Merge branch 'lammps:develop' into mliappy_unified

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/Packages/MDI.cmake

@@ -6,13 +6,10 @@ else()
 endif()
 option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
 
-
-
-
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.10.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 "1c203b7fd462d9934834f643f09f3c06" 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/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

@@ -61,6 +61,7 @@ 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/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:: TBD
+
+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)
@@ -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

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/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/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/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_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_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_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

@@ -224,30 +224,29 @@ page for details.
 
 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
+"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::
 
@@ -434,7 +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`,
@@ -553,15 +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::
 
@@ -570,37 +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 "%"
+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
@@ -679,37 +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*, and *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
@@ -721,8 +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
@@ -736,17 +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*, and *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
@@ -754,39 +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
+the discussion above for how :math:`i` can be specified with a wildcard
-to 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
@@ -794,10 +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_image.rst

@@ -196,8 +196,8 @@ Only atoms in the specified group are rendered in the image.  The
 alter what atoms are included in the image.
 The filename suffix determines whether a JPEG, PNG, or PPM file is
 created with the *image* dump style.  If the suffix is ".jpg" or
-".jpeg," then a `JPEG format <jpeg_format_>`_ file is created, if the
+".jpeg", then a `JPEG format <jpeg_format_>`_ file is created, if the
-suffix is ".png," then a `PNG format <png_format_>`_ is created, else
+suffix is ".png", then a `PNG format <png_format_>`_ is created, else
 a `PPM (aka NETPBM) format <ppm_format_>`_ file is created.
 The JPEG and PNG files are binary; PPM has a text mode header followed
 by binary data. JPEG images have lossy compression, PNG has lossless
@@ -261,7 +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.
 
@@ -297,18 +297,18 @@ and sizes used by the `AtomEye <atomeye_>`_ visualization package.
 If other atom attributes are used for the *color* or *diameter*
 settings, they are interpreted in the following way.
 
-If "vx," for example, is used as the *color* setting, then the color
+If "vx", for example, is used as the *color* setting, then the color
 of the atom will depend on the x-component of its velocity.  The
 association of a per-atom value with a specific color is determined by
-a "color map," which can be specified via the dump_modify command, as
+a "color map", which can be specified via the dump_modify command, as
 described below.  The basic idea is that the atom-attribute will be
 within a range of values, and every value within the range is mapped
 to a specific color.  Depending on how the color map is defined, that
 mapping can take place via interpolation so that a value of -3.2 is
-halfway between "red" and "blue," or discretely so that the value of
+halfway between "red" and "blue", or discretely so that the value of
 -3.2 is "orange".
 
-If "vx," for example, is used as the *diameter* setting, then the atom
+If "vx", for example, is used as the *diameter* setting, then the atom
 will be rendered using the x-component of its velocity as the
 diameter.  If the per-atom value <= 0.0, them the atom will not be
 drawn.  Note that finite-size spherical particles, as defined by
@@ -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 :math:`X` of its atom attribute.
+atom, given the value :math:`X` of its atom attribute.  :math:`X` will
-:math:`X` will fall between 2 of the entry values.  The color of the atom is
+fall between 2 of the entry values.  The color of the atom is linearly
-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 :math:`X = -5.0` and the two
+with those entries.  For example, if :math:`X = -5.0` and the two
-surrounding entries are "red" at :math:`-10.0` and "blue" at :math:`0.0`,
+surrounding entries are "red" at :math:`-10.0` and "blue" at
-then the 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,
@@ -867,7 +866,7 @@ that bonds of each type will be drawn in the image.
 The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
 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 "m\*" or "m\*n."  If :math:`N`
+types.  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 numerical 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 m to :math:`N`

doc/src/dump_modify.rst

@@ -176,6 +176,31 @@ 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
@@ -365,7 +390,7 @@ 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
@@ -373,7 +398,7 @@ 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.
@@ -388,30 +413,6 @@ performed with dump style *xtc*\ .
 
 ----------
 
-.. 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.
-
-----------
-
 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*
@@ -498,6 +499,8 @@ 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.
 
 ----------
 
@@ -671,6 +674,8 @@ 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.
 
 ----------
 

doc/src/fix_adapt.rst

@@ -122,7 +122,7 @@ The *pstyle* argument is the name of the pair style.  If
 sub-styles using the same pair style, then *pstyle* should be specified
 as "style:N", where :math:`N` is which instance of the pair style you wish to
 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
+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
 fix.  See the doc pages for individual pair styles and their energy
@@ -245,7 +245,7 @@ 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 :math:`I,J` arguments to set the coefficients for multiple pairs of atom
-types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n."  If :math:`N`
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N`
 is the number of atom 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 m to :math:`N`
@@ -260,17 +260,17 @@ 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
@@ -288,13 +288,14 @@ 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 "m\*" or "m\*n."  If :math:`N`
+This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is
-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 :math:`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 m to :math:`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 (inclusive).
+: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
 hybrid/overlay as bond styles. The bond styles that currently work
@@ -323,13 +324,14 @@ 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 "m\*" or "m\*n."  If :math:`N`
+This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is
-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 :math:`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 m to :math:`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 (inclusive).
+: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
 hybrid/overlay as angle styles. The angle styles that currently work

doc/src/fix_adapt_fep.rst

@@ -115,7 +115,7 @@ overrides the parameters.
 
 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.  For example, *pstyle* could be specified as "soft"
-or "lubricate."  The *pparam* argument is the name of the parameter to
+or "lubricate".  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 fix.  See the doc pages for individual pair
 styles and their energy formulas for the meaning of these parameters:
@@ -209,7 +209,7 @@ 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 :math:`I,J` arguments to set the coefficients for multiple pairs of atom
-types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n."  If :math:`N` is
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is
 the number of atom 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 m to :math:`N`

doc/src/fix_addforce.rst

@@ -153,7 +153,7 @@ 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
 on individual atoms are changed by the fix.  The scalar and vector
-values calculated by this fix are "extensive."
+values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_addtorque.rst

@@ -75,7 +75,7 @@ accessed by various :doc:`output commands <Howto_output>`.  The scalar
 is the potential energy discussed above.  The vector is the total
 torque on the group of atoms before the forces on individual atoms are
 changed by the fix.  The scalar and vector values calculated by this
-fix are "extensive."
+fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_amoeba_bitorsion.rst

@@ -124,7 +124,7 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
 energy discussed above.  The scalar value calculated by this fix is
-"extensive."
+"extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_amoeba_pitorsion.rst

@@ -138,7 +138,7 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
 energy discussed above.  The scalar value calculated by this fix is
-"extensive."
+"extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_atc.rst

@@ -135,7 +135,7 @@ fix are listed below.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the energy
-discussed in the previous paragraph.  The scalar value is "extensive."
+discussed in the previous paragraph.  The scalar value is "extensive".
 
 No parameter of this fix can be used with the
 *start/stop* keywords of the :doc:`run <run>` command.  This fix is not

doc/src/fix_atom_swap.rst

@@ -167,7 +167,7 @@ the following global cumulative quantities:
 * 1 = swap attempts
 * 2 = swap accepts
 
-The vector values calculated by this fix are "extensive."
+The vector values calculated by this fix are "extensive".
 
 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/src/fix_ave_atom.rst

@@ -70,7 +70,7 @@ per-atom vectors.
 Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
 specify multiple values.  This takes the form "\*" or "\*n" or "m\*" or
-"m\*n."  If :math:`N` is the size of the vector (for *mode* = scalar) or the
+"m\*n".  If :math:`N` is the size of the vector (for *mode* = scalar) or the
 number of columns in the array (for *mode* = vector), then an asterisk
 with no numeric values means all indices from 1 to :math:`N`.  A leading
 asterisk means all indices from 1 to n (inclusive).  A trailing
@@ -127,7 +127,7 @@ specifying an input value from that compute.
    :doc:`compute property/atom <compute_property_atom>`
    command via its *xu*, *yu*, and *zu* attributes.
 
-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.  If no bracketed term is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed term containing an index :math:`I` is appended, the
@@ -137,7 +137,7 @@ used.  Users can also write code for their own compute styles and
 :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 previously
+If a value begins with "f\_", a fix ID must follow which has been previously
 defined in the input script.  If no bracketed term is appended, the per-atom
 vector calculated by the fix is used.  If a bracketed term containing an index
 :math:`I` is appended, the :math:`I^\text{th}` column of the per-atom array
@@ -148,7 +148,7 @@ 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 "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 as an
 :doc:`atom-style variable <variable>`. Variables of style *atom* can reference
 thermodynamic keywords or invoke other computes, fixes, or variables

doc/src/fix_ave_chunk.rst

@@ -288,7 +288,7 @@ together as one set of atoms to calculate their temperature.  The
 compute allows the center-of-mass velocity of each chunk to be
 subtracted before calculating the temperature; this fix does not.
 
-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.  If no bracketed integer is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -297,7 +297,7 @@ their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 See the discussion above for how 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.  If no bracketed integer is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -308,7 +308,7 @@ their own fix styles and :doc:`add them to LAMMPS <Modify>`.  See the
 discussion above for how 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.  Variables of style
 *atom* can reference thermodynamic keywords and various per-atom
 attributes, or invoke other computes, fixes, or variables when they
@@ -348,7 +348,7 @@ at each sampling step.
 
 If the *norm* setting is *none*, a similar computation as for the
 *sample* setting is done, except the individual "average sample
-values" are "summed sample values."  A summed sample value is simply
+values" are "summed sample values".  A summed sample value is simply
 the chunk value summed over atoms in the sample, without dividing by
 the number of atoms in the sample.  The output value for the chunk on
 the :math:`N_\text{freq}` timesteps is the average of the
@@ -494,21 +494,21 @@ relevant to this fix.
 
 This fix computes a global array of values which can be accessed by
 various :doc:`output commands <Howto_output>`.  The values can only be
-accessed on timesteps that are multiples of :math:`N_\text{freq}`, since that
+accessed on timesteps that are multiples of :math:`N_\text{freq}`, since
-is when averaging is performed.  The global array has # of rows = the number
+that is when averaging is performed.  The global array has # of rows =
-of chunks :math:`N_\text{chunk}`, as calculated by the specified
+the number of chunks :math:`N_\text{chunk}`, as calculated by the
-:doc:`compute chunk/atom <compute_chunk_atom>` command.  The # of columns is
+specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The #
-:math:`M+1+N_\text{values}`, where :math:`M \in \{1,\dotsc,4\}`,
+of columns is :math:`M+1+N_\text{values}`, where :math:`M \in
-depending on whether the optional
+\{1,\dotsc,4\}`, depending on whether the optional columns for OrigID
-columns for OrigID and CoordN are used, as explained above.  Following
+and CoordN are used, as explained above.  Following the optional
-the optional columns, the next column contains the count of atoms in
+columns, the next column contains the count of atoms in the chunk, and
-the chunk, and the remaining columns are the Nvalue quantities.  When
+the remaining columns are the Nvalue quantities.  When the array is
-the array is accessed with a row :math:`I` that exceeds the current number of
+accessed with a row :math:`I` that exceeds the current number of chunks,
-chunks, than a 0.0 is returned by the fix instead of an error, since
+than a 0.0 is returned by the fix instead of an error, since the number
-the number of chunks can vary as a simulation runs depending on how
+of chunks can vary as a simulation runs depending on how that value is
-that value is computed by the compute chunk/atom command.
+computed by the compute chunk/atom command.
 
-The array values calculated by this fix are treated as "intensive,"
+The array values calculated by this fix are treated as "intensive",
 since they are typically already normalized by the count of atoms in
 each chunk.
 

doc/src/fix_ave_correlate.rst

@@ -189,7 +189,7 @@ Also, if the *ave* keyword is set to *one* which is the default, then
 
 ----------
 
-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.  If no bracketed term is
 appended, the global scalar calculated by the compute is used.  If a
 bracketed term is appended, the :math:`I^\text{th}` element of the global
@@ -206,7 +206,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`.  See the doc pages for
 these commands which give the IDs of these computes.  Users can also
 write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  If no bracketed term is
 appended, the global scalar calculated by the fix is used.  If a
 bracketed term is appended, the :math:`I^\text{th}` element of the global
@@ -219,7 +219,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will
 result.  Users can also write code for their own fix styles and
 :doc:`add them to LAMMPS <Modify>`.
 
-If a value begins with "v\_," a variable name must follow which has been
+If a value begins with "v\_", a variable name must follow which has been
 previously defined in the input script.  Only equal-style or vector-style
 variables can be referenced; the latter requires a bracketed term to specify
 the :math:`I^\text{th}` element of the vector calculated by the variable.

doc/src/fix_ave_histo.rst

@@ -193,7 +193,7 @@ 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.  If *mode* = scalar, then if
 no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
@@ -215,7 +215,7 @@ these commands which give the IDs of these computes.  Users can also
 write code for their own compute styles and
 :doc:`add them to LAMMPS <Modify>`.
 
-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.  If *mode* = scalar, then if
 no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
@@ -232,7 +232,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will
 result.  Users can also write code for their own fix styles and
 :doc:`add them to LAMMPS <Modify>`.
 
-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.  If *mode* = scalar, then
 only equal-style or vector-style variables can be used, which both
 produce global values.  In this mode, a vector-style variable requires

doc/src/fix_ave_time.rst

@@ -358,11 +358,11 @@ of rows = length of the input vectors and # of columns = number of
 inputs.
 
 If the fix produces a scalar or vector, then the scalar and each
-element of the vector can be either "intensive" or "extensive,"
+element of the vector can be either "intensive" or "extensive",
 depending on whether the values contributing to the scalar or vector
-element are "intensive" or "extensive."  If the fix produces an array,
+element are "intensive" or "extensive".  If the fix produces an array,
 then all elements in the array must be the same, either "intensive" or
-"extensive."  If a compute or fix provides the value being time
+"extensive".  If a compute or fix provides the value being time
 averaged, then the compute or fix determines whether the value is
 intensive or extensive; see the page for that compute or fix for
 further info.  Values produced by a variable are treated as intensive.

doc/src/fix_balance.rst

@@ -361,7 +361,7 @@ The "SQUARES" section lists the node IDs of the four vertices in a
 rectangle for each processor (1 to 4).
 
 For a 3d problem, the syntax is similar but with eight vertices listed for
-each processor instead of four, and "SQUARES" replaced by "CUBES."
+each processor instead of four, and "SQUARES" replaced by "CUBES".
 
 ----------
 
@@ -387,7 +387,7 @@ number of particles (or total weight) per processor.
 
 These quantities can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar and vector values calculated
-by this fix are "intensive."
+by this fix are "intensive".
 
 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/src/fix_latte.rst

@@ -8,18 +8,27 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID latte peID
+   fix ID group-ID latte keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * latte = style name of this fix command
-* peID = NULL or ID of compute used to calculate per-atom energy
+* zero or more keyword/value pairs may be appended
+
+  .. parsed-literal::
+
+     keyword = *coulomb* or *exclude*
+       *coulomb* value = peID
+         peID = ID of compute used to calculate per-atom energy
+       *exclude* value = fixID
+         fixID = ID of fix which potentially excludes atoms before calling LATTE
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   fix dftb all latte NULL
+   fix dftb all latte
+   fix dftb all exclude GCMC
 
 Description
 """""""""""
@@ -48,10 +57,41 @@ found in examples/latte.
 
 A step-by-step tutorial can be followed at: `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_
 
-The *peID* argument is not yet supported by fix latte, so it must be
+Currently, LAMMPS must be run in serial or as a single MPI task, to
-specified as NULL.  Eventually it will be used to enable LAMMPS to
+use this fix.  This is because the version of the LATTE library LAMMPS
-calculate a Coulomb potential as an alternative to LATTE performing
+uses does not support MPI.  On the LAMMPS size, this is typically not
-the calculation.
+a bottleneck, since LATTE will be doing 99% or more of the work to
+compute quantum-accurate forces.  On the LATTE side, the LATTE library
+does support threaded parallelism via OpenMP.  You must build the
+LATTE library with OpenMP support, then set the OMP_NUM_THREADS
+environment variable before performing a LAMMPS + LATTE simulation to
+tell LATTE how many threads to invoke.
+
+.. note::
+
+   NEB calculations can be done using this fix using multiple
+   replicas and running LAMMPS in parallel.  However, each replica must
+   be run on a single MPI task.  For details, see the :doc:`neb <neb>`
+   command page and the :doc:`-partition command-line switch <Run_options>`
+
+----------
+
+The *coulomb* argument is not yet supported by fix latte (as of Sept
+2022).  Eventually it will be used to enable LAMMPS to calculate a
+Coulomb potential as an alternative to LATTE performing the
+calculation.
+
+The *exclude* argument allows this fix to work in tandem with another
+fix which may decide to delete one or more atoms of molecules.  The
+specified fixID is the ID of the other fix.
+
+The one current example of such a fix is the :doc:`fix gcmc
+<fix_gcmc>` command which performs Monte Carlo insertions and
+deletions.  If a trial deletion is performed, then LAMMPS needs to
+only pass LATTE the atoms which remain.  Fix gcmc does not actually
+remove any atoms until after the new energy is computed (in this case
+by LATTE), and a Monte Carlo accept/reject decision is made for the
+trial deletion.
 
 ----------
 
@@ -153,18 +193,8 @@ use this fix.
 
 LATTE does not currently compute per-atom energy or per-atom virial
 contributions.  So they will not show up as part of the calculations
-performed by the :doc:`compute pe/atom <compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>` commands.
+performed by the :doc:`compute pe/atom <compute_pe_atom>` or
-
+:doc:`compute stress/atom <compute_stress_atom>` commands.
-Currently, LAMMPS must be run in serial or as a single MPI task, to
-use this fix.  This is typically not a bottleneck, since LATTE will be
-doing 99% or more of the work to compute quantum-accurate forces.
-
-.. note::
-
-   NEB calculations can be done using this fix using multiple
-   replicas and running LAMMPS in parallel.  However, each replica must
-   be run on a single MPI task.  For details, see the :doc:`neb <neb>`
-   command page and the :doc:`-partition command-line switch <Run_options>`
 
 Related commands
 """"""""""""""""

doc/src/group.rst

@@ -318,7 +318,7 @@ Restrictions
 """"""""""""
 
 There can be no more than 32 groups defined at one time, including
-"all."
+"all".
 
 The parent group of a dynamic group cannot itself be a dynamic group.
 

doc/src/improper_coeff.rst

@@ -10,7 +10,7 @@ Syntax
 
    improper_coeff N args
 
-* N = improper type (see asterisk form below)
+* N = numeric improper type (see asterisk form below), or type label
 * args = coefficients for one or more improper types
 
 Examples
@@ -22,27 +22,34 @@ Examples
    improper_coeff * 80.2 -1 2
    improper_coeff *4 80.2 -1 2
 
+   labelmap improper 1 benzene
+   improper_coeff benzene 300.0 0.0
+
 Description
 """""""""""
 
 Specify the improper force field coefficients for one or more improper
 types.  The number and meaning of the coefficients depends on the
-improper style.  Improper coefficients can also be set in the data
+improper style.  Improper coefficients can also be set in the data file
-file read by the :doc:`read_data <read_data>` command or in a restart
+read by the :doc:`read_data <read_data>` command or in a restart file.
-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 improper types.  This takes
+type label, which is an alphanumeric string defined by the
-the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of improper
+:doc:`labelmap <labelmap>` command or in a section of a data file read
-types, then an asterisk with no numeric values means all types from 1
+by the :doc:`read_data <read_data>` command.
-to N.  A leading asterisk means all types from 1 to n (inclusive).  A
+
-trailing asterisk means all types from n to N (inclusive).  A middle
+For numeric values only, a wild-card asterisk can be used to set the
-asterisk means all types from m to n (inclusive).
+coefficients for multiple improper types.  This takes the form "\*" or
+"\*n" or "n\*" or "m\*n".  If :math:`N` = the number of improper 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 improper_coeff command can override a previous
-setting for the same improper type.  For example, these commands set
+setting for the same improper type.  For example, these commands set the
-the coeffs for all improper types, then overwrite the coeffs for just
+coeffs for all improper types, then overwrite the coeffs for just
 improper type 2:
 
 .. code-block:: LAMMPS
@@ -53,9 +60,9 @@ improper type 2:
 A line in a data file that specifies improper coefficients uses the
 exact same format as the arguments of the improper_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 "Improper Coeffs" section of a data file, the line that
+example, under the "Improper Coeffs" section of a data file, the line
-corresponds to the first example above would be listed as
+that corresponds to the first example above would be listed as
 
 .. parsed-literal::
 

doc/src/kim_commands.rst

@@ -981,7 +981,7 @@ In the last example, "new-property.edn" and
 "/home/mary/marys-kim-properties/dissociation-energy.edn" are the names of files
 that contain user-defined (local) property definitions.
 
-A KIM property instance takes the form of a "map," i.e. a set of key-value
+A KIM property instance takes the form of a "map", i.e. a set of key-value
 pairs akin to Perl's hash, Python's dictionary, or Java's Hashtable.  It
 consists of a set of property key names, each of which is referred to here by
 the *key_name* argument, that are defined as part of the relevant KIM Property

doc/src/labelmap.rst

@@ -0,0 +1,100 @@
+.. index:: labelmap
+
+labelmap command
+==================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   labelmap option args
+
+* *option* = *atom* or *bond* or *angle* or *dihedral* or *improper* or *clear* or *write*
+
+  .. parsed-literal::
+
+     *clear* = no args
+     *write* arg = filename
+     *atom* or *bond* or *angle* or *dihedral* or *improper*
+       args = list of one or more numeric-type/type-label pairs
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
+   labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """
+   labelmap atom $(label2type(atom,carbon)) C  # change type label from 'carbon' to 'C'
+   labelmap clear
+   labelmap write mymap.include
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Define alphanumeric type labels to associate with one or more numeric
+atom, bond, angle, dihedral or improper types.  A collection of type
+labels for all atom types, bond types, etc. is stored as a label map.
+
+The label map can also be defined by the :doc:`read_data <read_data>`
+command when it reads these sections in a data file: Atom Type Labels,
+Bond Type Labels, etc.  See the :doc:`Howto type labels
+<Howto_type_labels>` doc page for a general discussion of how type
+labels can be used.
+
+Valid type labels can contain any alphanumeric character, but must not
+start with a number, a '#', or a '*' character.  They can contain other
+standard ASCII characters such as angular or square brackets '<' and '>'
+or '[' and ']', parenthesis '(' and ')', dash '-', underscore '_', plus
+'+' and equals '=' signs and more.  They must not contain blanks or any
+other whitespace.  Note that type labels must be put in single or double
+quotation marks if they contain the '#' character or if they contain a
+double (") or single quotation mark (').  If the label contains both
+a single and a double quotation mark, then triple quotation (""") must
+be used.  When enclosing a type label with quotation marks, the
+LAMMPS input parser may require adding leading or trailing blanks
+around the type label so it can identify the enclosing quotation
+marks.  Those blanks will be removed when defining the label.
+
+A *labelmap* command can only modify the label map for one type-kind
+(atom types, bond types, etc).  Any number of numeric-type/type-label
+pairs may follow.  If a type label already exists for the same numeric
+type, it will be overwritten.  Type labels must be unique; assigning the
+same type label to multiple numeric types within the same type-kind is
+not allowed.  When reading and writing data files, it is required that
+there is a label defined for *every* numeric type within a given
+type-kind in order to write out the type label section for that
+type-kind.
+
+The *clear* option resets the label map and thus discards all previous
+settings.
+
+The *write* option takes a filename as argument and writes the current
+label mappings to a file as a sequence of *labelmap* commands, so the
+file can be copied into a new LAMMPS input file or read in using the
+:doc:`include <include>` command.
+
+----------
+
+Restrictions
+""""""""""""
+
+This command must come after the simulation box is defined by a
+:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
+:doc:`create_box <create_box>` command.
+
+Label maps are currently not supported when using the KOKKOS package.
+
+Related commands
+""""""""""""""""
+
+:doc:`read_data <read_data>`, :doc:`write_data <write_data>`,
+:doc:`molecule <molecule>`, :doc:`fix bond/react <fix_bond_react>`
+
+Default
+"""""""
+
+none

doc/src/mass.rst

@@ -10,7 +10,7 @@ Syntax
 
    mass I value
 
-* I = atom type (see asterisk form below)
+* I = atom type (see asterisk form below), or type label
 * value = mass
 
 Examples
@@ -22,6 +22,9 @@ Examples
    mass * 62.5
    mass 2* 62.5
 
+   labelmap atom 1 C
+   mass C 12.01
+
 Description
 """""""""""
 
@@ -30,12 +33,16 @@ values can also be set in the :doc:`read_data <read_data>` data file
 using the "Masses" keyword.  See the :doc:`units <units>` command for
 what mass units to use.
 
-The I index can be specified in one of two ways.  An explicit numeric
+The I index can be specified in one of several ways.  An explicit
-value can be used, as in the first example above.  Or a wild-card
+numeric value can be used, as in the first example above.  Or I can be
-asterisk can be used to set the mass for multiple atom types.  This
+a type label, which is an alphanumeric string defined by the
-takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of
+:doc:`labelmap <labelmap>` command or in a section of a data file read
-atom types, then an asterisk with no numeric values means all types
+by the :doc:`read_data <read_data>` command, and which converts
-from 1 to N.  A leading asterisk means all types from 1 to n
+internally to a numeric type. Or a wild-card asterisk can be used to
+set the mass for multiple atom types.  This takes the form "\*" or
+"\*n" or "n\*" or "m\*n", where m and n are numbers.  If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from n to N
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).

doc/src/molecule.rst

@@ -70,8 +70,9 @@ and underscores.
 A single template can contain multiple molecules, listed one per file.
 Some of the commands listed above currently use only the first
 molecule in the template, and will issue a warning if the template
-contains multiple molecules.  The :doc:`atom_style template <atom_style>` command allows multiple-molecule templates
+contains multiple molecules.  The :doc:`atom_style template
-to define a system with more than one templated molecule.
+<atom_style>` command allows multiple-molecule templates to define a
+system with more than one templated molecule.
 
 Each filename can be followed by optional keywords which are applied
 only to the molecule in the file as used in this template.  This is to
@@ -88,6 +89,12 @@ molecule file.  E.g. if *toff* = 2, and the file uses atom types
 individual values will be ignored if the molecule template does not
 use that attribute (e.g. no bonds).
 
+.. note::
+
+   Offsets are **ignored** on lines using type labels, as the type
+   labels will determine the actual types directly depending on the
+   current :doc:`labelmap <labelmap>` settings.
+
 The *scale* keyword scales the size of the molecule.  This can be
 useful for modeling polydisperse granular rigid bodies.  The scale
 factor is applied to each of these properties in the molecule file, if
@@ -118,14 +125,18 @@ The format of an individual molecule file is similar but
 (not identical) to the data file read by the :doc:`read_data <read_data>`
 commands, and is as follows.
 
-A molecule file has a header and a body.  The header appears first.
+A molecule file has a header and a body.  The header appears first.  The
-The first line of the header is always skipped; it typically contains
+first line of the header and thus of the molecule file is *always* skipped;
-a description of the file.  Then lines are read one at a time.  Lines
+it typically contains a description of the file or a comment from the software
-can have a trailing comment starting with '#' that is ignored.  If the
+that created the file.
-line is blank (only white-space after comment is deleted), it is
+
+Then lines are read one line at a time.  Lines can have a trailing
+comment starting with '#' that is ignored.  There *must* be at least one
+blank between any valid content and the comment.  If the line is blank
+(i.e. contains only white-space after comments are deleted), it is
 skipped.  If the line contains a header keyword, the corresponding
-value(s) is read from the line.  If it does not contain a header
+value(s) is/are read from the line.  A line that is *not* blank and does
-keyword, the line begins the body of the file.
+*not* contains a header keyword begins the body of the file.
 
 The body of the file contains zero or more sections.  The first line
 of a section has only a keyword.  The next line is skipped.  The
@@ -173,31 +184,43 @@ These are the allowed section keywords for the body of the file.
 * *Special Bond Counts, Special Bonds* = special neighbor info
 * *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
 
+For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
+atom/bond/angle/etc type can be specified either as a number (numeric
+type) or as an alphanumeric type label.  The latter is only allowed if
+type labels have been defined, either by the :doc:`labelmap
+<labelmap>` command or in data files read by the :doc:`read_data
+<read_data>` command which have sections for Atom Type Labels, Bond
+Type Labels, Angle Type Labels, etc.  See the :doc:`Howto type labels
+<Howto_type_labels>` doc page for the allowed syntax of type labels
+and a general discussion of how type labels can be used.
+When using type labels, any values specified as *offset* are ignored.
+
 If a Bonds section is specified then the Special Bond Counts and
 Special Bonds sections can also be used, if desired, to explicitly
 list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
 details below).  This is optional since if these sections are not
 included, LAMMPS will auto-generate this information.  Note that
 LAMMPS uses this info to properly exclude or weight bonded pairwise
-interactions between bonded atoms.  See the
+interactions between bonded atoms.  See the :doc:`special_bonds
-:doc:`special_bonds <special_bonds>` command for more details.  One
+<special_bonds>` command for more details.  One reason to list the
-reason to list the special bond info explicitly is for the
+special bond info explicitly is for the :doc:`thermalized Drude
-:doc:`thermalized Drude oscillator model <Howto_drude>` which treats the
+oscillator model <Howto_drude>` which treats the bonds between nuclear
-bonds between nuclear cores and Drude electrons in a different manner.
+cores and Drude electrons in a different manner.
 
 .. note::
 
-   Whether a section is required depends on how the molecule
+   Whether a section is required depends on how the molecule template
-   template is used by other LAMMPS commands.  For example, to add a
+   is used by other LAMMPS commands.  For example, to add a molecule
-   molecule via the :doc:`fix deposit <fix_deposit>` command, the Coords
+   via the :doc:`fix deposit <fix_deposit>` command, the Coords and
-   and Types sections are required.  To add a rigid body via the :doc:`fix pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
+   Types sections are required.  To add a rigid body via the :doc:`fix
+   pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
    required, since the molecule will be treated as a rigid body.  Some
    sections are optional.  For example, the :doc:`fix pour <fix_pour>`
    command can be used to add "molecules" which are clusters of
    finite-size granular particles.  If the Diameters section is not
-   specified, each particle in the molecule will have a default diameter
+   specified, each particle in the molecule will have a default
-   of 1.0.  See the doc pages for LAMMPS commands that use molecule
+   diameter of 1.0.  See the doc pages for LAMMPS commands that use
-   templates for more details.
+   molecule templates for more details.
 
 Each section is listed below in alphabetic order.  The format of each
 section is described including the number of lines it must contain and
@@ -222,7 +245,7 @@ order.
 
 * one line per atom
 * line syntax: ID type
-* type = atom type of atom
+* type = atom type of atom (1-Natomtype, or type label)
 
 ----------
 
@@ -289,7 +312,7 @@ included, the default mass for each atom is derived from its volume
 
 * one line per bond
 * line syntax: ID type atom1 atom2
-* type = bond type (1-Nbondtype)
+* type = bond type (1-Nbondtype, or type label)
 * atom1,atom2 = IDs of atoms in bond
 
 The IDs for the two atoms in each bond should be values
@@ -301,7 +324,7 @@ from 1 to Natoms, where Natoms = # of atoms in the molecule.
 
 * one line per angle
 * line syntax: ID type atom1 atom2 atom3
-* type = angle type (1-Nangletype)
+* type = angle type (1-Nangletype, or type label)
 * atom1,atom2,atom3 = IDs of atoms in angle
 
 The IDs for the three atoms in each angle should be values from 1 to
@@ -315,7 +338,7 @@ which the angle is computed) is the atom2 in the list.
 
 * one line per dihedral
 * line syntax: ID type atom1 atom2 atom3 atom4
-* type = dihedral type (1-Ndihedraltype)
+* type = dihedral type (1-Ndihedraltype, or type label)
 * atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
 
 The IDs for the four atoms in each dihedral should be values from 1 to
@@ -328,7 +351,7 @@ ordered linearly within the dihedral.
 
 * one line per improper
 * line syntax: ID type atom1 atom2 atom3 atom4
-* type = improper type (1-Nimpropertype)
+* type = improper type (1-Nimpropertype, or type label)
 * atom1,atom2,atom3,atom4 = IDs of atoms in improper
 
 The IDs for the four atoms in each improper should be values from 1 to
@@ -447,11 +470,15 @@ This section is only needed when molecules created using the template
 will be constrained by SHAKE via the "fix shake" command.  The other
 two Shake sections must also appear in the file.
 
-The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
+The a,b,c values are bond types for all bonds in the SHAKE cluster that
-in the SHAKE cluster that this atom belongs to.  The number of values
+this atom belongs to.  Bond types may be either numbers (from 1 to Nbondtypes)
-that must appear is determined by the shake flag for the atom (see the
+or bond type labels as defined by the :doc:`labelmap <labelmap>` command
-Shake Flags section above).  All atoms in a particular cluster should
+or a "Bond Type Labels" section of a data file.
-list their a,b,c values identically.
+
+
+The number of values that must appear is determined by the shake flag
+for the atom (see the Shake Flags section above).  All atoms in a
+particular cluster should list their a,b,c values identically.
 
 If flag = 0, no a,b,c values are listed on the line, just the
 (ignored) ID.
@@ -459,8 +486,9 @@ If flag = 0, no a,b,c values are listed on the line, just the
 If flag = 1, a,b,c are listed, where a = bondtype of the bond between
 the central atom and the first non-central atom (value b in the Shake
 Atoms section), b = bondtype of the bond between the central atom and
-the second non-central atom (value c in the Shake Atoms section), and c =
+the second non-central atom (value c in the Shake Atoms section), and c
-the angle type (1 to Nangletypes) of the angle between the 3 atoms.
+= the angle type (1 to Nangletypes, or angle type label) of the angle
+between the 3 atoms.
 
 If flag = 2, only a is listed, where a = bondtype of the bond between
 the 2 atoms in the cluster.
@@ -473,9 +501,9 @@ and the second non-central atom (value c in the Shake Atoms section).
 If flag = 4, a,b,c are listed, where a = bondtype of the bond between
 the central atom and the first non-central atom (value b in the Shake
 Atoms section), b = bondtype of the bond between the central atom and
-the second non-central atom (value c in the Shake Atoms section), and c =
+the second non-central atom (value c in the Shake Atoms section), and c
-bondtype of the bond between the central atom and the third non-central
+= bondtype of the bond between the central atom and the third
-atom (value d in the Shake Atoms section).
+non-central atom (value d in the Shake Atoms section).
 
 See the :doc:`fix shake <fix_shake>` page for a further description
 of SHAKE clusters.