html,
-"tdpd/source"_fix_dpd_source.html,
-"temp/rescale/eff"_fix_temp_rescale_eff.html,
-"ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html,
-"wall/ees"_fix_wall_ees.html,
-"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
-
-:line
-
-Compute styles :h3
-
-See the "compute"_compute.html command for one-line descriptions of
-each style or click on the style itself for a full description. Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"aggregate/atom"_compute_cluster_atom.html,
-"angle"_compute_angle.html,
-"angle/local"_compute_angle_local.html,
-"angmom/chunk"_compute_angmom_chunk.html,
-"body/local"_compute_body_local.html,
-"bond"_compute_bond.html,
-"bond/local"_compute_bond_local.html,
-"centro/atom"_compute_centro_atom.html,
-"chunk/atom"_compute_chunk_atom.html,
-"cluster/atom"_compute_cluster_atom.html,
-"cna/atom"_compute_cna_atom.html,
-"com"_compute_com.html,
-"com/chunk"_compute_com_chunk.html,
-"contact/atom"_compute_contact_atom.html,
-"coord/atom"_compute_coord_atom.html,
-"damage/atom"_compute_damage_atom.html,
-"dihedral"_compute_dihedral.html,
-"dihedral/local"_compute_dihedral_local.html,
-"dilatation/atom"_compute_dilatation_atom.html,
-"dipole/chunk"_compute_dipole_chunk.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,
-"fragment/atom"_compute_cluster_atom.html,
-"global/atom"_compute_global_atom.html,
-"group/group"_compute_group_group.html,
-"gyration"_compute_gyration.html,
-"gyration/chunk"_compute_gyration_chunk.html,
-"heat/flux"_compute_heat_flux.html,
-"hexorder/atom"_compute_hexorder_atom.html,
-"improper"_compute_improper.html,
-"improper/local"_compute_improper_local.html,
-"inertia/chunk"_compute_inertia_chunk.html,
-"ke"_compute_ke.html,
-"ke/atom"_compute_ke_atom.html,
-"ke/rigid"_compute_ke_rigid.html,
-"msd"_compute_msd.html,
-"msd/chunk"_compute_msd_chunk.html,
-"msd/nongauss"_compute_msd_nongauss.html,
-"omega/chunk"_compute_omega_chunk.html,
-"orientorder/atom"_compute_orientorder_atom.html,
-"pair"_compute_pair.html,
-"pair/local"_compute_pair_local.html,
-"pe"_compute_pe.html,
-"pe/atom"_compute_pe_atom.html,
-"plasticity/atom"_compute_plasticity_atom.html,
-"pressure"_compute_pressure.html,
-"property/atom"_compute_property_atom.html,
-"property/local"_compute_property_local.html,
-"property/chunk"_compute_property_chunk.html,
-"rdf"_compute_rdf.html,
-"reduce"_compute_reduce.html,
-"reduce/region"_compute_reduce.html,
-"rigid/local"_compute_rigid_local.html,
-"slice"_compute_slice.html,
-"sna/atom"_compute_sna_atom.html,
-"snad/atom"_compute_sna_atom.html,
-"snav/atom"_compute_sna_atom.html,
-"stress/atom"_compute_stress_atom.html,
-"temp (k)"_compute_temp.html,
-"temp/asphere"_compute_temp_asphere.html,
-"temp/body"_compute_temp_body.html,
-"temp/chunk"_compute_temp_chunk.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,
-"torque/chunk"_compute_torque_chunk.html,
-"vacf"_compute_vacf.html,
-"vcm/chunk"_compute_vcm_chunk.html,
-"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
-
-These are additional compute styles in USER packages, 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,
-"cnp/atom"_compute_cnp_atom.html,
-"dpd"_compute_dpd.html,
-"dpd/atom"_compute_dpd_atom.html,
-"edpd/temp/atom"_compute_edpd_temp_atom.html,
-"fep"_compute_fep.html,
-"force/tally"_compute_tally.html,
-"heat/flux/tally"_compute_tally.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,
-"pe/tally"_compute_tally.html,
-"pe/mol/tally"_compute_tally.html,
-"pressure/uef"_compute_pressure_uef.html,
-"saed"_compute_saed.html,
-"smd/contact/radius"_compute_smd_contact_radius.html,
-"smd/damage"_compute_smd_damage.html,
-"smd/hourglass/error"_compute_smd_hourglass_error.html,
-"smd/internal/energy"_compute_smd_internal_energy.html,
-"smd/plastic/strain"_compute_smd_plastic_strain.html,
-"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
-"smd/rho"_compute_smd_rho.html,
-"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
-"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
-"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
-"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
-"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
-"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
-"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
-"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
-"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
-"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
-"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
-"smd/vol"_compute_smd_vol.html,
-"stress/tally"_compute_tally.html,
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
-"temp/drude"_compute_temp_drude.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,
-"temp/uef"_compute_temp_uef.html,
-"xrd"_compute_xrd.html :tb(c=6,ea=c)
-
-:line
-
-Pair_style potentials :h3
-
-See the "pair_style"_pair_style.html command for an overview of pair
-potentials. Click on the style itself for a full description. Many
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_pair_none.html,
-"zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
-"hybrid/overlay (k)"_pair_hybrid.html,
-"adp (o)"_pair_adp.html,
-"airebo (oi)"_pair_airebo.html,
-"airebo/morse (oi)"_pair_airebo.html,
-"beck (go)"_pair_beck.html,
-"body"_pair_body.html,
-"bop"_pair_bop.html,
-"born (go)"_pair_born.html,
-"born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_born.html,
-"born/coul/long (go)"_pair_born.html,
-"born/coul/long/cs"_pair_born.html,
-"born/coul/msm (o)"_pair_born.html,
-"born/coul/wolf (go)"_pair_born.html,
-"born/coul/wolf/cs"_pair_born.html,
-"brownian (o)"_pair_brownian.html,
-"brownian/poly (o)"_pair_brownian.html,
-"buck (giko)"_pair_buck.html,
-"buck/coul/cut (giko)"_pair_buck.html,
-"buck/coul/long (giko)"_pair_buck.html,
-"buck/coul/long/cs"_pair_buck.html,
-"buck/coul/msm (o)"_pair_buck.html,
-"buck/long/coul/long (o)"_pair_buck_long.html,
-"colloid (go)"_pair_colloid.html,
-"comb (o)"_pair_comb.html,
-"comb3"_pair_comb.html,
-"coul/cut (gko)"_pair_coul.html,
-"coul/debye (gko)"_pair_coul.html,
-"coul/dsf (gko)"_pair_coul.html,
-"coul/long (gko)"_pair_coul.html,
-"coul/long/cs"_pair_coul.html,
-"coul/msm"_pair_coul.html,
-"coul/streitz"_pair_coul.html,
-"coul/wolf (ko)"_pair_coul.html,
-"coul/wolf/cs"_pair_coul.html,
-"dpd (gio)"_pair_dpd.html,
-"dpd/tstat (go)"_pair_dpd.html,
-"dsmc"_pair_dsmc.html,
-"eam (gikot)"_pair_eam.html,
-"eam/alloy (gikot)"_pair_eam.html,
-"eam/fs (gikot)"_pair_eam.html,
-"eim (o)"_pair_eim.html,
-"gauss (go)"_pair_gauss.html,
-"gayberne (gio)"_pair_gayberne.html,
-"gran/hertz/history (o)"_pair_gran.html,
-"gran/hooke (o)"_pair_gran.html,
-"gran/hooke/history (o)"_pair_gran.html,
-"gw"_pair_gw.html,
-"gw/zbl"_pair_gw.html,
-"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
-"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
-"kim"_pair_kim.html,
-"lcbop"_pair_lcbop.html,
-"line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
-"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (giko)"_pair_charmm.html,
-"lj/charmm/coul/msm"_pair_charmm.html,
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
-"lj/charmmfsw/coul/long"_pair_charmm.html,
-"lj/class2 (gko)"_pair_class2.html,
-"lj/class2/coul/cut (ko)"_pair_class2.html,
-"lj/class2/coul/long (gko)"_pair_class2.html,
-"lj/cubic (go)"_pair_lj_cubic.html,
-"lj/cut (gikot)"_pair_lj.html,
-"lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/debye (gko)"_pair_lj.html,
-"lj/cut/coul/dsf (gko)"_pair_lj.html,
-"lj/cut/coul/long (gikot)"_pair_lj.html,
-"lj/cut/coul/long/cs"_pair_lj.html,
-"lj/cut/coul/msm (go)"_pair_lj.html,
-"lj/cut/coul/wolf (o)"_pair_lj.html,
-"lj/cut/dipole/cut (go)"_pair_dipole.html,
-"lj/cut/dipole/long"_pair_dipole.html,
-"lj/cut/tip4p/cut (o)"_pair_lj.html,
-"lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/expand (gko)"_pair_lj_expand.html,
-"lj/gromacs (gko)"_pair_gromacs.html,
-"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (io)"_pair_lj_long.html,
-"lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long"_pair_lj_long.html,
-"lj/smooth (o)"_pair_lj_smooth.html,
-"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
-"lj96/cut (go)"_pair_lj96.html,
-"lubricate (o)"_pair_lubricate.html,
-"lubricate/poly (o)"_pair_lubricate.html,
-"lubricateU"_pair_lubricateU.html,
-"lubricateU/poly"_pair_lubricateU.html,
-"meam"_pair_meam.html,
-"mie/cut (o)"_pair_mie.html,
-"morse (gkot)"_pair_morse.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
-"nm/cut (o)"_pair_nm.html,
-"nm/cut/coul/cut (o)"_pair_nm.html,
-"nm/cut/coul/long (o)"_pair_nm.html,
-"peri/eps"_pair_peri.html,
-"peri/lps (o)"_pair_peri.html,
-"peri/pmb (o)"_pair_peri.html,
-"peri/ves"_pair_peri.html,
-"polymorphic"_pair_polymorphic.html,
-"python"_pair_python.html,
-"reax"_pair_reax.html,
-"rebo (oi)"_pair_airebo.html,
-"resquared (go)"_pair_resquared.html,
-"snap (k)"_pair_snap.html,
-"soft (go)"_pair_soft.html,
-"sw (giko)"_pair_sw.html,
-"table (gko)"_pair_table.html,
-"tersoff (giko)"_pair_tersoff.html,
-"tersoff/mod (gko)"_pair_tersoff_mod.html,
-"tersoff/mod/c (o)"_pair_tersoff_mod.html,
-"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
-"tip4p/cut (o)"_pair_coul.html,
-"tip4p/long (o)"_pair_coul.html,
-"tri/lj"_pair_tri_lj.html,
-"ufm (got)"_pair_ufm.html,
-"vashishta (ko)"_pair_vashishta.html,
-"vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gok)"_pair_yukawa.html,
-"yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
-
-These are additional pair styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"agni (o)"_pair_agni.html,
-"awpmd/cut"_pair_awpmd.html,
-"buck/mdf"_pair_mdf.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
-"coul/diel (o)"_pair_coul_diel.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
-"coul/shield"_pair_coul_shield.html,
-"dpd/fdt"_pair_dpd_fdt.html,
-"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
-"eam/cd (o)"_pair_eam.html,
-"edip (o)"_pair_edip.html,
-"edip/multi"_pair_edip.html,
-"edpd"_pair_meso.html,
-"eff/cut"_pair_eff.html,
-"exp6/rx (k)"_pair_exp6_rx.html,
-"extep"_pair_extep.html,
-"gauss/cut"_pair_gauss.html,
-"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
-"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
-"lennard/mdf"_pair_mdf.html,
-"list"_pair_list.html,
-"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
-"lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/thole/long (o)"_pair_thole.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
-"lj/mdf"_pair_mdf.html,
-"lj/sdk (gko)"_pair_sdk.html,
-"lj/sdk/coul/long (go)"_pair_sdk.html,
-"lj/sdk/coul/msm (o)"_pair_sdk.html,
-"mdpd"_pair_meso.html,
-"mdpd/rhosum"_pair_meso.html,
-"meam/c"_pair_meam.html,
-"meam/spline (o)"_pair_meam_spline.html,
-"meam/sw/spline"_pair_meam_sw_spline.html,
-"mgpt"_pair_mgpt.html,
-"momb"_pair_momb.html,
-"morse/smooth/linear"_pair_morse.html,
-"morse/soft"_pair_morse.html,
-"multi/lucy"_pair_multi_lucy.html,
-"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"oxdna/coaxstk"_pair_oxdna.html,
-"oxdna/excv"_pair_oxdna.html,
-"oxdna/hbond"_pair_oxdna.html,
-"oxdna/stk"_pair_oxdna.html,
-"oxdna/xstk"_pair_oxdna.html,
-"oxdna2/coaxstk"_pair_oxdna2.html,
-"oxdna2/dh"_pair_oxdna2.html,
-"oxdna2/excv"_pair_oxdna2.html,
-"oxdna2/stk"_pair_oxdna2.html,
-"quip"_pair_quip.html,
-"reax/c (ko)"_pair_reaxc.html,
-"smd/hertz"_pair_smd_hertz.html,
-"smd/tlsph"_pair_smd_tlsph.html,
-"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
-"smd/ulsph"_pair_smd_ulsph.html,
-"smtbq"_pair_smtbq.html,
-"snap (k)"_pair_snap.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,
-"srp"_pair_srp.html,
-"table/rx (k)"_pair_table_rx.html,
-"tdpd"_pair_meso.html,
-"tersoff/table (o)"_pair_tersoff.html,
-"thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
-
-:line
-
-Bond_style potentials :h3
-
-See the "bond_style"_bond_style.html command for an overview of bond
-potentials. Click on the style itself for a full description. Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_bond_none.html,
-"zero"_bond_zero.html,
-"hybrid"_bond_hybrid.html,
-"class2 (ko)"_bond_class2.html,
-"fene (iko)"_bond_fene.html,
-"fene/expand (o)"_bond_fene_expand.html,
-"gromos (o)"_bond_gromos.html,
-"harmonic (ko)"_bond_harmonic.html,
-"morse (o)"_bond_morse.html,
-"nonlinear (o)"_bond_nonlinear.html,
-"quartic (o)"_bond_quartic.html,
-"table (o)"_bond_table.html :tb(c=4,ea=c)
-
-These are additional bond styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna.html,
-"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c)
-
-:line
-
-Angle_style potentials :h3
-
-See the "angle_style"_angle_style.html command for an overview of
-angle potentials. Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_angle_none.html,
-"zero"_angle_zero.html,
-"hybrid"_angle_hybrid.html,
-"charmm (ko)"_angle_charmm.html,
-"class2 (ko)"_angle_class2.html,
-"cosine (o)"_angle_cosine.html,
-"cosine/delta (o)"_angle_cosine_delta.html,
-"cosine/periodic (o)"_angle_cosine_periodic.html,
-"cosine/squared (o)"_angle_cosine_squared.html,
-"harmonic (iko)"_angle_harmonic.html,
-"table (o)"_angle_table.html :tb(c=4,ea=c)
-
-These are additional angle styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift (o)"_angle_cosine_shift.html,
-"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
-"dipole (o)"_angle_dipole.html,
-"fourier (o)"_angle_fourier.html,
-"fourier/simple (o)"_angle_fourier_simple.html,
-"quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html :tb(c=4,ea=c)
-
-:line
-
-Dihedral_style potentials :h3
-
-See the "dihedral_style"_dihedral_style.html command for an overview
-of dihedral potentials. Click on the style itself for a full
-description. Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_dihedral_none.html,
-"zero"_dihedral_zero.html,
-"hybrid"_dihedral_hybrid.html,
-"charmm (iko)"_dihedral_charmm.html,
-"charmmfsw"_dihedral_charmm.html,
-"class2 (ko)"_dihedral_class2.html,
-"harmonic (io)"_dihedral_harmonic.html,
-"helix (o)"_dihedral_helix.html,
-"multi/harmonic (o)"_dihedral_multi_harmonic.html,
-"opls (iko)"_dihedral_opls.html :tb(c=4,ea=c)
-
-These are additional dihedral styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (io)"_dihedral_fourier.html,
-"nharmonic (o)"_dihedral_nharmonic.html,
-"quadratic (o)"_dihedral_quadratic.html,
-"spherical (o)"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html :tb(c=4,ea=c)
-
-:line
-
-Improper_style potentials :h3
-
-See the "improper_style"_improper_style.html command for an overview
-of improper potentials. Click on the style itself for a full
-description. Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_improper_none.html,
-"zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html,
-"class2 (ko)"_improper_class2.html,
-"cvff (io)"_improper_cvff.html,
-"harmonic (iko)"_improper_harmonic.html,
-"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
-
-These are additional improper styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cossq (o)"_improper_cossq.html,
-"distance"_improper_distance.html,
-"fourier (o)"_improper_fourier.html,
-"ring (o)"_improper_ring.html :tb(c=4,ea=c)
-
-:line
-
-Kspace solvers :h3
-
-See the "kspace_style"_kspace_style.html command for an overview of
-Kspace solvers. Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"ewald (o)"_kspace_style.html,
-"ewald/disp"_kspace_style.html,
-"msm (o)"_kspace_style.html,
-"msm/cg (o)"_kspace_style.html,
-"pppm (gok)"_kspace_style.html,
-"pppm/cg (o)"_kspace_style.html,
-"pppm/disp (i)"_kspace_style.html,
-"pppm/disp/tip4p"_kspace_style.html,
-"pppm/stagger"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt
deleted file mode 100644
index 150a6fb30e..0000000000
--- a/doc/compute_displace_atom.txt
+++ /dev/null
@@ -1,137 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-compute displace/atom command :h3
-
-[Syntax:]
-
-compute ID group-ID displace/atom :pre
-
-ID, group-ID are documented in "compute"_compute.html command :ulb,l
-displace/atom = style name of this compute command :l
-zero or more keyword/arg pairs may be appended :l
-keyword = {refresh} :l
- {replace} arg = per-atom variable ID :pre
-:ule
-
-[Examples:]
-
-compute 1 all displace/atom
-compute 1 all displace/atom refresh myVar :pre
-
-[Description:]
-
-Define a computation that calculates the current displacement of each
-atom in the group from its original (reference) coordinates, including
-all effects due to atoms passing thru periodic boundaries.
-
-A vector of four quantities per atom is calculated by this compute.
-The first 3 elements of the vector are the dx,dy,dz displacements.
-The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
-dz*dz).
-
-The displacement of an atom is from its original position at the time
-the compute command was issued. The value of the displacement will be
-0.0 for atoms not in the specified compute group.
-
-NOTE: Initial coordinates are stored in "unwrapped" form, by using the
-image flags associated with each atom. See the "dump
-custom"_dump.html command for a discussion of "unwrapped" coordinates.
-See the Atoms section of the "read_data"_read_data.html command for a
-discussion of image flags and how they are set for each atom. You can
-reset the image flags (e.g. to 0) before invoking this compute by
-using the "set image"_set.html command.
-
-NOTE: If you want the quantities calculated by this compute to be
-continuous when running from a "restart file"_read_restart.html, then
-you should use the same ID for this compute, as in the original run.
-This is so that the fix this compute creates to store per-atom
-quantities will also have the same ID, and thus be initialized
-correctly with time=0 atom coordinates from the restart file.
-
-:line
-
-The {refresh} option can be used in conjuction with the "dump_modify
-refresh" command to generate incremental dump files.
-
-The definition and motivation of an incremental dump file is as
-follows. Instead of outputting all atoms at each snapshot (with some
-associated values), you may only wish to output the subset of atoms
-with a value that has changed in some way compared to the value the
-last time that atom was output. In some scenarios this can result in
-a dramatically smaller dump file. If desired, by post-processing the
-sequence of snapshots, the values for all atoms at all timesteps can
-be inferred.
-
-A concrete example using this compute, is a simulation of atom
-diffusion in a solid, represented as atoms on a lattice. Diffusive
-hops are rare. Imagine that when a hop occurs an atom moves more than
-a distance {Dhop}. For any snapshot we only want to output atoms that
-have hopped since the last snapshot. This can be accomplished with
-something like the following commands:
-
-write_dump all custom tmp.dump id type x y z # see comment below :pre
-
-variable Dhop equal 0.6
-variable check atom "c_dsp[4] > v_Dhop"
-compute dsp all displace/atom refresh check
-dump 1 all custom 100 tmp.dump id type x y z
-dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} &
- refresh c_dsp delay 100 :pre
-
-The "dump_modify thresh"_dump_modify.html command will only ouptut
-atoms that have displaced more than 0.6 Angstroms on each snapshot
-(assuming metal units). The dump_modify {refresh} option triggers a
-call to this compute at the end of every dump.
-
-The {refresh} argument for this compute is the ID of an "atom-style
-variable"_variable.html which calculates a Boolean value (0 or 1)
-based on the same criterion used by dump_modify thresh. This compute
-evaluates the atom-style variable. For each atom that returns 1
-(true), the original (reference) coordinates of the atom (stored by
-this compute) are updated.
-
-The effect of these commands is that a particular atom will only be
-output in the dump file on the snapshot after it makes a diffusive
-hop. It will not be output again until it makes another hop.
-
-Note that in the first snapshot of a subsequent run, no atoms will be
-typically be output. That is because the initial displacement for all
-atoms is 0.0. If an initial dump snapshot is desired, containing the
-initial reference positions of all atoms, one way to do this is
-illustrated above. An initial write_dump command can be used before
-the first run. It will contain the positions of all the atoms,
-Options in the "dump_modify"_dump_modify.html command above will
-append new output to that same file and delay the output until a later
-timestep. The {delay} setting avoids a second time = 0 snapshot which
-would be empty.
-
-:line
-
-[Output info:]
-
-This compute calculates a per-atom array with 4 columns, which can be
-accessed by indices 1-4 by any command that uses per-atom values from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
-
-The per-atom array values will be in distance "units"_units.html.
-
-This compute supports the {refresh} option as explained above, for use
-in conjunction with "dump_modify refresh"_dump_modify.html to generate
-incremental dump files.
-
-[Restrictions:] none
-
-[Related commands:]
-
-"compute msd"_compute_msd.html, "dump custom"_dump.html, "fix
-store/state"_fix_store_state.html
-
-[Default:] none
diff --git a/doc/create_atoms.txt b/doc/create_atoms.txt
deleted file mode 100644
index 5d824ae1ef..0000000000
--- a/doc/create_atoms.txt
+++ /dev/null
@@ -1,335 +0,0 @@
-"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
-
-create_atoms command :h3
-
-[Syntax:]
-
-create_atoms type style args keyword values ... :pre
-
-type = atom type (1-Ntypes) of atoms to create (offset for molecule creation) :ulb,l
-style = {box} or {region} or {single} or {random} :l
- {box} args = none
- {region} args = region-ID
- region-ID = particles will only be created if contained in the region
- {single} args = x y z
- x,y,z = coordinates of a single particle (distance units)
- {random} args = N seed region-ID
- N = number of particles to create
- seed = random # seed (positive integer)
- region-ID = create atoms within this region, use NULL for entire simulation box :pre
-zero or more keyword/value pairs may be appended :l
-keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
- {mol} value = template-ID seed
- template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
- seed = random # seed (positive integer)
- {basis} values = M itype
- M = which basis atom
- itype = atom type (1-N) to assign to this basis atom
- {remap} value = {yes} or {no}
- {var} value = name = variable name to evaluate for test of atom creation
- {set} values = dim name
- dim = {x} or {y} or {z}
- name = name of variable to set with x, y, or z atom position
- {rotate} values = theta Rx Ry Rz
- theta = rotation angle for single molecule (degrees)
- Rx,Ry,Rz = rotation vector for single molecule
- {units} value = {lattice} or {box}
- {lattice} = the geometry is defined in lattice units
- {box} = the geometry is defined in simulation box units :pre
-:ule
-
-[Examples:]
-
-create_atoms 1 box
-create_atoms 3 region regsphere basis 2 3
-create_atoms 3 single 0 0 5
-create_atoms 1 box var v set x xpos set y ypos :pre
-
-[Description:]
-
-This command creates atoms (or molecules) on a lattice, or a single
-atom (or molecule), or a random collection of atoms (or molecules), as
-an alternative to reading in their coordinates explicitly via a
-"read_data"_read_data.html or "read_restart"_read_restart.html
-command. A simulation box must already exist, which is typically
-created via the "create_box"_create_box.html command. Before using
-this command, a lattice must also be defined using the
-"lattice"_lattice.html command, unless you specify the {single} style
-with units = box or the {random} style. For the remainder of this doc
-page, a created atom or molecule is referred to as a "particle".
-
-If created particles are individual atoms, they are assigned the
-specified atom {type}, though this can be altered via the {basis}
-keyword as discussed below. If molecules are being created, the type
-of each atom in the created molecule is specified in the file read by
-the "molecule"_molecule.html command, and those values are added to
-the specified atom {type}. E.g. if {type} = 2, and the file specifies
-atom types 1,2,3, then each created molecule will have atom types
-3,4,5.
-
-For the {box} style, the create_atoms command fills the entire
-simulation box with particles on the lattice. If your simulation box
-is periodic, you should insure its size is a multiple of the lattice
-spacings, to avoid unwanted atom overlaps at the box boundaries. If
-your box is periodic and a multiple of the lattice spacing in a
-particular dimension, LAMMPS is careful to put exactly one particle at
-the boundary (on either side of the box), not zero or two.
-
-For the {region} style, a geometric volume is filled with particles on
-the lattice. This volume what is inside the simulation box and is
-also consistent with the region volume. See the "region"_region.html
-command for details. Note that a region can be specified so that its
-"volume" is either inside or outside a geometric boundary. Also note
-that if your region is the same size as a periodic simulation box (in
-some dimension), LAMMPS does not implement the same logic described
-above as for the {box} style, to insure exactly one particle at
-periodic boundaries. if this is what you desire, you should either
-use the {box} style, or tweak the region size to get precisely the
-particles you want.
-
-For the {single} style, a single particle is added to the system at
-the specified coordinates. This can be useful for debugging purposes
-or to create a tiny system with a handful of particles at specified
-positions.
-
-For the {random} style, N particles are added to the system at
-randomly generated coordinates, which can be useful for generating an
-amorphous system. The particles are created one by one using the
-specified random number {seed}, resulting in the same set of particles
-coordinates, independent of how many processors are being used in the
-simulation. If the {region-ID} argument is specified as NULL, then
-the created particles will be anywhere in the simulation box. If a
-{region-ID} is specified, a geometric volume is filled which is both
-inside the simulation box and is also consistent with the region
-volume. See the "region"_region.html command for details. Note that
-a region can be specified so that its "volume" is either inside or
-outside a geometric boundary.
-
-NOTE: Particles generated by the {random} style will typically be
-highly overlapped which will cause many interatomic potentials to
-compute large energies and forces. Thus you should either perform an
-"energy minimization"_minimize.html or run dynamics with "fix
-nve/limit"_fix_nve_limit.html to equilibrate such a system, before
-running normal dynamics.
-
-Note that this command adds particles to those that already exist.
-This means it can be used to add particles to a system previously read
-in from a data or restart file. Or the create_atoms command can be
-used multiple times, to add multiple sets of particles to the
-simulation. For example, grain boundaries can be created, by
-interleaving create_atoms with "lattice"_lattice.html commands
-specifying different orientations. By using the create_atoms command
-in conjunction with the "delete_atoms"_delete_atoms.html command,
-reasonably complex geometries can be created, or a protein can be
-solvated with a surrounding box of water molecules.
-
-In all these cases, care should be taken to insure that new atoms do
-not overlap existing atoms inappropriately, especially if molecules
-are being added. The "delete_atoms"_delete_atoms.html command can be
-used to remove overlapping atoms or molecules.
-
-NOTE: You cannot use any of the styles explained above to create atoms
-that are outside the simulation box; they will just be ignored by
-LAMMPS. This is true even if you are using shrink-wrapped box
-boundaries, as specified by the "boundary"_boundary.html command.
-However, you can first use the "change_box"_change_box.html command to
-temporarily expand the box, then add atoms via create_atoms, then
-finally use change_box command again if needed to re-shrink-wrap the
-new atoms. See the "change_box"_change_box.html doc page for an
-example of how to do this, using the create_atoms {single} style to
-insert a new atom outside the current simulation box.
-
-:line
-
-Individual atoms are inserted by this command, unless the {mol}
-keyword is used. It specifies a {template-ID} previously defined
-using the "molecule"_molecule.html command, which reads a file that
-defines the molecule. The coordinates, atom types, charges, etc, as
-well as any bond/angle/etc and special neighbor information for the
-molecule can be specified in the molecule file. See the
-"molecule"_molecule.html command for details. The only settings
-required to be in this file are the coordinates and types of atoms in
-the molecule.
-
-Using a lattice to add molecules, e.g. via the {box} or {region} or
-{single} styles, is exactly the same as adding atoms on lattice
-points, except that entire molecules are added at each point, i.e. on
-the point defined by each basis atom in the unit cell as it tiles the
-simulation box or region. This is done by placing the geometric
-center of the molecule at the lattice point, and giving the molecule a
-random orientation about the point. The random {seed} specified with
-the {mol} keyword is used for this operation, and the random numbers
-generated by each processor are different. This means the coordinates
-of individual atoms (in the molecules) will be different when running
-on different numbers of processors, unlike when atoms are being
-created in parallel.
-
-Also note that because of the random rotations, it may be important to
-use a lattice with a large enough spacing that adjacent molecules will
-not overlap, regardless of their relative orientations.
-
-NOTE: If the "create_box"_create_box.html command is used to create
-the simulation box, followed by the create_atoms command with its
-{mol} option for adding molecules, then you typically need to use the
-optional keywords allowed by the "create_box"_create_box.html command
-for extra bonds (angles,etc) or extra special neighbors. This is
-because by default, the "create_box"_create_box.html command sets up a
-non-molecular system which doesn't allow molecules to be added.
-
-:line
-
-This is the meaning of the other allowed keywords.
-
-The {basis} keyword is only used when atoms (not molecules) are being
-created. It specifies an atom type that will be assigned to specific
-basis atoms as they are created. See the "lattice"_lattice.html
-command for specifics on how basis atoms are defined for the unit cell
-of the lattice. By default, all created atoms are assigned the
-argument {type} as their atom type.
-
-The {remap} keyword only applies to the {single} style. If it is set
-to {yes}, then if the specified position is outside the simulation
-box, it will mapped back into the box, assuming the relevant
-dimensions are periodic. If it is set to {no}, no remapping is done
-and no particle is created if its position is outside the box.
-
-The {var} and {set} keywords can be used together to provide a
-criterion for accepting or rejecting the addition of an individual
-atom, based on its coordinates. The {name} specified for the {var}
-keyword is the name of an "equal-style variable"_variable.html which
-should evaluate to a zero or non-zero value based on one or two or
-three variables which will store the x, y, or z coordinates of an atom
-(one variable per coordinate). If used, these other variables must be
-"internal-style variables"_variable.html defined in the input script;
-their initial numeric value can be anything. They must be
-internal-style variables, because this command resets their values
-directly. The {set} keyword is used to identify the names of these
-other variables, one variable for the x-coordinate of a created atom,
-one for y, and one for z.
-
-When an atom is created, its x,y,z coordinates become the values for
-any {set} variable that is defined. The {var} variable is then
-evaluated. If the returned value is 0.0, the atom is not created. If
-it is non-zero, the atom is created.
-
-As an example, these commands can be used in a 2d simulation, to
-create a sinusoidal surface. Note that the surface is "rough" due to
-individual lattice points being "above" or "below" the mathematical
-expression for the sinusoidal curve. If a finer lattice were used,
-the sinusoid would appear to be "smoother". Also note the use of the
-"xlat" and "ylat" "thermo_style"_thermo_style.html keywords which
-converts lattice spacings to distance. Click on the image for a
-larger version.
-
-dimension 2
-variable x equal 100
-variable y equal 25
-lattice hex 0.8442
-region box block 0 $x 0 $y -0.5 0.5
-create_box 1 box :pre
-
-variable xx internal 0.0
-variable yy internal 0.0
-variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
-create_atoms 1 box var v set x xx set y yy
-write_dump all atom sinusoid.lammpstrj :pre
-
-:c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
-
-The {rotate} keyword can only be used with the {single} style and
-when adding a single molecule. It allows to specify the orientation
-at which the molecule is inserted. The axis of rotation is
-determined by the rotation vector (Rx,Ry,Rz) that goes through the
-insertion point. The specified {theta} determines the angle of
-rotation around that axis. Note that the direction of rotation for
-the atoms around the rotation axis is consistent with the right-hand
-rule: if your right-hand's thumb points along {R}, then your fingers
-wrap around the axis in the direction of rotation.
-
-The {units} keyword determines the meaning of the distance units used
-to specify the coordinates of the one particle created by the {single}
-style. A {box} value selects standard distance units as defined by
-the "units"_units.html command, e.g. Angstroms for units = real or
-metal. A {lattice} value means the distance units are in lattice
-spacings.
-
-:line
-
-Atom IDs are assigned to created atoms in the following way. The
-collection of created atoms are assigned consecutive IDs that start
-immediately following the largest atom ID existing before the
-create_atoms command was invoked. This is done by the processor's
-communicating the number of atoms they each own, the first processor
-numbering its atoms from 1 to N1, the second processor from N1+1 to
-N2, etc. Where N1 = number of atoms owned by the first processor, N2
-= number owned by the second processor, etc. Thus when the same
-simulation is performed on different numbers of processors, there is
-no guarantee a particular created atom will be assigned the same ID in
-both simulations. If molecules are being created, molecule IDs are
-assigned to created molecules in a similar fashion.
-
-Aside from their ID, atom type, and xyz position, other properties of
-created atoms are set to default values, depending on which quantities
-are defined by the chosen "atom style"_atom_style.html. See the "atom
-style"_atom_style.html command for more details. See the
-"set"_set.html and "velocity"_velocity.html commands for info on how
-to change these values.
-
-charge = 0.0
-dipole moment magnitude = 0.0
-diameter = 1.0
-shape = 0.0 0.0 0.0
-density = 1.0
-volume = 1.0
-velocity = 0.0 0.0 0.0
-angular velocity = 0.0 0.0 0.0
-angular momentum = 0.0 0.0 0.0
-quaternion = (1,0,0,0)
-bonds, angles, dihedrals, impropers = none :ul
-
-If molecules are being created, these defaults can be overridden by
-values specified in the file read by the "molecule"_molecule.html
-command. E.g. the file typically defines bonds (angles,etc) between
-atoms in the molecule, and can optionally define charges on each atom.
-
-Note that the {sphere} atom style sets the default particle diameter
-to 1.0 as well as the density. This means the mass for the particle
-is not 1.0, but is PI/6 * diameter^3 = 0.5236.
-
-Note that the {ellipsoid} atom style sets the default particle shape
-to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
-particle, not an ellipsoid, and has a mass of 1.0.
-
-Note that the {peri} style sets the default volume and density to 1.0
-and thus also set the mass for the particle to 1.0.
-
-The "set"_set.html command can be used to override many of these
-default settings.
-
-:line
-
-[Restrictions:]
-
-An "atom_style"_atom_style.html must be previously defined to use this
-command.
-
-A rotation vector specified for a single molecule must be in
-the z-direction for a 2d model.
-
-[Related commands:]
-
-"lattice"_lattice.html, "region"_region.html, "create_box"_create_box.html,
-"read_data"_read_data.html, "read_restart"_read_restart.html
-
-[Default:]
-
-The default for the {basis} keyword is that all created atoms are
-assigned the argument {type} as their atom type (when single atoms are
-being created). The other defaults are {remap} = no, {rotate} =
-random, and {units} = lattice.
diff --git a/doc/delete_atoms.txt b/doc/delete_atoms.txt
deleted file mode 100644
index 1aa71d341f..0000000000
--- a/doc/delete_atoms.txt
+++ /dev/null
@@ -1,152 +0,0 @@
-"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
-
-delete_atoms command :h3
-
-[Syntax:]
-
-delete_atoms style args keyword value ... :pre
-
-style = {group} or {region} or {overlap} or {porosity} :ulb,l
- {group} args = group-ID
- {region} args = region-ID
- {overlap} args = cutoff group1-ID group2-ID
- cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
- group1-ID = one atom in pair must be in this group
- group2-ID = other atom in pair must be in this group
- {porosity} args = region-ID fraction seed
- region-ID = region within which to perform deletions
- fraction = delete this fraction of atoms
- seed = random number seed (positive integer) :pre
-zero or more keyword/value pairs may be appended :l
-keyword = {compress} or {bond} or {mol} :l
- {compress} value = {no} or {yes}
- {bond} value = {no} or {yes}
- {mol} value = {no} or {yes} :pre
-:ule
-
-[Examples:]
-
-delete_atoms group edge
-delete_atoms region sphere compress no
-delete_atoms overlap 0.3 all all
-delete_atoms overlap 0.5 solvent colloid
-delete_atoms porosity cube 0.1 482793 bond yes :pre
-
-[Description:]
-
-Delete the specified atoms. This command can be used to carve out
-voids from a block of material or to delete created atoms that are too
-close to each other (e.g. at a grain boundary).
-
-For style {group}, all atoms belonging to the group are deleted.
-
-For style {region}, all atoms in the region volume are deleted.
-Additional atoms can be deleted if they are in a molecule for which
-one or more atoms were deleted within the region; see the {mol}
-keyword discussion below.
-
-For style {overlap} pairs of atoms whose distance of separation is
-within the specified cutoff distance are searched for, and one of the
-2 atoms is deleted. Only pairs where one of the two atoms is in the
-first group specified and the other atom is in the second group are
-considered. The atom that is in the first group is the one that is
-deleted.
-
-Note that it is OK for the two group IDs to be the same (e.g. group
-{all}), or for some atoms to be members of both groups. In these
-cases, either atom in the pair may be deleted. Also note that if
-there are atoms which are members of both groups, the only guarantee
-is that at the end of the deletion operation, enough deletions will
-have occurred that no atom pairs within the cutoff will remain
-(subject to the group restriction). There is no guarantee that the
-minimum number of atoms will be deleted, or that the same atoms will
-be deleted when running on different numbers of processors.
-
-For style {porosity} a specified {fraction} of atoms are deleted
-within the specified region. For example, if fraction is 0.1, then
-10% of the atoms will be deleted. The atoms to delete are chosen
-randomly. There is no guarantee that the exact fraction of atoms will
-be deleted, or that the same atoms will be deleted when running on
-different numbers of processors.
-
-If the {compress} keyword is set to {yes}, then after atoms are
-deleted, then atom IDs are re-assigned so that they run from 1 to the
-number of atoms in the system. Note that this is not done for
-molecular systems (see the "atom_style"_atom_style.html command),
-regardless of the {compress} setting, since it would foul up the bond
-connectivity that has already been assigned. However, the
-"reset_ids"_reset_ids.html command can be used after this command to
-accomplish the same thing.
-
-Note that the re-assignement of IDs is not really a compression, where
-gaps in atom IDs are removed by decrementing atom IDs that are larger.
-Instead the IDs for all atoms are erased, and new IDs are assigned so
-that the atoms owned by individual processors have consecutive IDs, as
-the "create_atoms"_create_atoms.html command explains.
-
-A molecular system with fixed bonds, angles, dihedrals, or improper
-interactions, is one where the topology of the interactions is
-typically defined in the data file read by the
-"read_data"_read_data.html command, and where the interactions
-themselves are defined with the "bond_style"_bond_style.html,
-"angle_style"_angle_style.html, etc commands. If you delete atoms
-from such a system, you must be careful not to end up with bonded
-interactions that are stored by remaining atoms but which include
-deleted atoms. This will cause LAMMPS to generate a "missing atoms"
-error when the bonded interaction is computed. The {bond} and {mol}
-keywords offer two ways to do that.
-
-It the {bond} keyword is set to {yes} then any bond or angle or
-dihedral or improper interaction that includes a deleted atom is also
-removed from the lists of such interactions stored by non-deleted
-atoms. Note that simply deleting interactions due to dangling bonds
-(e.g. at a surface) may result in a inaccurate or invalid model for
-the remaining atoms.
-
-It the {mol} keyword is set to {yes}, then for every atom that is
-deleted, all other atoms in the same molecule (with the same molecule
-ID) will also be deleted. This is not done for atoms with molecule ID
-= 0, since such an ID is assumed to flag isolated atoms that are not
-part of molecules.
-
-NOTE: The molecule deletion operation in invoked after all individual
-atoms have been deleted using the rules described above for each
-style. This means additional atoms may be deleted that are not in the
-group or region, that are not required by the overlap cutoff
-criterion, or that will create a higher fraction of porosity than was
-requested.
-
-[Restrictions:]
-
-The {overlap} styles requires inter-processor communication to acquire
-ghost atoms and build a neighbor list. This means that your system
-must be ready to perform a simulation before using this command (force
-fields setup, atom masses set, etc). Since a neighbor list is used to
-find overlapping atom pairs, it also means that you must define a
-"pair style"_pair_style.html with the minimum force cutoff distance
-between any pair of atoms types (plus the "neighbor"_neighbor.html
-skin) >= the specified overlap cutoff.
-
-If the "special_bonds"_special_bonds.html command is used with a
-setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
-appear in the neighbor list, and thus will not be considered for
-deletion by the {overlap} styles. You probably don't want to be
-deleting one atom in a bonded pair anyway.
-
-The {bond yes} option cannot be used with molecular systems defined
-using molecule template files via the "molecule"_molecule.html and
-"atom_style template"_atom_style.html commands.
-
-[Related commands:]
-
-"create_atoms"_create_atoms.html, "reset_ids"_reset_ids.html
-
-[Default:]
-
-The option defaults are compress = yes, bond = no, mol = no.
diff --git a/doc/dump.txt b/doc/dump.txt
deleted file mode 100644
index 9c386e2410..0000000000
--- a/doc/dump.txt
+++ /dev/null
@@ -1,664 +0,0 @@
- "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 command :h3
-"dump vtk"_dump_vtk.html command :h3
-"dump h5md"_dump_h5md.html command :h3
-"dump molfile"_dump_molfile.html command :h3
-"dump netcdf"_dump_netcdf.html command :h3
-"dump image"_dump_image.html command :h3
-"dump movie"_dump_image.html command :h3
-
-[Syntax:]
-
-dump ID group-ID style N file args :pre
-
-ID = user-assigned name for the dump :ulb,l
-group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
-N = dump every this many timesteps :l
-file = name of file to write dump info to :l
-args = list of arguments for a particular style :l
- {atom} args = none
- {atom/gz} args = none
- {atom/mpiio} args = none
- {cfg} args = same as {custom} args, see below
- {cfg/gz} args = same as {custom} args, see below
- {cfg/mpiio} args = same as {custom} args, see below
- {custom}, {custom/gz}, {custom/mpiio} args = see below
- {dcd} args = none
- {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page
- {image} args = discussed on "dump image"_dump_image.html doc page
- {local} args = see below
- {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
- {movie} args = discussed on "dump image"_dump_image.html doc page
- {netcdf} args = discussed on "dump netcdf"_dump_netcdf.html doc page
- {netcdf/mpiio} args = discussed on "dump netcdf"_dump_netcdf.html doc page
- {vtk} args = same as {custom} args, see below, also "dump vtk"_dump_vtk.html doc page
- {xtc} args = none
- {xyz} args = none
- {xyz/gz} args = none
- {xyz/mpiio} args = none :pre
-
-{custom} or {custom/gz} or {custom/mpiio} or {netcdf} or {netcdf/mpiio} args = list of atom attributes :l
- possible attributes = id, mol, proc, procp1, type, element, mass,
- x, y, z, xs, ys, zs, xu, yu, zu,
- xsu, ysu, zsu, ix, iy, iz,
- vx, vy, vz, fx, fy, fz,
- q, mux, muy, muz, mu,
- radius, diameter, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz, tqx, tqy, tqz,
- c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
-
- id = atom ID
- mol = molecule ID
- proc = ID of processor that owns atom
- procp1 = ID+1 of processor that owns atom
- type = atom type
- element = name of atom element, as defined by "dump_modify"_dump_modify.html command
- mass = atom mass
- x,y,z = unscaled atom coordinates
- xs,ys,zs = scaled atom coordinates
- xu,yu,zu = unwrapped atom coordinates
- xsu,ysu,zsu = scaled unwrapped atom coordinates
- ix,iy,iz = box image that the atom is in
- vx,vy,vz = atom velocities
- fx,fy,fz = forces on atoms
- q = atom charge
- mux,muy,muz = orientation of dipole moment of atom
- mu = magnitude of dipole moment of atom
- radius,diameter = radius,diameter of spherical particle
- omegax,omegay,omegaz = angular velocity of spherical particle
- angmomx,angmomy,angmomz = angular momentum of aspherical particle
- tqx,tqy,tqz = torque on finite-size particles
- c_ID = per-atom vector calculated by a compute with ID
- c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
- f_ID = per-atom vector calculated by a fix with ID
- f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
- v_name = per-atom vector calculated by an atom-style variable with name
- d_name = per-atom floating point vector with name, managed by fix property/atom
- i_name = per-atom integer vector with name, managed by fix property/atom :pre
-
-{local} args = list of local attributes :l
- possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]
- index = enumeration of local values
- c_ID = local vector calculated by a compute with ID
- c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
- f_ID = local vector calculated by a fix with ID
- f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre
-
-:ule
-
-[Examples:]
-
-dump myDump all atom 100 dump.atom
-dump myDump all atom/mpiio 100 dump.atom.mpiio
-dump myDump all atom/gz 100 dump.atom.gz
-dump 2 subgroup atom 50 dump.run.bin
-dump 2 subgroup atom 50 dump.run.mpiio.bin
-dump 4a all custom 100 dump.myforce.* id type x y vx fx
-dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
-dump 4b flow custom 100 dump.%.myforce id type c_myF\[*\] v_ke
-dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
-dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress\[2\]
-dump 1 all xtc 1000 file.xtc :pre
-
-[Description:]
-
-Dump a snapshot of atom quantities to one or more files every N
-timesteps in one of several styles. The {image} and {movie} styles are
-the exception: the {image} style renders a JPG, PNG, or PPM image file
-of the atom configuration every N timesteps while the {movie} style
-combines and compresses them into a movie file; both are discussed in
-detail on the "dump image"_dump_image.html doc page. The timesteps on
-which dump output is written can also be controlled by a variable.
-See the "dump_modify every"_dump_modify.html command.
-
-Only information for atoms in the specified group is dumped. The
-"dump_modify thresh and region and refresh"_dump_modify.html commands
-can also alter what atoms are included. Not all styles support all
-these options; see details on the "dump_modify"_dump_modify.html doc
-page.
-
-As described below, the filename determines the kind of output (text
-or binary or gzipped, one big file or one per timestep, one big file
-or multiple smaller files).
-
-NOTE: Because periodic boundary conditions are enforced only on
-timesteps when neighbor lists are rebuilt, the coordinates of an atom
-written to a dump file may be slightly outside the simulation box.
-Re-neighbor timesteps will not typically coincide with the timesteps
-dump snapshots are written. See the "dump_modify
-pbc"_dump_modify.html command if you with to force coordinates to be
-strictly inside the simulation box.
-
-NOTE: Unless the "dump_modify sort"_dump_modify.html option is
-invoked, the lines of atom information written to dump files
-(typically one line per atom) will be in an indeterminate order for
-each snapshot. This is even true when running on a single processor,
-if the "atom_modify sort"_atom_modify.html option is on, which it is
-by default. In this case atoms are re-ordered periodically during a
-simulation, due to spatial sorting. It is also true when running in
-parallel, because data for a single snapshot is collected from
-multiple processors, each of which owns a subset of the atoms.
-
-For the {atom}, {custom}, {cfg}, and {local} styles, sorting is off by
-default. For the {dcd}, {xtc}, {xyz}, and {molfile} styles, sorting by
-atom ID is on by default. See the "dump_modify"_dump_modify.html doc
-page for details.
-
-The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are identical
-in command syntax to the corresponding styles without "gz", however,
-they generate compressed files using the zlib library. Thus the filename
-suffix ".gz" is mandatory. This is an alternative approach to writing
-compressed files via a pipe, as done by the regular dump styles, which
-may be required on clusters where the interface to the high-speed network
-disallows using the fork() library call (which is needed for a pipe).
-For the remainder of this doc page, you should thus consider the {atom}
-and {atom/gz} styles (etc) to be inter-changeable, with the exception
-of the required filename suffix.
-
-As explained below, the {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and
-{xyz/mpiio} styles are identical in command syntax and in the format
-of the dump files they create, to the corresponding styles without
-"mpiio", except the single dump file they produce is written in
-parallel via the MPI-IO library. For the remainder of this doc page,
-you should thus consider the {atom} and {atom/mpiio} styles (etc) to
-be inter-changeable. The one exception is how the filename is
-specified for the MPI-IO styles, as explained below.
-
-The precision of values output to text-based dump files can be
-controlled by the "dump_modify format"_dump_modify.html command and
-its options.
-
-:line
-
-The {style} keyword determines what atom quantities are written to the
-file and in what format. Settings made via the
-"dump_modify"_dump_modify.html command can also alter the format of
-individual values and the file itself.
-
-The {atom}, {local}, and {custom} styles create files in a simple text
-format that is self-explanatory when viewing a dump file. Many of the
-LAMMPS "post-processing tools"_Section_tools.html, including
-"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this
-format, as does the "rerun"_rerun.html command.
-
-For post-processing purposes the {atom}, {local}, and {custom} text
-files are self-describing in the following sense.
-
-The dimensions of the simulation box are included in each snapshot.
-For an orthogonal simulation box this information is is formatted as:
-
-ITEM: BOX BOUNDS xx yy zz
-xlo xhi
-ylo yhi
-zlo zhi :pre
-
-where xlo,xhi are the maximum extents of the simulation box in the
-x-dimension, and similarly for y and z. The "xx yy zz" represent 6
-characters that encode the style of boundary for each of the 6
-simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of
-the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
-or m = shrink wrapped with a minimum value. See the
-"boundary"_boundary.html command for details.
-
-For triclinic simulation boxes (non-orthogonal), an orthogonal
-bounding box which encloses the triclinic simulation box is output,
-along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
-formatted as follows:
-
-ITEM: BOX BOUNDS xy xz yz xx yy zz
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz :pre
-
-The presence of the text "xy xz yz" in the ITEM line indicates that
-the 3 tilt factors will be included on each of the 3 following lines.
-This bounding box is convenient for many visualization programs. The
-meaning of the 6 character flags for "xx yy zz" is the same as above.
-
-Note that the first two numbers on each line are now xlo_bound instead
-of xlo, etc, since they represent a bounding box. See "this
-section"_Section_howto.html#howto_12 of the doc pages for a geometric
-description of triclinic boxes, as defined by LAMMPS, simple formulas
-for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
-calculated from the triclinic parameters, and how to transform those
-parameters to and from other commonly used triclinic representations.
-
-The "ITEM: ATOMS" line in each snapshot lists column descriptors for
-the per-atom lines that follow. For example, the descriptors would be
-"id type xs ys zs" for the default {atom} style, and would be the atom
-attributes you specify in the dump command for the {custom} style.
-
-For style {atom}, atom coordinates are written to the file, along with
-the atom ID and atom type. By default, atom coords are written in a
-scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom
-is at a location 1/4 of the distance from xlo to xhi of the box
-boundaries. The format can be changed to unscaled coords via the
-"dump_modify"_dump_modify.html settings. Image flags can also be
-added for each atom via dump_modify.
-
-Style {custom} allows you to specify a list of atom attributes to be
-written to the dump file for each atom. Possible attributes are
-listed above and will appear in the order specified. You cannot
-specify a quantity that is not defined for a particular simulation -
-such as {q} for atom style {bond}, since that atom style doesn't
-assign charges. Dumps occur at the very end of a timestep, so atom
-attributes will include effects due to fixes that are applied during
-the timestep. An explanation of the possible dump custom attributes
-is given below.
-
-For style {local}, local output generated by "computes"_compute.html
-and "fixes"_fix.html is used to generate lines of output that is
-written to the dump file. This local data is typically calculated by
-each processor based on the atoms it owns, but there may be zero or
-more entities per atom, e.g. a list of bond distances. An explanation
-of the possible dump local attributes is given below. Note that by
-using input from the "compute
-property/local"_compute_property_local.html command with dump local,
-it is possible to generate information on bonds, angles, etc that can
-be cut and pasted directly into a data file read by the
-"read_data"_read_data.html command.
-
-Style {cfg} has the same command syntax as style {custom} and writes
-extended CFG format files, as used by the
-"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualization
-package. Since the extended CFG format uses a single snapshot of the
-system per file, a wildcard "*" must be included in the filename, as
-discussed below. The list of atom attributes for style {cfg} must
-begin with either "mass type xs ys zs" or "mass type xsu ysu zsu"
-since these quantities are needed to write the CFG files in the
-appropriate format (though the "mass" and "type" fields do not appear
-explicitly in the file). Any remaining attributes will be stored as
-"auxiliary properties" in the CFG files. Note that you will typically
-want to use the "dump_modify element"_dump_modify.html command with
-CFG-formatted files, to associate element names with atom types, so
-that AtomEye can render atoms appropriately. When unwrapped
-coordinates {xsu}, {ysu}, and {zsu} are requested, the nominal AtomEye
-periodic cell dimensions are expanded by a large factor UNWRAPEXPAND =
-10.0, which ensures atoms that are displayed correctly for up to
-UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond
-this, AtomEye will rewrap the unwrapped coordinates. The expansion
-causes the atoms to be drawn farther away from the viewer, but it is
-easy to zoom the atoms closer, and the interatomic distances are
-unaffected.
-
-The {dcd} style writes DCD files, a standard atomic trajectory format
-used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
-files are binary and thus may not be portable to different machines.
-The number of atoms per snapshot cannot change with the {dcd} style.
-The {unwrap} option of the "dump_modify"_dump_modify.html command
-allows DCD coordinates to be written "unwrapped" by the image flags
-for each atom. Unwrapped means that if the atom has passed through
-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.
-
-The {xtc} style writes XTC files, a compressed trajectory format used
-by the GROMACS molecular dynamics package, and described
-"here"_http://manual.gromacs.org/current/online/xtc.html.
-The precision used in XTC files can be adjusted via the
-"dump_modify"_dump_modify.html command. The default value of 1000
-means that coordinates are stored to 1/1000 nanometer accuracy. XTC
-files are portable binary files written in the NFS XDR data format,
-so that any machine which supports XDR should be able to read them.
-The number of atoms per snapshot cannot change with the {xtc} style.
-The {unwrap} option of the "dump_modify"_dump_modify.html command allows
-XTC coordinates to 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.
-
-The {xyz} style writes XYZ files, which is a simple text-based
-coordinate format that many codes can read. Specifically it has
-a line with the number of atoms, then a comment line that is
-usually ignored followed by one line per atom with the atom type
-and the x-, y-, and z-coordinate of that atom. You can use the
-"dump_modify element"_dump_modify.html option to change the output
-from using the (numerical) atom type to an element name (or some
-other label). This will help many visualization programs to guess
-bonds and colors.
-
-Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
-can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
-popular molecular viewing program.
-
-: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 also 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 (not allowed
-for {dcd} style). The "dump_modify every"_dump_modify.html command
-also allows a variable to be used to determine the sequence of
-timesteps on which dump files are written. In this mode a dump on the
-first timestep of a run will also not be written unless the
-"dump_modify first"_dump_modify.html command is used.
-
-The specified filename determines how the dump file(s) is written.
-The default is to write one large text file, which is opened when the
-dump command is invoked and closed when an "undump"_undump.html
-command is used or when LAMMPS exits. For the {dcd} and {xtc} styles,
-this is a single large binary file.
-
-Dump filenames can contain two wildcard characters. If a "*"
-character appears in the filename, then one file per snapshot is
-written and the "*" character is replaced with the timestep value.
-For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
-tmp.dump.20000, etc. This option is not available for the {dcd} and
-{xtc} styles. 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 read a series of dump files
-in order with some post-processing tools.
-
-If a "%" character appears in the filename, then each of P processors
-writes a portion of the dump file, and the "%" character is replaced
-with the processor ID from 0 to P-1. For example, tmp.dump.% becomes
-tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller
-files and can be a fast mode of output on parallel machines that
-support parallel I/O for output. This option is not available for the
-{dcd}, {xtc}, and {xyz} styles.
-
-By default, P = the number of processors meaning one file per
-processor, but P can be set to a smaller value via the {nfile} or
-{fileper} keywords of the "dump_modify"_dump_modify.html command.
-These options can be the most efficient way of writing out dump files
-when running on large numbers of processors.
-
-Note that using the "*" and "%" characters together can produce a
-large number of small dump files!
-
-For the {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio}
-styles, a single dump file is written in parallel via the MPI-IO
-library, which is part of the MPI standard for versions 2.0 and above.
-Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
-package installed, e.g.
-
-make yes-mpiio # installs the MPIIO package
-make mpi # build LAMMPS for your platform :pre
-
-Second, use a dump filename which contains ".mpiio". Note that it
-does not have to end in ".mpiio", just contain those characters.
-Unlike MPI-IO restart files, which must be both written and read using
-MPI-IO, the dump files produced by these MPI-IO styles are identical
-in format to the files produced by their non-MPI-IO style
-counterparts. This means you can write a dump file using MPI-IO and
-use the "read_dump"_read_dump.html command or perform other
-post-processing, just as if the dump file was not written using
-MPI-IO.
-
-Note that MPI-IO dump files are one large file which all processors
-write to. You thus cannot use the "%" wildcard character described
-above in the filename since that specifies generation of multiple
-files. You can use the ".bin" suffix described below in an MPI-IO
-dump file; again this file will be written in parallel and have the
-same binary format as if it were written without MPI-IO.
-
-If the filename ends with ".bin", the dump file (or files, if "*" or
-"%" is also used) is written in binary format. A binary dump file
-will be about the same size as a text version, but will typically
-write out much faster. Of course, when post-processing, you will need
-to convert it back to text format (see the "binary2txt
-tool"_Section_tools.html#binary) or write your own code to read the
-binary file. The format of the binary file can be understood by
-looking at the tools/binary2txt.cpp file. This option is only
-available for the {atom} and {custom} styles.
-
-If the filename ends with ".gz", the dump file (or files, if "*" or "%"
-is also used) is written in gzipped format. A gzipped dump file will
-be about 3x smaller than the text version, but will also take longer
-to write. This option is not available for the {dcd} and {xtc}
-styles.
-
-:line
-
-Note that in the discussion which follows, for styles which can
-reference values from a compute or fix, like the {custom}, {cfg}, or
-{local} styles, the bracketed index I can be specified using a
-wildcard asterisk with the index to effectively specify multiple
-values. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
-size of the vector (for {mode} = scalar) or the number of columns in
-the array (for {mode} = vector), then an asterisk with no numeric
-values means all indices from 1 to N. A leading asterisk means all
-indices from 1 to n (inclusive). A trailing asterisk means all
-indices from n to N (inclusive). A middle asterisk means all indices
-from m to n (inclusive).
-
-Using a wildcard is the same as if the individual columns of the array
-had been listed one by one. E.g. these 2 dump commands are
-equivalent, since the "compute stress/atom"_compute_stress_atom.html
-command creates a per-atom array with 6 columns:
-
-compute myPress all stress/atom NULL
-dump 2 all custom 100 tmp.dump id myPress\[*\]
-dump 2 all custom 100 tmp.dump id myPress\[1\] myPress\[2\] myPress\[3\] &
- myPress\[4\] myPress\[5\] myPress\[6\] :pre
-
-:line
-
-This section explains the local attributes that can be specified as
-part of the {local} style.
-
-The {index} attribute can be used to generate an index number from 1
-to N for each line written into the dump file, where N is the total
-number of local datums from all processors, or lines of output that
-will appear in the snapshot. Note that because data from different
-processors depend on what atoms they currently own, and atoms migrate
-between processor, there is no guarantee that the same index will be
-used for the same info (e.g. a particular bond) in successive
-snapshots.
-
-The {c_ID} and {c_ID\[I\]} attributes allow local vectors or arrays
-calculated by a "compute"_compute.html to be output. The ID in the
-attribute should be replaced by the actual ID of the compute that has
-been defined previously in the input script. See the
-"compute"_compute.html command for details. There are computes for
-calculating local information such as indices, types, and energies for
-bonds and angles.
-
-Note that computes which calculate global or per-atom quantities, as
-opposed to local quantities, cannot be output in a dump local command.
-Instead, global quantities can be output by the "thermo_style
-custom"_thermo_style.html command, and per-atom quantities can be
-output by the dump custom command.
-
-If {c_ID} is used as a attribute, then the local vector calculated by
-the compute is printed. If {c_ID\[I\]} is used, then I must be in the
-range from 1-M, which will print the Ith column of the local array
-with M columns calculated by the compute. See the discussion above
-for how I can be specified with a wildcard asterisk to effectively
-specify multiple values.
-
-The {f_ID} and {f_ID\[I\]} attributes allow local vectors or arrays
-calculated by a "fix"_fix.html to be output. The ID in the attribute
-should be replaced by the actual ID of the fix that has been defined
-previously in the input script.
-
-If {f_ID} is used as a attribute, then the local vector calculated by
-the fix is printed. If {f_ID\[I\]} is used, then I must be in the
-range from 1-M, which will print the Ith column of the local with M
-columns calculated by the fix. See the discussion above for how I can
-be specified with a wildcard asterisk to effectively specify multiple
-values.
-
-Here is an example of how to dump bond info for a system, including
-the distance and energy of each bond:
-
-compute 1 all property/local batom1 batom2 btype
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_2\[1\] c_2\[2\] :pre
-
-:line
-
-This section explains the atom attributes that can be specified as
-part of the {custom} and {cfg} styles.
-
-The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
-{vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory.
-
-{Id} is the atom ID. {Mol} is the molecule ID, included in the data
-file for molecular systems. {Proc} is the ID of the processor (0 to
-Nprocs-1) that currently owns the atom. {Procp1} is the proc ID+1,
-which can be convenient in place of a {type} attribute (1 to Ntypes)
-for coloring atoms in a visualization program. {Type} is the atom
-type (1 to Ntypes). {Element} is typically the chemical name of an
-element, which you must assign to each type via the "dump_modify
-element"_dump_modify.html command. More generally, it can be any
-string you wish to associated with an atom type. {Mass} is the atom
-mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components of
-atom velocity and force and atomic charge.
-
-There are several options for outputting atom coordinates. The {x},
-{y}, {z} attributes write atom coordinates "unscaled", in the
-appropriate distance "units"_units.html (Angstroms, sigma, etc). Use
-{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
-so that each value is 0.0 to 1.0. If the simulation box is triclinic
-(tilted), then all atom coords will still be between 0.0 and 1.0.
-I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
-the non-orthogonal vectors of the simulation box edges, as discussed
-in "Section 6.12"_Section_howto.html#howto_12.
-
-Use {xu}, {yu}, {zu} if you want the coordinates "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 using {xu}, {yu}, {zu} means
-that the coordinate values may be far outside the box bounds printed
-with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using
-{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
-the box size. Atoms that have passed through a periodic boundary will
-have the corresponding coordinate increased or decreased by 1.0.
-
-The image flags can be printed directly using the {ix}, {iy}, {iz}
-attributes. For periodic dimensions, they specify which image of the
-simulation box the atom is considered to be in. An image of 0 means
-it is inside the box as defined. A value of 2 means add 2 box lengths
-to get the true value. A value of -1 means subtract 1 box length to
-get the true value. LAMMPS updates these flags as atoms cross
-periodic boundaries during the simulation.
-
-The {mux}, {muy}, {muz} attributes are specific to dipolar systems
-defined with an atom style of {dipole}. They give the orientation of
-the atom's point dipole moment. The {mu} attribute gives the
-magnitude of the atom's dipole moment.
-
-The {radius} and {diameter} attributes are specific to spherical
-particles that have a finite size, such as those defined with an atom
-style of {sphere}.
-
-The {omegax}, {omegay}, and {omegaz} attributes are specific to
-finite-size spherical particles that have an angular velocity. Only
-certain atom styles, such as {sphere} define this quantity.
-
-The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
-finite-size aspherical particles that have an angular momentum. Only
-the {ellipsoid} atom style defines this quantity.
-
-The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
-can sustain a rotational torque due to interactions with other
-particles.
-
-The {c_ID} and {c_ID\[I\]} attributes allow per-atom vectors or arrays
-calculated by a "compute"_compute.html to be output. The ID in the
-attribute should be replaced by the actual ID of the compute that has
-been defined previously in the input script. See the
-"compute"_compute.html command for details. There are computes for
-calculating the per-atom energy, stress, centro-symmetry parameter,
-and coordination number of individual atoms.
-
-Note that computes which calculate global or local quantities, as
-opposed to per-atom quantities, cannot be output in a dump custom
-command. Instead, global quantities can be output by the
-"thermo_style custom"_thermo_style.html command, and local quantities
-can be output by the dump local command.
-
-If {c_ID} is used as a attribute, then the per-atom vector calculated
-by the compute is printed. If {c_ID\[I\]} is used, then I must be in
-the range from 1-M, which will print the Ith column of the per-atom
-array with M columns calculated by the compute. See the discussion
-above for how I can be specified with a wildcard asterisk to
-effectively specify multiple values.
-
-The {f_ID} and {f_ID\[I\]} attributes allow vector or array per-atom
-quantities calculated by a "fix"_fix.html to be output. The ID in the
-attribute should be replaced by the actual ID of the fix that has been
-defined previously in the input script. The "fix
-ave/atom"_fix_ave_atom.html command is one that calculates per-atom
-quantities. Since it can time-average per-atom quantities produced by
-any "compute"_compute.html, "fix"_fix.html, or atom-style
-"variable"_variable.html, this allows those time-averaged results to
-be written to a dump file.
-
-If {f_ID} is used as a attribute, then the per-atom vector calculated
-by the fix is printed. If {f_ID\[I\]} is used, then I must be in the
-range from 1-M, which will print the Ith column of the per-atom array
-with M columns calculated by the fix. See the discussion above for
-how I can be specified with a wildcard asterisk to effectively specify
-multiple values.
-
-The {v_name} attribute allows per-atom vectors calculated by a
-"variable"_variable.html to be output. The name in the attribute
-should be replaced by the actual name of the variable that has been
-defined previously in the input script. Only an atom-style variable
-can be referenced, since it is the only style that generates per-atom
-values. Variables of style {atom} can reference individual atom
-attributes, per-atom atom attributes, thermodynamic keywords, or
-invoke other computes, fixes, or variables when they are evaluated, so
-this is a very general means of creating quantities to output to a
-dump file.
-
-The {d_name} and {i_name} attributes allow to output custom per atom
-floating point or integer properties that are managed by
-"fix property/atom"_fix_property_atom.html.
-
-See "Section 10"_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 gzipped dump files, you must either compile LAMMPS with the
--DLAMMPS_GZIP option or use the styles from the COMPRESS package
-- see the "Making LAMMPS"_Section_start.html#start_2 section of
-the documentation.
-
-The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part
-of the COMPRESS package. They are only enabled if LAMMPS was built
-with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
-
-The {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles
-are part of the MPIIO package. They are only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
-
-The {xtc} style is part of the MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
-
-[Related commands:]
-
-"dump h5md"_dump_h5md.html, "dump image"_dump_image.html,
-"dump molfile"_dump_molfile.html, "dump_modify"_dump_modify.html,
-"undump"_undump.html
-
-[Default:]
-
-The defaults for the {image} and {movie} styles are listed on the
-"dump image"_dump_image.html doc page.
diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt
deleted file mode 100644
index 6de6de545e..0000000000
--- a/doc/dump_modify.txt
+++ /dev/null
@@ -1,1090 +0,0 @@
-"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
-these keywords apply to various dump styles :l
-keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
- {append} arg = {yes} or {no}
- {at} arg = N
- N = index of frame written upon first dump
- {buffer} arg = {yes} or {no}
- {delay} arg = Dstep
- Dstep = delay output until this timestep
- {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} args = {line} string, {int} string, {float} string, M string, or {none}
- string = C-style format string
- M = integer from 1 to N, where N = # of per-atom quantities being 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
- {pbc} arg = {yes} or {no} = remap atoms via periodic boundary conditions
- {precision} arg = power-of-10 value from 10 to 1000000
- {region} arg = region-ID or "none"
- {refresh} arg = c_ID = compute ID that supports a refresh operation
- {scale} arg = {yes} or {no}
- {sfactor} arg = coordinate scaling factor (> 0.0)
- {thermo} arg = {yes} or {no}
- {tfactor} arg = time scaling factor (> 0.0)
- {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 operator value
- attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
- operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
- value = numeric value to compare to, or LAST
- these 3 args can be replaced by the word "none" to turn off thresholding
- {unwrap} arg = {yes} or {no} :pre
-these keywords apply only to the {image} and {movie} "styles"_dump_image.html :l
-keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l
- {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
- {backcolor} arg = color
- color = name of color for background
- {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)
- {boxcolor} arg = color
- color = name of color for simulation box lines and processor sub-domain 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
- {bitrate} arg = rate
- rate = target bitrate for movie in kbps
- {framerate} arg = fps
- fps = frames per second for movie :pre
-:ule
-
-[Examples:]
-
-dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
-dump_modify 1 format float %20.15g 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 sfactor 0.1
-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.
-
-As explained on the "dump"_dump.html doc page, the {atom/mpiio},
-{custom/mpiio}, and {xyz/mpiio} dump styles are identical in command
-syntax and in the format of the dump files they create, to the
-corresponding styles without "mpiio", except the single dump file they
-produce is written in parallel via the MPI-IO library. Thus if a
-dump_modify option below is valid for the {atom} style, it is also
-valid for the {atom/mpiio} style, and similarly for the other styles
-which allow for use of MPI-IO.
-
-:line
-:line
-
-These keywords apply to various dump styles, including the "dump
-image"_dump_image.html and "dump movie"_dump_image.html styles. The
-description gives details.
-
-: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 or image/movie 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.
-
-:line
-
-The {at} keyword only applies to the {netcdf} dump style. It can only
-be used if the {append yes} keyword is also used. The {N} argument is
-the index of which frame to append to. A negative value can be
-specified for {N}, which means a frame counted from the end of the
-file. The {at} keyword can only be used if the dump_modify command is
-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 {buffer} keyword applies only to dump styles {atom}, {cfg},
-{custom}, {local}, and {xyz}. It also applies only to text output
-files, not to binary or gzipped files. If specified as {yes}, which
-is the default, then each processor writes its output into an internal
-text buffer, which is then sent to the processor(s) which perform file
-writes, and written by those processors(s) as one large chunk of text.
-If specified as {no}, each processor sends its per-atom data in binary
-format to the processor(s) which perform file wirtes, and those
-processor(s) format and write it line by line into the output file.
-
-The buffering mode is typically faster since each processor does the
-relatively expensive task of formatting the output for its own atoms.
-However it requires about twice the memory (per processor) for the
-extra buffering.
-
-:line
-
-The {delay} keyword applies to all dump styles. No snapshots will be
-output until the specified {Dstep} timestep or later. Specifying
-{Dstep} < 0 is the same as turning off the delay setting. This is a
-way to turn off unwanted output early in a simulation, for example,
-during an equilibration phase.
-
-:line
-
-The {element} keyword applies only to 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
-
-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}.
-
-:line
-
-The {format} keyword can be used to change the default numeric format
-output by the text-based dump styles: {atom}, {custom}, {cfg}, and
-{xyz} styles, and their MPIIO variants. Only the {line} or {none}
-options can be used with the {atom} and {xyz} styles.
-
-All the specified format strings are C-style formats, e.g. as used by
-the C/C++ printf() command. The {line} keyword takes a single
-argument which is the format string for an entire line of output for
-each atom (do not include a trailing "\n"), with N fields, which you
-must enclose in quotes if it is more than one field. The {int} and
-{float} keywords take a single format argument and are applied to all
-integer or floating-point quantities output. The setting for {M
-string} also takes a single format argument which is used for the Mth
-value output in each line, e.g. the 5th column is output in high
-precision for "format 5 %20.15g".
-
-NOTE: When using the {line} keyword for the {cfg} style, the first two
-fields (atom ID and type) are not actually written into the CFG file,
-however you must include formats for them in the format string.
-
-The {format} keyword can be used multiple times. The precedence is
-that for each value in a line of output, the {M} format (if specified)
-is used, else the {int} or {float} setting (if specified) is used,
-else the {line} setting (if specified) for that value is used, else
-the default setting is used. A setting of {none} clears all previous
-settings, reverting all values to their default format.
-
-NOTE: Atom and molecule IDs are stored internally as 4-byte or 8-byte
-signed integers, depending on how LAMMPS was compiled. When
-specifying the {format int} option you can use a "%d"-style format
-identifier in the format string and LAMMPS will convert this to the
-corresponding 8-byte form it it is needed when outputting those
-values. However, when specifying the {line} option or {format M
-string} option for those values, you should specify a format string
-appropriate for an 8-byte signed integer, e.g. one with "%ld", if
-LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs.
-
-NOTE: Any value written to a text-based dump file that is a per-atom
-quantity calculated by a "compute"_compute.html or "fix"_fix.html is
-stored internally as a floating-point value. If the value is actually
-an integer and you wish it to appear in the text dump file as a
-(large) integer, then you need to use an appropriate format. For
-example, these commands:
-
-compute 1 all property/local batom1 batom2
-dump 1 all local 100 tmp.bonds index c_1\[1\] c_1\[2\]
-dump_modify 1 format "%d %0.0f %0.0f" :pre
-
-will output the two atom IDs for atoms in each bond as integers. If
-the dump_modify command were omitted, they would appear as
-floating-point values, assuming they were large integers (more than 6
-digits). The "index" keyword should use the "%d" format since it is
-not generated by a compute or fix, and is stored internally as an
-integer.
-
-:line
-
-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 information, 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}, {image}, {movie}, {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 {pbc} keyword applies to all the dump styles. As explained on the
-"dump"_dump.html doc page, atom coordinates in a dump file may be
-slightly outside the simulation box. This is because periodic
-boundary conditions are enforced only on timesteps when neighbor lists
-are rebuilt, which will not typically coincide with the timesteps dump
-snapshots are written. If the setting of this keyword is set to
-{yes}, then all atoms will be remapped to the periodic box before the
-snapshot is written, then restored to their original position. If it
-is set to {no} they will not be. The {no} setting is the default
-because it requires no extra computation.
-
-: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 {refresh} keyword only applies to the dump {custom}, {cfg},
-{image}, and {movie} styles. It allows an "incremental" dump file to
-be written, by refreshing a compute that is used as a threshold for
-determining which atoms are included in a dump snapshot. The
-specified {c_ID} gives the ID of the compute. It is prefixed by "c_"
-to indicate a compute, which is the only current option. At some
-point, other options may be added, e.g. fixes or variables.
-
-NOTE: This keyword can only be specified once for a dump. Refreshes
-of multiple computes cannot yet be performed.
-
-The definition and motivation of an incremental dump file is as
-follows. Instead of outputting all atoms at each snapshot (with some
-associated values), you may only wish to output the subset of atoms
-with a value that has changed in some way compared to the value the
-last time that atom was output. In some scenarios this can result in
-a dramatically smaller dump file. If desired, by post-processing the
-sequence of snapshots, the values for all atoms at all timesteps can
-be inferred.
-
-A concrete example is a simulation of atom diffusion in a solid,
-represented as atoms on a lattice. Diffusive hops are rare. Imagine
-that when a hop occurs an atom moves more than a distance {Dhop}. For
-any snapshot we only want to output atoms that have hopped since the
-last snapshot. This can be accomplished with something the following
-commands:
-
-variable Dhop equal 0.6
-variable check atom "c_dsp[4] > v_Dhop"
-compute dsp all displace/atom refresh check
-dump 1 all custom 20 tmp.dump id type x y z
-dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre
-
-The "compute displace/atom"_compute_displace_atom.html command
-calculates the displacement of each atom from its reference position.
-The "4" index is the scalar displacement; 1,2,3 are the xyz components
-of the displacement. The "dump_modify thresh"_dump_modify.html
-command will cause only atoms that have displaced more than 0.6
-Angstroms to be output on a given snapshot (assuming metal units).
-However, note that when an atom is output, we also need to update the
-reference position for that atom to its new coordinates. So that it
-will not be output in every snapshot thereafter. That reference
-position is stored by "compute
-displace/atom"_compute_displace_atom.html. So the dump_modify
-{refresh} option triggers a call to compute displace/atom at the end
-of every dump to perform that update. The {refresh check} option
-shown as part of the "compute
-displace/atom"_compute_displace_atom.html command enables the compute
-to respond to the call from the dump command, and update the
-appropriate reference positions. This is done be defining an
-"atom-style variable"_variable.html, {check} in this example, which
-calculates a Boolean value (0 or 1) for each atom, based on the same
-criterion used by dump_modify thresh.
-
-See the "compute displace/atom"_compute_displace_atom.html command for
-more details, including an example of how to produce output that
-includes an initial snapshot with the reference position of all atoms.
-
-Note that only computes with a {refresh} option will work with
-dump_modify refresh. See individual compute doc pages for details.
-Currently, only compute displace/atom supports this option. Others
-may be added at some point. If you use a compute that doesn't support
-refresh operations, LAMMPS will not complain; dump_modify refresh will
-simply do nothing.
-
-:line
-
-The {region} keyword only applies to the dump {custom}, {cfg},
-{image}, and {movie} styles. If specified, only atoms in the region
-will be written to the dump file or included in the image/movie. 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 simulation 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 {sfactor} and {tfactor} keywords only apply to the dump {xtc}
-style. They allow customization of the unit conversion factors used
-when writing to XTC files. By default they are initialized for
-whatever "units"_units.html style is being used, to write out
-coordinates in nanometers and time in picoseconds. I.e. for {real}
-units, LAMMPS defines {sfactor} = 0.1 and {tfactor} = 0.001, since the
-Angstroms and fmsec used by {real} units are 0.1 nm and 0.001 psec
-respectively. If you are using a units system with distance and time
-units far from nm and psec, you may wish to write XTC files with
-different units, since the compression algorithm used in XTC files is
-most effective when the typical magnitude of position data is between
-10.0 and 0.1.
-
-: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.
-
-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 {thermo} keyword only applies the dump {netcdf} style. It
-triggers writing of "thermo"_thermo.html information to the dump file
-alongside per-atom data. The values included in the dump file are
-identical to the values specified by "thermo_style"_thermo_style.html.
-
-:line
-
-The {thresh} keyword only applies to the dump {custom}, {cfg},
-{image}, and {movie} 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 a different attributes can be used than those output by the "dump
-custom"_dump.html command. E.g. you can output the coordinates and
-stress of atoms whose energy is above some threshold.
-
-If an atom-style variable is used as the attribute, then it can
-produce continuous numeric values or effective Boolean 0/1 values
-which may be useful for the comparison operator. Boolean values can
-be generated by variable formulas that use comparison or Boolean math
-operators or special functions like gmask() and rmask() and grmask().
-See the "variable"_variable.html command doc page for details.
-
-The specified value must be a simple numeric value or the word LAST.
-If LAST is used, it refers to the value of the attribute the last time
-the dump command was invoked to produce a snapshot. This is a way to
-only dump atoms whose attribute has changed (or not changed).
-Three examples follow.
-
-dump_modify ... thresh ix != LAST :pre
-
-This will dump atoms which have crossed the periodic x boundary of the
-simulation box since the last dump. (Note that atoms that crossed
-once and then crossed back between the two dump timesteps would not be
-included.)
-
-region foo sphere 10 20 10 15
-variable inregion atom rmask(foo)
-dump_modify ... thresh v_inregion |^ LAST
-
-This will dump atoms which crossed the boundary of the spherical
-region since the last dump.
-
-variable charge atom "(q > 0.5) || (q < -0.5)"
-dump_modify ... thresh v_charge |^ LAST
-
-This will dump atoms whose charge has changed from an absolute value
-less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
-E.g. due to reactions and subsequent charge equilibration in a
-reactive force field.
-
-The choice of operators listed above are the usual comparison
-operators. The XOR operation (exclusive or) is also included as "|^".
-In this context, XOR means that if either the attribute or value is
-0.0 and the other is non-zero, then the result is "true" and the
-threshold criterion is met. Otherwise it is not met.
-
-: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
-:line
-
-These keywords apply only to the "dump image"_dump_image.html and
-"dump movie"_dump_image.html styles. Any keyword that affects an
-image, also affects a movie, since the movie is simply a collection of
-images. Some of the keywords only affect the "dump
-movie"_dump_image.html style. The descriptions give details.
-
-:line
-
-The {acolor} keyword 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 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 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 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.
-
-Here is an example of using a sequential color map to color all the
-atoms in individual molecules with a different color. See the
-examples/pour/in.pour.2d.molecule input script for an example of how
-this is used.
-
-variable colors string &
- "red green blue yellow white &
- purple pink orange lime gray"
-variable mol atom mol%10
-dump 1 all image 250 image.*.jpg v_mol type &
- zoom 1.6 adiam 1.5
-dump_modify 1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
-
-In this case, 10 colors are defined, and molecule IDs are
-mapped to one of the colors, even if there are 1000s of molecules.
-
-:line
-
-The {backcolor} 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 {bcolor} keyword 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 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 {bitrate} keyword can be used with the "dump
-movie"_dump_image.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 the
-bitrate to be set. If not, the setting is silently ignored.
-
-:line
-
-The {boxcolor} keyword sets the color of the simulation box drawn
-around the atoms in each image as well as the color of processor
-sub-domain boundaries. See the "dump image box" command for how to
-specify that a box be drawn via the {box} keyword, and the sub-domain
-boundaries via the {subbox} keyword. 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 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 {framerate} keyword can be used with the "dump
-movie"_dump_image.html command to define the duration of the resulting
-movie file. Movie files written by the dump {movie} command have a
-default 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
-:line
-
-[Restrictions:] none
-
-[Related commands:]
-
-"dump"_dump.html, "dump image"_dump_image.html, "undump"_undump.html
-
-[Default:]
-
-The option defaults are
-
-append = no
-buffer = yes for dump styles {atom}, {custom}, {loca}, and {xyz}
-element = "C" for every atom type
-every = whatever it was set to via the "dump"_dump.html command
-fileper = # of processors
-first = no
-flush = yes
-format = %d and %g for each integer or floating point value
-image = no
-label = ENTRIES
-nfile = 1
-pad = 0
-pbc = no
-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
-
-acolor = * red/green/blue/yellow/aqua/cyan
-adiam = * 1.0
-amap = min max cf 0.0 2 min blue max red
-backcolor = black
-bcolor = * red/green/blue/yellow/aqua/cyan
-bdiam = * 0.5
-bitrate = 2000
-boxcolor = yellow
-color = 140 color names are pre-defined as listed below
-framerate = 24 :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/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 4f33d8bd95..0d7e069e06 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -497,6 +497,7 @@ in the command's documentation.
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
+"reset_ids"_reset_ids.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt
index decf0bc8b9..150a6fb30e 100644
--- a/doc/src/compute_displace_atom.txt
+++ b/doc/src/compute_displace_atom.txt
@@ -12,18 +12,23 @@ compute displace/atom command :h3
compute ID group-ID displace/atom :pre
-ID, group-ID are documented in "compute"_compute.html command
-displace/atom = style name of this compute command :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+displace/atom = style name of this compute command :l
+zero or more keyword/arg pairs may be appended :l
+keyword = {refresh} :l
+ {replace} arg = per-atom variable ID :pre
+:ule
[Examples:]
-compute 1 all displace/atom :pre
+compute 1 all displace/atom
+compute 1 all displace/atom refresh myVar :pre
[Description:]
Define a computation that calculates the current displacement of each
-atom in the group from its original coordinates, including all effects
-due to atoms passing thru periodic boundaries.
+atom in the group from its original (reference) coordinates, including
+all effects due to atoms passing thru periodic boundaries.
A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
@@ -49,6 +54,65 @@ This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with time=0 atom coordinates from the restart file.
+:line
+
+The {refresh} option can be used in conjuction with the "dump_modify
+refresh" command to generate incremental dump files.
+
+The definition and motivation of an incremental dump file is as
+follows. Instead of outputting all atoms at each snapshot (with some
+associated values), you may only wish to output the subset of atoms
+with a value that has changed in some way compared to the value the
+last time that atom was output. In some scenarios this can result in
+a dramatically smaller dump file. If desired, by post-processing the
+sequence of snapshots, the values for all atoms at all timesteps can
+be inferred.
+
+A concrete example using this compute, is a simulation of atom
+diffusion in a solid, represented as atoms on a lattice. Diffusive
+hops are rare. Imagine that when a hop occurs an atom moves more than
+a distance {Dhop}. For any snapshot we only want to output atoms that
+have hopped since the last snapshot. This can be accomplished with
+something like the following commands:
+
+write_dump all custom tmp.dump id type x y z # see comment below :pre
+
+variable Dhop equal 0.6
+variable check atom "c_dsp[4] > v_Dhop"
+compute dsp all displace/atom refresh check
+dump 1 all custom 100 tmp.dump id type x y z
+dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} &
+ refresh c_dsp delay 100 :pre
+
+The "dump_modify thresh"_dump_modify.html command will only ouptut
+atoms that have displaced more than 0.6 Angstroms on each snapshot
+(assuming metal units). The dump_modify {refresh} option triggers a
+call to this compute at the end of every dump.
+
+The {refresh} argument for this compute is the ID of an "atom-style
+variable"_variable.html which calculates a Boolean value (0 or 1)
+based on the same criterion used by dump_modify thresh. This compute
+evaluates the atom-style variable. For each atom that returns 1
+(true), the original (reference) coordinates of the atom (stored by
+this compute) are updated.
+
+The effect of these commands is that a particular atom will only be
+output in the dump file on the snapshot after it makes a diffusive
+hop. It will not be output again until it makes another hop.
+
+Note that in the first snapshot of a subsequent run, no atoms will be
+typically be output. That is because the initial displacement for all
+atoms is 0.0. If an initial dump snapshot is desired, containing the
+initial reference positions of all atoms, one way to do this is
+illustrated above. An initial write_dump command can be used before
+the first run. It will contain the positions of all the atoms,
+Options in the "dump_modify"_dump_modify.html command above will
+append new output to that same file and delay the output until a later
+timestep. The {delay} setting avoids a second time = 0 snapshot which
+would be empty.
+
+:line
+
[Output info:]
This compute calculates a per-atom array with 4 columns, which can be
@@ -59,6 +123,10 @@ options.
The per-atom array values will be in distance "units"_units.html.
+This compute supports the {refresh} option as explained above, for use
+in conjunction with "dump_modify refresh"_dump_modify.html to generate
+incremental dump files.
+
[Restrictions:] none
[Related commands:]
diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt
index ad13879c6d..5d824ae1ef 100644
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@@ -264,11 +264,15 @@ spacings.
Atom IDs are assigned to created atoms in the following way. The
collection of created atoms are assigned consecutive IDs that start
immediately following the largest atom ID existing before the
-create_atoms command was invoked. When a simulation is performed on
-different numbers of processors, there is no guarantee a particular
-created atom will be assigned the same ID. If molecules are being
-created, molecule IDs are assigned to created molecules in a similar
-fashion.
+create_atoms command was invoked. This is done by the processor's
+communicating the number of atoms they each own, the first processor
+numbering its atoms from 1 to N1, the second processor from N1+1 to
+N2, etc. Where N1 = number of atoms owned by the first processor, N2
+= number owned by the second processor, etc. Thus when the same
+simulation is performed on different numbers of processors, there is
+no guarantee a particular created atom will be assigned the same ID in
+both simulations. If molecules are being created, molecule IDs are
+assigned to created molecules in a similar fashion.
Aside from their ID, atom type, and xyz position, other properties of
created atoms are set to default values, depending on which quantities
diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt
index f3dfc7eba9..1aa71d341f 100644
--- a/doc/src/delete_atoms.txt
+++ b/doc/src/delete_atoms.txt
@@ -80,7 +80,15 @@ deleted, then atom IDs are re-assigned so that they run from 1 to the
number of atoms in the system. Note that this is not done for
molecular systems (see the "atom_style"_atom_style.html command),
regardless of the {compress} setting, since it would foul up the bond
-connectivity that has already been assigned.
+connectivity that has already been assigned. However, the
+"reset_ids"_reset_ids.html command can be used after this command to
+accomplish the same thing.
+
+Note that the re-assignement of IDs is not really a compression, where
+gaps in atom IDs are removed by decrementing atom IDs that are larger.
+Instead the IDs for all atoms are erased, and new IDs are assigned so
+that the atoms owned by individual processors have consecutive IDs, as
+the "create_atoms"_create_atoms.html command explains.
A molecular system with fixed bonds, angles, dihedrals, or improper
interactions, is one where the topology of the interactions is
@@ -137,7 +145,7 @@ using molecule template files via the "molecule"_molecule.html and
[Related commands:]
-"create_atoms"_create_atoms.html
+"create_atoms"_create_atoms.html, "reset_ids"_reset_ids.html
[Default:]
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index 1e6acc67e6..9c386e2410 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -120,9 +120,10 @@ which dump output is written can also be controlled by a variable.
See the "dump_modify every"_dump_modify.html command.
Only information for atoms in the specified group is dumped. The
-"dump_modify thresh and region"_dump_modify.html commands can also
-alter what atoms are included. Not all styles support all these
-options; see details below.
+"dump_modify thresh and region and refresh"_dump_modify.html commands
+can also alter what atoms are included. Not all styles support all
+these options; see details on the "dump_modify"_dump_modify.html doc
+page.
As described below, the filename determines the kind of output (text
or binary or gzipped, one big file or one per timestep, one big file
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index db727c2d4f..6de6de545e 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -15,11 +15,13 @@ 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
these keywords apply to various dump styles :l
-keyword = {append} or {at} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
{append} arg = {yes} or {no}
{at} arg = N
N = index of frame written upon first dump
{buffer} arg = {yes} or {no}
+ {delay} arg = Dstep
+ Dstep = delay output until this timestep
{element} args = E1 E2 ... EN, where N = # of atom types
E1,...,EN = element name, e.g. C or Fe or Ga
{every} arg = N
@@ -41,6 +43,7 @@ keyword = {append} or {at} or {buffer} or {element} or {every} or {fileper} or {
{pbc} arg = {yes} or {no} = remap atoms via periodic boundary conditions
{precision} arg = power-of-10 value from 10 to 1000000
{region} arg = region-ID or "none"
+ {refresh} arg = c_ID = compute ID that supports a refresh operation
{scale} arg = {yes} or {no}
{sfactor} arg = coordinate scaling factor (> 0.0)
{thermo} arg = {yes} or {no}
@@ -174,6 +177,14 @@ extra buffering.
:line
+The {delay} keyword applies to all dump styles. No snapshots will be
+output until the specified {Dstep} timestep or later. Specifying
+{Dstep} < 0 is the same as turning off the delay setting. This is a
+way to turn off unwanted output early in a simulation, for example,
+during an equilibration phase.
+
+:line
+
The {element} keyword applies only to 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
@@ -407,25 +418,70 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to
:line
-The {sfactor} and {tfactor} keywords only apply to the dump {xtc}
-style. They allow customization of the unit conversion factors used
-when writing to XTC files. By default they are initialized for
-whatever "units"_units.html style is being used, to write out
-coordinates in nanometers and time in picoseconds. I.e. for {real}
-units, LAMMPS defines {sfactor} = 0.1 and {tfactor} = 0.001, since the
-Angstroms and fmsec used by {real} units are 0.1 nm and 0.001 psec
-respectively. If you are using a units system with distance and time
-units far from nm and psec, you may wish to write XTC files with
-different units, since the compression algorithm used in XTC files is
-most effective when the typical magnitude of position data is between
-10.0 and 0.1.
-
-:line
-
-The {thermo} keyword ({netcdf} only) triggers writing of "thermo"_thermo.html
-information to the dump file alongside per-atom data. The data included in the
-dump file is identical to the data specified by
-"thermo_style"_thermo_style.html.
+The {refresh} keyword only applies to the dump {custom}, {cfg},
+{image}, and {movie} styles. It allows an "incremental" dump file to
+be written, by refreshing a compute that is used as a threshold for
+determining which atoms are included in a dump snapshot. The
+specified {c_ID} gives the ID of the compute. It is prefixed by "c_"
+to indicate a compute, which is the only current option. At some
+point, other options may be added, e.g. fixes or variables.
+
+NOTE: This keyword can only be specified once for a dump. Refreshes
+of multiple computes cannot yet be performed.
+
+The definition and motivation of an incremental dump file is as
+follows. Instead of outputting all atoms at each snapshot (with some
+associated values), you may only wish to output the subset of atoms
+with a value that has changed in some way compared to the value the
+last time that atom was output. In some scenarios this can result in
+a dramatically smaller dump file. If desired, by post-processing the
+sequence of snapshots, the values for all atoms at all timesteps can
+be inferred.
+
+A concrete example is a simulation of atom diffusion in a solid,
+represented as atoms on a lattice. Diffusive hops are rare. Imagine
+that when a hop occurs an atom moves more than a distance {Dhop}. For
+any snapshot we only want to output atoms that have hopped since the
+last snapshot. This can be accomplished with something the following
+commands:
+
+variable Dhop equal 0.6
+variable check atom "c_dsp[4] > v_Dhop"
+compute dsp all displace/atom refresh check
+dump 1 all custom 20 tmp.dump id type x y z
+dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre
+
+The "compute displace/atom"_compute_displace_atom.html command
+calculates the displacement of each atom from its reference position.
+The "4" index is the scalar displacement; 1,2,3 are the xyz components
+of the displacement. The "dump_modify thresh"_dump_modify.html
+command will cause only atoms that have displaced more than 0.6
+Angstroms to be output on a given snapshot (assuming metal units).
+However, note that when an atom is output, we also need to update the
+reference position for that atom to its new coordinates. So that it
+will not be output in every snapshot thereafter. That reference
+position is stored by "compute
+displace/atom"_compute_displace_atom.html. So the dump_modify
+{refresh} option triggers a call to compute displace/atom at the end
+of every dump to perform that update. The {refresh check} option
+shown as part of the "compute
+displace/atom"_compute_displace_atom.html command enables the compute
+to respond to the call from the dump command, and update the
+appropriate reference positions. This is done be defining an
+"atom-style variable"_variable.html, {check} in this example, which
+calculates a Boolean value (0 or 1) for each atom, based on the same
+criterion used by dump_modify thresh.
+
+See the "compute displace/atom"_compute_displace_atom.html command for
+more details, including an example of how to produce output that
+includes an initial snapshot with the reference position of all atoms.
+
+Note that only computes with a {refresh} option will work with
+dump_modify refresh. See individual compute doc pages for details.
+Currently, only compute displace/atom supports this option. Others
+may be added at some point. If you use a compute that doesn't support
+refresh operations, LAMMPS will not complain; dump_modify refresh will
+simply do nothing.
:line
@@ -449,6 +505,21 @@ value of {no} means they are written in absolute distance units
:line
+The {sfactor} and {tfactor} keywords only apply to the dump {xtc}
+style. They allow customization of the unit conversion factors used
+when writing to XTC files. By default they are initialized for
+whatever "units"_units.html style is being used, to write out
+coordinates in nanometers and time in picoseconds. I.e. for {real}
+units, LAMMPS defines {sfactor} = 0.1 and {tfactor} = 0.001, since the
+Angstroms and fmsec used by {real} units are 0.1 nm and 0.001 psec
+respectively. If you are using a units system with distance and time
+units far from nm and psec, you may wish to write XTC files with
+different units, since the compression algorithm used in XTC files is
+most effective when the typical magnitude of position data is between
+10.0 and 0.1.
+
+: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
@@ -472,6 +543,13 @@ as well as memory, versus unsorted output.
:line
+The {thermo} keyword only applies the dump {netcdf} style. It
+triggers writing of "thermo"_thermo.html information to the dump file
+alongside per-atom data. The values included in the dump file are
+identical to the values specified by "thermo_style"_thermo_style.html.
+
+:line
+
The {thresh} keyword only applies to the dump {custom}, {cfg},
{image}, and {movie} styles. Multiple thresholds can be specified.
Specifying {none} turns off all threshold criteria. If thresholds are
diff --git a/doc/reset_ids.txt b/doc/src/reset_ids.txt
similarity index 100%
rename from doc/reset_ids.txt
rename to doc/src/reset_ids.txt
--
GitLab