fixing merge conflicts

.github/workflows/compile-msvc.yml

@@ -3,9 +3,11 @@ name: "Native Windows Compilation and Unit Tests"
 
 on:
   push:
-    branches: [ develop ]
+    branches:
+      - develop
   pull_request:
-    branches: [ $default-branch ]
+    branches:
+      - develop
 
   workflow_dispatch:
 

.github/workflows/unittest-macos.yml

@@ -3,9 +3,11 @@ name: "Unittest for MacOS"
 
 on:
   push:
-    branches: [ develop ]
+    branches:
+      - develop
   pull_request:
-    branches: [ $default-branch ]
+    branches:
+      - develop
 
   workflow_dispatch:
 

cmake/CMakeLists.txt

@@ -376,6 +376,7 @@ pkg_depends(DIELECTRIC EXTRA-PAIR)
 pkg_depends(CG-DNA MOLECULE)
 pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
+pkg_depends(EXTRA-MOLECULE MOLECULE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)

cmake/Modules/LAMMPSUtils.cmake

@@ -110,14 +110,16 @@ function(FetchPotentials pkgfolder potfolder)
       math(EXPR plusone "${blank}+1")
       string(SUBSTRING ${line} 0 ${blank} pot)
       string(SUBSTRING ${line} ${plusone} -1 sum)
-      if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
+      if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
         file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
       endif()
       if(NOT sum STREQUAL oldsum)
-        message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
+        message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
-        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
+        string(MD5 TMP_EXT "${CMAKE_BINARY_DIR}")
+        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
           EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
-        file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
+        file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
+        file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
       endif()
     endforeach()
   endif()

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   enable_language(C)

cmake/presets/clang.cmake

@@ -3,6 +3,13 @@
 # prefer flang over gfortran, if available
 find_program(CLANG_FORTRAN NAMES flang gfortran f95)
 set(ENV{OMPI_FC} ${CLANG_FORTRAN})
+get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
+if (_tmp_fc STREQUAL "flang")
+  set(FC_STD_VERSION "-std=f2018")
+  set(BUILD_MPI OFF)
+else()
+  set(FC_STD_VERSION "-std=f2003")
+endif()
 
 set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
@@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "3 August 2022" "2022-8-3"
+.TH LAMMPS "1" "15 September 2022" "2022-9-15"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 3 August 2022
+\- Molecular Dynamics Simulator.  Version 15 September 2022
 
 .SH SYNOPSIS
 .B lmp

doc/src/Bibliography.rst

@@ -1373,7 +1373,7 @@ Bibliography
    Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
 
 **(Ziegler)**
-   J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
+   J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
 
 **(Zimmerman2004)**
    Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.

doc/src/Commands_all.rst

@@ -15,7 +15,9 @@
 General commands
 ================
 
-An alphabetic list of general LAMMPS commands.
+An alphabetic list of general LAMMPS commands.  Note that style
+commands with many variants, can be more easily accessed via the small
+table above.
 
 .. table_from_list::
    :columns: 5
@@ -61,6 +63,7 @@ An alphabetic list of general LAMMPS commands.
    * :doc:`kspace_modify <kspace_modify>`
    * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`
+   * :doc:`labelmap <labelmap>`
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`

doc/src/Commands_fix.rst

@@ -165,6 +165,7 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
+   * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`

doc/src/Developer_updating.rst

@@ -328,7 +328,7 @@ removed so this update is **required** to avoid compilation failure.
 Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. versionchanged:: TBD
+.. versionchanged:: 15Sep2022
 
 This change splits the GLOBAL and PERATOM modes of fix STORE into two
 separate fixes STORE/GLOBAL and STORE/PERATOM.  There was very little
@@ -387,7 +387,7 @@ This change is **required** or else the code will not compile.
 Use Output::get_dump_by_id() instead of Output::find_dump()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. versionchanged:: TBD
+.. versionchanged:: 15Sep2022
 
 The accessor function to individual dump style instances has been changed
 from ``Output::find_dump()`` returning the index of the dump instance in

doc/src/Developer_utils.rst

@@ -175,6 +175,12 @@ and parsing files or arguments.
 .. doxygenfunction:: is_double
    :project: progguide
 
+.. doxygenfunction:: is_id
+   :project: progguide
+
+.. doxygenfunction:: is_type
+   :project: progguide
+
 Potential file functions
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -205,6 +211,9 @@ Argument processing
 .. doxygenfunction:: expand_args
    :project: progguide
 
+.. doxygenfunction:: expand_type
+   :project: progguide
+
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Errors_messages.rst

@@ -5453,6 +5453,11 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Mass command must set a type from 1-N where N is the number of atom
    types.
 
+*Invalid label2type() function syntax in variable formula*
+   The first argument must be a label map kind (atom, bond, angle,
+   dihedral, or improper) and the second argument must be a valid type
+   label that has been assigned to a numeric type.
+
 *Invalid use of library file() function*
    This function is called through the library interface.  This
    error should not occur.  Contact the developers if it does.
@@ -5585,9 +5590,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *LJ6 off not supported in pair_style buck/long/coul/long*
    Self-explanatory.
 
+*Label map is incomplete: all types must be assigned a unique type label*
+   For a given type-kind (atom types, bond types, etc.) to be written to
+   the data file, all associated types must be assigned a type label, and
+   each type label can be assigned to only one numeric type.
+
 *Label wasn't found in input script*
    Self-explanatory.
 
+*Labelmap command before simulation box is defined*
+   The labelmap command cannot be used before a read_data,
+   read_restart, or create_box command.
+
 *Lattice orient vectors are not orthogonal*
    The three specified lattice orientation vectors must be mutually
    orthogonal.
@@ -5863,6 +5877,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Must not have multiple fixes change box parameter ...*
    Self-explanatory.
 
+*Must read Angle Type Labels before Angles*
+   An Angle Type Labels section of a data file must come before the Angles section.
+
+*Must read Atom Type Labels before Atoms*
+   An Atom Type Labels section of a data file must come before the Atoms section.
+
 *Must read Atoms before Angles*
    The Atoms section of a data file must come before an Angles section.
 
@@ -5893,6 +5913,15 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    The Atoms section of a data file must come before a Velocities
    section.
 
+*Must read Bond Type Labels before Bonds*
+   A Bond Type Labels section of a data file must come before the Bonds section.
+
+*Must read Dihedral Type Labels before Dihedrals*
+   An Dihedral Type Labels section of a data file must come before the Dihedrals section.
+
+*Must read Improper Type Labels before Impropers*
+   An Improper Type Labels section of a data file must come before the Impropers section.
+
 *Must re-specify non-restarted pair style (xxx) after read_restart*
    For pair styles, that do not store their settings in a restart file,
    it must be defined with a new 'pair_style' command after read_restart.
@@ -7849,6 +7878,10 @@ keyword to allow for additional bonds to be formed
    Number of local atoms times number of columns must fit in a 32-bit
    integer for dump.
 
+*Topology type exceeds system topology type*
+   The number of bond, angle, etc types exceeds the system setting. See
+   the create_box or read_data command for how to specify these values.
+
 *Tree structure in joint connections*
    Fix poems cannot (yet) work with coupled bodies whose joints connect
    the bodies in a tree structure.
@@ -7873,6 +7906,13 @@ keyword to allow for additional bonds to be formed
 *Two groups cannot be the same in fix spring couple*
    Self-explanatory.
 
+*The %s type label %s is already in use for type %s*
+   For a given type-kind (atom types, bond types, etc.), a given type
+   label can be assigned to only one numeric type.
+
+*Type label string %s for %s type %s is invalid*
+   See the labelmap command documentation for valid type labels.
+
 *Unable to initialize accelerator for use*
    There was a problem initializing an accelerator for the gpu package
 

doc/src/Howto.rst

@@ -34,6 +34,7 @@ Settings howto
    :maxdepth: 1
 
    Howto_2d
+   Howto_type_labels
    Howto_triclinic
    Howto_thermostat
    Howto_barostat

doc/src/Howto_type_labels.rst

@@ -0,0 +1,126 @@
+Type labels
+===========
+
+.. versionadded:: 15Sep2022
+
+Each atom in LAMMPS has an associated numeric atom type. Similarly,
+each bond, angle, dihedral, and improper is assigned a bond type,
+angle type, and so on.  The primary use of these types is to map
+potential (force field) parameters to the interactions of the atom,
+bond, angle, dihedral, and improper.
+
+By default, type values are entered as integers from 1 to Ntypes
+wherever they appear in LAMMPS input or output files.  The total number
+Ntypes for each interaction is "locked in" when the simulation box
+is created.
+
+A recent addition to LAMMPS is the option to use strings - referred
+to as type labels - as an alternative.  Using type labels instead of
+numeric types can be advantageous in various scenarios.  For example,
+type labels can make inputs more readable and generic (i.e. usable through
+the :doc:`include command <include>` for different systems with different
+numerical values assigned to types.  This generality also applies to
+other inputs like data files read by :doc:`read_data <read_data>` or
+molecule template files read by the :doc:`molecule <molecule>`
+command.  See below for a list of other commands that can use
+type labels in different ways.
+
+LAMMPS will *internally* continue to use numeric types, which means
+that many previous restrictions still apply.  For example, the total
+number of types is locked in when creating the simulation box, and
+potential parameters for each type must be provided even if not used
+by any interactions.
+
+A collection of type labels for all type-kinds (atom types, bond types,
+etc.) is stored as a "label map" which is simply a list of numeric types
+and their associated type labels.  Within a type-kind, each type label
+must be unique.  It can be assigned to only one numeric type.  To read
+and write type labels to data files for a given type-kind, *all*
+associated numeric types need have a type label assigned.  Partial
+maps can be saved with the :doc:`labelmap write <labelmap>` command
+and read back with the :doc:`include <include>` command.
+
+Valid type labels can contain most ASCII characters, but cannot start
+with a number, a '#', or a '*'.  Also, labels must not contain whitespace
+characters.  When using the :doc:`labelmap command <labelmap>` in the
+LAMMPS input, if certain characters appear in the type label, such as
+the single (') or double (") quote or the '#' character, the label
+must be put in either double, single, or triple (""") quotes.  Triple
+quotes allow for the most generic type label strings, but they require
+to have a leading and trailing blank space.  When defining type labels
+the blanks will be ignored. Example:
+
+.. code-block:: LAMMPS
+
+   labelmap angle 1 """ C1'-C2"-C3# """
+
+This command will map the string ```C1'-C2"-C3#``` to the angle type 1.
+
+There are two ways to define label maps.  One is via the :doc:`labelmap
+<labelmap>` command.  The other is via the :doc:`read_data <read_data>`
+command.  A data file can have sections such as *Atom Type Labels*, *Bond
+Type Labels*, etc., which assign type labels to numeric types.  The
+label map can be written out to data files by the :doc:`write_data
+<write_data>` command.  This map is also written to and read from
+restart files, by the :doc:`write_restart <write_restart>` and
+:doc:`read_restart <read_restart>` commands.
+
+----------
+
+Use of type labels in LAMMPS input or output
+""""""""""""""""""""""""""""""""""""""""""""
+
+Many LAMMPS input script commands that take a numeric type as an
+argument can use the associated type label instead.  If a type label
+is not defined for a particular numeric type, only its numeric type
+can be used.
+
+This example assigns labels to the atom types, and then uses the type
+labels to redefine the pair coefficients.
+
+.. code-block:: LAMMPS
+
+   pair_coeff 1 2 1.0 1.0              # numeric types
+   labelmap atom 1 C 2 H
+   pair_coeff C H 1.0 1.0              # type labels
+
+Adding support for type labels to various commands is an ongoing
+project.  If an input script command (or a section in a file read by a
+command) allows substituting a type label for a numeric type argument,
+it will be explicitly mentioned in that command's documentation page.
+
+As a temporary measure, input script commands can take advantage of
+variables and how they can be expanded during processing of the input.
+The variables can use functions that will translate type label strings
+to their respective number as defined in the current label map.  See the
+:doc:`variable <variable>` command for details.
+
+For example, here is how the pair_coeff command could be used with
+type labels if it did not yet support them, either with an explicit
+variable command or an implicit variable used in the pair_coeff
+command.
+
+.. code-block:: LAMMPS
+
+   labelmap atom 1 C 2 H
+   variable atom1 equal label2type(atom,C)
+   variable atom2 equal label2type(atom,H)
+   pair_coeff ${atom1} ${atom2} 1.0 1.0
+
+.. code-block:: LAMMPS
+
+   labelmap atom 1 C 2 H
+   pair_coeff $(label2type(atom,C)) $(label2type(atom,H)) 80.0 1.2
+
+----------
+
+Commands that can use label types
+"""""""""""""""""""""""""""""""""
+
+Any workflow that involves reading multiple data files, molecule
+templates or a combination of the two can be streamlined by using type
+labels instead of numeric types, because types are automatically synced
+between the files.  The creation of simulation-ready reaction templates
+for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
+type labels, and results in templates that can be used without
+modification in multiple simulations or different systems.

doc/src/Packages_details.rst

@@ -276,7 +276,7 @@ the barostat as outlined in:
 
 N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
 accurately describe the structure, pressure, and compressibility of
-molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+molecular liquids", J. Chem. Phys. 143, 243148 (2015).
 
 **Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
 Pennsylvania State University)
@@ -652,7 +652,7 @@ short-range or long-range interactions.
 * :doc:`pair_style lj/cut/dipole/cut <pair_dipole>`
 * :doc:`pair_style lj/cut/dipole/long <pair_dipole>`
 * :doc:`pair_style lj/long/dipole/long <pair_dipole>`
-* :doc: `angle_style dipole <angle_dipole>`
+* :doc:`angle_style dipole <angle_dipole>`
 * examples/dipole
 
 ----------
@@ -932,6 +932,10 @@ EXTRA-MOLECULE package
 
 Additional bond, angle, dihedral, and improper styles that are less commonly used.
 
+**Install:**
+
+To use this package, also the :ref:`MOLECULE <PKG-MOLECULE>` package needs to be installed.
+
 **Supporting info:**
 
 * src/EXTRA-MOLECULE: filenames -> commands
@@ -1404,7 +1408,7 @@ This package has :ref:`specific installation instructions <machdyn>` on the :doc
 
 * src/MACHDYN: filenames -> commands
 * src/MACHDYN/README
-* doc/PDF/MACHDYN_LAMMPS_userguide.pdf
+* `doc/PDF/MACHDYN_LAMMPS_userguide.pdf <PDF/MACHDYN_LAMMPS_userguide.pdf>`_
 * examples/PACKAGES/machdyn
 * https://www.lammps.org/movies.html#smd
 
@@ -2703,7 +2707,7 @@ Dynamics, Ernst Mach Institute, Germany).
 
 * src/SPH: filenames -> commands
 * src/SPH/README
-* doc/PDF/SPH_LAMMPS_userguide.pdf
+* `doc/PDF/SPH_LAMMPS_userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_
 * examples/PACKAGES/sph
 * https://www.lammps.org/movies.html#sph
 

doc/src/Run_options.rst

@@ -495,7 +495,7 @@ run:
    write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
 
 Note that the specified restartfile and dumpfile names may contain
-wild-card characters ("\*","%") as explained on the
+wild-card characters ("\*" or "%") as explained on the
 :doc:`read_restart <read_restart>` and :doc:`write_dump <write_dump>` doc
 pages.  The use of "%" means that a parallel restart file and/or
 parallel dump file can be read and/or written.  Note that a filename

doc/src/Speed_intel.rst

@@ -536,6 +536,6 @@ supported.
 References
 """"""""""
 
-* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
+* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
 * Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
 * Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.

doc/src/accel_styles.rst

@@ -6,7 +6,7 @@ page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 
 These accelerated styles are part of the GPU, INTEL, KOKKOS,
-OPENMP and OPT packages, respectively.  They are only enabled if
+OPENMP, and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
 
 You can specify the accelerated styles explicitly in your input script

doc/src/angle_coeff.rst

@@ -10,7 +10,7 @@ Syntax
 
    angle_coeff N args
 
-* N = angle type (see asterisk form below)
+* N = numeric angle type (see asterisk form below), or type label
 * args = coefficients for one or more angle types
 
 Examples
@@ -22,6 +22,9 @@ Examples
    angle_coeff * 5.0
    angle_coeff 2*10 5.0
 
+   labelmap angle 1 hydroxyl
+   angle_coeff hydroxyl 300.0 107.0
+
 Description
 """""""""""
 
@@ -30,18 +33,24 @@ The number and meaning of the coefficients depends on the angle style.
 Angle coefficients can also be set in the data file read by the
 :doc:`read_data <read_data>` command or in a restart file.
 
-N can be specified in one of two ways.  An explicit numeric value can
+:math:`N` can be specified in one of two ways.  An explicit numeric
-be used, as in the first example above.  Or a wild-card asterisk can be
+value can be used, as in the first example above.  Or :math:`N` can be a
-used to set the coefficients for multiple angle types.  This takes the
+type label, which is an alphanumeric string defined by the
-form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of angle types,
+:doc:`labelmap <labelmap>` command or in a section of a data file read
-then an asterisk with no numeric values means all types from 1 to N.  A
+by the :doc:`read_data <read_data>` command.
-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).
 
-Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
+For numeric values only, a wild-card asterisk can be used to set the
-for the same angle type.  For example, these commands set the coeffs
+coefficients for multiple angle types.  This takes the form "\*" or
-for all angle types, then overwrite the coeffs for just angle type 2:
+"\*n" or "n\*" or "m\*n".  If :math:`N` is the number of angle types,
+then an asterisk with no numeric values means all types from 1 to
+:math:`N`.  A leading asterisk means all types from 1 to n (inclusive).
+A trailing asterisk means all types from n to :math:`N` (inclusive).  A
+middle asterisk means all types from m to n (inclusive).
+
+Note that using an :doc:`angle_coeff <angle_coeff>` command can
+override a previous setting for the same angle type.  For example,
+these commands set the coeffs for all angle types, then overwrite the
+coeffs for just angle type 2:
 
 .. code-block:: LAMMPS
 
@@ -49,11 +58,11 @@ for all angle types, then overwrite the coeffs for just angle type 2:
    angle_coeff 2 50.0 107.0
 
 A line in a data file that specifies angle coefficients uses the exact
-same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input
+same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
-script, except that wild-card asterisks should not be used since
+command in an input script, except that wild-card asterisks should not
-coefficients for all N types must be listed in the file.  For example,
+be used since coefficients for all :math:`N` types must be listed in the
-under the "Angle Coeffs" section of a data file, the line that
+file.  For example, under the "Angle Coeffs" section of a data file, the
-corresponds to the first example above would be listed as
+line that corresponds to the first example above would be listed as
 
 .. parsed-literal::
 
@@ -61,15 +70,14 @@ corresponds to the first example above would be listed as
 
 The :doc:`angle_style class2 <angle_class2>` is an exception to this
 rule, in that an additional argument is used in the input script to
-allow specification of the cross-term coefficients.   See its
+allow specification of the cross-term coefficients.  See its doc page
-doc page for details.
+for details.
 
 ----------
 
 The list of all angle styles defined in LAMMPS is given on the
 :doc:`angle_style <angle_style>` doc page.  They are also listed in more
-compact form on the :ref:`Commands angle <angle>` doc
+compact form on the :ref:`Commands angle <angle>` doc page.
-page.
 
 On either of those pages, click on the style to display the formula it
 computes and its coefficients as specified by the associated

doc/src/angle_mesocnt.rst

@@ -24,7 +24,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 15Sep2022
 
 The *mesocnt* angle style uses the potential
 

doc/src/bond_coeff.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_coeff N args
 
-* N = bond type (see asterisk form below)
+* N = numeric bond type (see asterisk form below), or type label
 * args = coefficients for one or more bond types
 
 Examples
@@ -21,7 +21,10 @@ Examples
    bond_coeff 5 80.0 1.2
    bond_coeff * 30.0 1.5 1.0 1.0
    bond_coeff 1*4 30.0 1.5 1.0 1.0
-   bond_coeff 1 harmonic 200.0 1.0
+   bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
+
+   labelmap bond 5 carbonyl
+   bond_coeff carbonyl 80.0 1.2
 
 Description
 """""""""""
@@ -31,14 +34,19 @@ The number and meaning of the coefficients depends on the bond style.
 Bond coefficients can also be set in the data file read by the
 :doc:`read_data <read_data>` command or in a restart file.
 
-N can be specified in one of two ways.  An explicit numeric value can
+:math:`N` can be specified in one of several ways.  An explicit numeric
-be used, as in the first example above.  Or a wild-card asterisk can be
+value can be used, as in the first example above.  Or :math:`N` can be a
-used to set the coefficients for multiple bond types.  This takes the
+type label, which is an alphanumeric string defined by the
-form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of bond types,
+:doc:`labelmap <labelmap>` command or in a section of a data file read
-then an asterisk with no numeric values means all types from 1 to N.  A
+by the :doc:`read_data <read_data>` command.
+
+For numeric values only, a wild-card asterisk can be used to set the
+coefficients for multiple bond types.  This takes the form "\*" or "\*n"
+or "n\*" or "m\*n".  If :math:`N` is the number of bond types, then an
+asterisk with no numeric values means all types from 1 to :math:`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
+asterisk means all types from n to :math:`N` (inclusive).  A middle
-means all types from m to n (inclusive).
+asterisk means all types from m to n (inclusive).
 
 Note that using a bond_coeff command can override a previous setting
 for the same bond type.  For example, these commands set the coeffs
@@ -52,8 +60,8 @@ for all bond types, then overwrite the coeffs for just bond type 2:
 A line in a data file that specifies bond coefficients uses the exact
 same format as the arguments of the bond_coeff command in an input
 script, except that wild-card asterisks should not be used since
-coefficients for all N types must be listed in the file.  For example,
+coefficients for all :math:`N` types must be listed in the file.  For
-under the "Bond Coeffs" section of a data file, the line that
+example, under the "Bond Coeffs" section of a data file, the line that
 corresponds to the first example above would be listed as
 
 .. parsed-literal::

doc/src/bond_mesocnt.rst

@@ -22,7 +22,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 15Sep2022
 
 The *mesocnt* bond style is a wrapper for the :doc:`harmonic
 <bond_harmonic>` style, and uses the potential

doc/src/commands_list.rst

@@ -56,6 +56,7 @@ Commands
    kspace_modify
    kspace_style
    label
+   labelmap
    lattice
    log
    mass

doc/src/compute_angmom_chunk.rst

@@ -78,7 +78,7 @@ These values can be accessed by any command that uses global array
 values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 mass-velocity-distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_born_matrix.rst

@@ -182,7 +182,7 @@ by any command that uses global values from a compute as input. See
 the :doc:`Howto output <Howto_output>` doc page for an overview of
 LAMMPS output options.
 
-The array values calculated by this compute are all "extensive."
+The array values calculated by this compute are all "extensive".
 
 Restrictions
 """"""""""""

doc/src/compute_com.rst

@@ -49,7 +49,7 @@ accessed by indices 1--3 by any command that uses global vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The vector values are "intensive."  The vector values will be in
+The vector values are "intensive".  The vector values will be in
 distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_com_chunk.rst

@@ -77,7 +77,7 @@ values can be accessed by any command that uses global array values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_dipole.rst

@@ -54,7 +54,7 @@ the computed dipole moment and a global vector of length 3 with the
 dipole vector.  See the :doc:`Howto output <Howto_output>` page for
 an overview of LAMMPS output options.
 
-The computed values are "intensive."  The array values will be in
+The computed values are "intensive".  The array values will be in
 dipole units (i.e., charge :doc:`units <units>` times distance
 :doc:`units <units>`).
 

doc/src/compute_dipole_chunk.rst

@@ -86,7 +86,7 @@ chunk. These values can be accessed by any command that uses global
 array values from a compute as input.  See the :doc:`Howto output
 <Howto_output>` page for an overview of LAMMPS output options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 dipole units (i.e., charge :doc:`units <units>` times distance
 :doc:`units <units>`).
 

doc/src/compute_erotate_asphere.rst

@@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_erotate_rigid.rst

@@ -48,7 +48,7 @@ of all the rigid bodies).  This value can be used by any command that
 uses a global scalar value from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_erotate_sphere.rst

@@ -44,7 +44,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_event_displace.rst

@@ -40,7 +40,7 @@ further than the threshold distance.
    If the system is undergoing significant center-of-mass motion,
    due to thermal motion, an external force, or an initial net momentum,
    then this compute will not be able to distinguish that motion from
-   local atom displacements and may generate "false positives."
+   local atom displacements and may generate "false positives".
 
 Output info
 """""""""""
@@ -50,7 +50,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
 scalar value will be a 0 or 1 as explained above.
 
 Restrictions

doc/src/compute_fep.rst

@@ -299,7 +299,7 @@ These output results can be used by any command that uses a global
 scalar or vector from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
 
-The values calculated by this compute are "extensive."
+The values calculated by this compute are "extensive".
 
 Restrictions
 """"""""""""

doc/src/compute_group_group.rst

@@ -140,7 +140,7 @@ vector values from a compute as input.  See the
 options.
 
 Both the scalar and vector values calculated by this compute are
-"extensive."  The scalar value will be in energy :doc:`units <units>`.
+"extensive".  The scalar value will be in energy :doc:`units <units>`.
 The vector values will be in force :doc:`units <units>`.
 
 Restrictions

doc/src/compute_gyration.rst

@@ -69,7 +69,7 @@ vector values from a compute as input.  See the :doc:`Howto output <Howto_output
 options.
 
 The scalar and vector values calculated by this compute are
-"intensive."  The scalar and vector values will be in distance and
+"intensive".  The scalar and vector values will be in distance and
 distance\ :math:`^2` :doc:`units <units>`, respectively.
 
 Restrictions

doc/src/compute_gyration_shape.rst

@@ -78,7 +78,7 @@ vector values from a compute as input.  See the
 options.
 
 The vector values calculated by this compute are
-"intensive."  The first five vector values will be in
+"intensive".  The first five vector values will be in
 distance\ :math:`2` :doc:`units <units>` while the sixth one is dimensionless.
 
 Restrictions

doc/src/compute_gyration_shape_chunk.rst

@@ -80,7 +80,7 @@ See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
 output options.
 
 The array calculated by this compute is
-"intensive."  The first five columns will be in
+"intensive".  The first five columns will be in
 distance\ :math:`^2` :doc:`units <units>` while the sixth one is dimensionless.
 
 Restrictions

doc/src/compute_heat_flux.rst

@@ -142,14 +142,14 @@ command that uses global vector values from a compute as input.
 See the :doc:`Howto output <Howto_output>` documentation for an overview of
 LAMMPS output options.
 
-The vector values calculated by this compute are "extensive," meaning
+The vector values calculated by this compute are "extensive", meaning
 they scale with the number of atoms in the simulation.  They can be
-divided by the appropriate volume to get a flux, which would then be
+divided by the appropriate volume to get a flux, which would then be an
-an "intensive" value, meaning independent of the number of atoms in
+"intensive" value, meaning independent of the number of atoms in the
-the simulation.  Note that if the compute is "all," then the
+simulation.  Note that if the compute group is "all", then the
-appropriate volume to divide by is the simulation box volume.
+appropriate volume to divide by is the simulation box volume.  However,
-However, if a sub-group is used, it should be the volume containing
+if a group with a subset of atoms is used, it should be the volume
-those atoms.
+containing those atoms.
 
 The vector values will be in energy\*velocity :doc:`units <units>`.  Once
 divided by a volume the units will be that of flux, namely

doc/src/compute_hma.rst

@@ -172,7 +172,7 @@ requested as arguments to the command (the potential energy, pressure and/or hea
 capacity).  The elements of the vector can be accessed by indices 1--n by any
 command that uses global vector values as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
 
-The vector values calculated by this compute are "extensive."  The
+The vector values calculated by this compute are "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_inertia_chunk.rst

@@ -84,7 +84,7 @@ by any command that uses global array values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 mass\*distance\ :math:`^2` :doc:`units <units>`.
 
 Restrictions

doc/src/compute_ke.rst

@@ -52,7 +52,7 @@ can be used by any command that uses a global scalar value from a
 compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_ke_rigid.rst

@@ -48,7 +48,7 @@ global scalar value from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_momentum.rst

@@ -37,7 +37,7 @@ length 3. This value can be used by any command that uses a global
 vector value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The vector value calculated by this compute is "extensive." The vector
+The vector value calculated by this compute is "extensive". The vector
 value will be in mass\*velocity :doc:`units <units>`.
 
 Restrictions

doc/src/compute_msd.rst

@@ -105,7 +105,7 @@ accessed by indices 1--4 by any command that uses global vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The vector values are "intensive."  The vector values will be in
+The vector values are "intensive".  The vector values will be in
 distance\ :math:`^2` :doc:`units <units>`.
 
 Restrictions

doc/src/compute_msd_chunk.rst

@@ -121,7 +121,7 @@ These values can be accessed by any command that uses global array values from
 a compute as input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 distance\ :math:`^2` :doc:`units <units>`.
 
 Restrictions

doc/src/compute_msd_nongauss.rst

@@ -67,7 +67,7 @@ accessed by indices 1--3 by any command that uses global vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The vector values are "intensive."  The first vector value will be in
+The vector values are "intensive".  The first vector value will be in
 distance\ :math:`^2` :doc:`units <units>`, the second is in
 distance\ :math:`^4` units, and the third is dimensionless.
 

doc/src/compute_omega_chunk.rst

@@ -84,7 +84,7 @@ These values can be accessed by any command that uses global array
 values from a compute as input.  See the :doc:`Howto output <Howto_output>`
 page for an overview of LAMMPS output options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 velocity/distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_pair.rst

@@ -93,7 +93,9 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`
+:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`,
+:doc:`fix pair <fix_pair>`
+
 
 Default
 """""""

doc/src/compute_pe.rst

@@ -27,7 +27,7 @@ Description
 """""""""""
 
 Define a computation that calculates the potential energy of the
-entire system of atoms.  The specified group must be "all."  See the
+entire system of atoms.  The specified group must be "all".  See the
 :doc:`compute pe/atom <compute_pe_atom>` command if you want per-atom
 energies.  These per-atom values could be summed for a group of atoms
 via the :doc:`compute reduce <compute_reduce>` command.
@@ -73,7 +73,7 @@ value can be used by any command that uses a global scalar value from
 a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_plasticity_atom.rst

@@ -73,5 +73,5 @@ none
 .. _Mitchell:
 
 **(Mitchell)** Mitchell, "A non-local, ordinary-state-based
-viscoelasticity model for peridynamics," Sandia National Lab Report,
+viscoelasticity model for peridynamics", Sandia National Lab Report,
 8064:1-28 (2011).

doc/src/compute_pressure.rst

@@ -29,7 +29,7 @@ Description
 """""""""""
 
 Define a computation that calculates the pressure of the entire system
-of atoms.  The specified group must be "all."  See the
+of atoms.  The specified group must be "all".  See the
 :doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom
 pressure (stress).  These per-atom values could be summed for a group
 of atoms via the :doc:`compute reduce <compute_reduce>` command.
@@ -115,7 +115,7 @@ LAMMPS starts up, as if this command were in the input script:
    compute thermo_press all pressure thermo_temp
 
 where thermo_temp is the ID of a similarly defined compute of style
-"temp."  See the :doc:`thermo_style <thermo_style>` command for more details.
+"temp".  See the :doc:`thermo_style <thermo_style>` command for more details.
 
 ----------
 
@@ -137,7 +137,7 @@ The ordering of values in the symmetric pressure tensor is as follows:
 :math:`p_{xz},` :math:`p_{yz}.`
 
 The scalar and vector values calculated by this compute are
-"intensive."  The scalar and vector values will be in pressure
+"intensive".  The scalar and vector values will be in pressure
 :doc:`units <units>`.
 
 Restrictions

doc/src/compute_property_atom.rst

@@ -167,7 +167,7 @@ triangular particles and define the corner points of each triangle.
 In addition, the various per-atom quantities listed above for specific
 packages are only accessible by this command.
 
-.. versionchanged:: TBD
+.. versionchanged:: 15Sep2022
 
   The *espin* property was previously called *spin*.
 
@@ -198,8 +198,8 @@ Related commands
 """"""""""""""""
 
 :doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`,
-:doc::doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk
+:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
-:doc:<fix_ave_chunk>`, `fix property/atom <fix_property_atom>`
+:doc:`fix property/atom <fix_property_atom>`
 
 Default
 """""""

doc/src/compute_property_chunk.rst

@@ -110,7 +110,7 @@ accessed by any command that uses global values from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The vector or array values are "intensive."  The values will be
+The vector or array values are "intensive".  The values will be
 unitless or in the units discussed above.
 
 Restrictions

doc/src/compute_property_local.rst

@@ -164,7 +164,7 @@ the type of the bond, from 1 to Nbtypes = # of bond types.  The number
 of bond types is defined in the data file read by the
 :doc:`read_data <read_data>` command.
 
-The attributes that start with "a," "d," and "i" refer to similar values
+The attributes that start with "a", "d", and "i" refer to similar values
 for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and
 :doc:`impropers <improper_style>`.
 

doc/src/compute_rdf.rst

@@ -166,7 +166,7 @@ by any command that uses a global values from a compute as input.  See
 the :doc:`Howto output <Howto_output>` page for an overview of
 LAMMPS output options.
 
-The array values calculated by this compute are all "intensive."
+The array values calculated by this compute are all "intensive".
 
 The first column of array values will be in distance
 :doc:`units <units>`.  The :math:`g(r)` columns of array values are normalized

doc/src/compute_reduce.rst

@@ -128,7 +128,7 @@ inputs to this fix by using the
 :doc:`compute property/atom <compute_property_atom>` command and then specifying
 an input value from that compute.
 
-If a value begins with "c\_," a compute ID must follow which has been
+If a value begins with "c\_", a compute ID must follow which has been
 previously defined in the input script.  Computes can generate
 per-atom or local quantities.  See the individual
 :doc:`compute <compute>` page for details.  If no bracketed integer
@@ -139,7 +139,7 @@ compute styles and :doc:`add them to LAMMPS <Modify>`.  See the
 discussion above for how :math:`I` can be specified with a wildcard asterisk
 to effectively specify multiple values.
 
-If a value begins with "f\_," a fix ID must follow which has been
+If a value begins with "f\_", a fix ID must follow which has been
 previously defined in the input script.  Fixes can generate per-atom
 or local quantities.  See the individual :doc:`fix <fix>` page for
 details.  Note that some fixes only produce their values on certain
@@ -152,7 +152,7 @@ is used.  Users can also write code for their own fix style and
 :math:`I` can be specified with a wildcard asterisk to effectively specify
 multiple values.
 
-If a value begins with "v\_," a variable name must follow which has
+If a value begins with "v\_", a variable name must follow which has
 been previously defined in the input script.  It must be an
 :doc:`atom-style variable <variable>`.  Atom-style variables can
 reference thermodynamic keywords and various per-atom attributes, or
@@ -197,7 +197,7 @@ global vector of values, the length of which is equal to the number of
 inputs specified.
 
 As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s)
-produced by this compute are all "extensive," meaning their value
+produced by this compute are all "extensive", meaning their value
 scales linearly with the number of atoms involved.  If normalized
 values are desired, this compute can be accessed by the
 :doc:`thermo_style custom <thermo_style>` command with
@@ -218,9 +218,9 @@ compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
 All the scalar or vector values calculated by this compute are
-"intensive," except when the *sum*, *sumabs*, or *sumsq* modes are used on
+"intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on
 per-atom or local vectors, in which case the calculated values are
-"extensive."
+"extensive".
 
 The scalar or vector values will be in whatever :doc:`units <units>` the
 quantities being reduced are in.

doc/src/compute_reduce_chunk.rst

@@ -102,7 +102,7 @@ The commands below can be added to the examples/in.micelle script.
 
 Imagine a collection of polymer chains or small molecules with
 hydrophobic end groups.  All the hydrophobic (HP) atoms are assigned
-to a group called "phobic."
+to a group called "phobic".
 
 These commands will assign a unique cluster ID to all HP atoms within
 a specified distance of each other.  A cluster will contain all HP

doc/src/compute_stress_atom.rst

@@ -222,6 +222,26 @@ result. I.e. the last 2 columns of thermo output will be the same:
    <pair_modify>` command, since those are contributions to the global
    system pressure.
 
+The compute stress/atom can be used in a number of ways.  Here is an
+example to compute a 1-d pressure profile in z-direction across the
+complete simulation box. You will need to adjust the number of bins and the
+selections for time averaging to your specific simulation.  This assumes
+that the dimensions of the simulation cell does not change.
+
+.. code-block:: LAMMPS
+
+   # set number of bins
+   variable nbins index 20
+   variable fraction equal 1.0/v_nbins
+   # define bins as chunks
+   compute cchunk all chunk/atom bin/1d x lower ${fraction} units reduced
+   compute stress all stress/atom NULL
+   # apply conversion to pressure early since we have no variable style for processing chunks
+   variable press atom -(c_stress[1]+c_stress[2]+c_stress[3])/(3.0*vol*${fraction})
+   compute binpress all reduce/chunk cchunk sum v_press
+   fix avg all ave/time 10 40 400 c_binpress mode vector file ave_stress.txt
+
+
 Output info
 """""""""""
 

doc/src/compute_stress_profile.rst

@@ -114,7 +114,7 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
   compute p all stress/cartesian x 0.1
   fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
 
-The values calculated by this compute are "intensive."  The stress
+The values calculated by this compute are "intensive".  The stress
 values will be in pressure :doc:`units <units>`. The number density
 values are in inverse volume :doc:`units <units>`.
 

doc/src/compute_tally.rst

@@ -182,7 +182,7 @@ Output info
   from individual atoms in both groups).
 
 Both the scalar and vector values calculated by this compute are
-"extensive."
+"extensive".
 
 Restrictions
 """"""""""""

doc/src/compute_temp.rst

@@ -91,7 +91,7 @@ vector values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
 vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The

doc/src/compute_temp_asphere.rst

@@ -134,8 +134,8 @@ vector values from a compute as input.
 See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
 output options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_body.rst

@@ -117,8 +117,8 @@ vector values from a compute as input.
 See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
 output options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.
 The vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_chunk.rst

@@ -242,8 +242,8 @@ can be accessed by any command that uses global array values from a
 compute as input.  Again, see the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."  The array values are "intensive."
+vector values are "extensive".  The array values are "intensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.  The array values

doc/src/compute_temp_com.rst

@@ -87,8 +87,8 @@ vector values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.
 The vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_cs.rst

@@ -101,8 +101,8 @@ vector of length 6 (KE tensor), which can be accessed by indices 1--6.
 These values can be used by any command that uses global scalar or
 vector values from a compute as input.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_deform.rst

@@ -134,7 +134,7 @@ vector values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
 vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.

doc/src/compute_temp_deform_eff.rst

@@ -53,8 +53,8 @@ vector values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_drude.rst

@@ -67,8 +67,8 @@ vector values from a compute as input.  See the
 options.
 
 Both the scalar value and the first two values of the vector
-calculated by this compute are "intensive."  The other four vector values
+calculated by this compute are "intensive".  The other four vector values
-are "extensive."
+are "extensive".
 
 Restrictions
 """"""""""""

doc/src/compute_temp_eff.rst

@@ -88,9 +88,9 @@ thermostatting.
 Output info
 """""""""""
 
-The scalar value calculated by this compute is "intensive," meaning it
+The scalar value calculated by this compute is "intensive", meaning it
 is independent of the number of atoms in the simulation.  The vector
-values are "extensive," meaning they scale with the number of atoms in
+values are "extensive", meaning they scale with the number of atoms in
 the simulation.
 
 Restrictions

doc/src/compute_temp_partial.rst

@@ -94,8 +94,8 @@ vector values from a compute as input.
 See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
 output options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_profile.rst

@@ -183,8 +183,8 @@ vector or array values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."  The array values are "intensive."
+vector values are "extensive".  The array values are "intensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.  The first column

doc/src/compute_temp_ramp.rst

@@ -106,8 +106,8 @@ vector values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_region.rst

@@ -99,8 +99,8 @@ vector values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.
 The vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_region_eff.rst

@@ -46,8 +46,8 @@ vector values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_rotate.rst

@@ -86,8 +86,8 @@ vector values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/src/compute_temp_sphere.rst

@@ -122,8 +122,8 @@ vector values from a compute as input.
 See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
 output options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-vector values are "extensive."
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/src/compute_ti.rst

@@ -125,7 +125,7 @@ value can be used by any command that uses a global scalar value from
 a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive."
+The scalar value calculated by this compute is "extensive".
 
 The scalar value will be in energy :doc:`units <units>`.
 

doc/src/compute_torque_chunk.rst

@@ -83,7 +83,7 @@ array values from a compute as input.
 See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 force-distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_vacf.rst

@@ -66,7 +66,7 @@ accessed by indices 1--4 by any command that uses global vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The vector values are "intensive."  The vector values will be in
+The vector values are "intensive".  The vector values will be in
 velocity\ :math:`^2` :doc:`units <units>`.
 
 Restrictions

doc/src/compute_vcm_chunk.rst

@@ -69,7 +69,7 @@ each chunk. These values can be accessed by any command that uses global array
 values from a compute as input.  See the :doc:`Howto output <Howto_output>`
 page for an overview of LAMMPS output options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 velocity :doc:`units <units>`.
 
 Restrictions

doc/src/compute_viscosity_cos.rst

@@ -134,9 +134,9 @@ These values can be used by any command that uses global scalar or
 vector values from a compute as input.
 See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
-first six elements of vector values are "extensive,"
+first six elements of vector values are "extensive",
-and the seventh element of vector values is "intensive."
+and the seventh element of vector values is "intensive".
 
 The scalar value will be in temperature :doc:`units <units>`.
 The first six elements of vector values will be in energy :doc:`units <units>`.

doc/src/compute_voronoi_atom.rst

@@ -198,7 +198,7 @@ Voronoi volume, the second is the neighbor count, as described above
 (read above for the output data in case the *occupation* keyword is
 specified).  These values can be accessed by any command that uses
 per-atom values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
-options. If the *peratom* keyword is set to "no," the per-atom array
+options. If the *peratom* keyword is set to "no", the per-atom array
 is still created, but it is not accessible.
 
 If the *edge_histo* keyword is used, then this compute generates a

doc/src/compute_xrd.rst

@@ -219,7 +219,7 @@ The array can be accessed by any command that uses global values from
 a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-All array values calculated by this compute are "intensive."
+All array values calculated by this compute are "intensive".
 
 Restrictions
 """"""""""""

doc/src/create_atoms.rst

@@ -95,7 +95,7 @@ typically created via the :doc:`create_box <create_box>` command.
 Before using this command, a lattice must also be defined using the
 :doc:`lattice <lattice>` 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."
+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*
@@ -352,7 +352,7 @@ 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
+the sinusoid would appear to be "smoother".  Also note the use of the
 "xlat" and "ylat" :doc:`thermo_style <thermo_style>` keywords, which
 converts lattice spacings to distance.
 

doc/src/dihedral_coeff.rst

@@ -10,7 +10,7 @@ Syntax
 
    dihedral_coeff N args
 
-* N = dihedral type (see asterisk form below)
+* N = numeric dihedral type (see asterisk form below) or alphanumeric type label
 * args = coefficients for one or more dihedral types
 
 Examples
@@ -22,26 +22,35 @@ Examples
    dihedral_coeff * 80.0 1 3 0.5
    dihedral_coeff 2* 80.0 1 3 0.5
 
+   labelmap dihedral 1 backbone
+   dihedral_coeff backbone 80.0 1 3
+
 Description
 """""""""""
 
-Specify the dihedral force field coefficients for one or more dihedral types.
+Specify the dihedral force field coefficients for one or more dihedral
-The number and meaning of the coefficients depends on the dihedral style.
+types.  The number and meaning of the coefficients depends on the
-Dihedral coefficients can also be set in the data file read by the
+dihedral style.  Dihedral coefficients can also be set in the data file
-:doc:`read_data <read_data>` command or in a restart file.
+read by the :doc:`read_data <read_data>` command or in a restart file.
 
-N can be specified in one of two ways.  An explicit numeric value can
+:math:`N` can be specified in one of two ways.  An explicit numeric
-be used, as in the first example above.  Or a wild-card asterisk can be
+value can be used, as in the first example above.  Or :math:`N` can be
-used to set the coefficients for multiple dihedral types.  This takes the
+an alphanumeric type label, which is a string defined by the
-form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is the number of dihedral
+:doc:`labelmap <labelmap>` command or in a corresponding section of a
-types, then an asterisk with no numeric values means all types from 1 to
+data file read by the :doc:`read_data <read_data>` command.
-:math:`N`.  A leading asterisk means all types from 1 to n (inclusive).  A
+
-trailing asterisk means all types from m to N (inclusive).  A middle asterisk
+For numeric values only, a wild-card asterisk can be used to set the
-means all types from m to n (inclusive).
+coefficients for multiple dihedral types.  This takes the form "\*" or
+"\*n" or "n\*" or "m\*n".  If :math:`N` is the number of dihedral types,
+then an asterisk with no numeric values means all types from 1 to
+:math:`N`.  A leading asterisk means all types from 1 to n (inclusive).
+A trailing asterisk means all types from n to :math:`N` (inclusive).  A
+middle asterisk means all types from m to n (inclusive).
 
 Note that using a dihedral_coeff command can override a previous setting
 for the same dihedral type.  For example, these commands set the coeffs
-for all dihedral types, then overwrite the coeffs for just dihedral type 2:
+for all dihedral types, then overwrite the coeffs for just dihedral type
+2:
 
 .. code-block:: LAMMPS
 

doc/src/dump.rst

@@ -55,24 +55,24 @@ dump command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID style N file args
 
 * ID = user-assigned name for the dump
 * group-ID = ID of the group of atoms to be dumped
-* style = *atom* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
+* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
-* N = dump every this many timesteps
+* N = dump on timesteps which are multiples of N
 * file = name of file to write dump info to
 * args = list of arguments for a particular style
 
   .. parsed-literal::
 
        *atom* args = none
+       *atom/adios* args = none,  discussed on :doc:`dump atom/adios <dump_adios>` page
        *atom/gz* args = none
        *atom/zstd* args = none
        *atom/mpiio* args = none
-       *atom/adios* args = none,  discussed on :doc:`dump atom/adios <dump_adios>` page
        *cfg* args = same as *custom* args, see below
        *cfg/gz* args = same as *custom* args, see below
        *cfg/zstd* args = same as *custom* args, see below
@@ -176,14 +176,15 @@ Examples
 Description
 """""""""""
 
-Dump a snapshot of atom quantities to one or more files every :math:`N`
+Dump a snapshot of atom quantities to one or more files once every
-timesteps in one of several styles.  The *image* and *movie* styles are
+:math:`N` timesteps in one of several styles.  The *image* and *movie*
-the exception: the *image* style renders a JPG, PNG, or PPM image file
+styles are the exception: the *image* style renders a JPG, PNG, or PPM
-of the atom configuration every :math:`N` timesteps while the *movie* style
+image file of the atom configuration every :math:`N` timesteps while
-combines and compresses them into a movie file; both are discussed in
+the *movie* style combines and compresses them into a movie file; both
-detail on the :doc:`dump image <dump_image>` page.  The timesteps on
+are discussed in detail on the :doc:`dump image <dump_image>` page.
-which dump output is written can also be controlled by a variable.
+The timesteps on which dump output is written can also be controlled
-See the :doc:`dump_modify every <dump_modify>` command.
+by a variable.  See the :doc:`dump_modify every <dump_modify>`
+command.
 
 Only information for atoms in the specified group is dumped.  The
 :doc:`dump_modify thresh and region and refresh <dump_modify>` commands
@@ -225,28 +226,27 @@ The *atom/gz*, *cfg/gz*, *custom/gz*, *local/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
+alternative approach to writing compressed files via a pipe, as done by
-by the regular dump styles, which may be required on clusters where
+the regular dump styles, which may be required on clusters where the
-the interface to the high-speed network disallows using the fork()
+interface to the high-speed network disallows using the fork() library
-library call (which is needed for a pipe).  For the remainder of this
+call (which is needed for a pipe).  For the remainder of this page, you
-page, you should thus consider the *atom* and *atom/gz* styles
+should thus consider the *atom* and *atom/gz* styles (etc.) to be
-(etc.) to be inter-changeable, with the exception of the required
+inter-changeable, with the exception of the required filename suffix.
-filename suffix.
 
-Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*,
+Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and
-and *xyz/zstd* styles are identical to the gz styles, but use the Zstd
+*xyz/zstd* styles are identical to the gz styles, but use the Zstd
 compression library instead and require the ".zst" suffix. See the
-:doc:`dump_modify <dump_modify>` page for details on how to control
+:doc:`dump_modify <dump_modify>` page for details on how to control the
-the compression level in both variants.
+compression level in both variants.
 
 As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
-*xyz/mpiio* styles are identical in command syntax and in the format
+*xyz/mpiio* styles are identical in command syntax and in the format of
-of the dump files they create, to the corresponding styles without
+the dump files they create, to the corresponding styles without "mpiio",
-"mpiio," except the single dump file they produce is written in
+except the single dump file they produce is written in parallel via the
-parallel via the MPI-IO library.  For the remainder of this page,
+MPI-IO library.  For the remainder of this page, you should thus
-you should thus consider the *atom* and *atom/mpiio* styles (etc.) to
+consider the *atom* and *atom/mpiio* styles (etc.) to be
-be inter-changeable.  The one exception is how the filename is
+inter-changeable.  The one exception is how the filename is specified
-specified for the MPI-IO styles, as explained below.
+for the MPI-IO styles, as explained below.
 
 .. warning::
 
@@ -287,13 +287,13 @@ where xlo,xhi are the maximum extents of the simulation box in the
 :math:`x`-dimension, and similarly for :math:`y` and :math:`z`.  The
 "xx yy zz" terms are six characters that encode the style of boundary for each
 of the six simulation box boundaries (xlo,xhi; ylo,yhi; and zlo,zhi).  Each of
-the six characters is either p (periodic), f (fixed), s (shrink wrap),
+the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap),
-or m (shrink wrapped with a minimum value).  See the
+or *m* (shrink wrapped with a minimum value).  See the
 :doc:`boundary <boundary>` 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,
+along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
 formatted as follows:
 
 .. parsed-literal::
@@ -332,8 +332,8 @@ 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 -
+specify a quantity that is not defined for a particular simulation---such as
-such as *q* for atom style *bond*, since that atom style does not
+*q* for atom style *bond*, since that atom style does not
 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
@@ -433,7 +433,7 @@ Below is an example for a YAML format dump created by the following commands.
    dump out all yaml 100 dump.yaml id type x y z vx vy vz ix iy iz
    dump_modify out time yes units yes thermo yes format 1 %5d format "% 10.6e"
 
-The tags "time," "units," and "thermo" are optional and enabled by the
+The tags "time", "units", and "thermo" are optional and enabled by the
 dump_modify command. The list under the "box" tag has three lines for
 orthogonal boxes and four lines for triclinic boxes, where the first three are
 the box boundaries and the fourth the three tilt factors (:math:`xy`,
@@ -485,21 +485,29 @@ popular molecular viewing program.
 
 ----------
 
-Dumps are performed on timesteps that are a multiple of :math:`N` (including
+Dumps are performed on timesteps that are a multiple of :math:`N`
-timestep 0) and on the last timestep of a minimization if the
+(including timestep 0) and on the last timestep of a minimization if
-minimization converges.  Note that this means a dump will not be
+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 :math:`N`.  This behavior can be
+if the current timestep is not a multiple of :math:`N`.  This behavior
-changed via the :doc:`dump_modify first <dump_modify>` command, which
+can be changed via the :doc:`dump_modify first <dump_modify>` command,
-can also be useful if the dump command is invoked after a minimization
+which can also be useful if the dump command is invoked after a
-ended on an arbitrary timestep.  :math:`N` can be changed between runs by
+minimization ended on an arbitrary timestep.
-using the :doc:`dump_modify every <dump_modify>` command (not allowed
+
-for *dcd* style).  The :doc:`dump_modify every <dump_modify>` command
+The value of :math:`N` can be changed between runs by using the
-also allows a variable to be used to determine the sequence of
+:doc:`dump_modify every <dump_modify>` command (not allowed for *dcd*
-timesteps on which dump files are written.  In this mode a dump on the
+style).  The :doc:`dump_modify every <dump_modify>` command also
-first timestep of a run will also not be written unless the
+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
 :doc:`dump_modify first <dump_modify>` command is used.
 
+If you instead want to dump snapshots based on simulation time (in
+time units of the :doc:`units` command), the :doc:`dump_modify
+every/time <dump_modify>` command can be used.  This can be useful
+when the timestep size varies during a simulation run, e.g. by use of
+the :doc:`fix dt/reset <fix_dt_reset>` command.
+
 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 :doc:`undump <undump>`
@@ -544,15 +552,14 @@ package installed, viz.,
    make yes-mpiio    # installs the MPIIO package
    make mpi          # build LAMMPS for your platform
 
-Second, use a dump filename which contains ".mpiio."  Note that it
+Second, use a dump filename which contains ".mpiio".  Note that it does
-does not have to end in ".mpiio," just contain those characters.
+not have to end in ".mpiio", just contain those characters.  Unlike
-Unlike MPI-IO restart files, which must be both written and read using
+MPI-IO restart files, which must be both written and read using MPI-IO,
-MPI-IO, the dump files produced by these MPI-IO styles are identical
+the dump files produced by these MPI-IO styles are identical in format
-in format to the files produced by their non-MPI-IO style
+to the files produced by their non-MPI-IO style counterparts.  This
-counterparts.  This means you can write a dump file using MPI-IO and
+means you can write a dump file using MPI-IO and use the :doc:`read_dump
-use the :doc:`read_dump <read_dump>` command or perform other
+<read_dump>` command or perform other post-processing, just as if the
-post-processing, just as if the dump file was not written using
+dump file was not written using MPI-IO.
-MPI-IO.
 
 .. warning::
 
@@ -561,37 +568,40 @@ 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
+above in the filename since that specifies generation of multiple files.
-files.  You can use the ".bin" or ".lammpsbin" suffix described below in an
+You can use the ".bin" or ".lammpsbin" suffix described below in an
-MPI-IO dump file; again this file will be written in parallel and have the
+MPI-IO dump file; again this file will be written in parallel and have
-same binary format as if it were written without MPI-IO.
+the same binary format as if it were written without MPI-IO.
 
-If the filename ends with ".bin" or ".lammpsbin", the dump file (or files, if
+If the filename ends with ".bin" or ".lammpsbin", the dump file (or
-"\*" or "%" is also used) is written in binary format.  A binary dump file
+files, if "\*" or "%" is also used) is written in binary format.  A
-will be about the same size as a text version, but will typically
+binary dump file will be about the same size as a text version, but will
-write out much faster.  Of course, when post-processing, you will need
+typically write out much faster.  Of course, when post-processing, you
-to convert it back to text format (see the :ref:`binary2txt tool <binary>`) or
+will need to convert it back to text format (see the :ref:`binary2txt
-write your own code to read the binary file.  The format of the binary file can
+tool <binary>`) or write your own code to read the binary file.  The
-be understood by looking at the :file:`tools/binary2txt.cpp` file.  This option
+format of the binary file can be understood by looking at the
-is only available for the *atom* and *custom* styles.
+:file:`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
+is also used) is written in gzipped format.  A gzipped dump file will be
-:math:`3\times` smaller than the text version, but will also take longer
+about :math:`3\times` smaller than the text version, but will also take
-to write.  This option is not available for the *dcd* and *xtc* styles.
+longer to write.  This option is not available for the *dcd* and *xtc*
+styles.
 
 ----------
 
 Note that in the discussion which follows, for styles which can
-reference values from a compute or fix or custom atom property, like
+reference values from a compute or fix or custom atom property, like the
-the *custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i` can
+*custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i`
-be specified using a wildcard asterisk with the index to effectively
+can be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form "\*" or "\*n" or "m\*"
+specify multiple values.  This takes the form "\*" or "\*n" or "m\*" or
-or "m\*n."  If :math:`N` is the number of columns in the array, then an
+"m\*n".  If :math:`N` is the number of columns in the array, then an
-asterisk with no numeric values means all column indices from 1 to :math:`N`.
+asterisk with no numeric values means all column indices from 1 to
-A leading asterisk means all indices from 1 to n (inclusive).  A
+:math:`N`.  A leading asterisk means all indices from 1 to n
-trailing asterisk means all indices from m to :math:`N` (inclusive).  A middle
+(inclusive).  A trailing asterisk means all indices from m to :math:`N`
-asterisk means all indices from m to n (inclusive).
+(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.  For example, these two dump commands are
@@ -670,37 +680,38 @@ The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*,
 
 *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
-:math:`N_\text{procs}-1`) that currently owns the atom.
+:math:`N_\text{procs}-1`) that currently owns the atom.  *Procp1* is the
-*Procp1* is the proc ID+1, which can be convenient in place of a *type*
+proc ID+1, which can be convenient in place of a *type* attribute (1 to
-attribute (1 to :math:`N_\text{types}`) for coloring atoms in a visualization
+:math:`N_\text{types}`) for coloring atoms in a visualization program.
-program.  *Type* is the atom type (1 to :math:`N_\text{types}`).  *Element* is
+*Type* is the atom type (1 to :math:`N_\text{types}`).  *Element* is
-typically the chemical name of an element, which you must assign to each type
+typically the chemical name of an element, which you must assign to each
-via the :doc:`dump_modify element <dump_modify>` command.  More generally, it
+type via the :doc:`dump_modify element <dump_modify>` command.  More
-can be any string you wish to associated with an atom type.  *Mass* is the atom
+generally, it can be any string you wish to associated with an atom
-mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components
+type.  *Mass* is the atom mass. The quantities *vx*, *vy*, *vz*, *fx*,
-of atom velocity and force and atomic charge.
+*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*, and *z* attributes write atom coordinates "unscaled," in the
+*y*, and *z* attributes write atom coordinates "unscaled", in the
 appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`,
-:math:`\sigma`, etc.).  Use *xs*, *ys*, *zs* if you want the coordinates
+:math:`\sigma`, etc.).  Use *xs*, *ys*, and *zs* if you want the
-"scaled" to the box size, so that each value is 0.0 to 1.0.  If the simulation
+coordinates "scaled" to the box size so that each value is 0.0 to 1.0.
-box is triclinic (tilted), then all atom coords will still be between 0.0 and
+If the simulation box is triclinic (tilted), then all atom coords will
-1.0.  The  actual unscaled :math:`(x,y,z)` coordinate is
+still be between 0.0 and 1.0.  The actual unscaled :math:`(x,y,z)`
-:math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal
+coordinate is :math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are
-vectors of the simulation box edges, as discussed on the
+the non-orthogonal vectors of the simulation box edges, as discussed on
-:doc:`Howto triclinic <Howto_triclinic>` page.
+the :doc:`Howto triclinic <Howto_triclinic>` page.
 
 Use *xu*, *yu*, and *zu* if you want the coordinates "unwrapped" by the
-image flags for each atom.  Unwrapped means that if the atom has
+image flags for each atom.  Unwrapped means that if the atom has passed
-passed through a periodic boundary one or more times, the value is
+through a periodic boundary one or more times, the value is printed for
-printed for what the coordinate would be if it had not been wrapped
+what the coordinate would be if it had not been wrapped back into the
-back into the periodic box.  Note that using *xu*, *yu*, and *zu* means
+periodic box.  Note that using *xu*, *yu*, and *zu* means that the
-that the coordinate values may be far outside the box bounds printed
+coordinate values may be far outside the box bounds printed with the
-with the snapshot.  Using *xsu*, *ysu*, and *zsu* is similar to using
+snapshot.  Using *xsu*, *ysu*, and *zsu* is similar to using *xu*, *yu*,
-*xu*, *yu*, and *zu*, except that the unwrapped coordinates are scaled by
+and *zu*, except that the unwrapped coordinates are scaled by the box
-the box size. Atoms that have passed through a periodic boundary will
+size. Atoms that have passed through a periodic boundary will have the
-have the corresponding coordinate increased or decreased by 1.0.
+corresponding coordinate increased or decreased by 1.0.
 
 The image flags can be printed directly using the *ix*, *iy*, and *iz*
 attributes.  For periodic dimensions, they specify which image of the
@@ -712,8 +723,8 @@ periodic boundaries during the simulation.
 
 The *mux*, *muy*, and *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
+the atom's point dipole moment.  The *mu* attribute gives the magnitude
-magnitude of the atom's dipole moment.
+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
@@ -727,17 +738,17 @@ 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
+The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles
-can sustain a rotational torque due to interactions with other
+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 :doc:`compute <compute>` 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
+been defined previously in the input script.  See the :doc:`compute
-:doc:`compute <compute>` command for details.  There are computes for
+<compute>` command for details.  There are computes for calculating the
-calculating the per-atom energy, stress, centro-symmetry parameter,
+per-atom energy, stress, centro-symmetry parameter, and coordination
-and coordination number of individual atoms.
+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
@@ -745,39 +756,39 @@ command.  Instead, global quantities can be output by the
 :doc:`thermo_style custom <thermo_style>` 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
+If *c_ID* is used as a attribute, then the per-atom vector calculated by
-by the compute is printed.  If *c_ID[i]* is used, then :math:`i` must be in
+the compute is printed.  If *c_ID[i]* is used, then :math:`i` must be in
-the range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
+the range from 1 to :math:`M`, which will print the :math:`i`\ th column
-per-atom array with :math:`M` columns calculated by the compute.  See the
+of the per-atom array with :math:`M` columns calculated by the compute.
-discussion above for how :math:`i` can be specified with a wildcard asterisk to
+See the discussion above for how :math:`i` can be specified with a
-effectively specify multiple values.
+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 :doc:`fix <fix>` to be output.  The ID in
+quantities calculated by a :doc:`fix <fix>` to be output.  The ID in the
-the attribute should be replaced by the actual ID of the fix that has
+attribute should be replaced by the actual ID of the fix that has been
-been defined previously in the input script.  The :doc:`fix ave/atom
+defined previously in the input script.  The :doc:`fix ave/atom
 <fix_ave_atom>` command is one that calculates per-atom quantities.
 Since it can time-average per-atom quantities produced by any
-:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style
+:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style :doc:`variable
-:doc:`variable <variable>`, this allows those time-averaged results to
+<variable>`, this allows those time-averaged results to be written to a
-be written to a dump file.
+dump file.
 
-If *f_ID* is used as a attribute, then the per-atom vector calculated
+If *f_ID* is used as a attribute, then the per-atom vector calculated by
-by the fix is printed.  If *f_ID[i]* is used, then :math:`i` must be in the
+the fix is printed.  If *f_ID[i]* is used, then :math:`i` must be in the
-range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
+range from 1 to :math:`M`, which will print the :math:`i`\ th column of
-per-atom array with :math:`M` columns calculated by the fix.  See the
+the per-atom array with :math:`M` columns calculated by the fix.  See
-discussion above for how :math:`i` can be specified with a wildcard asterisk to
+the discussion above for how :math:`i` can be specified with a wildcard
-effectively specify multiple values.
+asterisk to effectively specify multiple values.
 
 The *v_name* attribute allows per-atom vectors calculated by a
 :doc:`variable <variable>` 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
+defined previously in the input script.  Only an atom-style variable can
-can be referenced, since it is the only style that generates per-atom
+be referenced, since it is the only style that generates per-atom
 values.  Variables of style *atom* can reference individual atom
-attributes, per-atom attributes, thermodynamic keywords, or invoke
+attributes, per-atom attributes, thermodynamic keywords, or invoke other
-other computes, fixes, or variables when they are evaluated, so this
+computes, fixes, or variables when they are evaluated, so this is a very
-is a very general means of creating quantities to output to a dump file.
+general means of creating quantities to output to a dump file.
 
 The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
 per-atom integer and floating-point vectors or arrays that have been
@@ -785,10 +796,11 @@ added via the :doc:`fix property/atom <fix_property_atom>` command.
 When that command is used specific names are given to each attribute
 which are the "name" portion of these keywords.  For arrays *i2_name*
 and *d2_name*, the column of the array must also be included following
-the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is in the
+the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
-range from 1 to :math:`M`, where :math:`M` is the number of columns in the
+in the range from 1 to :math:`M`, where :math:`M` is the number of
-custom array). See the discussion above for how :math:`i` can be specified with
+columns in the custom array). See the discussion above for how :math:`i`
-a wildcard asterisk to effectively specify multiple values.
+can be specified with a wildcard asterisk to effectively specify
+multiple values.
 
 See the :doc:`Modify <Modify>` page for information on how to add
 new compute and fix styles to LAMMPS to calculate per-atom quantities

doc/src/dump_adios.rst

@@ -10,10 +10,9 @@ dump custom/adios command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID atom/adios N file.bp
-
    dump ID group-ID custom/adios N file.bp args
 
 * ID = user-assigned name for the dump
@@ -21,7 +20,7 @@ Syntax
 * adios = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
 * N = dump every this many timesteps
 * file.bp = name of file/stream to write to
-* args = same options as in :doc:`\ *dump custom*\ <dump>` command
+* args = same options as in :doc:`dump custom <dump>` command
 
 Examples
 """"""""
@@ -35,10 +34,10 @@ Examples
 Description
 """""""""""
 
-Dump a snapshot of atom coordinates every N timesteps in the `ADIOS
+Dump a snapshot of atom coordinates every :math:`N` timesteps in the `ADIOS
-<adios_>`_ based "BP" file format, or using different I/O solutions in
+<adios_>`_-based "BP" file format, or using different I/O solutions in
 ADIOS, to a stream that can be read on-line by another program.
-ADIOS-BP files are binary, portable and self-describing.
+ADIOS-BP files are binary, portable, and self-describing.
 
 .. _adios: https://github.com/ornladios/ADIOS2
 
@@ -67,7 +66,7 @@ create a new file at each individual dump.
 Restrictions
 """"""""""""
 
-The number of atoms per snapshot CAN change with the adios style.
+The number of atoms per snapshot **can** change with the adios style.
 When using the ADIOS tool 'bpls' to list the content of a .bp file,
 bpls will print *__* for the size of the output table indicating that
 its size is changing every step.

doc/src/dump_cfg_uef.rst

@@ -6,7 +6,7 @@ dump cfg/uef command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID cfg/uef N file mass type xs ys zs args
 
@@ -32,9 +32,8 @@ Description
 
 This command is used to dump atomic coordinates in the
 reference frame of the applied flow field when
-:doc:`fix nvt/uef <fix_nh_uef>` or
+:doc:`fix nvt/uef <fix_nh_uef>` or :doc:`fix npt/uef <fix_nh_uef>` is used.
-:doc:`fix npt/uef <fix_nh_uef>` or is used. Only the atomic
+Only the atomic coordinates and frame-invariant scalar quantities
-coordinates and frame-invariant scalar quantities
 will be in the flow frame. If velocities are selected
 as output, for example, they will not be in the same
 reference frame as the atomic positions.
@@ -43,7 +42,8 @@ Restrictions
 """"""""""""
 
 This fix is part of the UEF package. It is only enabled if LAMMPS
-was built with that package. See the :doc:`Build package <Build_package>` page for more info.
+was built with that package. See the :doc:`Build package <Build_package>`
+page for more info.
 
 This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`
 or :doc:`fix npt/uef <fix_nh_uef>` is active.

doc/src/dump_image.rst

@@ -12,7 +12,7 @@ dump movie command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID style N file color diameter keyword value ...
 
@@ -28,7 +28,7 @@ Syntax
 
   .. parsed-literal::
 
-       *atom* = yes/no = do or do not draw atoms
+       *atom* = *yes* or *no* = do or do not draw atoms
        *adiam* size = numeric value for atom diameter (distance units)
        *bond* values = color width = color and width of bonds
          color = *atom* or *type* or *none*
@@ -68,21 +68,20 @@ Syntax
        *box* values = yes/no diam = draw outline of simulation box
          yes/no = do or do not draw simulation box lines
          diam = diameter of box lines as fraction of shortest box length
-       *axes* values = yes/no length diam = draw xyz axes
+       *axes* values = axes length diam = draw xyz axes
-         yes/no = do or do not draw xyz axes lines next to simulation box
+         axes = *yes* or *no = do or do not draw xyz axes lines next to simulation box
          length = length of axes lines as fraction of respective box lengths
          diam = diameter of axes lines as fraction of shortest box length
-       *subbox* values = yes/no diam = draw outline of processor sub-domains
+       *subbox* values = lines diam = draw outline of processor sub-domains
-         yes/no = do or do not draw sub-domain lines
+         lines = *yes* or *no* = do or do not draw sub-domain lines
          diam = diameter of sub-domain lines as fraction of shortest box length
        *shiny* value = sfactor = shinyness of spheres and cylinders
          sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
-       *ssao* value = yes/no seed dfactor = SSAO depth shading
+       *ssao* value = shading seed dfactor = SSAO depth shading
-         yes/no = turn depth shading on/off
+         shading = *yes* or *no* = turn depth shading on/off
          seed = random # seed (positive integer)
          dfactor = strength of shading from 0.0 to 1.0
 
-
 .. _dump_modify_image:
 
 dump_modify options for dump image/movie
@@ -162,7 +161,7 @@ Examples
 Description
 """""""""""
 
-Dump a high-quality rendered image of the atom configuration every N
+Dump a high-quality rendered image of the atom configuration every :math:`N`
 timesteps and save the images either as a sequence of JPEG or PNG or
 PPM files, or as a single movie file.  The options for this command as
 well as the :doc:`dump_modify <dump_modify>` command control what is
@@ -179,7 +178,7 @@ has been run, using the :doc:`rerun <rerun>` command to read snapshots
 from an existing dump file, and using these dump commands in the rerun
 script to generate the images/movie.
 
-Here are two sample images, rendered as 1024x1024 JPEG files.
+Here are two sample images, rendered as :math:`1024\times 1024` JPEG files.
 
 .. |dump1| image:: img/dump1.jpg
    :width: 48%
@@ -232,22 +231,22 @@ details.
 
 ----------
 
-Dumps are performed on timesteps that are a multiple of N (including
+Dumps are performed on timesteps that are a multiple of :math:`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
+if the current timestep is not a multiple of :math:`N`.  This behavior can be
 changed via the :doc:`dump_modify first <dump_modify>` command, which
 can be useful if the dump command is invoked after a minimization
-ended on an arbitrary timestep.  N can be changed between runs by
+ended on an arbitrary timestep. :math:`N` can be changed between runs by
 using the :doc:`dump_modify every <dump_modify>` command.
 
-Dump *image* filenames must contain a wildcard character "\*", so that
+Dump *image* filenames must contain a wildcard character "\*" so that
 one image file per snapshot is written.  The "\*" character is replaced
 with the timestep value.  For example, tmp.dump.\*.jpg becomes
 tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc.  Note
 that the :doc:`dump_modify pad <dump_modify>` command can be used to
-insure all timestep numbers are the same length (e.g. 00010), which
+insure all timestep numbers are the same length (e.g., 00010), which
 can make it easier to convert a series of images into a movie in the
 correct ordering.
 
@@ -262,7 +261,7 @@ atoms rendered in the image.  They can be any atom attribute defined
 for the :doc:`dump custom <dump>` command, including *type* and
 *element*\ .  This includes per-atom quantities calculated by a
 :doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
-which are prefixed by "c\_", "f\_", or "v\_" respectively.  Note that the
+which are prefixed by "c\_", "f\_", or "v\_", respectively.  Note that the
 *diameter* setting can be overridden with a numeric value applied to
 all atoms by the optional *adiam* keyword.
 
@@ -277,7 +276,7 @@ to colors is as follows:
 * type 5 = aqua
 * type 6 = cyan
 
-and repeats itself for types > 6.  This mapping can be changed by the
+and repeats itself for types :math:`> 6`.  This mapping can be changed by the
 "dump_modify acolor" command, as described below.
 
 If *type* is specified for the *diameter* setting then the diameter of
@@ -773,10 +772,11 @@ the number 5.0 would be used.  But for a fractional map, the number
 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
+consecutive colors to.  For example, if the range is from :math:`-10.0` to
-10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
+:math:`10.0` and a *delta* of :math:`1.0` is used, then 20 colors will be
-the range.  The first will be from -10.0 <= color1 < -9.0, then second
+assigned to the range.  The first will be from
-from -9.0 <= color2 < -8.0, etc.
+:math:`-10.0 \le \text{color1} < -9.0`, then second from
+:math:`-9.0 \le 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
@@ -792,14 +792,14 @@ 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
+Here is how the entries are used to determine the color of an individual
-individual atom, given the value X of its atom attribute.  X will fall
+atom, given the value :math:`X` of its atom attribute.  :math:`X` will
-between 2 of the entry values.  The color of the atom is linearly
+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
+interpolated (in each of the RGB values) between the 2 colors associated
-associated with those entries.  For example, if X = -5.0 and the 2
+with those entries.  For example, if :math:`X = -5.0` and the two
-surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
+surrounding entries are "red" at :math:`-10.0` and "blue" at
-atom's color will be halfway between "red" and "blue", which happens
+:math:`0.0`, then the atom's color will be halfway between "red" and
-to be "purple".
+"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
@@ -807,19 +807,18 @@ 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
+can be specified either as absolute numbers or as fractions (0.0 to 1.0)
-1.0) of the range, depending on the "a" or "f" in the style setting
+of the range, depending on the "a" or "f" in the style setting for the
-for the color map.
+color map.
 
-Here is how the entries are used to determine the color of an
+Here is how the entries are used to determine the color of an individual
-individual atom, given the value X of its atom attribute.  The entries
+atom, given the value X of its atom attribute.  The entries are scanned
-are scanned from first to last.  The first time that *lo* <= X <=
+from first to last.  The first time that *lo* <= X <= *hi*, X is
-*hi*, X is assigned the color associated with that entry.  You can
+assigned the color associated with that entry.  You can think of the
-think of the last entry as assigning a default color (since it will
+last entry as assigning a default color (since it will always be matched
-always be matched by X), and the earlier entries as colors that
+by X), and the earlier entries as colors that override the default.
-override the default.  Also note that no interpolation of a color RGB
+Also note that no interpolation of a color RGB is done.  All atoms will
-is done.  All atoms will be drawn with one of the colors in the list
+be drawn with one of the colors in the list of entries.
-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,
@@ -864,20 +863,20 @@ The *bcolor* keyword can be used with the dump image 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
+The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
-number of bond types.  A wildcard asterisk can be used in place of or
+is 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 =
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N`
-the number of bond types, then an asterisk with no numeric values
+is the number of bond types, then an asterisk with no numerical values
-means all types from 1 to N.  A leading asterisk means all types from
+means all types from 1 to :math:`N`.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to :math:`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
+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.
@@ -885,13 +884,13 @@ of the specified bond types.
 ----------
 
 The *bdiam* keyword can be used with the dump image command, with its
-*bond* keyword, when its diam setting is *type*, to set the diameter
+*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 :doc:`units <units>` you are
-using, e.g. Angstroms.
+using (e.g., Angstroms).
 
 ----------
 
@@ -922,7 +921,7 @@ dump_modify color option.
 ----------
 
 The *color* keyword allows definition of a new color name, in addition
-to the 140-predefined colors (see below), and associates 3
+to the 140-predefined colors (see below), and associates three
 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
@@ -959,15 +958,15 @@ PNG library.
 
 To write *movie* dumps, you must use the -DLAMMPS_FFMPEG switch when
 building LAMMPS and have the FFmpeg executable available on the
-machine where LAMMPS is being run.  Typically it's name is lowercase,
+machine where LAMMPS is being run.  Typically its name is lowercase
-i.e. ffmpeg.
+(i.e., "ffmpeg").
 
 See the :doc:`Build settings <Build_settings>` page for details.
 
 Note that since FFmpeg is run as an external program via a pipe,
 LAMMPS has limited control over its execution and no knowledge about
 errors and warnings printed by it. Those warnings and error messages
-will be printed to the screen only. Due to the way image data is
+will be printed to the screen only. Due to the way image data are
 communicated to FFmpeg, it will often print the message
 
 .. parsed-literal::
@@ -976,7 +975,7 @@ communicated to FFmpeg, it will often print the message
 
 which can be safely ignored. Other warnings
 and errors have to be addressed according to the FFmpeg documentation.
-One known issue is that certain movie file formats (e.g. MPEG level 1
+One known issue is that certain movie file formats (e.g., MPEG level 1
 and 2 format streams) have video bandwidth limits that can be crossed
 when rendering too large of image sizes. Typical warnings look like
 this:
@@ -987,10 +986,9 @@ this:
    [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
    [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018
 
-In this case it is recommended to either reduce the size of the image
+In this case it is recommended either to reduce the size of the image
-or encode in a different format that is also supported by your copy of
+or to encode in a different format that is also supported by your copy of
-FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
+FFmpeg and which does not have this limitation (e.g., .avi, .mkv, mp4).
-mp4).
 
 Related commands
 """"""""""""""""

doc/src/dump_modify.rst

@@ -17,7 +17,7 @@ Syntax
 * one or more keyword/value pairs may be appended
 
 * these keywords apply to various dump styles
-* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
+* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
 
   .. parsed-literal::
 
@@ -35,10 +35,10 @@ Syntax
        *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 = dump on timesteps which are a multiple of N
          N can be a variable (see below)
        *every/time* arg = Delta
-         Delta = dump every this interval in simulation time (time units)
+         Delta = dump once every Delta interval of simulation time (time units)
          Delta can be a variable (see below)
        *fileper* arg = Np
          Np = write one file for every this many processors
@@ -65,6 +65,8 @@ Syntax
        *refresh* arg = c_ID = compute ID that supports a refresh operation
        *scale* arg = *yes* or *no*
        *sfactor* arg = coordinate scaling factor (> 0.0)
+       *skip* arg = v_name
+         v_name = variable with name which evaluates to non-zero (skip) or 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
@@ -176,6 +178,31 @@ extra buffering.
 
 ----------
 
+.. versionadded:: 4May2022
+
+The *colname* keyword can be used to change the default header keyword
+for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
+and MPIIO variants.  The setting for *ID string* replaces the default
+text with the provided string.  *ID* can be a positive integer when it
+represents the column number counting from the left, a negative integer
+when it represents the column number from the right (i.e. -1 is the last
+column/keyword), or a custom dump keyword (or compute, fix, property, or
+variable reference) and then it replaces the string for that specific
+keyword. For *atom* dump styles only the keywords "id", "type", "x",
+"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
+whether scaled or unwrapped coordinates were enabled or disabled, and
+it always assumes 8 columns for indexing regardless of whether image
+flags are enabled or not.  For dump style *cfg* only changes to the
+"auxiliary" keywords (6th or later keyword) will become visible.
+
+The *colname* keyword can be used multiple times. If multiple *colname*
+settings refer to the same keyword, the last setting has precedence.  A
+setting of *default* clears all previous settings, reverting all values
+to their default names. Using the *scale* or *image* keyword will also
+reset all header keywords to their default values.
+
+----------
+
 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
@@ -207,13 +234,10 @@ will be accepted.
 ----------
 
 The *every* keyword can be used with any dump style except the *dcd*
-and *xtc* styles.  It does two things.  It specifies that the interval
+and *xtc* styles.  It specifies that the output of dump snapshots will
-between dump snapshots will be set in timesteps, which is the default
+now be performed on timesteps which are a multiple of a new :math:`N`
-if the *every* or *every/time* keywords are not used.  See the
+value, This overrides the dump frequency originally specified by the
-*every/time* keyword for how to specify the interval in simulation
+:doc:`dump <dump>` command.
-time, i.e. in time units of the :doc:`units <units>` command.  The
-*every* keyword also sets the interval value, which overrides the dump
-frequency originally specified by the :doc:`dump <dump>` command.
 
 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
@@ -273,6 +297,17 @@ in file tmp.times:
 
 ----------
 
+The *every/time* keyword can be used with any dump style except the
+*dcd* and *xtc* styles.  It changes the frequency of dump snapshots
+from being based on the current timestep to being determined by
+elapsed simulation time, i.e. in time units of the :doc:`units
+<units>` command, and specifies *Delta* for the interval between
+snapshots.  This can be useful when the timestep size varies during a
+simulation run, e.g. by use of the :doc:`fix dt/reset <fix_dt_reset>`
+command.  The default is to perform output on timesteps which a
+multiples of specified timestep value :math:`N`; see the *every*
+keyword.
+
 The *every/time* keyword can be used with any dump style except the
 *dcd* and *xtc* styles.  It does two things.  It specifies that the
 interval between dump snapshots will be set in simulation time
@@ -357,7 +392,7 @@ always occur if the current timestep is a multiple of $N$, the
 frequency specified in the :doc:`dump <dump>` command or
 :doc:`dump_modify every <dump_modify>` command, including timestep 0.
 It will also always occur if the current simulation time is a multiple
-of *Delta*, the time interval specified in the doc:`dump_modify
+of *Delta*, the time interval specified in the :doc:`dump_modify
 every/time <dump_modify>` command.
 
 But if this is not the case, a dump snapshot will only be written if
@@ -365,7 +400,7 @@ the setting of this keyword is *yes*\ .  If it is *no*, which is the
 default, then it will not be written.
 
 Note that if the argument to the :doc:`dump_modify every
-<dump_modify>` doc:`dump_modify every/time <dump_modify>` commands is
+<dump_modify>` :doc:`dump_modify every/time <dump_modify>` commands is
 a variable and not a numeric value, then specifying *first yes* is the
 only way to write a dump snapshot on the first timestep after the dump
 command is invoked.
@@ -380,6 +415,7 @@ performed with dump style *xtc*\ .
 
 ----------
 
+<<<<<<< HEAD
 .. versionadded:: 4May2022
 
 The *colname* keyword can be used to change the default header keyword
@@ -404,6 +440,8 @@ to their default names.
 
 ----------
 
+=======
+>>>>>>> develop
 The *format* keyword can be used to change the default numeric format output
 by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
 *xyz* styles, and their MPIIO variants. Only the *line* or *none*
@@ -490,6 +528,8 @@ boundary twice and is really two 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.
+Using this keyword will reset all custom header names set with
+*dump_modify colname* to their respective default values.
 
 ----------
 
@@ -663,6 +703,8 @@ value of *yes* means atom coords are written in normalized units from
 (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., :math:`\mathrm{\mathring A}` or :math:`\sigma`).
+Using this keyword will reset all custom header names set with
+*dump_modify colname* to their respective default values.
 
 ----------
 
@@ -681,14 +723,33 @@ most effective when the typical magnitude of position data is between
 
 ----------
 
+.. versionadded:: 15Sep2022
+
+The *skip* keyword can be used with all dump styles.  It allows a dump
+snapshot to be skipped (not written to the dump file), if a condition
+is met.  The condition is computed by an :doc:`equal-style variable
+<variable>`, which should be specified as v_name, where name is the
+variable name.  If the variable evaluation returns a non-zero value,
+then the dump snapshot is skipped.  If it returns zero, the dump
+proceeds as usual.  Note that :doc:`equal-style variable <variable>`
+can contain Boolean operators which effectively evaluate as a true
+(non-zero) or false (zero) result.
+
+The *skip* keyword can be useful for debugging purposes, e.g. to dump
+only on a particular timestep.  Or to limit output to conditions of
+interest, e.g. only when the force on some atom exceeds a threshold
+value.
+
+----------
+
 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
+parallel.  This is the case even in serial if the :doc:`atom_modify sort
-:doc:`atom_modify sort <atom_modify>` option is turned on, which it is by
+<atom_modify>` option is turned on, which it is by default, to improve
-default, to improve performance.  A sort value of *id* means sort the output by
+performance.  A sort value of *id* means sort the output by atom ID.  A
-atom ID.  A sort value of :math:`N` or :math:`-N` means sort the output by the
+sort value of :math:`N` or :math:`-N` means sort the output by the value
-value in the :math:`N`\ th column of per-atom info in either ascending or
+in the :math:`N`\ th column of per-atom info in either ascending or
 descending order.
 
 The dump *local* style cannot be sorted by atom ID, since there are
@@ -732,8 +793,8 @@ attributes that can be tested for are the same as those that can be
 specified in the :doc:`dump custom <dump>` 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
-:doc:`dump custom <dump>` command.  For example, you can output the coordinates
+:doc:`dump custom <dump>` command.  For example, you can output the
-and stress of atoms whose energy is above some threshold.
+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,

doc/src/dump_vtk.rst

@@ -6,13 +6,13 @@ dump vtk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID vtk N file args
 
 * ID = user-assigned name for the dump
 * group-ID = ID of the group of atoms to be dumped
-* vtk = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* vtk = style of dump command (other styles such as *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
 * N = dump every this many timesteps
 * file = name of file to write dump info to
 * args = same as arguments for :doc:`dump_style custom <dump>`
@@ -28,17 +28,18 @@ Examples
 Description
 """""""""""
 
-Dump a snapshot of atom quantities to one or more files every N
+Dump a snapshot of atom quantities to one or more files every :math:`N`
 timesteps in a format readable by the `VTK visualization toolkit <http://www.vtk.org>`_ or other visualization tools that use it,
-e.g. `ParaView <http://www.paraview.org>`_.  The timesteps on which dump
+such as `ParaView <http://www.paraview.org>`_.  The time steps on which dump
 output is written can also be controlled by a variable; see the
 :doc:`dump_modify every <dump_modify>` command for details.
 
 This dump style is similar to :doc:`dump_style custom <dump>` but uses
-the VTK library to write data to VTK simple legacy or XML format
+the VTK library to write data to VTK simple legacy or XML format,
 depending on the filename extension specified for the dump file.  This
 can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*,
-respectively, for XML format; see the `VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
+respectively, for XML format; see the
+`VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
 description of these formats.  Since this naming convention conflicts
 with the way binary output is usually specified (see below), the
 :doc:`dump_modify binary <dump_modify>` command allows setting of a

doc/src/fix.rst

@@ -312,6 +312,7 @@ accelerated styles exist.
 * :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
 * :doc:`orient/eco <fix_orient_eco>` - add generalized grain boundary migration force
 * :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
+* :doc:`pair <fix_pair>` - access per-atom info from pair styles
 * :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
 * :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
 * :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane

doc/src/fix_accelerate_cos.rst

@@ -6,8 +6,7 @@ fix accelerate/cos command
 Syntax
 """"""
 
-
+.. code-block:: LAMMPS
-.. parsed-literal::
 
    fix ID group-ID accelerate value
 
@@ -19,7 +18,6 @@ Syntax
 Examples
 """"""""
 
-
 .. code-block:: LAMMPS
 
    fix 1 all accelerate/cos 0.02e-5
@@ -34,8 +32,8 @@ The acceleration is a periodic function along the z-direction:
 
    a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)
 
-where :math:`A` is the acceleration amplitude, :math:`l_z` is the z-length
+where :math:`A` is the acceleration amplitude, :math:`l_z` is the
-of the simulation box.
+:math:`z`-length of the simulation box.
 At steady state, the acceleration generates a velocity profile:
 
 .. math::
@@ -49,17 +47,18 @@ shear viscosity :math:`\eta` by:
 
    V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}
 
-
 and it can be obtained from ensemble average of the velocity profile:
 
 .. math::
 
-   V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}}
+   V = \frac{\sum\limits_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum\limits_i m_{i}},
 
-where :math:`m_i`, :math:`v_{i,x}` and :math:`z_i` are the mass,
+where :math:`m_i`, :math:`v_{i,x}`, and :math:`z_i` are the mass,
-x-component velocity and z coordinate of a particle.
+:math:`x`-component velocity, and :math:`z`-coordinate of a particle,
+respectively.
 
-The velocity amplitude :math:`V` can be calculated with :doc:`compute viscosity/cos <compute_viscosity_cos>`,
+The velocity amplitude :math:`V` can be calculated with
+:doc:`compute viscosity/cos <compute_viscosity_cos>`,
 which enables viscosity calculation with periodic perturbation method,
 as described by :ref:`Hess<Hess2>`.
 Because the applied acceleration drives the system away from equilibration,
@@ -79,15 +78,17 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to binary restart files.
 None of the fix_modify options are relevant to this fix.
-No global or per-atom quantities are stored by this fix for access by various output commands.
+No global or per-atom quantities are stored by this fix for access by various
-No parameter of this fix can be used with the start/stop keywords of the run command.
+output commands.  No parameter of this fix can be used with the start/stop
+keywords of the run command.
 This fix is not invoked during energy minimization.
 
 Restrictions
 """"""""""""
 
 This command is only available when LAMMPS was built with the MISC package.
-Since this fix depends on the z-coordinate of atoms, it cannot be used in 2d simulations.
+Since this fix depends on the :math:`z`-coordinate of atoms, it cannot be used
+in 2d simulations.
 
 Related commands
 """"""""""""""""
@@ -96,10 +97,10 @@ Related commands
 
 Default
 """""""
- none
+none
 
 ----------
 
 .. _Hess2:
 
-**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
+**(Hess)** Hess, B. Journal of Chemical Physics 2002, 116 (1), 209--217.

doc/src/fix_acks2_reaxff.rst

@@ -9,7 +9,7 @@ Accelerator Variants: *acks2/reaxff/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID acks2/reaxff Nevery cutlo cuthi tolerance params args
 
@@ -37,10 +37,10 @@ Examples
 Description
 """""""""""
 
-Perform the atom-condensed Kohn-Sham DFT to second order (ACKS2) charge
+Perform the atom-condensed Kohn--Sham DFT to second order (ACKS2) charge
 equilibration method as described in :ref:`(Verstraelen) <Verstraelen>`.
 ACKS2 impedes unphysical long-range charge transfer sometimes seen with
-QEq (e.g. for dissociation of molecules), at increased computational
+QEq (e.g., for dissociation of molecules), at increased computational
 cost.  It is typically used in conjunction with the ReaxFF force field
 model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
 command, but it can be used with any potential in LAMMPS, so long as it
@@ -71,7 +71,8 @@ potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
 bond cutoff distance.  Note that these 4 quantities are also in the
 ReaxFF potential file, except that eta is defined here as twice the eta
 value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
-of this fix are hard-coded to be A, eV, and electronic charge.
+of this fix are hard-coded to be :math:`\mathrm{\mathring{A}}`, eV, and
+electronic charge.
 
 The optional *maxiter* keyword allows changing the max number
 of iterations in the linear solver. The default value is 200.
@@ -110,7 +111,7 @@ LAMMPS was built with that package. See the :doc:`Build package
 
 This fix does not correctly handle interactions involving multiple
 periodic images of the same atom.  Hence, it should not be used for
-periodic cell dimensions less than 10 angstroms.
+periodic cell dimensions less than :math:`10~\mathrm{\mathring{A}}`.
 
 This fix may be used in combination with :doc:`fix efield <fix_efield>`
 and will apply the external electric field during charge equilibration,
@@ -132,7 +133,7 @@ maxiter 200
 
 .. _O'Hearn:
 
-**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1-C22 (2020).
+**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020).
 
 .. _Verstraelen:
 

doc/src/fix_adapt.rst

@@ -6,7 +6,7 @@ fix adapt command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID adapt N attribute args ... keyword value ...
 
@@ -19,24 +19,24 @@ Syntax
   .. parsed-literal::
 
        *pair* args = pstyle pparam I J v_name
-         pstyle = pair style name, e.g. lj/cut
+         pstyle = pair style name (e.g., lj/cut)
          pparam = parameter to adapt over time
          I,J = type pair(s) to set parameter for
          v_name = variable with name that calculates value of pparam
        *bond* args = bstyle bparam I v_name
-         bstyle = bond style name, e.g. harmonic
+         bstyle = bond style name (e.g., harmonic)
          bparam = parameter to adapt over time
          I = type bond to set parameter for
          v_name = variable with name that calculates value of bparam
        *angle* args = astyle aparam I v_name
-         astyle = angle style name, e.g. harmonic
+         astyle = angle style name (e.g., harmonic)
          aparam = parameter to adapt over time
          I = type angle to set parameter for
          v_name = variable with name that calculates value of aparam
        *kspace* arg = v_name
-         v_name = variable with name that calculates scale factor on K-space terms
+         v_name = variable with name that calculates scale factor on :math:`k`-space terms
        *atom* args = atomparam v_name
-         atomparam = parameter to adapt over time
+         atomparam = *charge* or *diameter* or *diameter/disc* = parameter to adapt over time
          v_name = variable with name that calculates value of atomparam
 
 * zero or more keyword/value pairs may be appended
@@ -44,15 +44,15 @@ Syntax
 
   .. parsed-literal::
 
-       *scale* value = *no* or *yes*
+     *scale* value = *no* or *yes*
-         *no* = the variable value is the new setting
+       *no* = the variable value is the new setting
-         *yes* = the variable value multiplies the original setting
+       *yes* = the variable value multiplies the original setting
-       *reset* value = *no* or *yes*
+     *reset* value = *no* or *yes*
-         *no* = values will remain altered at the end of a run
+       *no* = values will remain altered at the end of a run
-         *yes* = reset altered values to their original values at the end of a run
+       *yes* = reset altered values to their original values at the end of a run
-       *mass* value = *no* or *yes*
+     *mass* value = *no* or *yes*
-         *no* = mass is not altered by changes in diameter
+       *no* = mass is not altered by changes in diameter
-         *yes* = mass is altered by changes in diameter
+       *yes* = mass is altered by changes in diameter
 
 Examples
 """"""""
@@ -70,22 +70,22 @@ Examples
 Description
 """""""""""
 
-Change or adapt one or more specific simulation attributes or settings
+Change or adapt one or more specific simulation attributes or settings over
-over time as a simulation runs.  Pair potential and K-space and atom
+time as a simulation runs.  Pair potential and :math:`k`-space and atom
-attributes which can be varied by this fix are discussed below.  Many
+attributes which can be varied by this fix are discussed below.  Many other
-other fixes can also be used to time-vary simulation parameters,
+fixes can also be used to time-vary simulation parameters (e.g., the
-e.g. the "fix deform" command will change the simulation box
+:doc:`fix deform <fix_deform>` command will change the simulation box
-size/shape and the "fix move" command will change atom positions and
+size/shape and the :doc:`fix move <fix_move>` command will change atom
-velocities in a prescribed manner.  Also note that many commands allow
+positions and velocities in a prescribed manner).  Also note that many commands
-variables as arguments for specific parameters, if described in that
+allow variables as arguments for specific parameters, if described in that
 manner on their doc pages.  An equal-style variable can calculate a
-time-dependent quantity, so this is another way to vary a simulation
+time-dependent quantity, so this is another way to vary a simulation parameter
-parameter over time.
+over time.
 
-If *N* is specified as 0, the specified attributes are only changed
+If :math:`N` is specified as 0, the specified attributes are only changed
 once, before the simulation begins.  This is all that is needed if the
-associated variables are not time-dependent.  If *N* > 0, then changes
+associated variables are not time-dependent.  If :math:`N > 0`, then changes
-are made every *N* steps during the simulation, presumably with a
+are made every :math:`N` steps during the simulation, presumably with a
 variable that is time-dependent.
 
 Depending on the value of the *reset* keyword, attributes changed by
@@ -98,9 +98,9 @@ If the *scale* keyword is set to *no*, which is the default, then
 the value of the altered parameter will be whatever the variable
 generates.  If the *scale* keyword is set to *yes*, then the value
 of the altered parameter will be the initial value of that parameter
-multiplied by whatever the variable generates.  I.e. the variable is
+multiplied by whatever the variable generates (i.e., the variable is
 now a "scale factor" applied in (presumably) a time-varying fashion to
-the parameter.
+the parameter).
 
 Note that whether scale is *no* or *yes*, internally, the parameters
 themselves are actually altered by this fix.  Make sure you use the
@@ -120,8 +120,8 @@ The *pstyle* argument is the name of the pair style.  If
 :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
 *pstyle* should be a sub-style name.  If there are multiple
 sub-styles using the same pair style, then *pstyle* should be specified
-as "style:N" where N is which instance of the pair style you wish to
+as "style:N", where :math:`N` is which instance of the pair style you wish to
-adapt, e.g. the first, second, etc.  For example, *pstyle* could be
+adapt (e.g., the first or second).  For example, *pstyle* could be
 specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2".  The
 *pparam* argument is the name of the parameter to change.  This is the
 current list of pair styles and parameters that can be varied by this
@@ -216,60 +216,61 @@ formulas for the meaning of these parameters:
    to this list.  All it typically takes is adding an extract() method to
    the pair\_\*.cpp file associated with the potential.
 
-Some parameters are global settings for the pair style, e.g. the
+Some parameters are global settings for the pair style (e.g., the
-viscosity setting "mu" for :doc:`pair_style lubricate <pair_lubricate>`.
+viscosity setting "mu" for :doc:`pair_style lubricate <pair_lubricate>`).
-Other parameters apply to atom type pairs within the pair style,
+Other parameters apply to atom type pairs within the pair style (e.g., the
-e.g. the prefactor "a" for :doc:`pair_style soft <pair_soft>`.
+prefactor :math:`a` for :doc:`pair_style soft <pair_soft>`).
 
 Note that for many of the potentials, the parameter that can be varied
 is effectively a prefactor on the entire energy expression for the
-potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"
+potential (e.g., the lj/cut epsilon).  The parameters listed as "scale"
 are exactly that, since the energy expression for the
 :doc:`coul/cut <pair_coul>` potential (for example) has no labeled
 prefactor in its formula.  To apply an effective prefactor to some
 potentials, multiple parameters need to be altered.  For example, the
-:doc:`Buckingham potential <pair_buck>` needs both the A and C terms
+:doc:`Buckingham potential <pair_buck>` needs both the :math:`A` and
-altered together.  To scale the Buckingham potential, you should thus
+:math:`C` terms altered together.  To scale the Buckingham potential, you
-list the pair style twice, once for A and once for C.
+should thus list the pair style twice, once for :math:`A` and once for
+:math:`C`.
 
-If a type pair parameter is specified, the *I* and *J* settings should
+If a type pair parameter is specified, the :math:`I` and :math:`J` settings
-be specified to indicate which type pairs to apply it to.  If a global
+should be specified to indicate which type pairs to apply it to.  If a global
-parameter is specified, the *I* and *J* settings still need to be
+parameter is specified, the :math:`I` and :math:`J` settings still need to be
 specified, but are ignored.
 
-Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
+Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and :math:`J`
-specified in one of two ways.  Explicit numeric values can be used for
+can be specified in one of two ways.  Explicit numeric values can be used for
-each, as in the first example above.  I <= J is required.  LAMMPS sets
+each, as in the first example above.  :math:`I \le J` is required.  LAMMPS sets
-the coefficients for the symmetric J,I interaction to the same values.
+the coefficients for the symmetric :math:`J,I` interaction to the same values.
 
 A wild-card asterisk can be used in place of or in conjunction with
-the I,J arguments to set the coefficients for multiple pairs of atom
+the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N`
-the number of atom types, then an asterisk with no numeric values
+is 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
+means all types from 1 to :math:`N`.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
 (inclusive).  A middle asterisk means all types from m to n
-(inclusive).  Note that only type pairs with I <= J are considered; if
+(inclusive).  Note that only type pairs with :math:`I \le J` are considered; if
-asterisks imply type pairs where J < I, they are ignored.
+asterisks imply type pairs where :math:`J < I`, they are ignored.
 
-IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
+IMPORTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
 <pair_hybrid>` is being used, then the *pstyle* will be a sub-style
-name.  You must specify I,J arguments that correspond to type pair
+name.  You must specify :math:`I,J` arguments that correspond to type pair
 values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
 that sub-style.
 
 The *v_name* argument for keyword *pair* is the name of an
-:doc:`equal-style variable <variable>` which will be evaluated each
+:doc:`equal-style variable <variable>` which will be evaluated each time
-time this fix is invoked to set the parameter to a new value.  It
+this fix is invoked to set the parameter to a new value.  It should be
-should be specified as v_name, where name is the variable name.
+specified as v_name, where name is the variable name.  Equal-style
-Equal-style variables can specify formulas with various mathematical
+variables can specify formulas with various mathematical functions, and
-functions, and include :doc:`thermo_style <thermo_style>` command
+include :doc:`thermo_style <thermo_style>` command keywords for the
-keywords for the simulation box parameters and timestep and elapsed
+simulation box parameters and timestep and elapsed time.  Thus it is
-time.  Thus it is easy to specify parameters that change as a function
+easy to specify parameters that change as a function of time or span
-of time or span consecutive runs in a continuous fashion.  For the
+consecutive runs in a continuous fashion.  For the latter, see the
-latter, see the *start* and *stop* keywords of the :doc:`run <run>`
+*start* and *stop* keywords of the :doc:`run <run>` command and the
-command and the *elaplong* keyword of :doc:`thermo_style custom
+*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for
-<thermo_style>` for details.
+details.
 
 For example, these commands would change the prefactor coefficient of
 the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a
@@ -287,13 +288,13 @@ a bond coefficient over time, very similar to how the *pair* keyword
 operates. The only difference is that now a bond coefficient for a
 given bond type is adapted.
 
-A wild-card asterisk can be used in place of or in conjunction with
+A wild-card asterisk can be used in place of or in conjunction with the
-the bond type argument to set the coefficients for multiple bond
+bond type argument to set the coefficients for multiple bond types.
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is
-the number of bond types, then an asterisk with no numeric values
+the number of bond types, then an asterisk with no numeric values means
-means all types from 1 to N.  A leading asterisk means all types from
+all types from 1 to :math:`N`.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to
-(inclusive).  A middle asterisk means all types from m to n
+:math:`N` (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
 
 Currently *bond* does not support bond_style hybrid nor bond_style
@@ -323,13 +324,13 @@ an angle coefficient over time, very similar to how the *pair* keyword
 operates. The only difference is that now an angle coefficient for a
 given angle type is adapted.
 
-A wild-card asterisk can be used in place of or in conjunction with
+A wild-card asterisk can be used in place of or in conjunction with the
-the angle type argument to set the coefficients for multiple angle
+angle type argument to set the coefficients for multiple angle types.
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is
-the number of angle types, then an asterisk with no numeric values
+the number of angle types, then an asterisk with no numeric values means
-means all types from 1 to N.  A leading asterisk means all types from
+all types from 1 to :math:`N`.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to
-(inclusive).  A middle asterisk means all types from m to n
+:math:`N` (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
 
 Currently *angle* does not support angle_style hybrid nor angle_style
@@ -348,7 +349,7 @@ this fix uses to reset theta0 needs to generate values in radians.
 ----------
 
 The *kspace* keyword used the specified variable as a scale factor on
-the energy, forces, virial calculated by whatever K-Space solver is
+the energy, forces, virial calculated by whatever :math:`k`-space solver is
 defined by the :doc:`kspace_style <kspace_style>` command.  If the
 variable has a value of 1.0, then the solver is unaltered.
 
@@ -373,17 +374,17 @@ with equal-style variables.  The new value is assigned to the
 corresponding attribute for all atoms in the fix group.
 
 If the atom parameter is *diameter* and per-atom density and per-atom
-mass are defined for particles (e.g. :doc:`atom_style granular
+mass are defined for particles (e.g., :doc:`atom_style granular
 <atom_style>`), then the mass of each particle is, by default, also
 changed when the diameter changes. The mass is set from the particle
 volume for 3d systems (density is assumed to stay constant). For 2d,
 the default is for LAMMPS to model particles with a radius attribute
 as spheres. However, if the atom parameter is *diameter/disc*, then the
 mass is set from the particle area (the density is assumed to be in
-mass/distance^2 units). The mass of the particle may also be kept constant
+mass/distance\ :math:`^2` units). The mass of the particle may also be kept
-if the *mass* keyword is set to *no*. This can be useful to account for
+constant if the *mass* keyword is set to *no*. This can be useful to account
-diameter changes that do not involve mass changes, e.g., thermal expansion.
+for diameter changes that do not involve mass changes (e.g., thermal
-
+expansion).
 
 For example, these commands would shrink the diameter of all granular
 particles in the "center" group from 1.0 to 0.1 in a linear fashion
@@ -405,11 +406,11 @@ their original values at the end of the last restarted run.
 
 Note that all the parameters changed by this fix are written into a
 restart file in their current changed state.  A new restarted
-simulation does not know their original time=0 values, unless the
+simulation does not know the original time=0 values, unless the
 input script explicitly resets the parameters (after the restart file
-is read), to their original values.
+is read) to the original values.
 
-Also note, that the time-dependent variable(s) used in the restart
+Also note that the time-dependent variable(s) used in the restart
 script should typically be written as a function of time elapsed since
 the original simulation began.
 
@@ -430,8 +431,8 @@ the one used in the original script.
 
 In a restarted run, if the *reset* keyword is set to *yes*, and the
 run ends in this script (as opposed to just writing more restart
-files, parameters will be restored to the values they were at the
+files), parameters will be restored to the values they were at the
-beginning of the run command in the restart script.  Which as
+beginning of the run command in the restart script, which as
 explained above, may or may not be the original values of the
 parameters.  Again, an exception is if the *atom* keyword is being
 used with *reset yes* (in all the runs). In that case, the original

doc/src/fix_adapt_fep.rst

@@ -6,7 +6,7 @@ fix adapt/fep command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID adapt/fep N attribute args ... keyword value ...
 
@@ -19,7 +19,7 @@ Syntax
   .. parsed-literal::
 
        *pair* args = pstyle pparam I J v_name
-         pstyle = pair style name, e.g. lj/cut
+         pstyle = pair style name (e.g., lj/cut)
          pparam = parameter to adapt over time
          I,J = type pair(s) to set parameter for
          v_name = variable with name that calculates value of pparam
@@ -66,12 +66,12 @@ Change or adapt one or more specific simulation attributes or settings
 over time as a simulation runs.
 
 This is an enhanced version of the :doc:`fix adapt <fix_adapt>` command
-with two differences,
+with two differences:
 
 * It is possible to modify the charges of chosen atom types only,
   instead of scaling all the charges in the system.
-* There is a new option *after* for better compatibility with "fix
+* There is a new option *after* for better compatibility with
-  ave/time".
+  :doc:`fix ave/time <fix_ave_time>`.
 
 This version is suited for free energy calculations using
 :doc:`compute ti <compute_ti>` or :doc:`compute fep <compute_fep>`.
@@ -92,8 +92,8 @@ If the *scale* keyword is set to *no*, then the value the parameter is
 set to will be whatever the variable generates.  If the *scale*
 keyword is set to *yes*, then the value of the altered parameter will
 be the initial value of that parameter multiplied by whatever the
-variable generates.  I.e. the variable is now a "scale factor" applied
+variable generates (i.e., the variable is now a "scale factor" applied
-in (presumably) a time-varying fashion to the parameter.  Internally,
+in (presumably) a time-varying fashion to the parameter).  Internally,
 the parameters themselves are actually altered; make sure you use the
 *reset yes* option if you want the parameters to be restored to their
 initial values after the run.
@@ -188,7 +188,7 @@ styles and their energy formulas for the meaning of these parameters:
 
 Note that for many of the potentials, the parameter that can be varied
 is effectively a prefactor on the entire energy expression for the
-potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"
+potential (e.g., the lj/cut epsilon).  The parameters listed as "scale"
 are exactly that, since the energy expression for the
 :doc:`coul/cut <pair_coul>` potential (for example) has no labeled
 prefactor in its formula.  To apply an effective prefactor to some
@@ -204,23 +204,23 @@ specified, but are ignored.
 
 Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
 specified in one of two ways.  Explicit numeric values can be used for
-each, as in the first example above.  I <= J is required.  LAMMPS sets
+each, as in the first example above.  :math:`I \le J` is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same values.
 
 A wild-card asterisk can be used in place of or in conjunction with
-the I,J arguments to set the coefficients for multiple pairs of atom
+the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is
-number of atom types, then an asterisk with no numeric values means
+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
+all types from 1 to :math:`N`.  A leading asterisk means all types from 1 to n
-(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A trailing asterisk means all types from m to :math:`N`
 (inclusive).  A middle asterisk means all types from m to n
-(inclusive).  Note that only type pairs with I <= J are considered; if
+(inclusive).  Note that only type pairs with :math:`I \le J` are considered; if
-asterisks imply type pairs where J < I, they are ignored.
+asterisks imply type pairs where :math:`J < I`, they are ignored.
 
-IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is being used, then the *pstyle* will
+IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is
-be a sub-style name.  You must specify I,J arguments that correspond
+being used, then the *pstyle* will be a sub-style name.  You must specify
-to type pair values defined (via the :doc:`pair_coeff <pair_coeff>`
+:math:`I,J` arguments that correspond to type pair values defined (via the
-command) for that sub-style.
+:doc:`pair_coeff <pair_coeff>` command) for that sub-style.
 
 The *v_name* argument for keyword *pair* is the name of an
 :doc:`equal-style variable <variable>` which will be evaluated each time
@@ -232,8 +232,7 @@ simulation box parameters and timestep and elapsed time.  Thus it is
 easy to specify parameters that change as a function of time or span
 consecutive runs in a continuous fashion.  For the latter, see the
 *start* and *stop* keywords of the :doc:`run <run>` command and the
-*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for
+*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for details.
-details.
 
 For example, these commands would change the prefactor coefficient of
 the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a
@@ -247,7 +246,7 @@ linear fashion over the course of a simulation:
 ----------
 
 The *kspace* keyword used the specified variable as a scale factor on
-the energy, forces, virial calculated by whatever K-Space solver is
+the energy, forces, virial calculated by whatever :math:`k`-space solver is
 defined by the :doc:`kspace_style <kspace_style>` command.  If the
 variable has a value of 1.0, then the solver is unaltered.
 
@@ -263,8 +262,8 @@ current list of atom parameters that can be varied by this fix:
 * charge = charge on particle
 * diameter = diameter of particle
 
-The *I* argument indicates which atom types are affected. A wild-card
+The :math:`I` argument indicates which atom types are affected. A wild-card
-asterisk can be used in place of or in conjunction with the I argument
+asterisk can be used in place of or in conjunction with the :math:`I` argument
 to set the coefficients for multiple atom types.
 
 The *v_name* argument of the *atom* keyword is the name of an
@@ -276,9 +275,9 @@ variables.  The new value is assigned to the corresponding attribute
 for all atoms in the fix group.
 
 If the atom parameter is *diameter* and per-atom density and per-atom
-mass are defined for particles (e.g. :doc:`atom_style granular <atom_style>`), then the mass of each particle is also
+mass are defined for particles (e.g., :doc:`atom_style granular <atom_style>`),
-changed when the diameter changes (density is assumed to stay
+then the mass of each particle is also changed when the diameter changes
-constant).
+(density is assumed to stay constant).
 
 For example, these commands would shrink the diameter of all granular
 particles in the "center" group from 1.0 to 0.1 in a linear fashion
@@ -297,11 +296,14 @@ parameters on the outermost rRESPA level.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to
+:doc:`binary restart files <restart>`.
+None of the :doc:`fix_modify <fix_modify>` options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
@@ -310,7 +312,8 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`
+:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`,
+:doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`
 
 Default
 """""""

doc/src/fix_addforce.rst

@@ -6,7 +6,7 @@ fix addforce command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID addforce fx fy fz keyword value ...
 
@@ -24,7 +24,7 @@ Syntax
   .. parsed-literal::
 
        *every* value = Nevery
-         Nevery = add force every this many timesteps
+         Nevery = add force every this many time steps
        *region* value = region-ID
          region-ID = ID of region atoms must be in to have added force
        *energy* value = v_name
@@ -42,31 +42,31 @@ Examples
 Description
 """""""""""
 
-Add fx,fy,fz to the corresponding component of force for each atom in
+Add :math:`(f_x,f_y,f_z)` to the corresponding component of the force for each
-the group.  This command can be used to give an additional push to
+atom in the group.  This command can be used to give an additional push to
 atoms in a simulation, such as for a simulation of Poiseuille flow in
 a channel.
 
-Any of the 3 quantities defining the force components can be specified
+Any of the three quantities defining the force components, namely :math:`f_x`,
-as an equal-style or atom-style :doc:`variable <variable>`, namely *fx*,
+:math:`f_y`, and :math:`f_z`, can be specified as an equal-style or atom-style
-*fy*, *fz*\ .  If the value is a variable, it should be specified as
+:doc:`variable <variable>`.  If the value is a variable, it should be specified
-v_name, where name is the variable name.  In this case, the variable
+as v_name, where name is the variable name.  In this case, the variable
-will be evaluated each timestep, and its value(s) used to determine
+will be evaluated each time step, and its value(s) will be used to determine
-the force component.
+the force component(s).
 
 Equal-style variables can specify formulas with various mathematical
-functions, and include :doc:`thermo_style <thermo_style>` command
+functions and include :doc:`thermo_style <thermo_style>` command
-keywords for the simulation box parameters and timestep and elapsed
+keywords for the simulation box parameters, time step, and elapsed time.
-time.  Thus it is easy to specify a time-dependent force field.
+Thus, it is easy to specify a time-dependent force field.
 
 Atom-style variables can specify the same formulas as equal-style
 variables but can also include per-atom values, such as atom
-coordinates.  Thus it is easy to specify a spatially-dependent force
+coordinates.  Thus, it is easy to specify a spatially-dependent force
 field with optional time-dependence as well.
 
 If the *every* keyword is used, the *Nevery* setting determines how
 often the forces are applied.  The default value is 1, for every
-timestep.
+time step.
 
 If the *region* keyword is used, the atom must also be in the
 specified geometric :doc:`region <region>` in order to have force added
@@ -83,10 +83,14 @@ potential energy to formulate a self-consistent minimization problem
 (see below).
 
 The *energy* keyword is not allowed if the added force is a constant
-vector F = (fx,fy,fz), with all components defined as numeric
+vector :math:`\vec F = (f_x,f_y,f_z)`, with all components defined as numeric
 constants and not as variables.  This is because LAMMPS can compute
-the energy for each atom directly as E = -x dot F = -(x\*fx + y\*fy +
+the energy for each atom directly as
-z\*fz), so that -Grad(E) = F.
+
+.. math::
+   E = -\vec x \cdot \vec F = -(x f_x + y f_y + z f_z),
+
+so that :math:`-\vec\nabla E = \vec F`.
 
 The *energy* keyword is optional if the added force is defined with
 one or more variables, and if you are performing dynamics via the
@@ -98,16 +102,16 @@ one or more variables, and you are performing energy minimization via
 the "minimize" command.  The keyword specifies the name of an
 atom-style :doc:`variable <variable>` which is used to compute the
 energy of each atom as function of its position.  Like variables used
-for *fx*, *fy*, *fz*, the energy variable is specified as v_name,
+for :math:`f_x`, :math:`f_y`, :math:`f_z`, the energy variable is specified as
-where name is the variable name.
+v_name, where name is the variable name.
 
 Note that when the *energy* keyword is used during an energy
 minimization, you must insure that the formula defined for the
 atom-style :doc:`variable <variable>` is consistent with the force
-variable formulas, i.e. that -Grad(E) = F.  For example, if the force
+variable formulas (i.e., that :math:`-\vec\nabla E = \vec F`).
-were a spring-like F = kx, then the energy formula should be E =
+For example, if the force were a spring-like, :math:`\vec F = -k\vec x`, then
--0.5kx\^2.  If you don't do this correctly, the minimization will not
+the energy formula should be :math:`E = \frac12 kx^2`.  If you do not do this
-converge properly.
+correctly, the minimization will not converge properly.
 
 ----------
 
@@ -128,8 +132,8 @@ the global potential energy of the system as part of
 this fix is :doc:`fix_modify energy no <fix_modify>`.  Note that this
 energy is a fictitious quantity but is needed so that the
 :doc:`minimize <minimize>` command can include the forces added by
-this fix in a consistent manner.  I.e. there is a decrease in
+this fix in a consistent manner (i.e., there is a decrease in
-potential energy when atoms move in the direction of the added force.
+potential energy when atoms move in the direction of the added force).
 
 The :doc:`fix_modify <fix_modify>` *virial* option is supported by
 this fix to add the contribution due to the added forces on atoms to
@@ -144,7 +148,7 @@ fix. This allows to set at which level of the :doc:`r-RESPA
 <run_style>` integrator the fix is adding its forces. Default is the
 outermost level.
 
-This fix computes a global scalar and a global 3-vector of forces,
+This fix computes a global scalar and a global three-vector of forces,
 which can be accessed by various :doc:`output commands
 <Howto_output>`.  The scalar is the potential energy discussed above.
 The vector is the total force on the group of atoms before the forces
@@ -157,7 +161,7 @@ the :doc:`run <run>` command.
 The forces due to this fix are imposed during an energy minimization,
 invoked by the :doc:`minimize <minimize>` command.  You should not
 specify force components with a variable that has time-dependence for
-use with a minimizer, since the minimizer increments the timestep as
+use with a minimizer, since the minimizer increments the time step as
 the iteration count during the minimization.
 
 .. note::