Merge branch 'develop' into distributed-grids

# Conflicts:
#	doc/src/Developer_utils.rst
#	doc/src/dump.rst
#	doc/src/fix_ave_chunk.rst
#	src/utils.h

.github/workflows/compile-msvc.yml

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

.github/workflows/coverity.yml

@@ -0,0 +1,103 @@
+name: "Run Coverity Scan"
+
+on:
+  schedule:
+    - cron: "0 0 * * FRI"
+
+  workflow_dispatch:
+
+jobs:
+  analyze:
+    name: Analyze
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-latest
+    container:
+      image: lammps/buildenv:ubuntu20.04
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 2
+
+    - name: Create Build and Download Folder
+      run: mkdir build download
+
+    - name: Cache Coverity
+      id: cache-coverity
+      uses: actions/cache@v3
+      with:
+        path: ./download/
+        key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}
+
+    - name: Download Coverity if necessary
+      if: steps.cache-coverity.outputs.cache-hit != 'true'
+      working-directory: download
+      run: |
+        wget -nv https://scan.coverity.com/download/linux64 --post-data "token=${{ secrets.COVERITY_TOKEN }}&project=LAMMPS" -O coverity_tool.tgz
+        wget -nv https://scan.coverity.com/download/linux64 --post-data "token=${{ secrets.COVERITY_TOKEN }}&project=LAMMPS&md5=1" -O coverity_tool.md5
+        echo " coverity_tool.tgz" >> coverity_tool.md5
+        md5sum -c coverity_tool.md5
+
+    - name: Setup Coverity
+      run: |
+        tar xzf download/coverity_tool.tgz
+        ln -s cov-analysis-linux64-* coverity
+
+    - name: Configure LAMMPS via CMake
+      shell: bash
+      working-directory: build
+      run: |
+        cmake \
+        -C ../cmake/presets/clang.cmake \
+        -C ../cmake/presets/most.cmake \
+        -C ../cmake/presets/kokkos-openmp.cmake \
+        -D CMAKE_BUILD_TYPE="RelWithDebug" \
+        -D CMAKE_TUNE_FLAGS="-Wall -Wextra -Wno-unused-result" \
+        -D BUILD_MPI=on \
+        -D BUILD_OMP=on \
+        -D BUILD_SHARED_LIBS=on \
+        -D LAMMPS_SIZES=SMALLBIG \
+        -D LAMMPS_EXCEPTIONS=off \
+        -D PKG_MESSAGE=on \
+        -D PKG_MPIIO=on \
+        -D PKG_ATC=on \
+        -D PKG_AWPMD=on \
+        -D PKG_BOCS=on \
+        -D PKG_EFF=on \
+        -D PKG_H5MD=on \
+        -D PKG_INTEL=on \
+        -D PKG_LATBOLTZ=on \
+        -D PKG_MANIFOLD=on \
+        -D PKG_MGPT=on \
+        -D PKG_ML-PACE=on \
+        -D PKG_ML-RANN=on \
+        -D PKG_MOLFILE=on \
+        -D PKG_NETCDF=on \
+        -D PKG_PTM=on \
+        -D PKG_QTB=on \
+        -D PKG_SMTBQ=on \
+        -D PKG_TALLY=on \
+        ../cmake
+
+    - name: Run Coverity Scan
+      shell: bash
+      working-directory: build
+      run: |
+        export PATH=$GITHUB_WORKSPACE/coverity/bin:$PATH
+        cov-build --dir cov-int cmake --build . --parallel 2
+
+    - name: Create tarball with scan results
+      shell: bash
+      working-directory: build
+      run: tar czf lammps.tgz cov-int
+
+    - name: Upload scan result to Coverity
+      shell: bash
+      run: |
+        curl --form token=${{ secrets.COVERITY_TOKEN }} \
+             --form email=${{ secrets.COVERITY_EMAIL }} \
+             --form file=@build/lammps.tgz \
+             --form version=${{ github.sha }} \
+             --form description="LAMMPS automated build" \
+             https://scan.coverity.com/builds?project=LAMMPS

.github/workflows/unittest-macos.yml

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

cmake/CMakeLists.txt

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

cmake/Modules/LAMMPSUtils.cmake

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

cmake/Modules/Packages/MDI.cmake

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

cmake/presets/clang.cmake

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

doc/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/Commands_bond.rst

@@ -44,6 +44,7 @@ OPT.
    * :doc:`harmonic (iko) <bond_harmonic>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`mesocnt <bond_mesocnt>`
    * :doc:`mm3 <bond_mm3>`
    * :doc:`morse (o) <bond_morse>`
    * :doc:`nonlinear (o) <bond_nonlinear>`
@@ -92,6 +93,7 @@ OPT.
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
    * :doc:`gaussian <angle_gaussian>`
    * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
    * :doc:`spica (o) <angle_spica>`

doc/src/Commands_pair.rst

@@ -201,6 +201,7 @@ OPT.
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
+   * :doc:`mesocnt/viscous <pair_mesocnt>`
    * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`

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
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -208,6 +214,9 @@ Argument processing
 .. doxygenfunction:: parse_gridid
    :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

@@ -932,6 +932,10 @@ EXTRA-MOLECULE package
 
 Additional bond, angle, dihedral, and improper styles that are less commonly used.
 
+**Install:**
+
+To use this package, also the :ref:`MOLECULE <PKG-MOLECULE>` package needs to be installed.
+
 **Supporting info:**
 
 * src/EXTRA-MOLECULE: filenames -> commands
@@ -1404,7 +1408,7 @@ This package has :ref:`specific installation instructions <machdyn>` on the :doc
 
 * src/MACHDYN: filenames -> commands
 * src/MACHDYN/README
-* doc/PDF/MACHDYN_LAMMPS_userguide.pdf
+* `doc/PDF/MACHDYN_LAMMPS_userguide.pdf <PDF/MACHDYN_LAMMPS_userguide.pdf>`_
 * examples/PACKAGES/machdyn
 * https://www.lammps.org/movies.html#smd
 
@@ -1556,31 +1560,40 @@ MESONT package
 
 **Contents:**
 
-MESONT is a LAMMPS package for simulation of nanomechanics of
+MESONT is a LAMMPS package for simulation of nanomechanics of nanotubes
-nanotubes (NTs). The model is based on a coarse-grained representation
+(NTs). The model is based on a coarse-grained representation of NTs as
-of NTs as "flexible cylinders" consisting of a variable number of
+"flexible cylinders" consisting of a variable number of
 segments. Internal interactions within a NT and the van der Waals
 interaction between the tubes are described by a mesoscopic force field
 designed and parameterized based on the results of atomic-level
 molecular dynamics simulations. The description of the force field is
-provided in the papers listed below. This package contains two
+provided in the papers listed below.
-independent implementations of this model: :doc:`pair_style mesocnt
+
-<pair_mesocnt>` is a (minimal) C++ implementation, and :doc:`pair_style
+This package contains two independent implementations of this model:
-mesont/tpm <pair_mesont_tpm>` is a more general and feature rich
+:doc:`pair_style mesont/tpm <pair_mesont_tpm>` is the original
-implementation based on a Fortran library in the ``lib/mesont`` folder.
+implementation of the model based on a Fortran library in the
+``lib/mesont`` folder. The second implementation is provided by the
+mesocnt styles (:doc:`bond_style mesocnt <bond_mesocnt>`,
+:doc:`angle_style mesocnt <angle_mesocnt>` and :doc:`pair_style mesocnt
+<pair_mesocnt>`).  The mesocnt implementation has the same features as
+the original implementation with the addition of friction, but is
+directly implemented in C++, interfaces more cleanly with general LAMMPS
+functionality, and is typically faster. It also does not require its own
+atom style and can be installed without any external libraries.
 
 **Download of potential files:**
 
-The potential files for these pair styles are *very* large and thus
+The potential files for these pair styles are *very* large and thus are
-are not included in the regular downloaded packages of LAMMPS or the
+not included in the regular downloaded packages of LAMMPS or the git
-git repositories.  Instead, they will be automatically downloaded
+repositories.  Instead, they will be automatically downloaded from a web
-from a web server when the package is installed for the first time.
+server when the package is installed for the first time.
 
 **Authors of the *mesont* styles:**
 
-Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)
+Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University
+of Alabama), Leonid V. Zhigilei (University of Virginia)
 
-**Author of the *mesocnt* pair style:**
+**Author of the *mesocnt* styles:**
 Philipp Kloza (U Cambridge)
 
 **Supporting info:**
@@ -1590,6 +1603,8 @@ Philipp Kloza (U Cambridge)
 * :doc:`atom_style mesont <atom_style>`
 * :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
 * :doc:`compute mesont <compute_mesont>`
+* :doc:`bond_style mesocnt <bond_mesocnt>`
+* :doc:`angle_style mesocnt <angle_mesocnt>`
 * :doc:`pair_style mesocnt <pair_mesocnt>`
 * examples/PACKAGES/mesont
 * tools/mesont
@@ -2692,7 +2707,7 @@ Dynamics, Ernst Mach Institute, Germany).
 
 * src/SPH: filenames -> commands
 * src/SPH/README
-* doc/PDF/SPH_LAMMPS_userguide.pdf
+* `doc/PDF/SPH_LAMMPS_userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_
 * examples/PACKAGES/sph
 * https://www.lammps.org/movies.html#sph
 

doc/src/accel_styles.rst

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

doc/src/angle_coeff.rst

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

doc/src/angle_mesocnt.rst

@@ -0,0 +1,146 @@
+.. index:: angle_style mesocnt
+
+angle_style mesocnt command
+===========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   angle_style mesocnt
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style mesocnt
+   angle_coeff 1 buckling C 10 10 20.0
+   angle_coeff 4 harmonic C 8 4 10.0
+   angle_coeff 2 buckling custom 400.0 50.0 5.0
+   angle_coeff 1 harmonic custom 300.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+The *mesocnt* angle style uses the potential
+
+.. math::
+
+   E = K_\text{H} \Delta \theta^2, \qquad |\Delta \theta| < \Delta
+   \theta_\text{B} \\
+   E = K_\text{H} \Delta \theta_\text{B}^2 +
+   K_\text{B} (\Delta \theta - \Delta \theta_\text{B}), \qquad |\Delta
+   \theta| \geq \Delta \theta_\text{B}
+
+where :math:`\Delta \theta = \theta - \pi` is the bending angle of the
+nanotube, :math:`K_\text{H}` and :math:`K_\text{B}` are prefactors for
+the harmonic and linear regime respectively and :math:`\Delta
+\theta_\text{B}` is the buckling angle. Note that the usual 1/2 factor
+for the harmonic potential is included in :math:`K_\text{H}`.
+
+The style implements parameterization presets of :math:`K_\text{H}`,
+:math:`K_\text{B}` and :math:`\Delta \theta_\text{B}` for mesoscopic
+simulations of carbon nanotubes based on the atomistic simulations of
+:ref:`(Srivastava) <Srivastava_2>` and buckling considerations of
+:ref:`(Zhigilei) <Zhigilei1_1>`.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle_coeff <angle_coeff>` command as in the examples above, or
+in the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands:
+
+* mode = *buckling* or *harmonic*
+* preset = *C* or *custom*
+* additional parameters depending on preset
+
+If mode *harmonic* is chosen, the potential is simply harmonic and
+does not switch to the linear term when the buckling angle is
+reached. In *buckling* mode, the full piecewise potential is used.
+
+Preset *C* is for carbon nanotubes, and the additional parameters are:
+
+* chiral index :math:`n` (unitless)
+* chiral index :math:`m` (unitless)
+* :math:`r_0` (distance)
+
+Here, :math:`r_0` is the equilibrium distance of the bonds included in
+the angle, see :doc:`bond_style mesocnt <bond_mesocnt>`.
+
+In harmonic mode with preset *custom*, the additional parameter is:
+
+* :math:`K_\text{H}` (energy)
+
+Hence, this setting is simply a wrapper for :doc:`bond_style harmonic
+<bond_harmonic>` with an equilibrium angle of 180 degrees.
+
+In harmonic mode with preset *custom*, the additional parameters are:
+
+* :math:`K_\text{H}` (energy)
+* :math:`K_\text{B}` (energy)
+* :math:`\Delta \theta_\text{B}` (degrees)
+
+:math:`\Delta \theta_\text{B}` is specified in degrees, but LAMMPS
+converts it to radians internally; hence :math:`K_\text{H}` is
+effectively energy per radian\^2 and :math:`K_\text{B}` is energy per
+radian.
+
+----------
+
+In *buckling* mode, this angle style adds the *buckled* property to
+all atoms in the simulation, which is an integer flag indicating
+whether the bending angle at a given atom has exceeded :math:`\Delta
+\theta_\text{B}`. It can be accessed as an atomic variable, e.g. for
+custom dump commands, as *i_buckled*.
+
+.. note::
+
+   If the initial state of the simulation contains buckled nanotubes
+   and :doc:`pair_style mesocnt <pair_mesocnt>` is used, the
+   *i_buckled* atomic variable needs to be initialized before the
+   pair_style is defined by doing a *run 0* command straight after the
+   angle_style command. See below for an example.
+
+If CNTs are already buckled at the start of the simulation, this
+script will correctly initialize *i_buckled*:
+
+.. code-block:: LAMMPS
+
+   angle_style mesocnt
+   angle_coeff 1 buckling C 10 10 20.0
+
+   run 0
+
+   pair_style mesocnt 60.0
+   pair_coeff * * C_10_10.mesocnt 1
+
+Restrictions
+""""""""""""
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE and MESONT packages.  See the :doc:`Build package
+<Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_coeff <angle_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Srivastava_2:
+
+**(Srivastava)** Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417
+(2005).
+
+.. _Zhigilei1_1:
+
+**(Zhigilei)** Volkov and Zhigilei, ACS Nano 4, 6187 (2010).

doc/src/angle_style.rst

@@ -90,6 +90,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
 * :doc:`gaussian <angle_gaussian>` - multi-centered Gaussian-based angle potential
 * :doc:`harmonic <angle_harmonic>` - harmonic angle
+* :doc:`mesocnt <angle_mesocnt>` - piecewise harmonic and linear angle for bending-buckling of nanotubes
 * :doc:`mm3 <angle_mm3>` - anharmonic angle
 * :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
 * :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms

doc/src/bond_coeff.rst

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

doc/src/bond_mesocnt.rst

@@ -0,0 +1,84 @@
+.. index:: bond_style mesocnt
+
+bond_style mesocnt command
+===========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style mesocnt
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style mesocnt
+   bond_coeff 1 C 10 10 20.0
+   bond_coeff 4 custom 800.0 10.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+The *mesocnt* bond style is a wrapper for the :doc:`harmonic
+<bond_harmonic>` style, and uses the potential
+
+.. math::
+
+   E = K (r - r_0)^2
+
+where :math:`r_0` is the equilibrium bond distance.  Note that the
+usual 1/2 factor is included in :math:`K`.  The style implements
+parameterization presets of :math:`K` for mesoscopic simulations of
+carbon nanotubes based on the atomistic simulations of
+:ref:`(Srivastava) <Srivastava_1>`.
+
+Other presets can be readily implemented in the future.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands:
+
+* preset = *C* or *custom*
+* additional parameters depending on preset
+
+Preset *C* is for carbon nanotubes, and the additional parameters are:
+
+* chiral index :math:`n` (unitless)
+* chiral index :math:`m` (unitless)
+* :math:`r_0` (distance)
+
+Preset *custom* is simply a direct wrapper for the :doc:`harmonic
+<bond_harmonic>` style, and the additional parameters are:
+
+* :math:`K` (energy/distance\^2)
+* :math:`r_0` (distance)
+
+Restrictions
+""""""""""""
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+and MESONT packages.  See the :doc:`Build package <Build_package>`
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Srivastava_1:
+
+**(Srivastava)** Zhigilei, Wei and Srivastava, Phys. Rev. B 71, 165417
+(2005).

doc/src/bond_style.rst

@@ -95,6 +95,7 @@ accelerated styles exist.
 * :doc:`harmonic <bond_harmonic>` - harmonic bond
 * :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
 * :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
+* :doc:`mesocnt <bond_mesocnt>` - Harmonic bond wrapper with parameterization presets for nanotubes
 * :doc:`mm3 <bond_mm3>` - MM3 anharmonic bond
 * :doc:`morse <bond_morse>` - Morse bond
 * :doc:`nonlinear <bond_nonlinear>` - nonlinear bond

doc/src/commands_list.rst

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

doc/src/compute_property_atom.rst

@@ -198,8 +198,8 @@ Related commands
 """"""""""""""""
 
 :doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`,
-:doc::doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk
+:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
-:doc:<fix_ave_chunk>`, `fix property/atom <fix_property_atom>`
+:doc:`fix property/atom <fix_property_atom>`
 
 Default
 """""""

doc/src/compute_stress_atom.rst

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

doc/src/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

@@ -56,24 +56,24 @@ dump command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID style N file args
 
 * ID = user-assigned name for the dump
 * group-ID = ID of the group of atoms to be dumped
-* style = *atom* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *grid* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
+* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *grid* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
-* N = dump every this many timesteps
+* N = dump on timesteps which are multiples of N
 * file = name of file to write dump info to
 * args = list of arguments for a particular style
 
   .. parsed-literal::
 
        *atom* args = none
+       *atom/adios* args = none,  discussed on :doc:`dump atom/adios <dump_adios>` page
        *atom/gz* args = none
        *atom/zstd* args = none
        *atom/mpiio* args = none
-       *atom/adios* args = none,  discussed on :doc:`dump atom/adios <dump_adios>` page
        *cfg* args = same as *custom* args, see below
        *cfg/gz* args = same as *custom* args, see below
        *cfg/zstd* args = same as *custom* args, see below
@@ -190,14 +190,15 @@ Examples
 Description
 """""""""""
 
-Dump a snapshot of atom quantities to one or more files every :math:`N`
+Dump a snapshot of atom quantities to one or more files once every
-timesteps in one of several styles.  The *image* and *movie* styles are
+:math:`N` timesteps in one of several styles.  The *image* and *movie*
-the exception: the *image* style renders a JPG, PNG, or PPM image file
+styles are the exception: the *image* style renders a JPG, PNG, or PPM
-of the atom configuration every :math:`N` timesteps while the *movie* style
+image file of the atom configuration every :math:`N` timesteps while
-combines and compresses them into a movie file; both are discussed in
+the *movie* style combines and compresses them into a movie file; both
-detail on the :doc:`dump image <dump_image>` page.  The timesteps on
+are discussed in detail on the :doc:`dump image <dump_image>` page.
-which dump output is written can also be controlled by a variable.
+The timesteps on which dump output is written can also be controlled
-See the :doc:`dump_modify every <dump_modify>` command.
+by a variable.  See the :doc:`dump_modify every <dump_modify>`
+command.
 
 Only information for atoms in the specified group is dumped.  The
 :doc:`dump_modify thresh and region and refresh <dump_modify>` commands
@@ -256,7 +257,7 @@ the 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
 of the dump files they create, to the corresponding styles without
-"mpiio," except the single dump file they produce is written in
+"mpiio", except the single dump file they produce is written in
 parallel via the MPI-IO library.  For the remainder of this page,
 you should thus consider the *atom* and *atom/mpiio* styles (etc.) to
 be inter-changeable.  The one exception is how the filename is
@@ -301,13 +302,13 @@ where xlo,xhi are the maximum extents of the simulation box in the
 :math:`x`-dimension, and similarly for :math:`y` and :math:`z`.  The
 "xx yy zz" terms are six characters that encode the style of boundary for each
 of the six simulation box boundaries (xlo,xhi; ylo,yhi; and zlo,zhi).  Each of
-the six characters is either p (periodic), f (fixed), s (shrink wrap),
+the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap),
-or m (shrink wrapped with a minimum value).  See the
+or *m* (shrink wrapped with a minimum value).  See the
 :doc:`boundary <boundary>` command for details.
 
 For triclinic simulation boxes (non-orthogonal), an orthogonal
 bounding box which encloses the triclinic simulation box is output,
-along with the 3 tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
+along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
 formatted as follows:
 
 .. parsed-literal::
@@ -346,8 +347,8 @@ added for each atom via dump_modify.
 Style *custom* allows you to specify a list of atom attributes to be
 written to the dump file for each atom.  Possible attributes are
 listed above and will appear in the order specified.  You cannot
-specify a quantity that is not defined for a particular simulation -
+specify a quantity that is not defined for a particular simulation---such as
-such as *q* for atom style *bond*, since that atom style does not
+*q* for atom style *bond*, since that atom style does not
 assign charges.  Dumps occur at the very end of a timestep, so atom
 attributes will include effects due to fixes that are applied during
 the timestep.  An explanation of the possible dump custom attributes
@@ -447,7 +448,7 @@ 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`,
@@ -499,21 +500,29 @@ popular molecular viewing program.
 
 ----------
 
-Dumps are performed on timesteps that are a multiple of :math:`N` (including
+Dumps are performed on timesteps that are a multiple of :math:`N`
-timestep 0) and on the last timestep of a minimization if the
+(including timestep 0) and on the last timestep of a minimization if
-minimization converges.  Note that this means a dump will not be
+the minimization converges.  Note that this means a dump will not be
 performed on the initial timestep after the dump command is invoked,
-if the current timestep is not a multiple of :math:`N`.  This behavior can be
+if the current timestep is not a multiple of :math:`N`.  This behavior
-changed via the :doc:`dump_modify first <dump_modify>` command, which
+can be changed via the :doc:`dump_modify first <dump_modify>` command,
-can also be useful if the dump command is invoked after a minimization
+which can also be useful if the dump command is invoked after a
-ended on an arbitrary timestep.  :math:`N` can be changed between runs by
+minimization ended on an arbitrary timestep.
-using the :doc:`dump_modify every <dump_modify>` command (not allowed
+
-for *dcd* style).  The :doc:`dump_modify every <dump_modify>` command
+The value of :math:`N` can be changed between runs by using the
-also allows a variable to be used to determine the sequence of
+:doc:`dump_modify every <dump_modify>` command (not allowed for *dcd*
-timesteps on which dump files are written.  In this mode a dump on the
+style).  The :doc:`dump_modify every <dump_modify>` command also
-first timestep of a run will also not be written unless the
+allows a variable to be used to determine the sequence of timesteps on
+which dump files are written.  In this mode a dump on the first
+timestep of a run will also not be written unless the
 :doc:`dump_modify first <dump_modify>` command is used.
 
+If you instead want to dump snapshots based on simulation time (in
+time units of the :doc:`units` command), the :doc:`dump_modify
+every/time <dump_modify>` command can be used.  This can be useful
+when the timestep size varies during a simulation run, e.g. by use of
+the :doc:`fix dt/reset <fix_dt_reset>` command.
+
 The specified filename determines how the dump file(s) is written.
 The default is to write one large text file, which is opened when the
 dump command is invoked and closed when an :doc:`undump <undump>`
@@ -559,7 +568,7 @@ package installed, viz.,
    make mpi          # build LAMMPS for your platform
 
 Second, use a dump filename which contains ".mpiio."  Note that it
-does not have to end in ".mpiio," just contain those characters.
+does not have to end in ".mpiio", just contain those characters.
 Unlike MPI-IO restart files, which must be both written and read using
 MPI-IO, the dump files produced by these MPI-IO styles are identical
 in format to the files produced by their non-MPI-IO style
@@ -582,19 +591,19 @@ and have 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 "\*" or "%" is also used) is written in binary format.  A
-binary dump file will be about the same size as a text version, but
+binary dump file will be about the same size as a text version, but will
-will typically write out much faster.  Of course, when
+typically write out much faster.  Of course, when post-processing, you
-post-processing, you will need to convert it back to text format (see
+will need to convert it back to text format (see the :ref:`binary2txt
-the :ref:`binary2txt tool <binary>`) or write your own code to read
+tool <binary>`) or write your own code to read the binary file.  The
-the binary file.  The format of the binary file can be understood by
+format of the binary file can be understood by looking at the
-looking at the :file:`tools/binary2txt.cpp` file.  This option is only
+:file:`tools/binary2txt.cpp` file.  This option is only available for
-available for the *atom* and *custom* styles.
+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
+is also used) is written in gzipped format.  A gzipped dump file will be
-will be about :math:`3\times` smaller than the text version, but will
+about :math:`3\times` smaller than the text version, but will also take
-also take longer to write.  This option is not available for the *dcd*
+longer to write.  This option is not available for the *dcd* and *xtc*
-and *xtc* styles.
+styles.
 
 ----------
 
@@ -643,10 +652,10 @@ mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components
 of atom velocity and force and atomic charge.
 
 There are several options for outputting atom coordinates.  The *x*,
-*y*, and *z* attributes write atom coordinates "unscaled," in the
+*y*, and *z* attributes write atom coordinates "unscaled", in the
 appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`,
-:math:`\sigma`, etc.).  Use *xs*, *ys*, *zs* if you want the coordinates
+:math:`\sigma`, etc.).  Use *xs*, *ys*, and *zs* if you want the coordinates
-"scaled" to the box size, so that each value is 0.0 to 1.0.  If the simulation
+"scaled" to the box size so that each value is 0.0 to 1.0.  If the simulation
 box is triclinic (tilted), then all atom coords will still be between 0.0 and
 1.0.  The actual unscaled :math:`(x,y,z)` coordinate is
 :math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal
@@ -689,7 +698,7 @@ The *angmomx*, *angmomy*, and *angmomz* attributes are specific to
 finite-size aspherical particles that have an angular momentum.  Only
 the *ellipsoid* atom style defines this quantity.
 
-The *tqx*, *tqy*, *tqz* attributes are for finite-size particles that
+The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles that
 can sustain a rotational torque due to interactions with other
 particles.
 
@@ -728,8 +737,8 @@ If *f_ID* is used as a attribute, then the per-atom vector calculated
 by the fix is printed.  If *f_ID[i]* is used, then :math:`i` must be in the
 range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
 per-atom array with :math:`M` columns calculated by the fix.  See the
-discussion above for how :math:`i` can be specified with a wildcard asterisk to
+discussion above for how :math:`i` can be specified with a wildcard asterisk
-effectively specify multiple values.
+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

doc/src/dump_adios.rst

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

doc/src/dump_cfg_uef.rst

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

doc/src/dump_image.rst

@@ -12,7 +12,7 @@ dump movie command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID style N file color diameter keyword value ...
 
@@ -28,7 +28,7 @@ Syntax
 
   .. parsed-literal::
 
-       *atom* = yes/no = do or do not draw atoms
+       *atom* = *yes* or *no* = do or do not draw atoms
        *adiam* size = numeric value for atom diameter (distance units)
        *bond* values = color width = color and width of bonds
          color = *atom* or *type* or *none*
@@ -68,21 +68,20 @@ Syntax
        *box* values = yes/no diam = draw outline of simulation box
          yes/no = do or do not draw simulation box lines
          diam = diameter of box lines as fraction of shortest box length
-       *axes* values = yes/no length diam = draw xyz axes
+       *axes* values = axes length diam = draw xyz axes
-         yes/no = do or do not draw xyz axes lines next to simulation box
+         axes = *yes* or *no = do or do not draw xyz axes lines next to simulation box
          length = length of axes lines as fraction of respective box lengths
          diam = diameter of axes lines as fraction of shortest box length
-       *subbox* values = yes/no diam = draw outline of processor sub-domains
+       *subbox* values = lines diam = draw outline of processor sub-domains
-         yes/no = do or do not draw sub-domain lines
+         lines = *yes* or *no* = do or do not draw sub-domain lines
          diam = diameter of sub-domain lines as fraction of shortest box length
        *shiny* value = sfactor = shinyness of spheres and cylinders
          sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
-       *ssao* value = yes/no seed dfactor = SSAO depth shading
+       *ssao* value = shading seed dfactor = SSAO depth shading
-         yes/no = turn depth shading on/off
+         shading = *yes* or *no* = turn depth shading on/off
          seed = random # seed (positive integer)
          dfactor = strength of shading from 0.0 to 1.0
 
-
 .. _dump_modify_image:
 
 dump_modify options for dump image/movie
@@ -162,7 +161,7 @@ Examples
 Description
 """""""""""
 
-Dump a high-quality rendered image of the atom configuration every N
+Dump a high-quality rendered image of the atom configuration every :math:`N`
 timesteps and save the images either as a sequence of JPEG or PNG or
 PPM files, or as a single movie file.  The options for this command as
 well as the :doc:`dump_modify <dump_modify>` command control what is
@@ -179,7 +178,7 @@ has been run, using the :doc:`rerun <rerun>` command to read snapshots
 from an existing dump file, and using these dump commands in the rerun
 script to generate the images/movie.
 
-Here are two sample images, rendered as 1024x1024 JPEG files.
+Here are two sample images, rendered as :math:`1024\times 1024` JPEG files.
 
 .. |dump1| image:: img/dump1.jpg
    :width: 48%
@@ -197,8 +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
@@ -232,22 +231,22 @@ details.
 
 ----------
 
-Dumps are performed on timesteps that are a multiple of N (including
+Dumps are performed on timesteps that are a multiple of :math:`N` (including
 timestep 0) and on the last timestep of a minimization if the
 minimization converges.  Note that this means a dump will not be
 performed on the initial timestep after the dump command is invoked,
-if the current timestep is not a multiple of N.  This behavior can be
+if the current timestep is not a multiple of :math:`N`.  This behavior can be
 changed via the :doc:`dump_modify first <dump_modify>` command, which
 can be useful if the dump command is invoked after a minimization
-ended on an arbitrary timestep.  N can be changed between runs by
+ended on an arbitrary timestep. :math:`N` can be changed between runs by
 using the :doc:`dump_modify every <dump_modify>` command.
 
-Dump *image* filenames must contain a wildcard character "\*", so that
+Dump *image* filenames must contain a wildcard character "\*" so that
 one image file per snapshot is written.  The "\*" character is replaced
 with the timestep value.  For example, tmp.dump.\*.jpg becomes
 tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc.  Note
 that the :doc:`dump_modify pad <dump_modify>` command can be used to
-insure all timestep numbers are the same length (e.g. 00010), which
+insure all timestep numbers are the same length (e.g., 00010), which
 can make it easier to convert a series of images into a movie in the
 correct ordering.
 
@@ -262,7 +261,7 @@ atoms rendered in the image.  They can be any atom attribute defined
 for the :doc:`dump custom <dump>` command, including *type* and
 *element*\ .  This includes per-atom quantities calculated by a
 :doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
-which are prefixed by "c\_", "f\_", or "v\_" respectively.  Note that the
+which are prefixed by "c\_," "f\_," or "v\_," respectively.  Note that the
 *diameter* setting can be overridden with a numeric value applied to
 all atoms by the optional *adiam* keyword.
 
@@ -277,7 +276,7 @@ to colors is as follows:
 * type 5 = aqua
 * type 6 = cyan
 
-and repeats itself for types > 6.  This mapping can be changed by the
+and repeats itself for types :math:`> 6`.  This mapping can be changed by the
 "dump_modify acolor" command, as described below.
 
 If *type* is specified for the *diameter* setting then the diameter of
@@ -298,18 +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
@@ -773,10 +772,11 @@ the number 5.0 would be used.  But for a fractional map, the number
 The *delta* setting must be specified for all styles, but is only used
 for the sequential style; otherwise the value is ignored.  It
 specifies the bin size to use within the range for assigning
-consecutive colors to.  For example, if the range is from -10.0 to
+consecutive colors to.  For example, if the range is from :math:`-10.0` to
-10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
+:math:`10.0` and a *delta* of :math:`1.0` is used, then 20 colors will be
-the range.  The first will be from -10.0 <= color1 < -9.0, then second
+assigned to the range.  The first will be from
-from -9.0 <= color2 < -8.0, etc.
+:math:`-10.0 \le \text{color1} < -9.0`, then second from
+:math:`-9.0 \le color2 < -8.0`, etc.
 
 The *N* setting is how many entries follow.  The format of the entries
 depends on whether the color map style is continuous, discrete or
@@ -793,13 +793,13 @@ as absolute numbers or as fractions (0.0 to 1.0) of the range,
 depending on the "a" or "f" in the style setting for the color map.
 
 Here is how the entries are used to determine the color of an
-individual atom, given the value X of its atom attribute.  X will fall
+individual atom, given the value :math:`X` of its atom attribute.
-between 2 of the entry values.  The color of the atom is linearly
+:math:`X` will fall between 2 of the entry values.  The color of the atom is
-interpolated (in each of the RGB values) between the 2 colors
+linearly interpolated (in each of the RGB values) between the 2 colors
-associated with those entries.  For example, if X = -5.0 and the 2
+associated with those entries.  For example, if :math:`X = -5.0` and the two
-surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
+surrounding entries are "red" at :math:`-10.0` and "blue" at :math:`0.0`,
-atom's color will be halfway between "red" and "blue", which happens
+then the atom's color will be halfway between "red" and "blue," which happens
-to be "purple".
+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
@@ -864,20 +864,20 @@ The *bcolor* keyword can be used with the dump image command, with its
 *bond* keyword, when its color setting is *type*, to set the color
 that bonds of each type will be drawn in the image.
 
-The specified *type* should be an integer from 1 to Nbondtypes = the
+The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
-number of bond types.  A wildcard asterisk can be used in place of or
+is the number of bond types.  A wildcard asterisk can be used in place of or
 in conjunction with the *type* argument to specify a range of bond
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n."  If :math:`N`
-the number of bond types, then an asterisk with no numeric values
+is the number of bond types, then an asterisk with no numerical values
-means all types from 1 to N.  A leading asterisk means all types from
+means all types from 1 to :math:`N`.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
 
 The specified *color* can be a single color which is any of the 140
 pre-defined colors (see below) or a color name defined by the
 dump_modify color option.  Or it can be two or more colors separated
-by a "/" character, e.g. red/green/blue.  In the former case, that
+by a "/" character (e.g., red/green/blue).  In the former case, that
 color is assigned to all the specified bond types.  In the latter
 case, the list of colors are assigned in a round-robin fashion to each
 of the specified bond types.
@@ -885,13 +885,13 @@ of the specified bond types.
 ----------
 
 The *bdiam* keyword can be used with the dump image command, with its
-*bond* keyword, when its diam setting is *type*, to set the diameter
+*bond* keyword, when its *diam* setting is *type*, to set the diameter
 that bonds of each type will be drawn in the image.  The specified
 *type* should be an integer from 1 to Nbondtypes.  As with the
 *bcolor* keyword, a wildcard asterisk can be used as part of the
 *type* argument to specify a range of bond types.  The specified
 *diam* is the size in whatever distance :doc:`units <units>` you are
-using, e.g. Angstroms.
+using (e.g., Angstroms).
 
 ----------
 
@@ -922,7 +922,7 @@ dump_modify color option.
 ----------
 
 The *color* keyword allows definition of a new color name, in addition
-to the 140-predefined colors (see below), and associates 3
+to the 140-predefined colors (see below), and associates three
 red/green/blue RGB values with that color name.  The color name can
 then be used with any other dump_modify keyword that takes a color
 name as a value.  The RGB values should each be floating point values
@@ -959,15 +959,15 @@ PNG library.
 
 To write *movie* dumps, you must use the -DLAMMPS_FFMPEG switch when
 building LAMMPS and have the FFmpeg executable available on the
-machine where LAMMPS is being run.  Typically it's name is lowercase,
+machine where LAMMPS is being run.  Typically its name is lowercase
-i.e. ffmpeg.
+(i.e., "ffmpeg").
 
 See the :doc:`Build settings <Build_settings>` page for details.
 
 Note that since FFmpeg is run as an external program via a pipe,
 LAMMPS has limited control over its execution and no knowledge about
 errors and warnings printed by it. Those warnings and error messages
-will be printed to the screen only. Due to the way image data is
+will be printed to the screen only. Due to the way image data are
 communicated to FFmpeg, it will often print the message
 
 .. parsed-literal::
@@ -976,7 +976,7 @@ communicated to FFmpeg, it will often print the message
 
 which can be safely ignored. Other warnings
 and errors have to be addressed according to the FFmpeg documentation.
-One known issue is that certain movie file formats (e.g. MPEG level 1
+One known issue is that certain movie file formats (e.g., MPEG level 1
 and 2 format streams) have video bandwidth limits that can be crossed
 when rendering too large of image sizes. Typical warnings look like
 this:
@@ -987,10 +987,9 @@ this:
    [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
    [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018
 
-In this case it is recommended to either reduce the size of the image
+In this case it is recommended either to reduce the size of the image
-or encode in a different format that is also supported by your copy of
+or to encode in a different format that is also supported by your copy of
-FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
+FFmpeg and which does not have this limitation (e.g., .avi, .mkv, mp4).
-mp4).
 
 Related commands
 """"""""""""""""

doc/src/dump_modify.rst

@@ -35,10 +35,10 @@ Syntax
        *element* args = E1 E2 ... EN, where N = # of atom types
          E1,...,EN = element name (e.g., C or Fe or Ga)
        *every* arg = N
-         N = dump every this many timesteps
+         N = dump on timesteps which are a multiple of N
          N can be a variable (see below)
        *every/time* arg = Delta
-         Delta = dump every this interval in simulation time (time units)
+         Delta = dump once every Delta interval of simulation time (time units)
          Delta can be a variable (see below)
        *fileper* arg = Np
          Np = write one file for every this many processors
@@ -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
@@ -207,13 +232,10 @@ will be accepted.
 ----------
 
 The *every* keyword can be used with any dump style except the *dcd*
-and *xtc* styles.  It does two things.  It specifies that the interval
+and *xtc* styles.  It specifies that the output of dump snapshots will
-between dump snapshots will be set in timesteps, which is the default
+now be performed on timesteps which are a multiple of a new :math:`N`
-if the *every* or *every/time* keywords are not used.  See the
+value, This overrides the dump frequency originally specified by the
-*every/time* keyword for how to specify the interval in simulation
+:doc:`dump <dump>` command.
-time, i.e. in time units of the :doc:`units <units>` command.  The
-*every* keyword also sets the interval value, which overrides the dump
-frequency originally specified by the :doc:`dump <dump>` command.
 
 The *every* keyword can be specified in one of two ways.  It can be a
 numeric value in which case it must be > 0.  Or it can be an
@@ -273,6 +295,17 @@ in file tmp.times:
 
 ----------
 
+The *every/time* keyword can be used with any dump style except the
+*dcd* and *xtc* styles.  It changes the frequency of dump snapshots
+from being based on the current timestep to being determined by
+elapsed simulation time, i.e. in time units of the :doc:`units
+<units>` command, and specifies *Delta* for the interval between
+snapshots.  This can be useful when the timestep size varies during a
+simulation run, e.g. by use of the :doc:`fix dt/reset <fix_dt_reset>`
+command.  The default is to perform output on timesteps which a
+multiples of specified timestep value :math:`N`; see the *every*
+keyword.
+
 The *every/time* keyword can be used with any dump style except the
 *dcd* and *xtc* styles.  It does two things.  It specifies that the
 interval between dump snapshots will be set in simulation time
@@ -357,7 +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
@@ -365,7 +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.
@@ -380,30 +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*
@@ -490,6 +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.
 
 ----------
 
@@ -663,6 +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/dump_vtk.rst

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

doc/src/fix_accelerate_cos.rst

@@ -6,8 +6,7 @@ fix accelerate/cos command
 Syntax
 """"""
 
-
+.. code-block:: LAMMPS
-.. parsed-literal::
 
    fix ID group-ID accelerate value
 
@@ -19,7 +18,6 @@ Syntax
 Examples
 """"""""
 
-
 .. code-block:: LAMMPS
 
    fix 1 all accelerate/cos 0.02e-5
@@ -34,8 +32,8 @@ The acceleration is a periodic function along the z-direction:
 
    a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)
 
-where :math:`A` is the acceleration amplitude, :math:`l_z` is the z-length
+where :math:`A` is the acceleration amplitude, :math:`l_z` is the
-of the simulation box.
+:math:`z`-length of the simulation box.
 At steady state, the acceleration generates a velocity profile:
 
 .. math::
@@ -49,17 +47,18 @@ shear viscosity :math:`\eta` by:
 
    V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}
 
-
 and it can be obtained from ensemble average of the velocity profile:
 
 .. math::
 
-   V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}}
+   V = \frac{\sum\limits_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum\limits_i m_{i}},
 
-where :math:`m_i`, :math:`v_{i,x}` and :math:`z_i` are the mass,
+where :math:`m_i`, :math:`v_{i,x}`, and :math:`z_i` are the mass,
-x-component velocity and z coordinate of a particle.
+:math:`x`-component velocity, and :math:`z`-coordinate of a particle,
+respectively.
 
-The velocity amplitude :math:`V` can be calculated with :doc:`compute viscosity/cos <compute_viscosity_cos>`,
+The velocity amplitude :math:`V` can be calculated with
+:doc:`compute viscosity/cos <compute_viscosity_cos>`,
 which enables viscosity calculation with periodic perturbation method,
 as described by :ref:`Hess<Hess2>`.
 Because the applied acceleration drives the system away from equilibration,
@@ -79,15 +78,17 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to binary restart files.
 None of the fix_modify options are relevant to this fix.
-No global or per-atom quantities are stored by this fix for access by various output commands.
+No global or per-atom quantities are stored by this fix for access by various
-No parameter of this fix can be used with the start/stop keywords of the run command.
+output commands.  No parameter of this fix can be used with the start/stop
+keywords of the run command.
 This fix is not invoked during energy minimization.
 
 Restrictions
 """"""""""""
 
 This command is only available when LAMMPS was built with the MISC package.
-Since this fix depends on the z-coordinate of atoms, it cannot be used in 2d simulations.
+Since this fix depends on the :math:`z`-coordinate of atoms, it cannot be used
+in 2d simulations.
 
 Related commands
 """"""""""""""""
@@ -102,4 +103,4 @@ Default
 
 .. _Hess2:
 
-**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
+**(Hess)** Hess, B. Journal of Chemical Physics 2002, 116 (1), 209--217.

doc/src/fix_acks2_reaxff.rst

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

doc/src/fix_adapt.rst

@@ -6,7 +6,7 @@ fix adapt command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID adapt N attribute args ... keyword value ...
 
@@ -19,24 +19,24 @@ Syntax
   .. parsed-literal::
 
        *pair* args = pstyle pparam I J v_name
-         pstyle = pair style name, e.g. lj/cut
+         pstyle = pair style name (e.g., lj/cut)
          pparam = parameter to adapt over time
          I,J = type pair(s) to set parameter for
          v_name = variable with name that calculates value of pparam
        *bond* args = bstyle bparam I v_name
-         bstyle = bond style name, e.g. harmonic
+         bstyle = bond style name (e.g., harmonic)
          bparam = parameter to adapt over time
          I = type bond to set parameter for
          v_name = variable with name that calculates value of bparam
        *angle* args = astyle aparam I v_name
-         astyle = angle style name, e.g. harmonic
+         astyle = angle style name (e.g., harmonic)
          aparam = parameter to adapt over time
          I = type angle to set parameter for
          v_name = variable with name that calculates value of aparam
        *kspace* arg = v_name
-         v_name = variable with name that calculates scale factor on K-space terms
+         v_name = variable with name that calculates scale factor on :math:`k`-space terms
        *atom* args = atomparam v_name
-         atomparam = parameter to adapt over time
+         atomparam = *charge* or *diameter* or *diameter/disc* = parameter to adapt over time
          v_name = variable with name that calculates value of atomparam
 
 * zero or more keyword/value pairs may be appended
@@ -70,22 +70,22 @@ Examples
 Description
 """""""""""
 
-Change or adapt one or more specific simulation attributes or settings
+Change or adapt one or more specific simulation attributes or settings over
-over time as a simulation runs.  Pair potential and K-space and atom
+time as a simulation runs.  Pair potential and :math:`k`-space and atom
-attributes which can be varied by this fix are discussed below.  Many
+attributes which can be varied by this fix are discussed below.  Many other
-other fixes can also be used to time-vary simulation parameters,
+fixes can also be used to time-vary simulation parameters (e.g., the
-e.g. the "fix deform" command will change the simulation box
+:doc:`fix deform <fix_deform>` command will change the simulation box
-size/shape and the "fix move" command will change atom positions and
+size/shape and the :doc:`fix move <fix_move>` command will change atom
-velocities in a prescribed manner.  Also note that many commands allow
+positions and velocities in a prescribed manner).  Also note that many commands
-variables as arguments for specific parameters, if described in that
+allow variables as arguments for specific parameters, if described in that
 manner on their doc pages.  An equal-style variable can calculate a
-time-dependent quantity, so this is another way to vary a simulation
+time-dependent quantity, so this is another way to vary a simulation parameter
-parameter over time.
+over time.
 
-If *N* is specified as 0, the specified attributes are only changed
+If :math:`N` is specified as 0, the specified attributes are only changed
 once, before the simulation begins.  This is all that is needed if the
-associated variables are not time-dependent.  If *N* > 0, then changes
+associated variables are not time-dependent.  If :math:`N > 0`, then changes
-are made every *N* steps during the simulation, presumably with a
+are made every :math:`N` steps during the simulation, presumably with a
 variable that is time-dependent.
 
 Depending on the value of the *reset* keyword, attributes changed by
@@ -98,9 +98,9 @@ If the *scale* keyword is set to *no*, which is the default, then
 the value of the altered parameter will be whatever the variable
 generates.  If the *scale* keyword is set to *yes*, then the value
 of the altered parameter will be the initial value of that parameter
-multiplied by whatever the variable generates.  I.e. the variable is
+multiplied by whatever the variable generates (i.e., the variable is
 now a "scale factor" applied in (presumably) a time-varying fashion to
-the parameter.
+the parameter).
 
 Note that whether scale is *no* or *yes*, internally, the parameters
 themselves are actually altered by this fix.  Make sure you use the
@@ -120,9 +120,9 @@ The *pstyle* argument is the name of the pair style.  If
 :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
 *pstyle* should be a sub-style name.  If there are multiple
 sub-styles using the same pair style, then *pstyle* should be specified
-as "style:N" where N is which instance of the pair style you wish to
+as "style:N", where :math:`N` is which instance of the pair style you wish to
-adapt, e.g. the first, second, etc.  For example, *pstyle* could be
+adapt (e.g., the first or second).  For example, *pstyle* could be
-specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2".  The
+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
@@ -216,45 +216,46 @@ formulas for the meaning of these parameters:
    to this list.  All it typically takes is adding an extract() method to
    the pair\_\*.cpp file associated with the potential.
 
-Some parameters are global settings for the pair style, e.g. the
+Some parameters are global settings for the pair style (e.g., the
-viscosity setting "mu" for :doc:`pair_style lubricate <pair_lubricate>`.
+viscosity setting "mu" for :doc:`pair_style lubricate <pair_lubricate>`).
-Other parameters apply to atom type pairs within the pair style,
+Other parameters apply to atom type pairs within the pair style (e.g., the
-e.g. the prefactor "a" for :doc:`pair_style soft <pair_soft>`.
+prefactor :math:`a` for :doc:`pair_style soft <pair_soft>`).
 
 Note that for many of the potentials, the parameter that can be varied
 is effectively a prefactor on the entire energy expression for the
-potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"
+potential (e.g., the lj/cut epsilon).  The parameters listed as "scale"
 are exactly that, since the energy expression for the
 :doc:`coul/cut <pair_coul>` potential (for example) has no labeled
 prefactor in its formula.  To apply an effective prefactor to some
 potentials, multiple parameters need to be altered.  For example, the
-:doc:`Buckingham potential <pair_buck>` needs both the A and C terms
+:doc:`Buckingham potential <pair_buck>` needs both the :math:`A` and
-altered together.  To scale the Buckingham potential, you should thus
+:math:`C` terms altered together.  To scale the Buckingham potential, you
-list the pair style twice, once for A and once for C.
+should thus list the pair style twice, once for :math:`A` and once for
+:math:`C`.
 
-If a type pair parameter is specified, the *I* and *J* settings should
+If a type pair parameter is specified, the :math:`I` and :math:`J` settings
-be specified to indicate which type pairs to apply it to.  If a global
+should be specified to indicate which type pairs to apply it to.  If a global
-parameter is specified, the *I* and *J* settings still need to be
+parameter is specified, the :math:`I` and :math:`J` settings still need to be
 specified, but are ignored.
 
-Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
+Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and :math:`J`
-specified in one of two ways.  Explicit numeric values can be used for
+can be specified in one of two ways.  Explicit numeric values can be used for
-each, as in the first example above.  I <= J is required.  LAMMPS sets
+each, as in the first example above.  :math:`I \le J` is required.  LAMMPS sets
-the coefficients for the symmetric J,I interaction to the same values.
+the coefficients for the symmetric :math:`J,I` interaction to the same values.
 
 A wild-card asterisk can be used in place of or in conjunction with
-the I,J arguments to set the coefficients for multiple pairs of atom
+the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n."  If :math:`N`
-the number of atom types, then an asterisk with no numeric values
+is the number of atom types, then an asterisk with no numeric values
-means all types from 1 to N.  A leading asterisk means all types from
+means all types from 1 to :math:`N`.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
 (inclusive).  A middle asterisk means all types from m to n
-(inclusive).  Note that only type pairs with I <= J are considered; if
+(inclusive).  Note that only type pairs with :math:`I \le J` are considered; if
-asterisks imply type pairs where J < I, they are ignored.
+asterisks imply type pairs where :math:`J < I`, they are ignored.
 
-IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
+IMPORTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
 <pair_hybrid>` is being used, then the *pstyle* will be a sub-style
-name.  You must specify I,J arguments that correspond to type pair
+name.  You must specify :math:`I,J` arguments that correspond to type pair
 values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
 that sub-style.
 
@@ -289,12 +290,11 @@ given bond type is adapted.
 
 A wild-card asterisk can be used in place of or in conjunction with
 the bond type argument to set the coefficients for multiple bond
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n."  If :math:`N`
-the number of bond types, then an asterisk with no numeric values
+is the number of bond types, then an asterisk with no numeric values
-means all types from 1 to N.  A leading asterisk means all types from
+means all types from 1 to :math:`N`.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
-(inclusive).  A middle asterisk means all types from m to n
+(inclusive).  A middle asterisk means all types from m to n (inclusive).
-(inclusive).
 
 Currently *bond* does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The bond styles that currently work
@@ -325,12 +325,11 @@ given angle type is adapted.
 
 A wild-card asterisk can be used in place of or in conjunction with
 the angle type argument to set the coefficients for multiple angle
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n."  If :math:`N`
-the number of angle types, then an asterisk with no numeric values
+is the number of angle types, then an asterisk with no numeric values
-means all types from 1 to N.  A leading asterisk means all types from
+means all types from 1 to :math:`N`.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
-(inclusive).  A middle asterisk means all types from m to n
+(inclusive).  A middle asterisk means all types from m to n (inclusive).
-(inclusive).
 
 Currently *angle* does not support angle_style hybrid nor angle_style
 hybrid/overlay as angle styles. The angle styles that currently work
@@ -348,7 +347,7 @@ this fix uses to reset theta0 needs to generate values in radians.
 ----------
 
 The *kspace* keyword used the specified variable as a scale factor on
-the energy, forces, virial calculated by whatever K-Space solver is
+the energy, forces, virial calculated by whatever :math:`k`-space solver is
 defined by the :doc:`kspace_style <kspace_style>` command.  If the
 variable has a value of 1.0, then the solver is unaltered.
 
@@ -373,17 +372,17 @@ with equal-style variables.  The new value is assigned to the
 corresponding attribute for all atoms in the fix group.
 
 If the atom parameter is *diameter* and per-atom density and per-atom
-mass are defined for particles (e.g. :doc:`atom_style granular
+mass are defined for particles (e.g., :doc:`atom_style granular
 <atom_style>`), then the mass of each particle is, by default, also
 changed when the diameter changes. The mass is set from the particle
 volume for 3d systems (density is assumed to stay constant). For 2d,
 the default is for LAMMPS to model particles with a radius attribute
 as spheres. However, if the atom parameter is *diameter/disc*, then the
 mass is set from the particle area (the density is assumed to be in
-mass/distance^2 units). The mass of the particle may also be kept constant
+mass/distance\ :math:`^2` units). The mass of the particle may also be kept
-if the *mass* keyword is set to *no*. This can be useful to account for
+constant if the *mass* keyword is set to *no*. This can be useful to account
-diameter changes that do not involve mass changes, e.g., thermal expansion.
+for diameter changes that do not involve mass changes (e.g., thermal
-
+expansion).
 
 For example, these commands would shrink the diameter of all granular
 particles in the "center" group from 1.0 to 0.1 in a linear fashion
@@ -405,11 +404,11 @@ their original values at the end of the last restarted run.
 
 Note that all the parameters changed by this fix are written into a
 restart file in their current changed state.  A new restarted
-simulation does not know their original time=0 values, unless the
+simulation does not know the original time=0 values, unless the
 input script explicitly resets the parameters (after the restart file
-is read), to their original values.
+is read) to the original values.
 
-Also note, that the time-dependent variable(s) used in the restart
+Also note that the time-dependent variable(s) used in the restart
 script should typically be written as a function of time elapsed since
 the original simulation began.
 
@@ -430,8 +429,8 @@ the one used in the original script.
 
 In a restarted run, if the *reset* keyword is set to *yes*, and the
 run ends in this script (as opposed to just writing more restart
-files, parameters will be restored to the values they were at the
+files), parameters will be restored to the values they were at the
-beginning of the run command in the restart script.  Which as
+beginning of the run command in the restart script, which as
 explained above, may or may not be the original values of the
 parameters.  Again, an exception is if the *atom* keyword is being
 used with *reset yes* (in all the runs). In that case, the original

doc/src/fix_adapt_fep.rst

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

doc/src/fix_addforce.rst

@@ -6,7 +6,7 @@ fix addforce command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID addforce fx fy fz keyword value ...
 
@@ -42,26 +42,26 @@ Examples
 Description
 """""""""""
 
-Add fx,fy,fz to the corresponding component of force for each atom in
+Add :math:`(f_x,f_y,f_z)` to the corresponding component of the force for each
-the group.  This command can be used to give an additional push to
+atom in the group.  This command can be used to give an additional push to
 atoms in a simulation, such as for a simulation of Poiseuille flow in
 a channel.
 
-Any of the 3 quantities defining the force components can be specified
+Any of the three quantities defining the force components, namely :math:`f_x`,
-as an equal-style or atom-style :doc:`variable <variable>`, namely *fx*,
+:math:`f_y`, and :math:`f_z`, can be specified as an equal-style or atom-style
-*fy*, *fz*\ .  If the value is a variable, it should be specified as
+:doc:`variable <variable>`.  If the value is a variable, it should be specified
-v_name, where name is the variable name.  In this case, the variable
+as v_name, where name is the variable name.  In this case, the variable
-will be evaluated each timestep, and its value(s) used to determine
+will be evaluated each time step, and its value(s) will be used to determine
-the force component.
+the force component(s).
 
 Equal-style variables can specify formulas with various mathematical
-functions, and include :doc:`thermo_style <thermo_style>` command
+functions and include :doc:`thermo_style <thermo_style>` command
-keywords for the simulation box parameters and timestep and elapsed
+keywords for the simulation box parameters, time step, and elapsed time.
-time.  Thus it is easy to specify a time-dependent force field.
+Thus, it is easy to specify a time-dependent force field.
 
 Atom-style variables can specify the same formulas as equal-style
 variables but can also include per-atom values, such as atom
-coordinates.  Thus it is easy to specify a spatially-dependent force
+coordinates.  Thus, it is easy to specify a spatially-dependent force
 field with optional time-dependence as well.
 
 If the *every* keyword is used, the *Nevery* setting determines how
@@ -83,10 +83,14 @@ potential energy to formulate a self-consistent minimization problem
 (see below).
 
 The *energy* keyword is not allowed if the added force is a constant
-vector F = (fx,fy,fz), with all components defined as numeric
+vector :math:`\vec F = (f_x,f_y,f_z)`, with all components defined as numeric
 constants and not as variables.  This is because LAMMPS can compute
-the energy for each atom directly as E = -x dot F = -(x\*fx + y\*fy +
+the energy for each atom directly as
-z\*fz), so that -Grad(E) = F.
+
+.. math::
+   E = -\vec x \cdot \vec F = -(x f_x + y f_y + z f_z),
+
+so that :math:`-\vec\nabla E = \vec F`.
 
 The *energy* keyword is optional if the added force is defined with
 one or more variables, and if you are performing dynamics via the
@@ -98,16 +102,16 @@ one or more variables, and you are performing energy minimization via
 the "minimize" command.  The keyword specifies the name of an
 atom-style :doc:`variable <variable>` which is used to compute the
 energy of each atom as function of its position.  Like variables used
-for *fx*, *fy*, *fz*, the energy variable is specified as v_name,
+for :math:`f_x`, :math:`f_y`, :math:`f_z`, the energy variable is specified as
-where name is the variable name.
+v_name, where name is the variable name.
 
 Note that when the *energy* keyword is used during an energy
 minimization, you must insure that the formula defined for the
 atom-style :doc:`variable <variable>` is consistent with the force
-variable formulas, i.e. that -Grad(E) = F.  For example, if the force
+variable formulas (i.e., that :math:`-\vec\nabla E = \vec F`).
-were a spring-like F = kx, then the energy formula should be E =
+For example, if the force were a spring-like, :math:`\vec F = -k\vec x`, then
--0.5kx\^2.  If you don't do this correctly, the minimization will not
+the energy formula should be :math:`E = \frac12 kx^2`.  If you do not do this
-converge properly.
+correctly, the minimization will not converge properly.
 
 ----------
 
@@ -128,8 +132,8 @@ the global potential energy of the system as part of
 this fix is :doc:`fix_modify energy no <fix_modify>`.  Note that this
 energy is a fictitious quantity but is needed so that the
 :doc:`minimize <minimize>` command can include the forces added by
-this fix in a consistent manner.  I.e. there is a decrease in
+this fix in a consistent manner (i.e., there is a decrease in
-potential energy when atoms move in the direction of the added force.
+potential energy when atoms move in the direction of the added force).
 
 The :doc:`fix_modify <fix_modify>` *virial* option is supported by
 this fix to add the contribution due to the added forces on atoms to
@@ -144,12 +148,12 @@ fix. This allows to set at which level of the :doc:`r-RESPA
 <run_style>` integrator the fix is adding its forces. Default is the
 outermost level.
 
-This fix computes a global scalar and a global 3-vector of forces,
+This fix computes a global scalar and a global three-vector of forces,
 which can be accessed by various :doc:`output commands
 <Howto_output>`.  The scalar is the potential energy discussed above.
 The vector is the total force on the group of atoms before the forces
 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

@@ -6,7 +6,7 @@ fix addtorque command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID addtorque Tx Ty Tz
 
@@ -30,13 +30,13 @@ Add a set of forces to each atom in
 the group such that:
 
 * the components of the total torque applied on the group (around its
-  center of mass) are Tx,Ty,Tz
+  center of mass) are :math:`T_x`, :math:`T_y`, and :math:`T_z`
 * the group would move as a rigid body in the absence of other
   forces.
 
 This command can be used to drive a group of atoms into rotation.
 
-Any of the 3 quantities defining the torque components can be specified
+Any of the three quantities defining the torque components can be specified
 as an equal-style :doc:`variable <variable>`, namely *Tx*,
 *Ty*, *Tz*\ .  If the value is a variable, it should be specified as
 v_name, where name is the variable name.  In this case, the variable
@@ -53,7 +53,8 @@ time.  Thus it is easy to specify a time-dependent torque.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to
+:doc:`binary restart files <restart>`.
 
 The :doc:`fix_modify <fix_modify>` *energy* option is supported by
 this fix to add the potential "energy" inferred by the added torques
@@ -62,8 +63,8 @@ to the global potential energy of the system as part of
 this fix is :doc:`fix_modify energy no <fix_modify>`.  Note that this
 is a fictitious quantity but is needed so that the :doc:`minimize
 <minimize>` command can include the forces added by this fix in a
-consistent manner.  I.e. there is a decrease in potential energy when
+consistent manner (i.e., there is a decrease in potential energy when
-atoms move in the direction of the added forces.
+atoms move in the direction of the added forces).
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by
 this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
@@ -74,7 +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.
@@ -99,9 +100,9 @@ invoked by the :doc:`minimize <minimize>` command.
 Restrictions
 """"""""""""
 
-This fix is part of the EXTRA-FIX package.  It is only enabled if
+This fix is part of the EXTRA-FIX package.  It is only enabled if LAMMPS was
-LAMMPS was built with that package.  See the :doc:`Build package
+built with that package.  See the :doc:`Build package <Build_package>` page for
-<Build_package>` page for more info.
+more info.
 
 Related commands
 """"""""""""""""

doc/src/fix_amoeba_bitorsion.rst

@@ -6,7 +6,7 @@ fix amoeba/bitorsion command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ameoba/bitorsion filename
 
@@ -55,8 +55,8 @@ should have a line like this in its header section:
 
    N bitorsions
 
-where N is the number of bitorsion 5-body interactions.  It should
+where :math:`N` is the number of bitorsion 5-body interactions.  It should
-also have a section in the body of the data file like this with N
+also have a section in the body of the data file like this with :math:`N`
 lines:
 
 .. parsed-literal::
@@ -68,7 +68,7 @@ lines:
           [...]
           N       3     314     315     317      318    330
 
-The first column is an index from 1 to N to enumerate the bitorsion
+The first column is an index from 1 to :math:`N` to enumerate the bitorsion
 5-atom tuples; it is ignored by LAMMPS.  The second column is the
 *type* of the interaction; it is an index into the bitorsion force
 field file.  The remaining 5 columns are the atom IDs of the atoms in
@@ -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

@@ -6,7 +6,7 @@ fix amoeba/pitorsion command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ameoba/pitorsion
 
@@ -29,14 +29,16 @@ Description
 This command enables 6-body pitorsion interactions to be added to
 simulations which use the AMOEBA and HIPPO force fields.  It matches
 how the Tinker MD code computes its pitorsion interactions for the
-AMOEBA and HIPPO force fields.  See the :doc:`Howto amoeba
+AMOEBA and HIPPO force fields.  See the :doc:`Howto amoeba <Howto_amoeba>`
-<Howto_amoeba>` doc page for more information about the implementation
+doc page for more information about the implementation of AMOEBA and HIPPO in
-of AMOEBA and HIPPO in LAMMPS.
+LAMMPS.
 
 Pitorsion interactions add additional potential energy contributions
-to 6-tuples of atoms IJKLMN which have a bond between atoms K and L,
+to 6-tuples of atoms :math:`IJKLMN` that have a bond between atoms
-where both K and L are additionally bonded to exactly two other atoms.
+:math:`K` and :math:`L`, where both :math:`K` and :math:`L` are additionally
-Namely K is also bonded to I and J.  And L is also bonded to M and N.
+bonded to exactly two other atoms. Namely, :math:`K` is also bonded to
+:math:`I` and :math:`J`, and :math:`L` is also bonded to :math:`M` and
+:math:`N`.
 
 The examples/amoeba directory has a sample input script and data file
 for ubiquitin, which illustrates use of the fix amoeba/pitorsion
@@ -47,7 +49,7 @@ file that contains a listing of pitorsion interactions.
 
 The data file read by the :doc:`read_data <read_data>` command must
 contain the topology of all the pitorsion interactions, similar to the
-topology data for bonds, angles, dihedrals, etc.  Specifically it
+topology data for bonds, angles, dihedrals, etc.  Specifically, it
 should have two lines like these in its header section:
 
 .. parsed-literal::
@@ -55,9 +57,9 @@ should have two lines like these in its header section:
    M pitorsion types
    N pitorsions
 
-where N is the number of pitorsion 5-body interactions and M is the
+where :math:`N` is the number of pitorsion 5-body interactions and :math:`M` is
-number of pitorsion types.  It should also have two sections in the body
+the number of pitorsion types.  It should also have two sections in the body
-of the data file like these with M and N lines each:
+of the data file like these with :math:`M` and :math:`N` lines each:
 
 .. parsed-literal::
 
@@ -77,11 +79,11 @@ of the data file like these with M and N lines each:
           [...]
           N       3     314     315     317      318    330
 
-For PiTorsion Coeffs, the first column is an index from 1 to M to
+For PiTorsion Coeffs, the first column is an index from 1 to :math:`M` to
 enumerate the pitorsion types.  The second column is the single
 prefactor coefficient needed for each type.
 
-For PiTorsions, the first column is an index from 1 to N to enumerate
+For PiTorsions, the first column is an index from 1 to :math:`N` to enumerate
 the pitorsion 5-atom tuples; it is ignored by LAMMPS.  The second
 column is the "type" of the interaction; it is an index into the
 PiTorsion Coeffs.  The remaining 5 columns are the atom IDs of the
@@ -90,8 +92,8 @@ atoms in the two 4-atom dihedrals that overlap to create the pitorsion
 
 Note that the *pitorsion types* and *pitorsions* and *PiTorsion
 Coeffs* and *PiTorsions* keywords for the header and body sections of
-the data file match those specified in the :doc:`read_data
+the data file match those specified in the :doc:`read_data <read_data>`
-<read_data>` command following the data file name.
+command following the data file name.
 
 The data file should be generated by using the
 tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS
@@ -136,7 +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.
@@ -161,8 +163,8 @@ Restrictions
 """"""""""""
 
 To function as expected this fix command must be issued *before* a
-:doc:`read_data <read_data>` command but *after* a :doc:`read_restart
+:doc:`read_data <read_data>` command but *after* a
-<read_restart>` command.
+:doc:`read_restart <read_restart>` command.
 
 This fix can only be used if LAMMPS was built with the AMOEBA package.
 See the :doc:`Build package <Build_package>` page for more info.

doc/src/fix_append_atoms.rst

@@ -6,7 +6,7 @@ fix append/atoms command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID append/atoms face ... keyword value ...
 
@@ -66,7 +66,7 @@ specific basis atoms as they are created.  See the
 defined for the unit cell of the lattice.  By default, all created
 atoms are assigned type = 1 unless this keyword specifies differently.
 
-The *size* keyword defines the size in z of the chunk of material to
+The *size* keyword defines the size in :math:`z` of the chunk of material to
 be added.
 
 The *random* keyword will give the atoms random displacements around
@@ -79,7 +79,8 @@ measured from zhi and is set with the *extent* argument.
 The *units* keyword determines the meaning of the distance units used
 to define a wall position, but only when a numeric constant is used.
 A *box* value selects standard distance units as defined by the
-:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
+:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
+for units = real or metal.
 A *lattice* value means the distance units are in lattice spacings.
 The :doc:`lattice <lattice>` command must have been previously used to
 define the lattice spacings.
@@ -89,17 +90,21 @@ define the lattice spacings.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to
+:doc:`binary restart files <restart>`.  None of the
+:doc:`fix_modify <fix_modify>` options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
 This fix style is part of the SHOCK package.  It is only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package. See the
+:doc:`Build package <Build_package>` page for more info.
 
 The boundary on which atoms are added with append/atoms must be
 shrink/minimum.  The opposite boundary may be any boundary type other

doc/src/fix_atc.rst

@@ -6,7 +6,7 @@ fix atc command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix <fixID> <group> atc <type> <parameter_file>
 
@@ -40,8 +40,8 @@ This fix is the beginning to creating a coupled FE/MD simulation and/or
 an on-the-fly estimation of continuum fields. The coupled versions of
 this fix do Verlet integration and the post-processing does not. After
 instantiating this fix, several other fix_modify commands will be
-needed to set up the problem, e.g. define the finite element mesh and
+needed to set up the problem (i.e., define the finite element mesh and
-prescribe initial and boundary conditions.
+prescribe initial and boundary conditions).
 
 .. image:: JPG/atc_nanotube.jpg
    :align: center
@@ -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
@@ -147,7 +147,7 @@ Restrictions
 Thermal and two_temperature (coupling) types use a Verlet
 time-integration algorithm. The hardy type does not contain its own
 time-integrator and must be used with a separate fix that does contain
-one, e.g. nve, nvt, etc. In addition, currently:
+one (e.g., nve, nvt). In addition, currently:
 
 * the coupling is restricted to thermal physics
 * the FE computations are done in serial on each processor.
@@ -159,8 +159,8 @@ Related commands
 
 After specifying this fix in your input script, several
 :doc:`fix_modify AtC <fix_modify>` commands are used to setup the
-problem, e.g. define the finite element mesh and prescribe initial and
+problem (e.g., define the finite element mesh and prescribe initial and
-boundary conditions.  Each of these options has its own doc page.
+boundary conditions).  Each of these options has its own doc page.
 
 *fix_modify* commands for setup:
 
@@ -311,6 +311,6 @@ and Computation (2011), 7:1736.
 as a field variable from molecular dynamics simulations." Journal of
 Chemical Physics (2013), 139:054115.
 
-Please refer to the standard finite element (FE) texts, e.g. T.J.R
+Please refer to the standard finite element (FE) texts (e.g., T.J.R.
-Hughes " The finite element method ", Dover 2003, for the basics of FE
+Hughes, *The Finite Element Method,* Dover 2003) for the basics of FE
-simulation.
+simulations.

doc/src/fix_atom_swap.rst

@@ -6,7 +6,7 @@ fix atom/swap command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID atom/swap N X seed T keyword values ...
 
@@ -45,10 +45,10 @@ Description
 """""""""""
 
 This fix performs Monte Carlo swaps of atoms of one given atom type
-with atoms of the other given atom types. The specified T is used in
+with atoms of the other given atom types. The specified :math:`T` is used in
 the Metropolis criterion dictating swap probabilities.
 
-Perform X swaps of atoms of one type with atoms of another type
+Perform :math:`X` swaps of atoms of one type with atoms of another type
 according to a Monte Carlo probability. Swap candidates must be in the
 fix group, must be in the region (if specified), and must be of one of
 the listed types. Swaps are attempted between candidates that are
@@ -57,7 +57,7 @@ atoms. Swaps are not attempted between atoms of the same type since
 nothing would happen.
 
 All atoms in the simulation domain can be moved using regular time
-integration displacements, e.g. via :doc:`fix nvt <fix_nh>`, resulting
+integration displacements (e.g., via :doc:`fix nvt <fix_nh>`), resulting
 in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
 be needed when running such a hybrid simulation, especially if the
 swapped atoms are not well equilibrated.
@@ -83,9 +83,8 @@ canonical ensemble, the composition of the system can change. Note
 that when using *semi-grand*, atoms in the fix group whose type is not
 listed in the *types* keyword are ineligible for attempted
 conversion. An attempt is made to switch the selected atom (if
-eligible) to one of the other listed types with equal
+eligible) to one of the other listed types with equal probability.
-probability. Acceptance of each attempt depends upon the Metropolis
+Acceptance of each attempt depends upon the Metropolis criterion.
-criterion.
 
 The *mu* keyword allows users to specify chemical potentials. This is
 required and allowed only when using *semi-grand*\ .  All chemical
@@ -97,8 +96,8 @@ amount will have no effect on the simulation.
 
 This command may optionally use the *region* keyword to define swap
 volume.  The specified region must have been previously defined with a
-:doc:`region <region>` command.  It must be defined with side = *in*\
+:doc:`region <region>` command.  It must be defined with side = *in*\ .
-.  Swap attempts occur only between atoms that are both within the
+Swap attempts occur only between atoms that are both within the
 specified region. Swaps are not otherwise attempted.
 
 You should ensure you do not swap atoms belonging to a molecule, or
@@ -123,7 +122,7 @@ Since this fix computes total potential energies before and after
 proposed swaps, so even complicated potential energy calculations are
 OK, including the following:
 
-* long-range electrostatics (kspace)
+* long-range electrostatics (:math:`k`-space)
 * many body pair styles
 * hybrid pair styles
 * eam pair styles
@@ -137,7 +136,7 @@ include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
 <fix_temp_berendsen>`, :doc:`temp/rescale <fix_temp_rescale>`, and
 :doc:`wall fixes <fix_wall>`.  For that energy to be included in the
 total potential energy of the system (the quantity used when
-performing GCMC moves), you MUST enable the :doc:`fix_modify
+performing GCMC moves), you **must** enable the :doc:`fix_modify
 <fix_modify>` *energy* option for that fix.  The doc pages for
 individual :doc:`fix <fix>` commands specify if this should be done.
 
@@ -147,7 +146,7 @@ Restart, fix_modify, output, run start/stop, minimize info
 This fix writes the state of the fix to :doc:`binary restart files
 <restart>`.  This includes information about the random number
 generator seed, the next timestep for MC exchanges, the number of
-exchange attempts and successes etc.  See the :doc:`read_restart
+exchange attempts and successes, etc.  See the :doc:`read_restart
 <read_restart>` command for info on how to re-specify a fix in an
 input script that reads a restart file, so that the operation of the
 fix continues in an uninterrupted fashion.
@@ -168,7 +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

@@ -6,7 +6,7 @@ fix ave/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ...
 
@@ -15,8 +15,8 @@ Syntax
 * Nevery = use input values every this many timesteps
 * Nrepeat = # of times to use input values for calculating averages
 * Nfreq = calculate averages every this many timesteps
-  one or more input values can be listed
+* one or more input values can be listed
-* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name
+* value = *x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, c_ID, c_ID[i], f_ID, f_ID[i], v_name
 
   .. parsed-literal::
 
@@ -41,7 +41,9 @@ Description
 
 Use one or more per-atom vectors as inputs every few timesteps, and
 average them atom by atom over longer timescales.  The resulting
-per-atom averages can be used by other :doc:`output commands <Howto_output>` such as the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` commands.
+per-atom averages can be used by other :doc:`output commands <Howto_output>`
+such as the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>`
+commands.
 
 The group specified with the command means only atoms within the group
 have their averages computed.  Results are set to 0.0 for atoms not in
@@ -53,7 +55,8 @@ component) or can be the result of a :doc:`compute <compute>` or
 :doc:`variable <variable>`.  In the latter cases, the compute, fix, or
 variable must produce a per-atom vector, not a global quantity or
 local quantity.  If you wish to time-average global quantities from a
-compute, fix, or variable, then see the :doc:`fix ave/time <fix_ave_time>` command.
+compute, fix, or variable, then see the :doc:`fix ave/time <fix_ave_time>`
+command.
 
 Each per-atom value of each input vector is averaged independently.
 
@@ -66,18 +69,18 @@ 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 "n\*" or
+specify multiple values.  This takes the form "\*" or "\*n" or "m\*" or
-"m\*n".  If N = 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 N.  A leading
+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
-asterisk means all indices from n to N (inclusive).  A middle asterisk
+asterisk means all indices from m to :math:`N` (inclusive).  A middle asterisk
 means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual columns of the array
-had been listed one by one.  E.g. these 2 fix ave/atom commands are
+had been listed one by one.  For example, these two fix ave/atom commands are
 equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
-command creates a per-atom array with 6 columns:
+command creates a per-atom array with six columns:
 
 .. code-block:: LAMMPS
 
@@ -89,61 +92,66 @@ command creates a per-atom array with 6 columns:
 
 ----------
 
-The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
+The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
-timesteps the input values will be used in order to contribute to the
+arguments specify on what timesteps the input values will be used in order to
-average.  The final averaged quantities are generated on timesteps
+contribute to the average.  The final averaged quantities are generated on
-that are a multiple of *Nfreq*\ .  The average is over *Nrepeat*
+timesteps that are a multiple of :math:`N_\text{freq}`\ .  The average is over
-quantities, computed in the preceding portion of the simulation every
+:math:`N_\text{repeat}` quantities, computed in the preceding portion of the
-*Nevery* timesteps.  *Nfreq* must be a multiple of *Nevery* and
+simulation every :math:`N_\text{every}` timesteps.  :math:`N_\text{freq}` must
-*Nevery* must be non-zero even if *Nrepeat* is 1.  Also, the timesteps
+be a multiple of :math:`N_\text{every}` and :math:`N_\text{every}` must be
-contributing to the average value cannot overlap,
+non-zero even if :math:`N_\text{repeat}` is 1.  Also, the timesteps
-i.e. Nrepeat\*Nevery can not exceed Nfreq.
+contributing to the average value cannot overlap; that is,
+:math:`N_\text{repeat} N_\text{every}` cannot exceed :math:`N_\text{freq}`.
 
-For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
-timesteps 90,92,94,96,98,100 will be used to compute the final average
+:math:`N_\text{freq}=100`, then values on timesteps 90, 92, 94, 96, 98, and 100
-on timestep 100.  Similarly for timesteps 190,192,194,196,198,200 on
+will be used to compute the final average on time step 100.  Similarly for
-timestep 200, etc.
+timesteps 190, 192, 194, 196, 198, and 200 on time step 200, etc.
 
 ----------
 
-The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, and
-self-explanatory.  Note that other atom attributes can be used as
+*fz*) are self-explanatory.  Note that other atom attributes can be used as
-inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+inputs to this fix by using the
-an input value from that compute.
+:doc:`compute property/atom <compute_property_atom>` command and then
+specifying an input value from that compute.
 
 .. note::
 
-   The x,y,z attributes are values that are re-wrapped inside the
+   The *x*\ , *y*\ , and *z* attributes are values that are re-wrapped inside
-   periodic box whenever an atom crosses a periodic boundary.  Thus if
+   the periodic box whenever an atom crosses a periodic boundary.  Thus, if
-   you time average an atom that spends half its time on either side of
+   you time-average an atom that spends half of its time on either side of
    the periodic box, you will get a value in the middle of the box.  If
    this is not what you want, consider averaging unwrapped coordinates,
-   which can be provided by the :doc:`compute property/atom <compute_property_atom>` command via its xu,yu,zu
+   which can be provided by the
-   attributes.
+   :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 I is appended, the Ith column of
+bracketed term containing an index :math:`I` is appended, the
-the per-atom array calculated by the compute is used.  Users can also
+:math:`I^\text{th}` column of the per-atom array calculated by the compute is
-write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how I can
+used.  Users can also write code for their own compute styles and
-be specified with a wildcard asterisk to effectively specify multiple
+:doc:`add them to LAMMPS <Modify>`.  See the discussion above for how
-values.
+: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
-previously defined in the input script.  If no bracketed term is
+defined in the input script.  If no bracketed term is appended, the per-atom
-appended, the per-atom vector calculated by the fix is used.  If a
+vector calculated by the fix is used.  If a bracketed term containing an index
-bracketed term containing an index I is appended, the Ith column of
+:math:`I` is appended, the :math:`I^\text{th}` column of the per-atom array
-the per-atom array calculated by the fix is used.  Note that some
+calculated by the fix is used.  Note that some fixes only produce their values
-fixes only produce their values on certain timesteps, which must be
+on certain timesteps, which must be compatible with :math:`N_\text{every}`,
-compatible with *Nevery*, else an error will result.  Users can also
+else an error will result.  Users can also write code for their own fix styles
-write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how I can be
+and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how
-specified with a wildcard asterisk to effectively specify multiple
+:math:`I` can be specified with a wildcard asterisk to effectively specify
-values.
+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
+been previously defined in the input script as an
-thermodynamic keywords, or invoke other computes, fixes, or variables
+:doc:`atom-style variable <variable>`. Variables of style *atom* can reference
+thermodynamic keywords or invoke other computes, fixes, or variables
 when they are evaluated, so this is a very general means of generating
 per-atom quantities to time average.
 
@@ -152,19 +160,22 @@ per-atom quantities to time average.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to
-are relevant to this fix.  No global scalar or vector quantities are
+:doc:`binary restart files <restart>`.  None of the
-stored by this fix for access by various :doc:`output commands <Howto_output>`.
+:doc:`fix_modify <fix_modify>` options are relevant to this fix.
+No global scalar or vector quantities are stored by this fix for access by
+various :doc:`output commands <Howto_output>`.
 
 This fix produces a per-atom vector or array which can be accessed by
 various :doc:`output commands <Howto_output>`.  A vector is produced if
 only a single quantity is averaged by this fix.  If two or more
 quantities are averaged, then an array of values is produced.  The
 per-atom values can only be accessed on timesteps that are multiples
-of *Nfreq* since that is when averaging is performed.
+of :math:`N_\text{freq}` since that is when averaging is performed.
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
@@ -173,7 +184,8 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
 :doc:`variable <variable>`,
 
 Default

doc/src/fix_ave_chunk.rst

@@ -6,7 +6,7 @@ fix ave/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ...
 
@@ -17,7 +17,7 @@ Syntax
 * Nfreq = calculate averages every this many timesteps
 * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
 * one or more input values can be listed
-* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, mass, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
+* value = *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *density/mass*, *density/number*, *mass*, *temp*, c_ID, c_ID[I], f_ID, f_ID[I], v_name
 
   .. parsed-literal::
 
@@ -145,18 +145,18 @@ Note that for values from a compute or fix that produces a per-atom
 array (multiple values per atom), the bracketed index I can be
 specified using a wildcard asterisk with the index to effectively
 specify multiple values.  This takes the form "\*" or "\*n" or "n\*"
-or "m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+or "m\*n".  If :math:`N` = the size of the vector (for *mode* = scalar) or the
 number of columns in the array (for *mode* = vector), then an asterisk
-with no numeric values means all indices from 1 to N.  A leading
+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
-asterisk means all indices from n to N (inclusive).  A middle asterisk
+asterisk means all indices from m to :math:`N` (inclusive).  A middle asterisk
 means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual columns of the array
-had been listed one by one.  E.g. these 2 fix ave/chunk commands are
+had been listed one by one.  For example, these two fix ave/chunk commands are
 equivalent, since the :doc:`compute property/atom
 <compute_property_atom>` command creates, in this case, a per-atom
-array with 3 columns:
+array with three columns:
 
 .. code-block:: LAMMPS
 
@@ -166,105 +166,109 @@ array with 3 columns:
 
 .. note::
 
-   This fix works by creating an array of size *Nchunk* by Nvalues
+   This fix works by creating an array of size
-   on each processor.  *Nchunk* is the number of chunks which is defined
+   :math:`N_\text{chunk} \times N_\text{values}` on each processor.
-   by the :doc:`compute chunk/atom <compute_chunk_atom>` command.
+   :math:`N_\text{chunk}` is the number of chunks, which is defined by the
-   Nvalues is the number of input values specified.  Each processor loops
+   :doc:`compute chunk/atom <compute_chunk_atom>` command.
-   over its atoms, tallying its values to the appropriate chunk.  Then
+   :math:`N_\text{values}` is the number of input values specified.
-   the entire array is summed across all processors.  This means that
+   Each processor loops over its atoms, tallying its values to the appropriate
-   using a large number of chunks will incur an overhead in memory and
+   chunk.  Then the entire array is summed across all processors.  This means
+   that using a large number of chunks will incur an overhead in memory and
    computational cost (summing across processors), so be careful to
    define a reasonable number of chunks.
 
 ----------
 
-The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
+The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
-timesteps the input values will be accessed and contribute to the
+arguments specify on what time steps the input values will be accessed and
-average.  The final averaged quantities are generated on timesteps
+contribute to the average.  The final averaged quantities are generated on time
-that are a multiples of *Nfreq*\ .  The average is over *Nrepeat*
+steps that are a multiples of :math:`N_\text{freq}`\ .  The average is over
-quantities, computed in the preceding portion of the simulation every
+:math:`N_\text{repeat}` quantities, computed in the preceding portion of the
-*Nevery* timesteps.  *Nfreq* must be a multiple of *Nevery* and
+simulation every :math:`N_\text{every}` time steps.  :math:`N_\text{freq}`
-*Nevery* must be non-zero even if *Nrepeat* is 1.  Also, the timesteps
+must be a multiple of :math:`N_\text{every}` and :math:`N_\text{every}` must be
-contributing to the average value cannot overlap, i.e. Nrepeat\*Nevery
+non-zero even if :math:`N_\text{repeat} = 1`\ .  Also, the time steps
-can not exceed Nfreq.
+contributing to the average value cannot overlap (i.e.,
+:math:`N_\text{repeat}N_\text{every}` cannot exceed :math:`N_\text{freq}`).
 
-For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
+:math:`N_\text{freq}=100`, then values on
 time steps 90, 92, 94, 96, 98, 100 will be used to compute the final average
 on time step 100.  Similarly for time steps 190, 192, 194, 196, 198, 200 on
-timestep 200, etc.  If Nrepeat=1 and Nfreq = 100, then no time
+time step 200, etc.  If :math:`N_\text{repeat}=1` and
-averaging is done; values are simply generated on timesteps
+:math:`N_\text{freq} = 100`, then no time averaging is done; values are simply
-100,200,etc.
+generated on time steps 100, 200, etc.
 
 Each input value can also be averaged over the atoms in each chunk.
-The way the averaging is done across the *Nrepeat* timesteps to
+The way the averaging is done across the :math:`N_\text{repeat}` time steps to
-produce output on the *Nfreq* timesteps, and across multiple *Nfreq*
+produce output on the :math:`N_\text{freq}` time steps, and across multiple
-outputs, is determined by the *norm* and *ave* keyword settings, as
+:math:`N_\text{freq}` outputs, is determined by the *norm* and *ave* keyword
-discussed below.
+settings, as discussed below.
 
 .. note::
 
-   To perform per-chunk averaging within a *Nfreq* time window, the
+   To perform per-chunk averaging within a :math:`N_\text{freq}` time window,
-   number of chunks *Nchunk* defined by the :doc:`compute chunk/atom
+   the number of chunks :math:`N_\text{chunk}` defined by the
-   <compute_chunk_atom>` command must remain constant.  If the *ave*
+   :doc:`compute chunk/atom <compute_chunk_atom>` command must remain
-   keyword is set to *running* or *window* then *Nchunk* must remain
+   constant.  If the *ave* keyword is set to *running* or *window* then
-   constant for the duration of the simulation.  This fix forces the
+   :math:`N_\text{chunk}` must remain constant for the duration of the
-   chunk/atom compute specified by chunkID to hold *Nchunk* constant
+   simulation.  This fix forces the chunk/atom compute specified by chunkID to
-   for the appropriate time windows, by not allowing it to
+   hold :math:`N_\text{chunk}` constant for the appropriate time windows,
-   re-calculate *Nchunk*, which can also affect how it assigns chunk
+   by not allowing it to re-calculate :math:`N_\text{chunk}`, which can also
-   IDs to atoms.  This is particularly important to understand if the
+   affect how it assigns chunk IDs to atoms.  This is particularly important to
-   chunks defined by the :doc:`compute chunk/atom
+   understand if the chunks defined by the :doc:`compute chunk/atom
    <compute_chunk_atom>` command are spatial bins.  If its *units*
    keyword is set to *box* or *lattice*, then the number of bins
-   *Nchunk* and size of each bin will be fixed over the *Nfreq* time
+   :math:`N_\text{chunk}` and size of each bin will be fixed over the
-   window, which can affect which atoms are discarded if the
+   :math:`N_\text{freq}` time window, which can affect which atoms are
-   simulation box size changes.  If its *units* keyword is set to
+   discarded if the simulation box size changes.  If its *units* keyword is set
-   *reduced*, then the number of bins *Nchunk* will still be fixed,
+   to *reduced*, then the number of bins :math:`N_\text{chunk}` will still be
-   but the size of each bin can vary at each timestep if the
+   fixed, but the size of each bin can vary at each time step if the
-   simulation box size changes, e.g. for an NPT simulation.
+   simulation box size changes (e.g., for an NPT simulation).
 
 ----------
 
-The atom attribute values (vx,vy,vz,fx,fy,fz,mass) are
+The atom attribute values (*vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *mass*) are
 self-explanatory.  As noted above, any other atom attributes can be
 used as input values to this fix by using the :doc:`compute
 property/atom <compute_property_atom>` command and then specifying an
 input value from that compute.
 
 The *density/number* value means the number density is computed for
-each chunk, i.e. number/volume.  The *density/mass* value means the
+each chunk (i.e., number/volume).  The *density/mass* value means the
-mass density is computed for each chunk, i.e. total-mass/volume.  The
+mass density is computed for each chunk (i.e., total-mass/volume).  The
-output values are in units of 1/volume or density (mass/volume).  See
+output values are in units of 1/volume or mass density (mass/volume).  See
 the :doc:`units <units>` command page for the definition of density
-for each choice of units, e.g. gram/cm\^3.  If the chunks defined by
+for each choice of units (e.g., g/cm\ :math:`^3`).  If the chunks defined by
 the :doc:`compute chunk/atom <compute_chunk_atom>` command are spatial
-bins, the volume is the bin volume.  Otherwise it is the volume of the
+bins, the volume is the bin volume.  Otherwise, it is the volume of the
 entire simulation box.
 
-The *temp* value means the temperature is computed for each chunk, by
+The *temp* value means the temperature is computed for each chunk,
-the formula
+by the formula
 
 .. math::
 
    \text{KE} = \frac{\text{DOF}}{2} k_B T,
 
-where KE = total kinetic energy of the chunk of atoms (sum of
+where KE is the total kinetic energy of the chunk of atoms (sum of
-:math:`\frac{1}{2} m v^2`), DOF = the total number of degrees of freedom
+:math:`\frac{1}{2} m v^2`), DOF is the the total number of degrees of freedom
-for all atoms in the chunk, :math:`k_B` = Boltzmann constant, and
+for all atoms in the chunk, :math:`k_B` is the Boltzmann constant, and
-:math:`T` = temperature.
+:math:`T` is the absolute temperature.
 
-The DOF is calculated as N\*adof + cdof, where N = number of atoms in
+The DOF is calculated as :math:`N`\ \*adof + cdof, where :math:`N` is the
-the chunk, adof = degrees of freedom per atom, and cdof = degrees of
+number of atoms in the chunk, adof is the number of degrees of freedom per
-freedom per chunk.  By default adof = 2 or 3 = dimensionality of
+atom, and cdof is the number of degrees of freedom per chunk.  By default,
-system, as set via the :doc:`dimension <dimension>` command, and cdof =
+adof = 2 or 3 = dimensionality of system,
-0.0.  This gives the usual formula for temperature.
+as set via the :doc:`dimension <dimension>` command, and cdof = 0.0.
+This gives the usual formula for temperature.
 
 Note that currently this temperature only includes translational
 degrees of freedom for each atom.  No rotational degrees of freedom
-are included for finite-size particles.  Also no degrees of freedom
+are included for finite-size particles.  Also, no degrees of freedom
 are subtracted for any velocity bias or constraints that are applied,
-such as :doc:`compute temp/partial <compute_temp_partial>`, or
+such as :doc:`compute temp/partial <compute_temp_partial>`,
-:doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`.  This is
+:doc:`fix shake <fix_shake>`, or :doc:`fix rigid <fix_rigid>`.  This is
-because those degrees of freedom (e.g. a constrained bond) could apply
+because those degrees of freedom (e.g., a constrained bond) could apply
 to sets of atoms that are both included and excluded from a specific
 chunk, and hence the concept is somewhat ill-defined.  In some cases,
 you can use the *adof* and *cdof* keywords to adjust the calculated
@@ -285,27 +289,27 @@ 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
 calculated by the compute is used.  Users can also write code for
-their own compute styles and :doc:`add them to LAMMPS <Modify>`.  See
+their own compute styles and :doc:`add them to LAMMPS <Modify>`.
-the discussion above for how I can be specified with a wildcard
+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
 calculated by the fix is used.  Note that some fixes only produce
 their values on certain time steps, which must be compatible with
-*Nevery*, else an error results.  Users can also write code for their
+:math:`N_\text{every}`, else an error results.  Users can also write code for
-own fix styles and :doc:`add them to LAMMPS <Modify>`.  See the
+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
@@ -318,113 +322,113 @@ Additional optional keywords also affect the operation of this fix
 and its outputs.
 
 The *norm* keyword affects how averaging is done for the per-chunk
-values that are output every *Nfreq* timesteps.
+values that are output every :math:`N_\text{freq}` time steps.
 
-It the *norm* setting is *all*, which is the default, a chunk value is
+It the *norm* setting is *all*, which is the default, a chunk value is summed
-summed over all atoms in all *Nrepeat* samples, as is the count of
+over all atoms in all :math:`N_\text{repeat}` samples, as is the count of
 atoms in the chunk.  The averaged output value for the chunk on the
-*Nfreq* timesteps is Total-sum / Total-count.  In other words it is an
+:math:`N_\text{freq}` time steps is Total-sum / Total-count.  In other words it
-average over atoms across the entire *Nfreq* timescale.  For the
+is an average over atoms across the entire :math:`N_\text{freq}` timescale.
-*density/number* and *density/mass* values, the volume (bin volume or
+For the *density/number* and *density/mass* values, the volume (bin volume or
 system volume) used in the final normalization will be the volume at
-the final *Nfreq* timestep. For the *temp* values, degrees of freedom
+the final :math:`N_\text{freq}` time step. For the *temp* values, degrees of
-and kinetic energy are summed separately across the entire *Nfreq*
+freedom and kinetic energy are summed separately across the entire
-timescale, and the output value is calculated by dividing those two
+:math:`N_\text{freq}` timescale, and the output value is calculated by dividing
-sums.
+those two sums.
 
 If the *norm* setting is *sample*, the chunk value is summed over
 atoms for each sample, as is the count, and an "average sample value"
-is computed for each sample, i.e. Sample-sum / Sample-count.  The
+is computed for each sample (i.e., Sample-sum / Sample-count).  The
-output value for the chunk on the *Nfreq* timesteps is the average of
+output value for the chunk on the :math:`N_\text{freq}` time steps is the
-the *Nrepeat* "average sample values", i.e. the sum of *Nrepeat*
+average of the :math:`N_\text{repeat}` "average sample values" (i.e., the sum
-"average sample values" divided by *Nrepeat*\ .  In other words it is an
+of :math:`N_\text{repeat}` "average sample values" divided by
-average of an average.  For the *density/number* and *density/mass*
+:math:`N_\text{repeat}`\ ).  In other words, it is an average of an average.
-values, the volume (bin volume or system volume) used in the
+For the *density/number* and *density/mass* values, the volume (bin volume or
-per-sample normalization will be the current volume at each sampling
+system volume) used in the per-sample normalization will be the current volume
-step.
+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 *Nfreq* timesteps is the average of the *Nrepeat* "summed sample
+the :math:`N_\text{freq}` timesteps is the average of the
-values", i.e. the sum of *Nrepeat* "summed sample values" divided by
+:math:`N_\text{repeat}` "summed sample values" (i.e., the sum of
-*Nrepeat*\ .  For the *density/number* and *density/mass* values, the
+:math:`N_\text{repeat}` "summed sample values" divided by
+:math:`N_\text{repeat}`\ ).
+For the *density/number* and *density/mass* values, the
 volume (bin volume or system volume) used in the per-sample sum
 normalization will be the current volume at each sampling step.
 
 ----------
 
 The *ave* keyword determines how the per-chunk values produced every
-*Nfreq* steps are averaged with values produced on previous steps that
+:math:`N_\text{freq}` steps are averaged with values produced on previous steps
-were multiples of *Nfreq*, before they are accessed by another output
+that were multiples of :math:`N_\text{freq}`, before they are accessed by
-command or written to a file.
+another output command or written to a file.
 
 If the *ave* setting is *one*, which is the default, then the chunk
-values produced on timesteps that are multiples of *Nfreq* are
+values produced on timesteps that are multiples of :math:`N_\text{freq}` are
-independent of each other; they are output as-is without further
+independent of each other; they are output as-is without further averaging.
-averaging.
 
 If the *ave* setting is *running*, then the chunk values produced on
-timesteps that are multiples of *Nfreq* are summed and averaged in a
+timesteps that are multiples of :math:`N_\text{freq}` are summed and averaged
-cumulative sense before being output.  Each output chunk value is thus
+in a cumulative sense before being output.  Each output chunk value is thus
 the average of the chunk value produced on that timestep with all
 preceding values for the same chunk.  This running average begins when
 the fix is defined; it can only be restarted by deleting the fix via
-the :doc:`unfix <unfix>` command, or re-defining the fix by
+the :doc:`unfix <unfix>` command, or re-defining the fix by re-specifying it.
-re-specifying it.
 
 If the *ave* setting is *window*, then the chunk values produced on
-timesteps that are multiples of *Nfreq* are summed and averaged within
+timesteps that are multiples of :math:`N_\text{freq}` are summed and averaged
-a moving "window" of time, so that the last M values for the same
+within a moving "window" of time, so that the last :math:`M` values for the
-chunk are used to produce the output.  E.g. if M = 3 and Nfreq = 1000,
+same chunk are used to produce the output.  For example, if :math:`M = 3` and
-then the output on step 10000 will be the average of the individual
+:math:`N_\text{freq} = 1000`, then the output on step 10000 will be the average
-chunk values on steps 8000,9000,10000.  Outputs on early steps will
+of the individual chunk values on time steps 8000, 9000, and 10000.  Outputs on
-average over less than M values if they are not available.
+early steps will average over less than :math:`M` values if they are not
+available.
 
 ----------
 
 The *bias* keyword specifies the ID of a temperature compute that
-removes a "bias" velocity from each atom, specified as *bias-ID*\ .  It
+removes a "bias" velocity from each atom, specified as *bias-ID*\ .
-is only used when the *temp* value is calculated, to compute the
+It is only used when the *temp* value is calculated, to compute the
 thermal temperature of each chunk after the translational kinetic
-energy components have been altered in a prescribed way, e.g.  to
+energy components have been altered in a prescribed way (e.g., to
-remove a flow velocity profile.  See the doc pages for individual
+remove a flow velocity profile).  See the doc pages for individual
-computes that calculate a temperature to see which ones implement a
+computes that calculate a temperature to see which ones implement a bias.
-bias.
 
 The *adof* and *cdof* keywords define the values used in the degree of
 freedom (DOF) formula described above for temperature calculation
 for each chunk.  They are only used when the *temp* value is
 calculated.  They can be used to calculate a more appropriate
-temperature for some kinds of chunks.  Here are 3 examples:
+temperature for some kinds of chunks.  Here are three examples:
 
 If spatially binned chunks contain some number of water molecules and
 :doc:`fix shake <fix_shake>` is used to make each molecule rigid, then
-you could calculate a temperature with 6 degrees of freedom (DOF) (3
+you could calculate a temperature with six degrees of freedom (DOF) (three
-translational, 3 rotational) per molecule by setting *adof* to 2.0.
+translational, three rotational) per molecule by setting *adof* to 2.0.
 
 If :doc:`compute temp/partial <compute_temp_partial>` is used with the
-*bias* keyword to only allow the x component of velocity to contribute
+*bias* keyword to only allow the :math:`x` component of velocity to contribute
 to the temperature, then *adof* = 1.0 would be appropriate.
 
 If each chunk consists of a large molecule, with some number of its
 bonds constrained by :doc:`fix shake <fix_shake>` or the entire molecule
 by :doc:`fix rigid/small <fix_rigid>`, *adof* = 0.0 and *cdof* could be
 set to the remaining degrees of freedom for the entire molecule
-(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
+(entire chunk in this case), that is, 6 for 3d or 3 for 2d for a rigid
 molecule.
 
 ----------
 
-The *file* keyword allows a filename to be specified.  Every *Nfreq*
+The *file* keyword allows a filename to be specified.  Every
-timesteps, a section of chunk info will be written to a text file in
+:math:`N_\text{freq}` timesteps, a section of chunk info will be written to a
-the following format.  A line with the timestep and number of chunks
+text file in the following format.  A line with the timestep and number of
-is written.  Then one line per chunk is written, containing the chunk
+chunks is written.  Then one line per chunk is written, containing the chunk
-ID (1-Nchunk), an optional original ID value, optional coordinate
+ID :math:`(1-N_\text{chunk}),` an optional original ID value, optional
-values for chunks that represent spatial bins, the number of atoms in
+coordinate values for chunks that represent spatial bins, the number of atoms
-the chunk, and one or more calculated values.  More explanation of the
+in the chunk, and one or more calculated values.  More explanation of the
 optional values is given below.  The number of values in each line
 corresponds to the number of values specified in the fix ave/chunk
 command.  The number of atoms and the value(s) are summed or average
@@ -437,10 +441,10 @@ output.  This option can only be used with the *ave running* setting.
 The *format* keyword sets the numeric format of each value when it is
 printed to a file via the *file* keyword.  Note that all values are
 floating point quantities.  The default format is %g.  You can specify
-a higher precision if desired, e.g. %20.16g.
+a higher precision if desired (e.g., %20.16g).
 
 The *title1* and *title2* and *title3* keywords allow specification of
-the strings that will be printed as the first 3 lines of the output
+the strings that will be printed as the first three lines of the output
 file, assuming the *file* keyword was used.  LAMMPS uses default
 values for each of these, so they do not need to be specified.
 
@@ -455,34 +459,33 @@ By default, these header lines are as follows:
 In the first line, ID and name are replaced with the fix-ID and group
 name.  The second line describes the two values that are printed at
 the first of each section of output.  In the third line the values are
-replaced with the appropriate value names, e.g. fx or c_myCompute[2].
+replaced with the appropriate value names (e.g., *fx* or c_myCompute[2]).
 
 The words in parenthesis only appear with corresponding columns if the
 chunk style specified for the :doc:`compute chunk/atom
 <compute_chunk_atom>` command supports them.  The OrigID column is
 only used if the *compress* keyword was set to *yes* for the
 :doc:`compute chunk/atom <compute_chunk_atom>` command.  This means
-that the original chunk IDs (e.g. molecule IDs) will have been
+that the original chunk IDs (e.g., molecule IDs) will have been
 compressed to remove chunk IDs with no atoms assigned to them.  Thus a
 compressed chunk ID of 3 may correspond to an original chunk ID or
-molecule ID of
+molecule ID of 415.  The OrigID column will list 415 for the third chunk.
-415.  The OrigID column will list 415 for the third chunk.
 
 The CoordN columns only appear if a *binning* style was used in the
 :doc:`compute chunk/atom <compute_chunk_atom>` command.  For *bin/1d*,
 *bin/2d*, and *bin/3d* styles the column values are the center point
 of the bin in the corresponding dimension.  Just Coord1 is used for
-*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\
+*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\ .
-.  For *bin/sphere*, just Coord1 is used, and it is the radial
+For *bin/sphere*, just Coord1 is used, and it is the radial
 coordinate.  For *bin/cylinder*, Coord1 and Coord2 are used.  Coord1
 is the radial coordinate (away from the cylinder axis), and coord2 is
 the coordinate along the cylinder axis.
 
 Note that if the value of the *units* keyword used in the
 :doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or
-*lattice*, the coordinate values will be in distance :doc:`units
+*lattice*, the coordinate values will be in distance :doc:`units <units>`.
-<units>`.  If the value of the *units* keyword is *reduced*, the
+If the value of the *units* keyword is *reduced*, the
-coordinate values will be in unitless reduced units (0-1).  This is
+coordinate values will be in unitless reduced units (0--1).  This is
 not true for the Coord1 value of style *bin/sphere* or *bin/cylinder*
 which both represent radial dimensions.  Those values are always in
 distance :doc:`units <units>`.
@@ -498,20 +501,21 @@ 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 *Nfreq* since that is when
+accessed on timesteps that are multiples of :math:`N_\text{freq}`, since that
-averaging is performed.  The global array has # of rows = the number
+is when averaging is performed.  The global array has # of rows = the number
-of chunks *Nchunk* as calculated by the specified :doc:`compute
+of chunks :math:`N_\text{chunk}`, as calculated by the specified
-chunk/atom <compute_chunk_atom>` command.  The # of columns =
+:doc:`compute chunk/atom <compute_chunk_atom>` command.  The # of columns is
-M+1+Nvalues, where M = 1 to 4, depending on whether the optional
+:math:`M+1+N_\text{values}`, where :math:`M \in \{1,\dotsc,4\}`,
+depending on whether the optional
 columns for OrigID and CoordN are used, as explained above.  Following
 the optional columns, the next column contains the count of atoms in
 the chunk, and the remaining columns are the Nvalue quantities.  When
-the array is accessed with a row I that exceeds the current number of
+the array is accessed with a row :math:`I` that exceeds the current number of
 chunks, than a 0.0 is returned by the fix instead of an error, since
 the number of chunks can vary as a simulation runs depending on how
 that value is 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.
 
@@ -526,7 +530,8 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
+:doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
 :doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`
 
 Default

doc/src/fix_ave_correlate.rst

@@ -6,7 +6,7 @@ fix ave/correlate command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
 
@@ -73,10 +73,12 @@ Description
 
 Use one or more global scalar values as inputs every few timesteps,
 calculate time correlations between them at varying time intervals,
-and average the correlation data over longer timescales.  The
+and average the correlation data over longer timescales.  The resulting
-resulting correlation values can be time integrated by
+correlation values can be time integrated by
-:doc:`variables <variable>` or used by other :doc:`output commands <Howto_output>` such as :doc:`thermo_style custom <thermo_style>`, and can also be written to a file.  See the
+:doc:`variables <variable>` or used by other
-:doc:`fix ave/correlate/long <fix_ave_correlate_long>` command for an
+:doc:`output commands <Howto_output>` such as
+:doc:`thermo_style custom <thermo_style>`, and can also be written to a file.
+See the :doc:`fix ave/correlate/long <fix_ave_correlate_long>` command for an
 alternate method for computing correlation functions efficiently over
 very long time windows.
 
@@ -89,9 +91,11 @@ Each listed value can be the result of a :doc:`compute <compute>` or
 :doc:`variable <variable>`.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.  If
 you wish to spatial- or time-average or histogram per-atom quantities
-from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
+from a compute, fix, or variable, then see the
+:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
 :doc:`fix ave/histo <fix_ave_histo>` commands.  If you wish to convert a
-per-atom quantity into a single global value, see the :doc:`compute reduce <compute_reduce>` command.
+per-atom quantity into a single global value, see the
+:doc:`compute reduce <compute_reduce>` command.
 
 The input values must be all scalars.  What kinds of
 correlations between input values are calculated is determined by the
@@ -110,16 +114,16 @@ be used, since they produce per-atom values.
 For input values from a compute or fix or variable , the bracketed
 index I can be specified using a wildcard asterisk with the index to
 effectively specify multiple values.  This takes the form "\*" or
-"\*n" or "n\*" or "m\*n".  If N = the size of the vector, then an
+"\*n" or "m\*" or "m\*n".  If :math:`N` is the size of the vector, then an
-asterisk with no numeric values means all indices from 1 to N.  A
+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 asterisk means all indices from n to N (inclusive).  A middle
+trailing asterisk means all indices from m to :math:`N` (inclusive).
-asterisk means all indices from m to n (inclusive).
+A middle asterisk means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual elements of the
-vector had been listed one by one.  E.g. these 2 fix ave/correlate
+vector had been listed one by one.  For example, the following two fix
-commands are equivalent, since the :doc:`compute pressure
+ave/correlate commands are equivalent, since the :doc:`compute pressure
-<compute_pressure>` command creates a global vector with 6 values.
+<compute_pressure>` command creates a global vector with six values:
 
 .. code-block:: LAMMPS
 
@@ -139,151 +143,161 @@ commands are equivalent, since the :doc:`compute pressure
 
 ----------
 
-The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
+The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
-timesteps the input values will be used to calculate correlation data.
+arguments specify on what timesteps the input values will be used to calculate
-The input values are sampled every *Nevery* timesteps.  The
+correlation data.  The input values are sampled every :math:`N_\text{every}`
-correlation data for the preceding samples is computed on timesteps
+time steps.  The correlation data for the preceding samples is computed on
-that are a multiple of *Nfreq*\ .  Consider a set of samples from some
+time steps that are a multiple of :math:`N_\text{freq}`\ .  Consider a set of
-initial time up to an output timestep.  The initial time could be the
+samples from some initial time up to an output timestep.  The initial time
-beginning of the simulation or the last output time; see the *ave*
+could be the beginning of the simulation or the last output time; see the *ave*
 keyword for options.  For the set of samples, the correlation value
-Cij is calculated as:
+:math:`C_{ij}` is calculated as:
 
-.. parsed-literal::
+.. math::
 
-   Cij(delta) = ave(Vi(t)\*Vj(t+delta))
+   C_{ij}(\Delta t) = \left\langle V_i(t) V_j(t+\Delta t)\right\rangle,
 
-which is the correlation value between input values Vi and Vj,
+which is the correlation value between input values :math:`V_i` and
-separated by time delta.  Note that the second value Vj in the pair is
+:math:`V_j`, separated by time :math:`\Delta t`.  Note that the second value
-always the one sampled at the later time.  The ave() represents an
+:math:`V_j` in the pair is always the one sampled at the later time.  The
-average over every pair of samples in the set that are separated by
+average is an average over every pair of samples in the set that are separated
-time delta.  The maximum delta used is of size (\ *Nrepeat*\ -1)\*\ *Nevery*\ .
+by time :math:`\Delta t`.  The maximum :math:`\Delta t` used is of size
-Thus the correlation between a pair of input values yields *Nrepeat*
+:math:`(N_\text{repeat} - 1) N_\text{every}`\ .
-correlation datums:
+Thus the correlation between a pair of input values yields
+:math:`N_\text{repeat}` correlation data:
 
-.. parsed-literal::
+.. math::
 
-   Cij(0), Cij(Nevery), Cij(2\*Nevery), ..., Cij((Nrepeat-1)\*Nevery)
+   C_{ij}(0), C_{ij}(N_\text{every}), C_{ij}(2N_\text{every}), \dotsc,
+     C_{ij}\bigl((N_\text{repeat}-1) N_\text{every}\bigr)
 
-For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
+For example, if :math:`N_\text{every}=5`, :math:`N_\text{repeat}=6`, and
-timesteps 0,5,10,15,...,100 will be used to compute the final averages
+:math:`N_\text{freq}=100`, then values on time steps
-on timestep 100.  Six averages will be computed: Cij(0), Cij(5),
+:math:`0, 5, 10, 15,\dotsc,100` will be used to compute the final averages
-Cij(10), Cij(15), Cij(20), and Cij(25).  Cij(10) on timestep 100 will
+on time step 100.  Six averages will be computed: :math:`C_{ij}(0)`,
-be the average of 19 samples, namely Vi(0)\*Vj(10), Vi(5)\*Vj(15),
+:math:`C_{ij}(5)`, :math:`C_{ij}(10)`, :math:`C_{ij}(15)`, :math:`C_{ij}(20)`,
-Vi(10)\*V j20), Vi(15)\*Vj(25), ..., Vi(85)\*Vj(95), Vi(90)\*Vj(100).
+and :math:`C_{ij}(25)`.  :math:`C_{ij}(10)` on time step 100 will
+be the average of 19 samples, namely :math:`V_i(0) V_j(10)`,
+:math:`V_i(5) V_j(15)`, :math:`V_i(10) V_j(20)`,
+:math:`V_i(15) V_j(25), \dotsc,`
+:math:`V_i(85) V_j(95)`, and :math:`V_i(90) V_j(100)`.
 
-*Nfreq* must be a multiple of *Nevery*\ ; *Nevery* and *Nrepeat* must be
+:math:`N_\text{freq}` must be a multiple of :math:`N_\text{every}`;
-non-zero.  Also, if the *ave* keyword is set to *one* which is the
+:math:`N_\text{every}` and :math:`N_\text{repeat}` must be non-zero.
-default, then *Nfreq* >= (\ *Nrepeat*\ -1)\*\ *Nevery* is required.
+Also, if the *ave* keyword is set to *one* which is the default, then
+:math:`N_\text{freq} \ge (N_\text{repeat} -1) N_\text{every}` is required.
 
 ----------
 
-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 Ith element of the global vector
+bracketed term is appended, the :math:`I^\text{th}` element of the global
-calculated by the compute is used.  See the discussion above for how I
+vector calculated by the compute is used.  See the discussion above for how
-can be specified with a wildcard asterisk to effectively specify
+:math:`I` can be specified with a wildcard asterisk to effectively specify
 multiple values.
 
 Note that there is a :doc:`compute reduce <compute_reduce>` command
-which can sum per-atom quantities into a global scalar or vector which
+that can sum per-atom quantities into a global scalar or vector which
-can thus be accessed by fix ave/correlate.  Or it can be a compute
+can then be accessed by fix ave/correlate.  It can also be a compute defined
-defined not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
+not in your input script, but by :doc:`thermodynamic output <thermo_style>`
+or other fixes such as :doc:`fix nvt <fix_nh>`
 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 Ith element of the global vector
+bracketed term is appended, the :math:`I^\text{th}` element of the global
-calculated by the fix is used.  See the discussion above for how I can
+vector calculated by the fix is used.  See the discussion above for how
-be specified with a wildcard asterisk to effectively specify multiple
+:math:`I` can be specified with a wildcard asterisk to effectively specify
-values.
+multiple values.
 
 Note that some fixes only produce their values on certain timesteps,
-which must be compatible with *Nevery*, else an error will result.
+which must be compatible with :math:`N_\text{every}`, else an error will
-Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
+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
-been previously defined in the input script.  Only equal-style or
+previously defined in the input script.  Only equal-style or vector-style
-vector-style variables can be referenced; the latter requires a
+variables can be referenced; the latter requires a bracketed term to specify
-bracketed term to specify the Ith element of the vector calculated by
+the :math:`I^\text{th}` element of the vector calculated by the variable.
-the variable.  See the :doc:`variable <variable>` command for details.
+See the :doc:`variable <variable>` command for details. Note that variables of
-Note that variables of style *equal* or *vector* define a formula
+style *equal* or *vector* define a formula which can reference individual atom
-which can reference individual atom properties or thermodynamic
+properties or thermodynamic keywords, or they can invoke other computes, fixes,
-keywords, or they can invoke other computes, fixes, or variables when
+or variables when they are evaluated, so this is a very general means of
-they are evaluated, so this is a very general means of specifying
+specifying quantities to time correlate.
-quantities to time correlate.
 
 ----------
 
 Additional optional keywords also affect the operation of this fix.
 
 The *type* keyword determines which pairs of input values are
-correlated with each other.  For N input values Vi, for i = 1 to N,
+correlated with each other.  For :math:`N` input values :math:`V_i`,
-let the number of pairs = Npair.  Note that the second value in the
+with :math:`i \in \{1,\dotsc,N\}`, let the number of pairs be
-pair Vi(t)\*Vj(t+delta) is always the one sampled at the later time.
+:math:`N_\text{pair}`.  Note that the second value in the
+pair, :math:`V_i(t) V_j(t+\Delta t)`, is always the one sampled at the later
+time.
 
 * If *type* is set to *auto* then each input value is correlated with
-  itself.  I.e. Cii = Vi\*Vi, for i = 1 to N, so Npair = N.
+  itself (i.e., :math:`C_{ii} = V_i^2` for :math:`i \in \{1,\dotsc,N\}`,
-* If *type* is set
+  so :math:`N_\text{pair} = N`).
-  to *upper* then each input value is correlated with every succeeding
+* If *type* is set to *upper* then each input value is correlated with every
-  value.  I.e. Cij = Vi\*Vj, for i < j, so Npair = N\*(N-1)/2.
+  succeeding value (i.e., :math:`C_{ij} = V_i V_j` for :math:`i < j`, so
-* If *type* is set
+  :math:`N_\text{pair} = N (N-1)/2`).
-  to *lower* then each input value is correlated with every preceding
+* If *type* is set to *lower* then each input value is correlated with every
-  value.  I.e. Cij = Vi\*Vj, for i > j, so Npair = N\*(N-1)/2.
+  preceding value (i.e., :math:`C_{ij} = V_i V_j` for :math:`i > j`, so
+  :math:`N_\text{pair} = N(N-1)/2`).
 * If *type* is set to *auto/upper* then each input value is correlated
-  with itself and every succeeding value.  I.e. Cij = Vi\*Vj, for i >= j,
+  with itself and every succeeding value (i.e., :math:`C_{ij} = V_i V_j`
-  so Npair = N\*(N+1)/2.
+  for :math:`i \ge j`, so :math:`N_\text{pair} = N(N+1)/2`).
 * If *type* is set to *auto/lower* then each input value is correlated
-  with itself and every preceding value.  I.e. Cij = Vi\*Vj, for i <= j,
+  with itself and every preceding value (i.e., :math:`C_{ij} = V_i V_j`
-  so Npair = N\*(N+1)/2.
+  for :math:`i \le j`, so :math:`N_\text{pair} = N(N+1)/2`).
 * If *type* is set to *full* then each input value is correlated with
-  itself and every other value.  I.e. Cij = Vi\*Vj, for i,j = 1,N so
+  itself and every other value (i.e., :math:`C_{ij} = V_i V_j` for
-  Npair = N\^2.
+  :math:`\{i,j\} = \{1,N\}`, so :math:`N_\text{pair} = N^2`).
 
-The *ave* keyword determines what happens to the accumulation of
+The *ave* keyword determines what happens to the accumulation of correlation
-correlation samples every *Nfreq* timesteps.  If the *ave* setting is
+samples every :math:`N_\text{freq}` timesteps.  If the *ave* setting is *one*,
-*one*, then the accumulation is restarted or zeroed every *Nfreq*
+then the accumulation is restarted or zeroed every :math:`N_\text{freq}`
-timesteps.  Thus the outputs on successive *Nfreq* timesteps are
+timesteps.  Thus the outputs on successive :math:`N_\text{freq}` timesteps are
 essentially independent of each other.  The exception is that the
-Cij(0) = Vi(T)\*Vj(T) value at a timestep T, where T is a multiple of
+:math:`C_{ij}(0) = V_i(t) V_j(t)` value at a time step :math:`t,` where
-*Nfreq*, contributes to the correlation output both at time T and at
+:math:`t` is a multiple of :math:`N_\text{freq}`, contributes to the
-time T+Nfreq.
+correlation output both at time :math:`t` and at time :math:`t+N_\text{freq}`.
 
-If the *ave* setting is *running*, then the accumulation is never
+If the *ave* setting is *running*, then the accumulation is never zeroed.
-zeroed.  Thus the output of correlation data at any timestep is the
+Thus the output of correlation data at any timestep is the average over samples
-average over samples accumulated every *Nevery* steps since the fix
+accumulated every :math:`N_\text{every}` steps since the fix was defined.
-was defined.  it can only be restarted by deleting the fix via the
+It can only be restarted by deleting the fix via the :doc:`unfix <unfix>`
-:doc:`unfix <unfix>` command, or by re-defining the fix by re-specifying
+command, or by re-defining the fix by re-specifying it.
-it.
 
 The *start* keyword specifies what time step the accumulation of
 correlation samples will begin on.  The default is step 0.  Setting it
 to a larger value can avoid adding non-equilibrated data to the
 correlation averages.
 
-The *prefactor* keyword specifies a constant which will be used as a
+The *prefactor* keyword specifies a constant which will be used as a multiplier
-multiplier on the correlation data after it is averaged.  It is
+on the correlation data after it is averaged.  It is effectively a scale factor
-effectively a scale factor on Vi\*Vj, which can be used to account for
+on :math:`V_i V_j`, which can be used to account for the size of the time
-the size of the time window or other unit conversions.
+window or other unit conversions.
 
-The *file* keyword allows a filename to be specified.  Every *Nfreq*
+The *file* keyword allows a filename to be specified.  Every
-steps, an array of correlation data is written to the file.  The
+:math:`N_\text{freq}` steps, an array of correlation data is written to the
-number of rows is *Nrepeat*, as described above.  The number of
+file.  The number of rows is :math:`N_\text{repeat}`, as described above.
-columns is the Npair+2, also as described above.  Thus the file ends
+The number of columns is :math:`N_\text{pair}+2`, also as described above.
-up to be a series of these array sections.
+Thus the file ends up to be a series of these array sections.
 
 The *overwrite* keyword will continuously overwrite the output file
 with the latest output, so that it only contains one timestep worth of
 output.  This option can only be used with the *ave running* setting.
 
-The *title1* and *title2* and *title3* keywords allow specification of
+The *title1*, *title2*, and *title3* keywords allow specification of
-the strings that will be printed as the first 3 lines of the output
+the strings that will be printed as the first three lines of the output file,
-file, assuming the *file* keyword was used.  LAMMPS uses default
+assuming the *file* keyword was used.  LAMMPS uses default values for each of
-values for each of these, so they do not need to be specified.
+these, so they do not need to be specified.
 
 By default, these header lines are as follows:
 
@@ -300,18 +314,19 @@ appropriate fields from the fix ave/correlate command.
 
 ----------
 
-Let Sij = a set of time correlation data for input values I and J,
+Let :math:`S_{ij}` be a set of time correlation data for input values
-namely the *Nrepeat* values:
+:math:`I` and :math:`J`, namely the :math:`N_\text{repeat}` values:
 
-.. parsed-literal::
+.. math::
 
-   Sij = Cij(0), Cij(Nevery), Cij(2\*Nevery), ..., Cij(\*Nrepeat-1)\*Nevery)
+   S_{ij} = C_{ij}(0), C_{ij}(N_\text{every}), C_{ij}(2N_\text{every}),
+    \dotsc, C_{ijI}\bigl((N_\text{repeat}-1) N_\text{every}\bigr)
 
-As explained below, these datums are output as one column of a global
+As explained below, these data are output as one column of a global
 array, which is effectively the correlation matrix.
 
 The *trap* function defined for :doc:`equal-style variables <variable>`
-can be used to perform a time integration of this vector of datums,
+can be used to perform a time integration of this vector of data,
 using a trapezoidal rule.  This is useful for calculating various
 quantities which can be derived from time correlation data.  If a
 normalization factor is needed for the time integration, it can be
@@ -322,40 +337,43 @@ included in the variable formula or via the *prefactor* keyword.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to
-are relevant to this fix.
+:doc:`binary restart files <restart>`.  None of the
+:doc:`fix_modify <fix_modify>` options are 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 *Nfreq* since that is when
+accessed on timesteps that are multiples of :math:`N_\text{freq}` since that is
-averaging is performed.  The global array has # of rows = *Nrepeat*
+when averaging is performed.  The global array has # of rows
-and # of columns = Npair+2.  The first column has the time delta (in
+:math:`N_\text{repeat}` and # of columns :math:`N_\text{pair}+2`.  The first
-timesteps) between the pairs of input values used to calculate the
+column has the time :math:`\Delta t` (in time steps) between the pairs of input
-correlation, as described above.  The second column has the number of
+values used to calculate the correlation, as described above.  The second
-samples contributing to the correlation average, as described above.
+column has the number of samples contributing to the correlation average, as
-The remaining Npair columns are for I,J pairs of the N input values,
+described above.  The remaining Npair columns are for :math:`I,J` pairs of the
-as determined by the *type* keyword, as described above.
+:math:`N` input values, as determined by the *type* keyword, as described
+above.
 
-* For *type* = *auto*, the Npair = N columns are ordered: C11, C22, ...,
+* For *type* = *auto*, the :math:`N_\text{pair} = N` columns are ordered:
-  CNN.
+  :math:`C_{11}, C_{22}, \dotsc, C_{NN}`
-* For *type* = *upper*, the Npair = N\*(N-1)/2 columns are ordered: C12,
+* For *type* = *upper*, the :math:`N_\text{pair} = N(N-1)/2` columns are
-  C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N.
+  ordered: :math:`C_{12}, C_{13}, \dotsc, C_{1N}, C_{23}, \dotsc, C_{2N},
-* For *type* = *lower*, the Npair = N\*(N-1)/2 columns are ordered: C21,
+  C_{34}, \dotsc, C_{N-1,N}`
-  C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1.
+* For *type* = *lower*, the :math:`N_\text{pair} = N(N-1)/2` columns are
-* For *type* = *auto/upper*, the Npair = N\*(N+1)/2 columns are ordered:
+  ordered: :math:`C_{21}, C_{31}, C_{32}, C_{41}, C_{42}, C_{43I}, \dotsc,
-  C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
+  C_{N1}, C_{N2}, \dotsc, C_{N,N-1}`
-  CNN.
+* For *type* = *auto/upper*, the :math:`N_\text{pair} = N(N+1)/2` columns are
-* For *type* = *auto/lower*, the Npair = N\*(N+1)/2 columns are ordered:
+  ordered: :math:`C_{11}, C_{12}, C_{13}, \dotsc, C_{1N}, C_{22}, C_{23},
-  C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
+  \dotsc, C_{2N}, C_{33}, C_{34}, \dotsc, C_{N-1,N}, C_{NN}`
-  CNN.
+* For *type* = *auto/lower*, the :math:`N_\text{pair} = N(N+1)/2` columns are
-* For *type* = *full*, the Npair = N\^2 columns are ordered: C11, C12,
+  ordered: :math:`C_{11}, C_{21}, C_{22}, C_{31}, C_{32}, C_{33}, C_{41},
-  ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
+  \dotsc, C_{44}, C_{N1}, C_{N2}, \dotsc, C_{N,N-1}, C_{NN}`
-  CNN.
+* For *type* = *full*, the :math:`N_\text{pair} = N^2` columns are ordered:
+  :math:`C_{11}, C_{12}, \dotsc, C_{1N}, C_{21}, C_{22}, \dotsc, C_{2N},
+  C_{31}, \dotsc, C_{3N}, \dotsc, C_{N1}, \dotsc, C_{N,N-1}, C_{NN}`
 
-The array values calculated by this fix are treated as intensive.  If
+The array values calculated by this fix are treated as extensive.  If
 you need to divide them by the number of atoms, you must do this in a
-later processing step, e.g. when using them in a
+later processing step (e.g., when using them in a :doc:`variable <variable>`).
-:doc:`variable <variable>`.
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
@@ -368,7 +386,8 @@ Related commands
 """"""""""""""""
 
 :doc:`fix ave/correlate/long <fix_ave_correlate_long>`,
-:doc:`compute <compute>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
+:doc:`compute <compute>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
 :doc:`fix ave/histo <fix_ave_histo>`, :doc:`variable <variable>`
 
 Default

doc/src/fix_ave_correlate_long.rst

@@ -6,7 +6,7 @@ fix ave/correlate/long command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ...
 
@@ -66,10 +66,11 @@ Examples
 Description
 """""""""""
 
-This fix is similar in spirit and syntax to the :doc:`fix ave/correlate <fix_ave_correlate>`.
+This fix is similar in spirit and syntax to the
+:doc:`fix ave/correlate <fix_ave_correlate>`.
 However, this fix allows the efficient calculation of time correlation
 functions on-the-fly over extremely long time windows with little
-additional CPU overhead, using a multiple-tau method
+additional CPU overhead, using a multiple-:math:`\tau` method
 :ref:`(Ramirez) <Ramirez>` that decreases the resolution of the stored
 correlation function with time.  It is not a full drop-in replacement.
 
@@ -78,37 +79,41 @@ specified values may represent calculations performed by computes and
 fixes which store their own "group" definitions.
 
 Each listed value can be the result of a compute or fix or the
-evaluation of an equal-style variable. See the :doc:`fix ave/correlate <fix_ave_correlate>` page for details.
+evaluation of an equal-style variable. See the
+:doc:`fix ave/correlate <fix_ave_correlate>` page for details.
 
 The *Nevery* and *Nfreq* arguments specify on what time steps the input
-values will be used to calculate correlation data, and the frequency
+values will be used to calculate correlation data and the frequency
-with which the time correlation functions will be output to a file.
+with which the time correlation functions will be output to a file,
-Note that there is no *Nrepeat* argument, unlike the :doc:`fix ave/correlate <fix_ave_correlate>` command.
+respectively.
+Note that there is no *Nrepeat* argument, unlike the
+:doc:`fix ave/correlate <fix_ave_correlate>` command.
 
 The optional keywords *ncorr*, *nlen*, and *ncount* are unique to this
 command and determine the number of correlation points calculated and
 the memory and CPU overhead used by this calculation. *Nlen* and
 *ncount* determine the amount of averaging done at longer correlation
-times.  The default values *nlen=16*, *ncount=2* ensure that the
+times.  The default values *nlen* = 16 and *ncount* = 2 ensure that the
-systematic error of the multiple-tau correlator is always below the
+systematic error of the multiple-:math:`\tau` correlator is always below the
 level of the statistical error of a typical simulation (which depends
 on the ensemble size and the simulation length).
 
 The maximum correlation time (in time steps) that can be reached is
-given by the formula (nlen-1) \* ncount\^(ncorr-1).  Longer correlation
+given by the formula :math:`(nlen-1) ncount^{(ncorr-1)}`.  Longer correlation
 times are discarded and not calculated.  With the default values of
-the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to
+the parameters (:math:`ncorr=20`, :math:`nlen=16` and :math:`ncount=2`),
-7864320 time steps.  If longer correlation times are needed, the value
+this corresponds to 7864320 time steps.  If longer correlation times are
-of ncorr should be increased. Using nlen=16 and ncount=2, with
+needed, the value of ncorr should be increased. Using :math:`nlen=16` and
-ncorr=30, the maximum number of steps that can be correlated is
+:math:`ncount=2`, with :math:`ncorr=30`, the maximum number of steps that can
-80530636808.  If ncorr=40, correlation times in excess of 8e12 time
+be correlated is 80530636808.  If :math:`ncorr=40`, correlation times in excess
-steps can be calculated.
+of :math:`8\times 10^{12}` time steps can be calculated.
 
 The total memory needed for each correlation pair is roughly
-4\*ncorr\*nlen\*8 bytes. With the default values of the parameters, this
+:math:`4 \times ncorr\times nlen \times 8` bytes.
-corresponds to about 10 KB.
+With the default values of the parameters, this corresponds to about 10 KB.
 
-For the meaning of the additional optional keywords, see the :doc:`fix ave/correlate <fix_ave_correlate>` doc page.
+For the meaning of the additional optional keywords, see the
+:doc:`fix ave/correlate <fix_ave_correlate>` doc page.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -128,7 +133,8 @@ Restrictions
 """"""""""""
 
 This compute is part of the EXTRA-FIX package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""
@@ -140,8 +146,9 @@ Default
 
 none
 
-The option defaults for keywords that are also keywords for the :doc:`fix ave/correlate <fix_ave_correlate>` command are as follows: type =
+The option defaults for keywords that are also keywords for the
-auto, start = 0, no file output, title 1,2 = strings as described on
+:doc:`fix ave/correlate <fix_ave_correlate>` command are as follows:
+type = auto, start = 0, no file output, title 1,2 = strings as described on
 the :doc:`fix ave/correlate <fix_ave_correlate>` doc page.
 
 The option defaults for keywords unique to this command are as

doc/src/fix_ave_histo.rst

@@ -10,7 +10,7 @@ fix ave/histo/weight command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ...
 
@@ -22,7 +22,7 @@ Syntax
 * lo,hi = lo/hi bounds within which to histogram
 * Nbin = # of histogram bins
 * one or more input values can be listed
-* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
+* value = *x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, c_ID, c_ID[N], f_ID, f_ID[N], v_name
 
   .. parsed-literal::
 
@@ -126,26 +126,27 @@ length.  The first value (a scalar or vector) is what is histogrammed
 into bins, in the same manner the fix ave/histo command operates.  The
 second value (a scalar or vector) is used as a "weight".  This means
 that instead of each value tallying a "1" to its bin, the
-corresponding weight is tallied.  E.g. The Nth entry (weight) in the
+corresponding weight is tallied.  For example, the :math:`N^\text{th}` entry
-second vector is tallied to the bin corresponding to the Nth entry in
+(weight) in the second vector is tallied to the bin corresponding to the
-the first vector.
+:math:`N^\text{th}` entry in the first vector.
 
 ----------
 
 For input values from a compute or fix or variable, the bracketed
 index I can be specified using a wildcard asterisk with the index to
 effectively specify multiple values.  This takes the form "\*" or
-"\*n" or "n\*" or "m\*n".  If N = the size of the vector (for *mode* =
+"\*n" or "m\*" or "m\*n".  If :math:`N` is the size of the vector
-scalar) or the number of columns in the array (for *mode* = vector),
+(for *mode* = scalar) or the number of columns in the array
-then an asterisk with no numeric values means all indices from 1 to N.
+(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 asterisk means all indices from n to N (inclusive).  A middle
+trailing asterisk means all indices from m to :math:`N` (inclusive).  A middle
 asterisk means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual elements of the
-vector or columns of the array had been listed one by one.  E.g. these
+vector or columns of the array had been listed one by one.  For example, the
-2 fix ave/histo commands are equivalent, since the :doc:`compute
+following two fix ave/histo commands are equivalent, since the :doc:`compute
-com/chunk <compute_com_chunk>` command creates a global array with 3
+com/chunk <compute_com_chunk>` command creates a global array with three
 columns:
 
 .. code-block:: LAMMPS
@@ -164,31 +165,35 @@ columns:
 
 ----------
 
-The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
+The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
-timesteps the input values will be used in order to contribute to the
+arguments specify on what time steps the input values will be used in order to
-histogram.  The final histogram is generated on timesteps that are
+contribute to the histogram.  The final histogram is generated on time steps
-multiple of *Nfreq*\ .  It is averaged over *Nrepeat* histograms,
+that are multiple of :math:`N_\text{freq}`\ .  It is averaged over
-computed in the preceding portion of the simulation every *Nevery*
+:math:`N_\text{repeat}` histograms, computed in the preceding portion of the
-timesteps.  *Nfreq* must be a multiple of *Nevery* and *Nevery* must
+simulation every :math:`N_\text{every}` time steps.
-be non-zero even if *Nrepeat* is 1.  Also, the timesteps
+:math:`N_\text{freq}` must be a multiple of :math:`N_\text{every}` and
-contributing to the histogram value cannot overlap,
+:math:`N_\text{every}` must be non-zero even if :math:`N_\text{repeat}` is 1.
-i.e. Nrepeat\*Nevery can not exceed Nfreq.
+Also, the time steps contributing to the histogram value cannot overlap
+(i.e., :math:`N_\text{repeat}\times N_\text{every}` cannot exceed
+:math:`N_\text{freq}`).
 
-For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
+For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
-on timesteps 90,92,94,96,98,100 will be used to compute the final
+:math:`N_\text{freq}=100`, then input values on time steps 90, 92, 94, 96, 98,
-histogram on timestep 100.  Similarly for timesteps
+and 100 will be used to compute the final histogram on timestep 100.
-190,192,194,196,198,200 on timestep 200, etc.  If Nrepeat=1 and Nfreq
+Similarly for timesteps 190, 192, 194, 196, 198, and 200 on timestep 200, etc.
-= 100, then no time averaging of the histogram is done; a histogram is
+If :math:`N_\text{repeat}=1` and :math:`N_\text{freq} = 100`, then no time
-simply generated on timesteps 100,200,etc.
+averaging of the histogram is done; a histogram is simply generated on
+timesteps 100, 200, etc.
 
 ----------
 
-The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, and
-self-explanatory.  Note that other atom attributes can be used as
+*fz*) are self-explanatory.  Note that other atom attributes can be used as
-inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+inputs to this fix by using the
-an input value from that compute.
+: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
@@ -201,35 +206,38 @@ how I can be specified with a wildcard asterisk to effectively specify
 multiple values.
 
 Note that there is a :doc:`compute reduce <compute_reduce>` command
-which can sum per-atom quantities into a global scalar or vector which
+that can sum per-atom quantities into a global scalar or vector, which
-can thus be accessed by fix ave/histo.  Or it can be a compute defined
+can then be accessed by fix ave/histo.  It can also be a compute defined
-not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
+not in your input script, but by :doc:`thermodynamic output <thermo_style>`
+or other fixes such as :doc:`fix nvt <fix_nh>`
 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>`.
+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
 global vector calculated by the fix is used.  If *mode* = vector, then
 if no bracketed term is appended, the global or per-atom or local
 vector calculated by the fix is used.  If a bracketed term is
-appended, the Ith column of the global or per-atom or local array
+appended, the :math:`I^\text{th}` column of the global or per-atom or local
-calculated by the fix is used.  See the discussion above for how I can
+array calculated by the fix is used.  See the discussion above for how
-be specified with a wildcard asterisk to effectively specify multiple
+:math:`I` can be specified with a wildcard asterisk to effectively specify
-values.
+multiple values.
 
 Note that some fixes only produce their values on certain timesteps,
-which must be compatible with *Nevery*, else an error will result.
+which must be compatible with :math:`N_\text{every}`, else an error will
-Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
+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
-a bracketed term to specify the Ith element of the vector calculated
+a bracketed term to specify the :math:`I^\text{th}` element of the vector
-by the variable.  If *mode* = vector, then only vector-style or
+calculated by the variable.  If *mode* = vector, then only vector-style or
 atom-style variables can be used, which produce a global or per-atom
 vector respectively.  The vector-style variable must be used without a
 bracketed term.  See the :doc:`variable <variable>` command for details.
@@ -259,44 +267,44 @@ keyword should be used to specify which output will be used.  The
 remaining input arguments must still be consistent.
 
 The *beyond* keyword determines how input values that fall outside the
-*lo* to *hi* bounds are treated.  Values such that *lo* <= value <=
+*lo* to *hi* bounds are treated.  Values such that *lo* :math:`\le` value
-*hi* are assigned to one bin.  Values on a bin boundary are assigned
+:math:`\le` *hi* are assigned to one bin.  Values on a bin boundary are
-to the lower of the 2 bins.  If *beyond* is set to *ignore* then
+assigned to the lower of the two bins.  If *beyond* is set to *ignore* then
-values < *lo* and values > *hi* are ignored, i.e. they are not binned.
+values :math:`<` *lo* and values :math:`>` *hi* are ignored (i.e., they are not
-If *beyond* is set to *end* then values < *lo* are counted in the
+binned). If *beyond* is set to *end*, then values :math:`<` *lo* are counted in
-first bin and values > *hi* are counted in the last bin.  If *beyond*
+the first bin and values :math:`>` *hi* are counted in the last bin.
-is set to *extend* then two extra bins are created, so that there are
+If *beyond* is set to *extend*, then two extra bins are created so that there
-Nbins+2 total bins.  Values < *lo* are counted in the first bin and
+are :math:`N_\text{bins}+2` total bins.  Values :math:`<` *lo* are counted in
-values > *hi* are counted in the last bin (Nbins+2).  Values between
+the first bin and values :math:`>` *hi* are counted in the last bin
-*lo* and *hi* (inclusive) are counted in bins 2 through Nbins+1.  The
+:math:`(N_\text{bins}+2)`\ .  Values between
-"coordinate" stored and printed for these two extra bins is *lo* and
+*lo* and *hi* (inclusive) are counted in bins 2 through
-*hi*\ .
+:math:`N_\text{bins}+1`\ .  The "coordinate" stored and printed for these two
+extra bins is *lo* and *hi*\ .
 
-The *ave* keyword determines how the histogram produced every *Nfreq*
+The *ave* keyword determines how the histogram produced every
-steps are averaged with histograms produced on previous steps that
+:math:`N_\text{freq}` steps are averaged with histograms produced on previous
-were multiples of *Nfreq*, before they are accessed by another output
+steps that were multiples of :math:`N_\text{freq}`, before they are accessed by
-command or written to a file.
+another output command or written to a file.
 
 If the *ave* setting is *one*, then the histograms produced on
-timesteps that are multiples of *Nfreq* are independent of each other;
+timesteps that are multiples of :math:`N_\text{freq}` are independent of each
-they are output as-is without further averaging.
+other; they are output as-is without further averaging.
 
 If the *ave* setting is *running*, then the histograms produced on
-timesteps that are multiples of *Nfreq* are summed and averaged in a
+timesteps that are multiples of :math:`N_\text{freq}` are summed and averaged
-cumulative sense before being output.  Each bin value in the histogram
+in a cumulative sense before being output.  Each bin value in the histogram
-is thus the average of the bin value produced on that timestep with
+is thus the average of the bin value produced on that timestep with all
-all preceding values for the same bin.  This running average begins
+preceding values for the same bin.  This running average begins when the fix is
-when the fix is defined; it can only be restarted by deleting the fix
+defined; it can only be restarted by deleting the fix via the
-via the :doc:`unfix <unfix>` command, or by re-defining the fix by
+:doc:`unfix <unfix>` command, or by re-defining the fix by re-specifying it.
-re-specifying it.
 
 If the *ave* setting is *window*, then the histograms produced on
-timesteps that are multiples of *Nfreq* are summed within a moving
+timesteps that are multiples of :math:`N_\text{freq}` are summed within a
-"window" of time, so that the last M histograms are used to produce
+moving "window" of time, so that the last :math:`M` histograms are used to
-the output.  E.g. if M = 3 and Nfreq = 1000, then the output on step
+produce the output (e.g., if :math:`M = 3` and :math:`N_\text{freq} = 1000`,
-10000 will be the combined histogram of the individual histograms on
+then the output on step 10000 will be the combined histogram of the individual
-steps 8000,9000,10000.  Outputs on early steps will be sums over less
+histograms on steps 8000, 9000, and 10000.  Outputs on early steps will be sums
-than M histograms if they are not available.
+over less than :math:`M` histograms if they are not available.
 
 The *start* keyword specifies what timestep histogramming will begin
 on.  The default is step 0.  Often input values can be 0.0 at time 0,
@@ -321,8 +329,8 @@ The *overwrite* keyword will continuously overwrite the output file
 with the latest output, so that it only contains one timestep worth of
 output.  This option can only be used with the *ave running* setting.
 
-The *title1* and *title2* and *title3* keywords allow specification of
+The *title1*, *title2*, and *title3* keywords allow specification of
-the strings that will be printed as the first 3 lines of the output
+the strings that will be printed as the first three lines of the output
 file, assuming the *file* keyword was used.  LAMMPS uses default
 values for each of these, so they do not need to be specified.
 
@@ -336,7 +344,7 @@ By default, these header lines are as follows:
 
 In the first line, ID is replaced with the fix-ID.  The second line
 describes the six values that are printed at the first of each section
-of output.  The third describes the 4 values printed for each bin in
+of output.  The third describes the four values printed for each bin in
 the histogram.
 
 ----------
@@ -344,13 +352,14 @@ the histogram.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to
-are relevant to this fix.
+:doc:`binary restart files <restart>`.
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
 
 This fix produces a global vector and global array which can be
 accessed by various :doc:`output commands <Howto_output>`.  The values
-can only be accessed on timesteps that are multiples of *Nfreq* since
+can only be accessed on timesteps that are multiples of :math:`N_\text{freq}`
-that is when a histogram is generated.  The global vector has 4
+since that is when a histogram is generated.  The global vector has four
 values:
 
 * 1 = total counts in the histogram
@@ -358,19 +367,20 @@ values:
 * 3 = min value of all input values, including ones not histogrammed
 * 4 = max value of all input values, including ones not histogrammed
 
-The global array has # of rows = Nbins and # of columns = 3.  The
+The global array has :math:`N_\text{bins}` rows and three columns.  The
 first column has the bin coordinate, the second column has the count of
 values in that histogram bin, and the third column has the bin count
 divided by the total count (not including missing counts), so that the
 values in the third column sum to 1.0.
 
 The vector and array values calculated by this fix are all treated as
-intensive.  If this is not the case, e.g. due to histogramming
+intensive.  If this is not the case (e.g., due to histogramming
-per-atom input values, then you will need to account for that when
+per-atom input values), then you will need to account for that when
 interpreting the values produced by this fix.
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.
+This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
@@ -379,7 +389,8 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
+:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
 :doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
 
 Default

doc/src/fix_ave_time.rst

@@ -6,7 +6,7 @@ fix ave/time command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
 
@@ -86,9 +86,11 @@ Each listed value can be the result of a :doc:`compute <compute>` or
 :doc:`variable <variable>`.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.  If
 you wish to spatial- or time-average or histogram per-atom quantities
-from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`,
+from a compute, fix, or variable, then see the
+:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`,
 or :doc:`fix ave/histo <fix_ave_histo>` commands.  If you wish to sum a
-per-atom quantity into a single global quantity, see the :doc:`compute reduce <compute_reduce>` command.
+per-atom quantity into a single global quantity, see the
+:doc:`compute reduce <compute_reduce>` command.
 
 :doc:`Computes <compute>` that produce global quantities are those which
 do not have the word *atom* in their style name.  Only a few
@@ -100,13 +102,13 @@ be used, since they produce per-atom values.
 
 The input values must either be all scalars or all vectors depending
 on the setting of the *mode* keyword.  In both cases, the averaging is
-performed independently on each input value.  I.e. each input scalar
+performed independently on each input value (i.e., each input scalar
 is averaged independently or each element of each input vector is
-averaged independently.
+averaged independently).
 
 If *mode* = scalar, then the input values must be scalars, or vectors
-with a bracketed term appended, indicating the Ith value of the vector
+with a bracketed term appended, indicating the :math:`I^\text{th}` value of the
-is used.
+vector is used.
 
 If *mode* = vector, then the input values must be vectors, or arrays
 with a bracketed term appended, indicating the Ith column of the array
@@ -118,17 +120,17 @@ the vector or number of rows in the array.
 For input values from a compute or fix or variable, the bracketed
 index I can be specified using a wildcard asterisk with the index to
 effectively specify multiple values.  This takes the form "\*" or
-"\*n" or "n\*" or "m\*n".  If N = the size of the vector (for *mode* =
+"\*n" or "m\*" or "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 N.
+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
+A leading asterisk means all indices from 1 to n (inclusive).  A trailing
-trailing asterisk means all indices from n to N (inclusive).  A middle
+asterisk means all indices from n to :math:`N` (inclusive).  A middle asterisk
-asterisk means all indices from m to n (inclusive).
+means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual elements of the
-vector or columns of the array had been listed one by one.  E.g. these
+vector or columns of the array had been listed one by one.  For example, the
-2 fix ave/time commands are equivalent, since the :doc:`compute rdf
+following two fix ave/time commands are equivalent, since the :doc:`compute rdf
-<compute_rdf>` command creates, in this case, a global array with 3
+<compute_rdf>` command creates, in this case, a global array with three
 columns, each of length 50:
 
 .. code-block:: LAMMPS
@@ -147,20 +149,22 @@ columns, each of length 50:
 
 ----------
 
-The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
+The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
-timesteps the input values will be used in order to contribute to the
+arguments specify on what time steps the input values will be used in order to
-average.  The final averaged quantities are generated on timesteps
+contribute to the average.  The final averaged quantities are generated on
-that are a multiple of *Nfreq*\ .  The average is over *Nrepeat*
+time steps that are a multiple of :math:`N_\text{freq}`\ .  The average is over
-quantities, computed in the preceding portion of the simulation every
+:math:`N_\text{repeat}` quantities, computed in the preceding portion of the
-*Nevery* timesteps.  *Nfreq* must be a multiple of *Nevery* and
+simulation every :math:`N_\text{every}` time steps.  :math:`N_\text{freq}` must
-*Nevery* must be non-zero even if *Nrepeat* is 1.  Also, the timesteps
+be a multiple of :math:`N_\text{every}` and :math:`N_\text{every}` must be
+non-zero even if :math:`N_\text{repeat} = 1`.  Also, the time steps
 contributing to the average value cannot overlap,
 i.e. Nrepeat\*Nevery can not exceed Nfreq.
 
-For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
-timesteps 90,92,94,96,98,100 will be used to compute the final average
+:math:`N_\text{freq}=100`, then values on time steps 90, 92, 94, 96, 98, and
-on timestep 100.  Similarly for timesteps 190,192,194,196,198,200 on
+100 will be used to compute the final average on time step 100.  Similarly for
-timestep 200, etc.  If Nrepeat=1 and Nfreq = 100, then no time
+time steps 190, 192, 194, 196, 198, and 200 on time step 200, etc.
+If :math:`N_\text{repeat}=1` and :math:`N_\text{freq} = 100`, then no time
 averaging is done; values are simply generated on time steps
 100, 200, etc.
 
@@ -178,8 +182,8 @@ See the discussion above for how I can be specified with a wildcard
 asterisk to effectively specify multiple values.
 
 Note that there is a :doc:`compute reduce <compute_reduce>` command
-which can sum per-atom quantities into a global scalar or vector which
+that can sum per-atom quantities into a global scalar or vector, which
-can thus be accessed by fix ave/time.  Or it can be a compute defined
+can then be accessed by fix ave/time.  It can also be a compute defined
 not in your input script, but by :doc:`thermodynamic output
 <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>` or
 :doc:`fix temp/rescale <fix_temp_rescale>`.  See the doc pages for
@@ -228,18 +232,18 @@ vectors, or columns of global arrays.  They can also be global arrays,
 which are converted into a series of global vectors (one per column),
 as explained above.
 
-The *ave* keyword determines how the values produced every *Nfreq*
+The *ave* keyword determines how the values produced every
-steps are averaged with values produced on previous steps that were
+:math:`N_\text{freq}` steps are averaged with values produced on previous steps
-multiples of *Nfreq*, before they are accessed by another output
+that were multiples of :math:`N_\text{freq}`, before they are accessed by
-command or written to a file.
+another output command or written to a file.
 
 If the *ave* setting is *one*, then the values produced on time steps
-that are multiples of *Nfreq* are independent of each other; they are
+that are multiples of :math:`N_\text{freq}` are independent of each other; they
-output as-is without further averaging.
+are output as-is without further averaging.
 
 If the *ave* setting is *running*, then the values produced on
-timesteps that are multiples of *Nfreq* are summed and averaged in a
+time steps that are multiples of :math:`N_\text{freq}` are summed and averaged
-cumulative sense before being output.  Each output value is thus the
+in a cumulative sense before being output.  Each output value is thus the
 average of the value produced on that time step with all preceding
 values.  This running average begins when the fix is defined; it can
 only be restarted by deleting the fix via the :doc:`unfix <unfix>`
@@ -248,10 +252,10 @@ command, or by re-defining the fix by re-specifying it.
 If the *ave* setting is *window*, then the values produced on
 time steps that are multiples of *Nfreq* are summed and averaged within
 a moving "window" of time, so that the last M values are used to
-produce the output.  E.g. if M = 3 and Nfreq = 1000, then the output
+produce the output.  For example, if :math:`M = 3` and
-on step 10000 will be the average of the individual values on steps
+:math:`N_\text{freq} = 1000`, then the output on step 10000 will be the average
-8000,9000,10000.  Outputs on early steps will average over less than M
+of the individual values on steps 8000, 9000, and 10000.  Outputs on early
-values if they are not available.
+steps will average over less than :math:`M` values if they are not available.
 
 The *start* keyword specifies what time step averaging will begin on.
 The default is step 0.  Often input values can be 0.0 at time 0, so
@@ -262,9 +266,9 @@ The *off* keyword can be used to flag any of the input values.  If a
 value is flagged, it will not be time averaged.  Instead the most
 recent input value will always be stored and output.  This is useful
 if one of more of the inputs produced by a compute or fix or variable
-are effectively constant or are simply current values.  E.g. they are
+are effectively constant or are simply current values (e.g., they are
 being written to a file with other time-averaged values for purposes
-of creating well-formatted output.
+of creating well-formatted output).
 
 The *file* keyword allows a filename to be specified.  Every *Nfreq*
 steps, one quantity or vector of quantities is written to the file for
@@ -294,7 +298,7 @@ output.  This option can only be used with the *ave running* setting.
 The *format* keyword sets the numeric format of each value when it is
 printed to a file via the *file* keyword.  Note that all values are
 floating point quantities.  The default format is %g.  You can specify
-a higher precision if desired, e.g. %20.16g.
+a higher precision if desired (e.g., %20.16g).
 
 The *title1* and *title2* and *title3* keywords allow specification of
 the strings that will be printed as the first 2 or 3 lines of the
@@ -341,7 +345,7 @@ a YAML format file this name will be in the list of keywords.
 This fix produces a global scalar or global vector or global array
 which can be accessed by various :doc:`output commands <Howto_output>`.
 The values can only be accessed on time steps that are multiples of
-*Nfreq* since that is when averaging is performed.
+:math:`N_\text{freq}` since that is when averaging is performed.
 
 A scalar is produced if only a single input value is averaged and
 *mode* = scalar.  A vector is produced if multiple input values are
@@ -354,17 +358,18 @@ 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.
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
@@ -373,7 +378,8 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
+:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
 :doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
 
 Default

doc/src/fix_aveforce.rst

@@ -6,7 +6,7 @@ fix aveforce command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID aveforce fx fy fz keyword value ...
 
@@ -48,13 +48,13 @@ component.  The actual force on each atom is then set to the average
 value plus the component specified in this command.  This means each
 atom in the group receives the same force.
 
-Any of the fx,fy,fz values can be specified as NULL which means the
+Any of the *fx*, *fy*, or *fz* values can be specified as :code:`NULL`, which
-force in that dimension is not changed.  Note that this is not the
+means the force in that dimension is not changed.  Note that this is not the
 same as specifying a 0.0 value, since that sets all forces to the same
 average value without adding in any additional force.
 
-Any of the 3 quantities defining the force components can be specified
+Any of the three quantities defining the force components, namely *fx*, *fy*,
-as an equal-style :doc:`variable <variable>`, namely *fx*, *fy*, *fz*\ .
+and *fz*, can be specified as an equal-style :doc:`variable <variable>`\ .
 If the value is a variable, it should be specified as v_name, where
 name is the variable name.  In this case, the variable will be
 evaluated each timestep, and its value used to determine the average
@@ -78,17 +78,17 @@ to it.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to
+:doc:`binary restart files <restart>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
 fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
 integrator the fix is adding its forces. Default is the outermost level.
 
-This fix computes a global 3-vector of forces, which can be accessed
+This fix computes a global three-vector of forces, which can be accessed
 by various :doc:`output commands <Howto_output>`.  This is the total
 force on the group of atoms before the forces on individual atoms are
-changed by the fix.  The vector values calculated by this fix are
+changed by the fix.  The vector values calculated by this fix are "extensive".
-"extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_balance.rst

@@ -6,7 +6,7 @@ fix balance command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID balance Nfreq thresh style args keyword args ...
 
@@ -19,7 +19,7 @@ Syntax
   .. parsed-literal::
 
        shift args = dimstr Niter stopthresh
-         dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
+         dimstr = sequence of letters containing *x* or *y* or *z*, each not more than once
          Niter = # of times to iterate within each dimension of dimstr sequence
          stopthresh = stop balancing when this imbalance threshold is reached
        *rcb* args = none
@@ -72,10 +72,10 @@ perform "static" balancing, before or between runs, see the
 Load-balancing is typically most useful if the particles in the
 simulation box have a spatially-varying density distribution or
 where the computational cost varies significantly between different
-atoms. E.g. a model of a vapor/liquid interface, or a solid with
+atoms (e.g., a model of a vapor/liquid interface, or a solid with
 an irregular-shaped geometry containing void regions, or
-:doc:`hybrid pair style simulations <pair_hybrid>` which combine
+:doc:`hybrid pair style simulations <pair_hybrid>` that combine
-pair styles with different computational cost.  In these cases, the
+pair styles with different computational cost).  In these cases, the
 LAMMPS default of dividing the simulation box volume into a
 regular-spaced grid of 3d bricks, with one equal-volume sub-domain
 per processor, may assign numbers of particles per processor in a
@@ -92,28 +92,30 @@ processor.
 .. note::
 
    The weighting options listed above are documented with the
-   :doc:`balance <balance>` command in :ref:`this section of the balance command <weighted_balance>` doc page.  That section
+   :doc:`balance <balance>` command in :ref:`this section of the balance
+   command <weighted_balance>` doc page.  That section
    describes the various weighting options and gives a few examples of
    how they can be used.  The weighting options are the same for both the
    fix balance and :doc:`balance <balance>` commands.
 
 Note that the :doc:`processors <processors>` command allows some control
 over how the box volume is split across processors.  Specifically, for
-a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
+a :math:`P_x \times P_y \times P_z` grid of processors, it allows choices of
-Pz, subject to the constraint that Px \* Py \* Pz = P, the total number
+:math:`P_x`, :math:`P_y`, and :math:`P_z` subject to the constraint that
-of processors.  This is sufficient to achieve good load-balance for
+:math:`P_x P_y P_z = P`, the total number of processors.
+This is sufficient to achieve good load-balance for
 some problems on some processor counts.  However, all the processor
-sub-domains will still have the same shape and same volume.
+sub-domains will still have the same shape and the same volume.
 
 On a particular time step, a load-balancing operation is only performed
 if the current "imbalance factor" in particles owned by each processor
 exceeds the specified *thresh* parameter.  The imbalance factor is
 defined as the maximum number of particles (or weight) owned by any
 processor, divided by the average number of particles (or weight) per
-processor.  Thus an imbalance factor of 1.0 is perfect balance.
+processor.  Thus, an imbalance factor of 1.0 is perfect balance.
 
 As an example, for 10000 particles running on 10 processors, if the
-most heavily loaded processor has 1200 particles, then the factor is
+most heavily loaded processor has 1200 particles, then the imbalance factor is
 1.2, meaning there is a 20% imbalance.  Note that re-balances can be
 forced even if the current balance is perfect (1.0) be specifying a
 *thresh* < 1.0.
@@ -125,28 +127,29 @@ forced even if the current balance is perfect (1.0) be specifying a
    may not be achieved.  For example, "grid" methods (defined below) that
    create a logical 3d grid cannot achieve perfect balance for many
    irregular distributions of particles.  Likewise, if a portion of the
-   system is a perfect lattice, e.g. the initial system is generated by
+   system is a perfect, non-rotated lattice (e.g., the initial system is
-   the :doc:`create_atoms <create_atoms>` command, then "grid" methods may
+   generated by the :doc:`create_atoms <create_atoms>` command with no
-   be unable to achieve exact balance.  This is because entire lattice
+   rotations), then "grid" methods may be unable to achieve exact balance.
-   planes will be owned or not owned by a single processor.
+   This is because entire lattice planes will be owned or not owned by a single
+   processor.
 
 .. note::
 
    The imbalance factor is also an estimate of the maximum speed-up
    you can hope to achieve by running a perfectly balanced simulation
-   versus an imbalanced one.  In the example above, the 10000 particle
+   versus an imbalanced one.  In the example above, the 10000-particle
    simulation could run up to 20% faster if it were perfectly balanced,
    versus when imbalanced.  However, computational cost is not strictly
    proportional to particle count, and changing the relative size and
    shape of processor sub-domains may lead to additional computational
-   and communication overheads, e.g. in the PPPM solver used via the
+   and communication overheads (e.g., in the PPPM solver used via the
-   :doc:`kspace_style <kspace_style>` command.  Thus you should benchmark
+   :doc:`kspace_style <kspace_style>` command).  Thus, you should benchmark
    the run times of a simulation before and after balancing.
 
 ----------
 
 The method used to perform a load balance is specified by one of the
-listed styles, which are described in detail below.  There are 2 kinds
+listed styles, which are described in detail below.  There are two kinds
 of styles.
 
 The *shift* style is a "grid" method which produces a logical 3d grid
@@ -198,11 +201,12 @@ The *group-ID* is ignored.  However the impact of balancing on
 different groups of atoms can be affected by using the *group* weight
 style as described below.
 
-The *Nfreq* setting determines how often a re-balance is performed.  If
+The :math:`N_\text{freq}` setting determines how often a re-balance is
-*Nfreq* > 0, then re-balancing will occur every *Nfreq* steps.  Each
+performed.  If :math:`N_\text{freq} > 0`, then re-balancing will occur every
-time a re-balance occurs, a reneighboring is triggered, so *Nfreq*
+:math:`N_\text{freq}` steps.  Each time a re-balance occurs, a reneighboring is
-should not be too small.  If *Nfreq* = 0, then re-balancing will be
+triggered, so :math:`N_\text{freq}` should not be too small.  If
-done every time reneighboring normally occurs, as determined by the
+:math:`N_\text{freq} = 0`, then re-balancing will be done every time
+reneighboring normally occurs, as determined by the
 the :doc:`neighbor <neighbor>` and :doc:`neigh_modify <neigh_modify>`
 command settings.
 
@@ -216,7 +220,7 @@ above.  It changes the positions of cutting planes between processors
 in an iterative fashion, seeking to reduce the imbalance factor.
 
 The *dimstr* argument is a string of characters, each of which must be
-an "x" or "y" or "z".  Each character can appear zero or one time,
+*x* or *y* or *z*.  Each character can appear zero or one time,
 since there is no advantage to balancing on a dimension more than
 once.  You should normally only list dimensions where you expect there
 to be a density variation in the particles.
@@ -224,8 +228,8 @@ to be a density variation in the particles.
 Balancing proceeds by adjusting the cutting planes in each of the
 dimensions listed in *dimstr*, one dimension at a time.  For a single
 dimension, the balancing operation (described below) is iterated on up
-to *Niter* times.  After each dimension finishes, the imbalance factor
+to :math:`N_\text{iter}` times.  After each dimension finishes, the imbalance
-is re-computed, and the balancing operation halts if the *stopthresh*
+factor is re-computed, and the balancing operation halts if the *stopthresh*
 criterion is met.
 
 A re-balance operation in a single dimension is performed using a
@@ -265,15 +269,15 @@ the normal reneighboring procedure.
    by the extent of a processor's sub-domain in one dimension.  The size
    of this bracketing region shrinks based on the local density, as
    described above, which should typically be 1/2 or more every
-   iteration.  Thus if *Niter* is specified as 10, the cutting plane will
+   iteration.  Thus if :math:`N_\text{iter}` is specified as 10, the cutting
-   typically be positioned to better than 1 part in 1000 accuracy
+   plane will typically be positioned to better than 1 part in 1000 accuracy
-   (relative to the perfect target position).  For *Niter* = 20, it will
+   (relative to the perfect target position).  For :math:`N_\text{iter} = 20`,
-   be accurate to better than 1 part in a million.  Thus there is no need
+   it will be accurate to better than 1 part in a million.  Thus there is no
-   to set *Niter* to a large value.  This is especially true if you are
+   need to set :math:`N_\text{iter}` to a large value.  This is especially true
-   re-balancing often enough that each time you expect only an incremental
+   if you are re-balancing often enough that each time you expect only an
-   adjustment in the cutting planes is necessary.  LAMMPS will check if
+   incremental adjustment in the cutting planes is necessary.  LAMMPS will
-   the threshold accuracy is reached (in a dimension) is less iterations
+   check if the threshold accuracy is reached (in a dimension) is less
-   than *Niter* and exit early.
+   iterations than :math:`N_\text{iter}` and exit early.
 
 ----------
 
@@ -281,12 +285,12 @@ The *rcb* style invokes a "tiled" method for balancing, as described
 above.  It performs a recursive coordinate bisectioning (RCB) of the
 simulation domain. The basic idea is as follows.
 
-The simulation domain is cut into 2 boxes by an axis-aligned cut in
+The simulation domain is cut into two boxes by an axis-aligned cut in
 the longest dimension, leaving one new box on either side of the cut.
-All the processors are also partitioned into 2 groups, half assigned
+All the processors are also partitioned into two groups, half assigned
 to the box on the lower side of the cut, and half to the box on the
-upper side.  (If the processor count is odd, one side gets an extra
+upper side.  If the processor count is odd, one side gets an extra
-processor.)  The cut is positioned so that the number of atoms in the
+processor.  The cut is positioned so that the number of atoms in the
 lower box is exactly the number that the processors assigned to that
 box should own for load balance to be perfect.  This also makes load
 balance for the upper box perfect.  The positioning is done
@@ -309,7 +313,7 @@ results of each re-balancing operation.  The file contains the bounds
 of the sub-domain for each processor after the balancing operation
 completes.  The format of the file is compatible with the
 `Pizza.py <pizza_>`_ *mdump* tool which has support for manipulating and
-visualizing mesh files.  An example is shown here for a balancing by 4
+visualizing mesh files.  An example is shown here for a balancing by four
 processors for a 2d problem:
 
 .. parsed-literal::
@@ -349,27 +353,28 @@ processors for a 2d problem:
    3 1 9 10 11 12
    4 1 13 14 15 16
 
-The coordinates of all the vertices are listed in the NODES section, 5
+The coordinates of all the vertices are listed in the NODES section, five
-per processor.  Note that the 4 sub-domains share vertices, so there
+per processor.  Note that the four sub-domains share vertices, so there
 will be duplicate nodes in the list.
 
-The "SQUARES" section lists the node IDs of the 4 vertices in a
+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 with 8 vertices listed for
+For a 3d problem, the syntax is similar but with eight vertices listed for
-each processor, instead of 4, and "SQUARES" replaced by "CUBES".
+each processor instead of four, and "SQUARES" replaced by "CUBES."
 
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to
-are relevant to this fix.
+:doc:`binary restart files <restart>`.  None of the
+:doc:`fix_modify <fix_modify>` options are relevant to this fix.
 
 This fix computes a global scalar which is the imbalance factor
 after the most recent re-balance and a global vector of length 3 with
-additional information about the most recent re-balancing.  The 3
+additional information about the most recent re-balancing.  The three
 values in the vector are as follows:
 
 * 1 = max # of particles per processor
@@ -380,22 +385,24 @@ As explained above, the imbalance factor is the ratio of the maximum
 number of particles (or total weight) on any processor to the average
 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
+These quantities can be accessed by various
-by this fix are "intensive".
+:doc:`output commands <Howto_output>`.  The scalar and vector values calculated
+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:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 ----------
 
 Restrictions
 """"""""""""
 
-For 2d simulations, the *z* style cannot be used.  Nor can a "z"
+For 2d simulations, the *z* style cannot be used, nor can *z*
 appear in *dimstr* for the *shift* style.
 
 Balancing through recursive bisectioning (\ *rcb* style) requires
-:doc:`comm_style tiled <comm_style>`
+:doc:`comm_style tiled <comm_style>`\ .
 
 Related commands
 """"""""""""""""

doc/src/fix_mdi_qm.rst

@@ -125,13 +125,14 @@ LAMMPS atom type corresponds to.  This is specified by the atomic
 number of the element, e.g. 13 for Al.  An atomic number must be
 specified for each of the ntypes LAMMPS atom types.  Ntypes is
 typically specified via the create_box command or in the data file
-read by the read_data command.  If this keyword is not specified, then
+read by the read_data command.
-this fix will send the LAMMPS atom type for each atom to the MDI
+
-engine.  If both the LAMMPS driver and the MDI engine are initialized
+If this keyword is specified, then this fix will send the MDI
-so that atom type values are consistent in both codes, then the
+">ELEMENTS" command to the engine, to insure the two codes are
-*elements* keyword is not needed.  Otherwise the keyword can be used
+consistent in their definition of atomic species.  If this keyword is
-to insure the two codes are consistent in their definition of atomic
+not specified, then this fix will send the MDI >TYPES command to the
-species.
+engine.  This is fine if both the LAMMPS driver and the MDI engine are
+initialized so that the atom type values are consistent in both codes.
 
 ----------
 

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/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 labelmap and thus discards all previous
+settings.
+
+The *write* option takes a filename as argument and writes the current
+label mappings to a file as 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.
+
+Labelmaps 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/mdi.rst

@@ -14,7 +14,7 @@ Syntax
 
   .. parsed-literal::
 
-     *engine* args = zero or more keyword arg pairs
+     *engine* args = zero or more keyword/args pairs
        keywords = *elements*
          *elements* args = N_1 N_2 ... N_ntypes
            N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
@@ -24,7 +24,7 @@ Syntax
        keywords = *mdi* or *infile* or *extra* or *command*
          *mdi* value = args passed to MDI for driver to operate with plugins (required)
          *infile* value = filename the engine will read at start-up (optional)
-         *extra* value = aditional command-line args to pass to engine library when loaded
+         *extra* value = aditional command-line args to pass to engine library when loaded (optional)
          *command* value = a LAMMPS input script command to execute (required)
      *connect* args = none
      *exit* args = none
@@ -289,11 +289,11 @@ are required.  The -name setting can be anything you choose.  MDI
 drivers and engines can query their names to verify they are values
 they expect.
 
-The *infile* keyword is also required.  It is the name of an input
+The *infile* keyword is optional.  It sets the name of an input script
-script which the engine will open and process.  MDI will pass it as a
+which the engine will open and process.  MDI will pass it as a
 command-line argument to the library when it is launched.  The file
 typically contains settings that an MD or QM code will use for its
-subsequent calculations.
+calculations.
 
 The *extra* keyword is optional.  It contains additional command-line
 arguments which MDI will pass to the library when it is launched.
@@ -309,12 +309,12 @@ could specify a filename with multiple LAMMPS commands.
 
 .. note::
 
-   When the single *command* is complete, LAMMPS will send an MDI
+   When the *command* is complete, LAMMPS will send an MDI EXIT
-   EXIT command to the plugin engine and the plugin will be removed.
+   command to the plugin engine and the plugin will be removed.  The
-   The "mdi plugin" command will then exit and the next command
+   "mdi plugin" command will then exit and the next command (if any)
-   (if any) in the LAMMPS input script will be processed.  A subsequent
+   in the LAMMPS input script will be processed.  A subsequent "mdi
-   "mdi plugin" command could then load the same library plugin or
+   plugin" command could then load the same or a different MDI
-   a different one if desired.
+   plugin if desired.
 
 ----------
 

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.

doc/src/pair_coeff.rst

@@ -10,7 +10,7 @@ Syntax
 
    pair_coeff I J args
 
-* I,J = atom types (see asterisk form below)
+* I,J = numeric atom types (see asterisk form below), or type labels
 * args = coefficients for one or more pairs of atom types
 
 Examples
@@ -26,6 +26,10 @@ Examples
    pair_coeff * 3 morse.table ENTRY1
    pair_coeff 1 2 lj/cut 1.0 1.0 2.5 # (for pair_style hybrid)
 
+   labelmap atom 1 C
+   labelmap atom 2 H
+   pair_coeff C H 1.0 1.0 2.5
+
 Description
 """""""""""
 
@@ -34,20 +38,27 @@ atom types.  The number and meaning of the coefficients depends on the
 pair style.  Pair coefficients can also be set in the data file read
 by the :doc:`read_data <read_data>` command or in a restart file.
 
-I and J can be specified in one of two ways.  Explicit numeric values
+I and J can be specified in one of several ways.  Explicit numeric
-can be used for each, as in the first example above.  I <= J is
+values can be used for each, as in the first example above.  Or, one
-required.  LAMMPS sets the coefficients for the symmetric J,I
+or both of the types in the I,J pair can be a type label, which is an
-interaction to the same values.
+alphanumeric string defined by the :doc:`labelmap <labelmap>` command
+or in a section of a data file read by the :doc:`read_data
+<read_data>` command, and which converts internally to a numeric type.
+Internally, LAMMPS will set coefficients for the symmetric J,I
+interaction to the same values as the I,J interaction.
 
-A wildcard asterisk can be used in place of or in conjunction with the
+For numeric values only, a wildcard asterisk can be used in place of or
-I,J arguments to set the coefficients for multiple pairs of atom
+in conjunction with the I,J arguments to set the coefficients for
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+multiple pairs of atom types.  This takes the form "\*" or "\*n" or
-number of atom types, then an asterisk with no numeric values means all
+"n\*" or "m\*n".  If :math:`N` is the number of atom types, then an
-types from 1 to N.  A leading asterisk means all types from 1 to n
+asterisk with no numeric values means all types from 1 to :math:`N`.  A
-(inclusive).  A trailing asterisk means all types from n to N
+leading asterisk means all types from 1 to n (inclusive).  A trailing
-(inclusive).  A middle asterisk means all types from m to n
+asterisk means all types from n to :math:`N` (inclusive).  A middle
-(inclusive).  Note that only type pairs with I <= J are considered; if
+asterisk means all types from m to n (inclusive).  For the asterisk
-asterisks imply type pairs where J < I, they are ignored.
+syntax, only type pairs with I <= J are considered; if asterisks imply
+type pairs where J < I, they are ignored. Again internally, LAMMPS will
+set the coefficients for the symmetric J,I interactions to the same
+values as the I <= J interactions.
 
 Note that a pair_coeff command can override a previous setting for the
 same I,J pair.  For example, these commands set the coeffs for all I,J
@@ -63,11 +74,11 @@ same format as the arguments of the pair_coeff command in an input
 script, with the exception of the I,J type arguments.  In each line of
 the "Pair Coeffs" section of a data file, only a single type I is
 specified, which sets the coefficients for type I interacting with
-type I.  This is because the section has exactly N lines, where N =
+type I.  This is because the section has exactly :math:`N` lines, where
-the number of atom types.  For this reason, the wild-card asterisk
+:math:`N` is the number of atom types.  For this reason, the wild-card
-should also not be used as part of the I argument.  Thus in a data
+asterisk should also not be used as part of the I argument.  Thus in a
-file, the line corresponding to the first example above would be listed
+data file, the line corresponding to the first example above would be
-as
+listed as
 
 .. parsed-literal::
 

doc/src/pair_dipole.rst

@@ -249,7 +249,7 @@ Style *lj/long/dipole/long* has the same functionality as style
 *lj/cut/dipole/long*, except it also has an option to compute 12/6
 Lennard-Jones interactions for use with a long-range dispersion kspace
 style.  This is done by setting its *flag_lj* argument to *long*.  For
-long-range LJ interactions, the doc:`kspace_style ewald/disp
+long-range LJ interactions, the :doc:`kspace_style ewald/disp
 <kspace_style>` command must be used.
 
 ----------

doc/src/pair_harmonic_cut.rst

@@ -33,7 +33,8 @@ Style *harmonic/cut* computes pairwise repulsive-only harmonic interactions with
 
    E = k (r_c - r)^2  \qquad r < r_c
 
-:math:`r_c` is the cutoff.
+where :math:`r_c` is the cutoff.  Note that the usual 1/2 factor is
+included in :math:`k`.
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -41,7 +42,7 @@ above, or in the data file or restart files read by the
 :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands:
 
-* :math:`k` (energy units)
+* :math:`k` (energy/distance^2 units)
 * :math:`r_c` (distance units)
 
 ----------

doc/src/pair_mesocnt.rst

@@ -1,68 +1,153 @@
 .. index:: pair_style mesocnt
+.. index:: pair_style mesocnt/viscous
 
 pair_style mesocnt command
 ==========================
 
+pair_style mesocnt/viscous command
+==================================
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   pair_style mesocnt
+   pair_style style neigh_cutoff mode neigh_mode
+
+* style = *mesocnt* or *mesocnt/viscous*
+* neigh_cutoff = neighbor list cutoff (distance units)
+* mode = *chain* or *segment* (optional)
+* neigh_mode = *id* or *topology* (optional)
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   pair_style mesocnt
+   pair_style mesocnt 30.0
-   pair_coeff * * 10_10.cnt
+   pair_coeff * * C_10_10.mesocnt 2
+
+   pair_style mesocnt/viscous 60.0 chain topology
+   pair_coeff * * C_10_10.mesocnt 0.001 20.0 0.2 2 4
 
 Description
 """""""""""
 
-Style *mesocnt* implements a mesoscopic potential
+Style *mesocnt* implements a mesoscopic potential for the interaction
-for the interaction of carbon nanotubes (CNTs). In this potential,
+of carbon nanotubes (CNTs), or other quasi-1D objects such as other
-CNTs are modelled as chains of cylindrical segments in which
+kinds of nanotubes or nanowires. In this potential, CNTs are modelled
-each infinitesimal surface element interacts with all other
+as chains of cylindrical segments in which each infinitesimal surface
-CNT surface elements with the Lennard-Jones (LJ) term adopted from
+element interacts with all other CNT surface elements with the
-the :doc:`airebo <pair_airebo>` style. The interaction energy
+Lennard-Jones (LJ) term adopted from the :doc:`airebo <pair_airebo>`
-is then computed by integrating over the surfaces of all interacting
+style. The interaction energy is then computed by integrating over the
-CNTs.
+surfaces of all interacting CNTs.
 
-The potential is based on interactions between one cylindrical
+In LAMMPS, cylindrical segments are represented by bonds. Each segment
-segment and infinitely or semi-infinitely long CNTs as described
+is defined by its two end points ("nodes") which correspond to atoms
-in :ref:`(Volkov1) <Volkov1>`. Chains of segments are
+in LAMMPS. For the exact functional form of the potential and
-converted to these (semi-)infinite CNTs bases on an approximate
+implementation details, the reader is referred to the original papers
-chain approach outlined in :ref:`(Volkov2) <Volkov2>`.
+:ref:`(Volkov1) <Volkov1>` and :ref:`(Volkov2) <Volkov2>`.
-This allows to simplify the computation of the interactions
-significantly and reduces the computational times to the
-same order of magnitude as for regular bead spring models
-where beads interact with the standard :doc:`pair_lj/cut <pair_lj>`
-potential.
 
-In LAMMPS, cylindrical segments are represented by bonds. Each
+.. versionchanged:: TBD
-segment is defined by its two end points ("nodes") which correspond
-to atoms in LAMMPS. For the exact functional form of the potential
-and implementation details, the reader is referred to the
-original papers :ref:`(Volkov1) <Volkov1>` and
-:ref:`(Volkov2) <Volkov2>`.
 
-The potential requires tabulated data provided in a single ASCII
+The potential supports two modes, *segment* and *chain*. By default,
-text file specified in the :doc:`pair_coeff <pair_coeff>` command.
+*chain* mode is enabled.  In *segment* mode, interactions are
-The first line of the file provides a time stamp and
+pair-wise between all neighboring segments based on a segment-segment
-general information. The second line lists four integers giving
+approach (keyword *segment* in pair_style command).  In *chain* mode,
-the number of data points provided in the subsequent four
+interactions are calculated between each segment and infinitely or
-data tables. The third line lists four floating point numbers:
+semi-infinitely long CNTs as described in :ref:`(Volkov1) <Volkov1>`.
-the CNT radius R, the LJ parameter sigma and two numerical
+Chains of segments are converted to these (semi-)infinite CNTs bases
-parameters delta1 and delta2. These four parameters are given
+on an approximate chain approach outlined in :ref:`(Volkov2)
-in Angstroms. This is followed by four data tables each separated
+<Volkov2>`. Hence, interactions are calculated on a segment-chain
-by a single empty line. The first two tables have two columns
+basis (keyword *chain* in the pair_style command).  Using *chain* mode
-and list the parameters uInfParallel and Gamma respectively.
+allows to simplify the computation of the interactions significantly
-The last two tables have three columns giving data on a quadratic
+and reduces the computational times to the same order of magnitude as
-array and list the parameters Phi and uSemiParallel respectively.
+for regular bead spring models where beads interact with the standard
-uInfParallel and uSemiParallel are given in eV/Angstrom, Phi is
+:doc:`pair_lj/cut <pair_lj>` potential. However, this method is only
-given in eV and Gamma is unitless.
+valid when the curvature of the CNTs in the system is small.  When
+CNTs are buckled (see :doc:`angle_mesocnt <angle_mesocnt>`), local
+curvature can be very high and the pair_style automatically switches
+to *segment* mode for interactions involving buckled CNTs.
+
+The potential further implements two different neighbor list
+construction modes. Mode *id* uses atom and mol IDs to construct
+neighbor lists while *topology* modes uses only the bond topology of
+the system. While *id* mode requires bonded atoms to have consecutive
+LAMMPS atom IDs and atoms in different CNTs to have different LAMMPS
+molecule IDs, *topology* mode has no such requirement. Using *id* mode
+is faster and is enabled by default.
+
+.. note::
+
+  Neighbor *id* mode requires all CNTs in the system to have distinct
+  LAMMPS molecule IDs and bonded atoms to have consecutive LAMMPS atom
+  IDs. If this is not possible (e.g. in simulations of CNT rings),
+  *topology* mode needs to be enabled in the pair_style command.
+
+.. versionadded:: TBD
+
+In addition to the LJ interactions described above, style
+*mesocnt/viscous* explicitly models friction between neighboring
+segments. Friction forces are a function of the relative velocity
+between a segment and its neighboring approximate chain (even in
+*segment* mode) and only act along the axes of the interacting segment
+and chain. In this potential, friction forces acting per unit length
+of a nanotube segment are modelled as a shifted logistic function:
+
+.. math::
+
+   F^{\text{FRICTION}}(v) / L = \frac{F^{\text{max}}}{1 +
+   \exp(-k(v-v_0))} - \frac{F^{\text{max}}}{1 + \exp(k v_0)}
+
+----------
+
+In the pair_style command, the modes described above can be toggled
+using the *segment* or *chain* keywords.  The neighbor list cutoff
+defines the cutoff within which atoms are included in the neighbor
+list for constructing neighboring CNT chains.  This is different from
+the potential cutoff, which is directly calculated from parameters
+specified in the potential file. We recommend using a neighbor list
+cutoff of at least 3 times the maximum segment length used in the
+simulation to ensure proper neighbor chain construction.
+
+.. note::
+
+   CNT ends are treated differently by all *mesocnt* styles. Atoms on
+   CNT ends need to be assigned different LAMMPS atom types than atoms
+   not on CNT ends.
+
+Style *mesocnt* requires tabulated data provided in a single ASCII
+text file, as well as a list of integers corresponding to all LAMMPS
+atom types representing CNT ends:
+
+* filename
+* :math:`N` CNT end atom types
+
+For example, if your LAMMPS simulation of (10, 10) nanotubes has 4
+atom types where atom types 1 and 3 are assigned to 'inner' nodes and
+atom types 2 and 4 are assigned to CNT end nodes, the pair_coeff
+command would be:
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * C_10_10.mesocnt 2 4
+
+Likewise, style *mesocnt/viscous* also requires the same information
+as style *mesocnt*, with the addition of 3 parameters for the viscous
+friction forces as listed above:
+
+* filename
+* :math:`F^{\text{max}}`
+* :math:`k`
+* :math:`v_0`
+* :math:`N` CNT end atom types
+
+Using the same example system as with style *mesocnt* with the
+addition of friction, the pair_coeff command is:
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * C_10_10.mesocnt 0.03 20.0 0.20 2 4
 
 Potential files for CNTs can be readily generated using the freely
 available code provided on
@@ -71,45 +156,51 @@ available code provided on
 
    https://github.com/phankl/cntpot
 
-Using the same approach, it should also be possible to
+Using the same approach, it should also be possible to generate
-generate potential files for other 1D systems such as
+potential files for other 1D systems mentioned above.
-boron nitride nanotubes.
 
 .. note::
 
-   Because of their size, *mesocnt* style potential files
+   Because of their size, *mesocnt* style potential files are not
-   are not bundled with LAMMPS.   When compiling LAMMPS from
+   bundled with LAMMPS.  When compiling LAMMPS from source code, the
-   source code, the file ``C_10_10.mesocnt`` should be downloaded
+   file ``C_10_10.mesocnt`` should be downloaded separately from
-   transparently from `https://download.lammps.org/potentials/C_10_10.mesocnt <https://download.lammps.org/potentials/C_10_10.mesocnt>`_
+   `https://download.lammps.org/potentials/C_10_10.mesocnt
-   This file has as number of data points per table 1001.
+   <https://download.lammps.org/potentials/C_10_10.mesocnt>`_
-   This is sufficient for NVT simulations. For proper energy
-   conservation, we recommend using a potential file where
-   the resolution for Phi is at least 2001 data points.
 
-.. note::
+   The first line of the potential file provides a time stamp and
+   general information. The second line lists four integers giving the
+   number of data points provided in the subsequent four data
+   tables. The third line lists four floating point numbers: the CNT
+   radius R, the LJ parameter sigma and two numerical parameters
+   delta1 and delta2. These four parameters are given in
+   Angstroms. This is followed by four data tables each separated by a
+   single empty line. The first two tables have two columns and list
+   the parameters uInfParallel and Gamma respectively.  The last two
+   tables have three columns giving data on a quadratic array and list
+   the parameters Phi and uSemiParallel respectively.  uInfParallel
+   and uSemiParallel are given in eV/Angstrom, Phi is given in eV and
+   Gamma is unitless.
 
-   The *mesocnt* style requires CNTs to be represented
+   If a simulation produces many warnings about segment-chain
-   as a chain of atoms connected by bonds. Atoms need
+   interactions falling outside the interpolation range, we recommend
-   to be numbered consecutively within one chain.
+   generating a potential file with lower values of delta1 and delta2.
-   Atoms belonging to different CNTs need to be assigned
-   different molecule IDs.
 
 ----------
 
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This pair style does not support mixing.
+These pair styles does not support mixing.
 
-This pair style does not support the :doc:`pair_modify <pair_modify>`
+These pair styles does not support the :doc:`pair_modify
-shift, table, and tail options.
+<pair_modify>` shift, table, and tail options.
 
-The *mesocnt* pair style do not write their information to :doc:`binary restart files <restart>`,
+These pair styles do not write their information to :doc:`binary
-since it is stored in tabulated potential files.
+restart files <restart>`, since it is stored in tabulated potential
-Thus, you need to re-specify the pair_style and pair_coeff commands in
+files.  Thus, you need to re-specify the pair_style and pair_coeff
-an input script that reads a restart file.
+commands in an input script that reads a restart file.
 
-This pair style can only be used via the *pair* keyword of the
+These pair styles can only be used via the *pair* keyword of the
 :doc:`run_style respa <run_style>` command.  They do not support the
 *inner*, *middle*, *outer* keywords.
 
@@ -118,12 +209,21 @@ This pair style can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-This style is part of the MESONT package.  It is only
+These styles are part of the MESONT package.  They are only enabled if
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
-This pair potential requires the :doc:`newton <newton>` setting to be
+These pair styles require the :doc:`newton <newton>` setting to be
 "on" for pair interactions.
 
+These pair styles require all 3 :doc:`special_bonds lj
+<special_bonds>` settings to be non-zero for proper neighbor list
+construction.
+
+Pair style *mesocnt/viscous* requires you to use the :doc:`comm_modify
+vel yes <comm_modify>` command so that velocities are stored by ghost
+atoms.
+
 Related commands
 """"""""""""""""
 
@@ -132,7 +232,7 @@ Related commands
 Default
 """""""
 
-none
+mode = chain, neigh_mode = id
 
 ----------
 

doc/src/pair_style.rst

@@ -81,12 +81,12 @@ only the global settings in that command are reset.  Any previous
 doc:`pair_coeff <pair_coeff>` and :doc:`pair_modify <pair_modify>`
 command settings are preserved.  The only exception is that if the
 global cutoff in the pair_style command is changed, it will override
-the corresponding cutoff in any of the previous doc:`pair_modify
+the corresponding cutoff in any of the previous :doc:`pair_modify
 <pair_coeff>` commands.
 
 Two pair styles which do not follow this rule are the pair_style
 *table* and *hybrid* commands.  A new pair_style command for these
-styles will wipe out all previously specified doc:`pair_coeff
+styles will wipe out all previously specified :doc:`pair_coeff
 <pair_coeff>` and :doc:`pair_modify <pair_modify>` settings, including
 for the sub-styles of the *hybrid* command.
 
@@ -278,7 +278,8 @@ accelerated styles exist.
 * :doc:`meam <pair_meam>` - modified embedded atom method (MEAM) in C
 * :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
 * :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
-* :doc:`mesocnt <pair_mesocnt>` - mesoscale model for (carbon) nanotubes
+* :doc:`mesocnt <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes
+* :doc:`mesocnt/viscous <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes with friction
 * :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
 * :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
 * :doc:`mie/cut <pair_mie>` - Mie potential

doc/src/read_data.rst

@@ -164,6 +164,12 @@ other types already exist.  All five offset values must be specified,
 but individual values will be ignored if the data file 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 *shift* keyword can be used to specify an (Sx, Sy, Sz)
 displacement applied to the coordinates of each atom.  Sz must be 0.0
 for a 2d simulation.  This is a mechanism for adding structured
@@ -227,22 +233,27 @@ The file will be read line by line, but there is a limit of 254
 characters per line and characters beyond that limit will be ignored.
 
 A data file has a header and a body.  The header appears first.  The
-first line of the header is always skipped; it typically contains a
+first line of the header and thus of the data file is *always* skipped;
-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
-can have a trailing comment starting with '#' that is ignored.  If the
+software that created the file.
-line is blank (only white-space after comment is 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
-keyword, the line begins the body of the file.
 
-The body of the file contains zero or more sections.  The first line
+Then lines are read one line at a time.  Lines can have a trailing
-of a section has only a keyword.  This line can have a trailing
+comment starting with '#' that is ignored.  There *must* be at least one
-comment starting with '#' that is either ignored or can be used to
+blank between any valid content and the comment. If a line is blank
-check for a style match, as described below.  The next line is
+(i.e. contains only white-space after comments are deleted), it is
-skipped.  The remaining lines of the section contain values.  The
+skipped.  If the line contains a header keyword, the corresponding
-number of lines depends on the section keyword as described below.
+value(s) is/are read from the line.  A line that is *not* blank and does
-Zero or more blank lines can be used between sections.  Sections can
+*not* contain a header keyword begins the body of the file.
-appear in any order, with a few exceptions as noted below.
+
+The body of the file contains zero or more sections.  The first line of
+a section has only a keyword.  This line can have a trailing comment
+starting with '#' that is either ignored or can be used to check for a
+style match, as described below.  There must be a blank between the
+keyword and any comment. The *next* line is *always* skipped.  The
+remaining lines of the section contain values.  The number of lines
+depends on the section keyword as described below.  Zero or more blank
+lines can be used *between* sections.  Sections can appear in any order,
+with a few exceptions as noted below.
 
 The keyword *fix* can be used one or more times.  Each usage specifies
 a fix that will be used to process a specific portion of the data
@@ -477,6 +488,7 @@ These are the section keywords for the body of the file.
 
 * *Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies* = atom-property sections
 * *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
+* *Atom Type Labels, Bond Type Labels, Angle Type Labels, Dihedral Type Labels, Improper Type Labels* = type label maps
 * *Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs,    Improper Coeffs* = force field sections
 * *BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs,    EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs,    BondBond13 Coeffs, AngleAngle Coeffs* = class 2 force field sections
 
@@ -503,7 +515,8 @@ section is described including the number of lines it must contain and
 rules (if any) for where it can appear in the data file.
 
 Any individual line in the various sections can have a trailing
-comment starting with "#" for annotation purposes.  E.g. in the
+comment starting with "#" for annotation purposes. There must be at least
+one blank between valid content and the comment. E.g. in the
 Atoms section:
 
 .. parsed-literal::
@@ -536,6 +549,26 @@ input script.
 
 ----------
 
+*Angle Type Labels* section:
+
+* one line per angle type
+* line syntax: ID label
+
+  .. parsed-literal::
+
+       ID = angle type (1-N)
+       label = alphanumeric type label
+
+Define alphanumeric type labels for each numeric angle type.  These
+can be used in the Angles section in place of a numeric type, but only
+if the this section appears before the Angles section.
+
+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.
+
+----------
+
 *AngleAngle Coeffs* section:
 
 * one line per improper type
@@ -568,7 +601,7 @@ input script.
   .. parsed-literal::
 
        ID = number of angle (1-Nangles)
-       type = angle type (1-Nangletype)
+       type = angle type (1-Nangletype, or type label)
        atom1,atom2,atom3 = IDs of 1st,2nd,3rd atom in angle
 
 example:
@@ -580,8 +613,15 @@ example:
 The 3 atoms are ordered linearly within the angle.  Thus the central
 atom (around which the angle is computed) is the atom2 in the list.
 E.g. H,O,H for a water molecule.  The *Angles* section must appear
-after the *Atoms* section.  All values in this section must be
+after the *Atoms* section.
-integers (1, not 1.0).
+
+All values in this section must be integers (1, not 1.0).  However,
+the type can be a numeric value or an alphanumeric label.  The latter
+is only allowed if the type label has been defined by the
+:doc:`labelmap <labelmap>` command or an Angle Type Labels section
+earlier in the data file.  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.
 
 ----------
 
@@ -597,6 +637,26 @@ integers (1, not 1.0).
 
 ----------
 
+*Atom Type Labels* section:
+
+* one line per atom type
+* line syntax: ID label
+
+  .. parsed-literal::
+
+       ID = numeric atom type (1-N)
+       label = alphanumeric type label
+
+Define alphanumeric type labels for each numeric atom type.  These
+can be used in the Atoms section in place of a numeric type, but only
+if the Atom Type Labels section appears before the Atoms section.
+
+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.
+
+----------
+
 *Atoms* section:
 
 * one line per atom
@@ -670,7 +730,7 @@ of analysis.
 The per-atom values have these meanings and units, listed alphabetically:
 
 * atom-ID = integer ID of atom
-* atom-type = type of atom (1-Ntype)
+* atom-type = type of atom (1-Ntype, or type label)
 * bodyflag = 1 for body particles, 0 for point particles
 * bond_nt = bond NT factor for MESONT particles (?? units)
 * buckling = buckling factor for MESONT particles (?? units)
@@ -722,6 +782,13 @@ not used (e.g. an atomic system with no bonds), and you don't care if
 unique atom IDs appear in dump files, then the atom-IDs can all be set
 to 0.
 
+The atom-type can be a numeric value or an alphanumeric label.  The
+latter is only allowed if the type label has been defined by the
+:doc:`labelmap <labelmap>` command or an Atom Type Labels section
+earlier in the data file.  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.
+
 The molecule ID is a second identifier attached to an atom.  Normally, it
 is a number from 1 to N, identifying which molecule the atom belongs
 to.  It can be 0 if it is a non-bonded atom or if you don't care to
@@ -932,6 +999,26 @@ script.
 
 ----------
 
+*Bond Type Labels* section:
+
+* one line per bond type
+* line syntax: ID label
+
+  .. parsed-literal::
+
+       ID = bond type (1-N)
+       label = alphanumeric type label
+
+Define alphanumeric type labels for each numeric bond type.  These can
+be used in the Bonds section in place of a numeric type, but only if
+the this section appears before the Angles section.
+
+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.
+
+----------
+
 *BondAngle Coeffs* section:
 
 * one line per angle type
@@ -976,7 +1063,7 @@ script.
   .. parsed-literal::
 
        ID = bond number (1-Nbonds)
-       type = bond type (1-Nbondtype)
+       type = bond type (1-Nbondtype, or type label)
        atom1,atom2 = IDs of 1st,2nd atom in bond
 
 * example:
@@ -985,8 +1072,15 @@ script.
 
        12 3 17 29
 
-The *Bonds* section must appear after the *Atoms* section.  All values
+The *Bonds* section must appear after the *Atoms* section.
-in this section must be integers (1, not 1.0).
+
+All values in this section must be integers (1, not 1.0).  However,
+the type can be a numeric value or an alphanumeric label.  The latter
+is only allowed if the type label has been defined by the
+:doc:`labelmap <labelmap>` command or a Bond Type Labels section
+earlier in the data file.  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.
 
 ----------
 
@@ -1014,6 +1108,26 @@ Coefficients can also be set via the
 
 ----------
 
+*Dihedral Type Labels* section:
+
+* one line per dihedral type
+* line syntax: ID label
+
+  .. parsed-literal::
+
+       ID = dihedral type (1-N)
+       label = alphanumeric type label
+
+Define alphanumeric type labels for each numeric dihedral type.  These
+can be used in the Dihedrals section in place of a numeric type, but
+only if the this section appears before the Dihedrals section.
+
+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.
+
+----------
+
 *Dihedrals* section:
 
 * one line per dihedral
@@ -1022,7 +1136,7 @@ Coefficients can also be set via the
   .. parsed-literal::
 
        ID = number of dihedral (1-Ndihedrals)
-       type = dihedral type (1-Ndihedraltype)
+       type = dihedral type (1-Ndihedraltype, or type label)
        atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in dihedral
 
 * example:
@@ -1032,8 +1146,15 @@ Coefficients can also be set via the
        12 4 17 29 30 21
 
 The 4 atoms are ordered linearly within the dihedral.  The *Dihedrals*
-section must appear after the *Atoms* section.  All values in this
+section must appear after the *Atoms* section.
-section must be integers (1, not 1.0).
+
+All values in this section must be integers (1, not 1.0).  However,
+the type can be a numeric value or an alphanumeric label.  The latter
+is only allowed if the type label has been defined by the
+:doc:`labelmap <labelmap>` command or a Dihedral Type Labels section
+earlier in the data file.  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.
 
 ----------
 
@@ -1115,6 +1236,26 @@ Coefficients can also be set via the
 
 ----------
 
+*Improper Type Labels* section:
+
+* one line per improper type
+* line syntax: ID label
+
+  .. parsed-literal::
+
+       ID = improper type (1-N)
+       label = alphanumeric type label
+
+Define alphanumeric type labels for each numeric improper type.  These
+can be used in the Impropers section in place of a numeric type, but
+only if the this section appears before the Impropers section.
+
+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.
+
+----------
+
 *Impropers* section:
 
 * one line per improper
@@ -1123,7 +1264,7 @@ Coefficients can also be set via the
   .. parsed-literal::
 
        ID = number of improper (1-Nimpropers)
-       type = improper type (1-Nimpropertype)
+       type = improper type (1-Nimpropertype, or type label)
        atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in improper
 
 * example:
@@ -1133,11 +1274,19 @@ Coefficients can also be set via the
        12 3 17 29 13 100
 
 The ordering of the 4 atoms determines the definition of the improper
-angle used in the formula for each :doc:`improper style <improper_style>`.  See the doc pages for individual styles
+angle used in the formula for each :doc:`improper style
-for details.
+<improper_style>`.  See the doc pages for individual styles for
+details.
 
-The *Impropers* section must appear after the *Atoms* section.  All
+The *Impropers* section must appear after the *Atoms* section.
-values in this section must be integers (1, not 1.0).
+
+All values in this section must be integers (1, not 1.0).  However,
+the type can be a numeric value or an alphanumeric label.  The latter
+is only allowed if the type label has been defined by the
+:doc:`labelmap <labelmap>` command or a Improper Type Labels section
+earlier in the data file.  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.
 
 ----------
 
@@ -1181,7 +1330,7 @@ The *Lines* section must appear after the *Atoms* section.
 
   .. parsed-literal::
 
-       ID = atom type (1-N)
+       ID = atom type (1-N or atom type label)
        mass = mass value
 
 * example:
@@ -1195,6 +1344,13 @@ This defines the mass of each atom type.  This can also be set via the
 used for atom styles that define a mass for individual atoms -
 e.g. :doc:`atom_style sphere <atom_style>`.
 
+Using type labels instead of atom type numbers is only allowed if the
+type label has been defined by the :doc:`labelmap <labelmap>` command or
+a Atom Type Labels section earlier in the data file.  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.
+
 ----------
 
 *MiddleBondTorsion Coeffs* section:
@@ -1363,11 +1519,14 @@ To read gzipped data files, you must compile LAMMPS with the
 -DLAMMPS_GZIP option.  See the :doc:`Build settings <Build_settings>`
 doc page for details.
 
+Labelmaps are currently not supported when using the KOKKOS package.
+
 Related commands
 """"""""""""""""
 
 :doc:`read_dump <read_dump>`, :doc:`read_restart <read_restart>`,
-:doc:`create_atoms <create_atoms>`, :doc:`write_data <write_data>`
+:doc:`create_atoms <create_atoms>`, :doc:`write_data <write_data>`,
+:doc:`labelmap <labelmap>`
 
 Default
 """""""

doc/src/restart.rst

@@ -12,7 +12,7 @@ Syntax
    restart N root keyword value ...
    restart N file1 file2 keyword value ...
 
-* N = write a restart file every this many timesteps
+* N = write a restart file on timesteps which are multipls of N
 * N can be a variable (see below)
 * root = filename to which timestep # is appended
 * file1,file2 = two full filenames, toggle between them when writing file
@@ -42,13 +42,14 @@ Description
 """""""""""
 
 Write out a binary restart file with the current state of the
-simulation every so many timesteps, in either or both of two modes, as
+simulation on timesteps which are a multiple of N.  A value of N = 0
-a run proceeds.  A value of 0 means do not write out any restart
+means do not write out any restart files, which is the default.
-files.  The two modes are as follows.  If one filename is specified, a
+Restart files are written in one (or both) of two modes as a run
-series of filenames will be created which include the timestep in the
+proceeds.  If one filename is specified, a series of filenames will be
-filename.  If two filenames are specified, only 2 restart files will
+created which include the timestep in the filename.  If two filenames
-be created, with those names.  LAMMPS will toggle between the 2 names
+are specified, only 2 restart files will be created, with those names.
-as it writes successive restart files.
+LAMMPS will toggle between the 2 names as it writes successive restart
+files.
 
 Note that you can specify the restart command twice, once with a
 single filename and once with two filenames.  This would allow you,

doc/src/variable.rst

@@ -66,7 +66,7 @@ Syntax
                            bound(group,dir,region), gyration(group,region), ke(group,reigon),
                            angmom(group,dim,region), torque(group,dim,region),
                            inertia(group,dimdim,region), omega(group,dim,region)
-         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name)
+         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label)
          feature functions = is_active(category,feature), is_available(category,feature), is_defined(category,id)
          atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
          atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
@@ -505,7 +505,7 @@ references, and references to other variables.
 +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Region functions   | count(ID,IDR), mass(ID,IDR), charge(ID,IDR),      xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR),      bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR),      angmom(ID,dim,IDR), torque(ID,dim,IDR),      inertia(ID,dimdim,IDR), omega(ID,dim,IDR)                                                                                                    |
 +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Special functions  | sum(x), min(x), max(x), ave(x), trap(x),      slope(x), gmask(x), rmask(x), grmask(x,y), next(x)                                                                                                                                                                                                                                                          |
+| Special functions  | sum(x), min(x), max(x), ave(x), trap(x),      slope(x), gmask(x), rmask(x), grmask(x,y), next(x),  label2type(kind,label)                                                                                                                                                                                                                                 |
 +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Atom values        | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i],              vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]                                                                                                                                                                                                                                            |
 +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -962,6 +962,12 @@ types, bond types and so on. For the full list of available keywords
 *name* and their meaning, see the documentation for extract_setting()
 via the link in this paragraph.
 
+The label2type() function converts type labels into numeric types, using label
+maps created by the :doc:`labelmap <labelmap>` or :doc:`read_data <read_data>`
+commands.  The first argument is the label map kind (atom, bond, angle,
+dihedral, or improper) and the second argument is the label.  The function
+returns the corresponding numeric type.
+
 ----------
 
 Feature Functions

doc/src/write_data.rst

@@ -12,12 +12,14 @@ Syntax
 
 * file = name of data file to write out
 * zero or more keyword/value pairs may be appended
-* keyword = *pair* or *nocoeff*
+* keyword = *pair* or *nocoeff* or *nofix* or *nolabelmap*
 
   .. parsed-literal::
 
        *nocoeff* = do not write out force field info
        *nofix* = do not write out extra sections read by fixes
+       *nolabelmap* = do not write out type labels
+       *types* value = *numeric* or *labels*
        *pair* value = *ii* or *ij*
          *ii* = write one line of pair coefficient info per atom type
          *ij* = write one line of pair coefficient info per IJ atom type pair
@@ -94,16 +96,39 @@ data file is read.
 
 ----------
 
-The *nocoeff* keyword requests that no force field parameters should
+Use of the *nocoeff* keyword means no force field parameters are
-be written to the data file. This can be very helpful, if one wants
+written to the data file. This can be helpful, for example, if you
-to make significant changes to the force field or if the parameters
+want to make significant changes to the force field or if the force
-are read in separately anyway, e.g. from an include file.
+field parameters are read in separately, e.g. from an include file.
 
-The *nofix* keyword requests that no extra sections read by fixes
+Use of the *nofix* keyword means no extra sections read by fixes are
-should be written to the data file (see the *fix* option of the
+written to the data file (see the *fix* option of the :doc:`read_data
-:doc:`read_data <read_data>` command for details). For example, this
+<read_data>` command for details). For example, this option excludes
-option excludes sections for user-created per-atom properties
+sections for user-created per-atom properties from :doc:`fix
-from :doc:`fix property/atom <fix_property_atom>`.
+property/atom <fix_property_atom>`.
+
+The *nolabelmap* and *types* keywords refer to type labels that may be
+defined for numeric atom types, bond types, angle types, etc.  The
+label map can be defined in two ways, 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.
+
+Use of the *nolabelmap* keyword means that even if type labels exist
+for a given type-kind (Atoms, Bonds, Angles, etc.), type labels are
+not written to the data file.  By default, they are written if they
+exist.  A type label must be defined for every numeric type (within a
+given type-kind) to be written to the data file.
+
+The *types* keyword determines how atom types, bond types, angle
+types, etc are written into these data file sections: Atoms, Bonds,
+Angles, etc.  The default is the *numeric* setting, even if type label
+maps exist.  If the *labels* setting is used, type labels will be
+written to the data file, if the corresponding label map exists.  Note
+that when using *types labels*, the *nolabelmap* keyword cannot be
+used.
 
 The *pair* keyword lets you specify in what format the pair
 coefficient information is written into the data file.  If the value
@@ -144,4 +169,4 @@ Related commands
 Default
 """""""
 
-The option defaults are pair = ii.
+The option defaults are pair = ii and types_style = numeric.

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -6,7 +6,7 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
 "clear", "comm_modify", "comm_style",
 "compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms",
 "delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
-"displace_atoms", "dump_modify", "dynamical_matrix", "echo",
+"displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else",
 "fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
 "improper_style", "include", "info", "jump", "kim",
 "kspace_modify", "kspace_style", "label", "lattice",
@@ -16,8 +16,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
 "partition", "prd", "print", "processors", "python", "quit", "read_data",
 "read_dump", "read_restart", "replicate", "rerun", "reset_ids",
 "reset_timestep", "restart", "run", "run_style", "server", "set", "shell",
-"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt",
+"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt", "then",
-"thermo", "thermo_modify", "thermo_style", "then", "third_order", "timer", "timestep",
+"thermo", "thermo_modify", "thermo_style", "third_order", "timer", "timestep",
 "units", "velocity", "write_coeff",
 "write_data", "write_restart")
 

doc/utils/sphinx-config/false_positives.txt

@@ -61,6 +61,7 @@ ajs
 akohlmey
 Aktulga
 al
+alabel
 alain
 Alain
 Alamos
@@ -287,6 +288,7 @@ bitrates
 Bitzek
 Bjerrum
 Bkappa
+blabel
 Blaise
 blanchedalmond
 blocksize
@@ -750,6 +752,7 @@ dissipative
 Dissipative
 distharm
 dl
+dlabel
 dlambda
 DLAMMPS
 dll
@@ -1427,6 +1430,7 @@ ijk
 ijkl
 ik
 Ikeshoji
+ilabel
 Ilie
 ilmenau
 Ilmenau
@@ -1716,6 +1720,8 @@ Kusters
 Kutta
 Kuznetsov
 kx
+labelmap
+Labelmap
 Lachet
 Lackmann
 Ladd
@@ -1939,6 +1945,8 @@ Manolopoulos
 manpages
 manybody
 MANYBODY
+mapID
+mapIDs
 Maras
 Marchetti
 Marchi
@@ -2252,6 +2260,7 @@ nanoparticles
 nanotube
 Nanotube
 nanotubes
+nanowires
 Narulkar
 nasa
 nasr
@@ -2259,6 +2268,7 @@ natively
 Natoli
 natoms
 Natoms
+Natomtype
 Nattempt
 navajowhite
 Navier
@@ -3555,6 +3565,7 @@ typeargs
 typedefs
 typeI
 typeJ
+typelabel
 typeN
 typesafe
 Tz

examples/PACKAGES/mesont/in.cnt

@@ -1,38 +0,0 @@
-#Initialisation
-
-units             nano
-dimension         3
-boundary          p p p
-atom_style        full
-comm_modify       cutoff 11.0
-neighbor          7.80 bin
-newton            on
-
-#Read data
-
-read_data           cnt.data
-replicate 1 2 2
-
-#Force field
-
-bond_style        harmonic
-bond_coeff        1 268896.77 2.0
-
-angle_style       harmonic
-angle_coeff       1 46562.17 180.0
-
-pair_style        mesocnt
-pair_coeff      * * C_10_10.mesocnt
-
-#Output
-
-thermo          1000
-dump            xyz all xyz 1000 cnt.xyz
-
-#Simulation setup
-
-timestep        1.0e-05
-
-#Nose-Hoover thermostat
-fix             nvt all nvt temp 300 300 0.001
-run             10000

examples/PACKAGES/mesont/in.film_mesocnt

@@ -0,0 +1,46 @@
+# initialisation
+
+units             metal
+dimension         3
+boundary          p p s
+atom_style        full
+special_bonds     lj 1 1 1
+neigh_modify      every 5 delay 0 check yes
+newton            on
+
+read_data         data.film_mesocnt
+
+# force field
+
+bond_style        mesocnt
+bond_coeff        1 C 10 10 10
+
+angle_style       mesocnt
+angle_coeff       1 buckling C 10 10 10
+
+pair_style        mesocnt 40 chain
+pair_coeff        * * C_10_10.mesocnt 1
+
+# output
+
+compute         epair all pe pair
+compute         ebond all pe bond
+compute         eangle all pe angle
+
+compute         epair_atom all pe/atom pair
+compute         ebond_atom all pe/atom bond
+compute         eangle_atom all pe/atom angle
+
+fix             angle_mesocnt_buckled all property/atom i_buckled ghost yes
+
+thermo_style    custom step temp etotal ke pe c_ebond c_eangle c_epair
+thermo 10
+#dump            custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
+
+# simulation setup
+
+velocity        all create 600.0 2022 loop geom
+timestep        0.01
+fix             nvt all nvt temp 300.0 300.0 1
+
+run             100

examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.1

@@ -0,0 +1,126 @@
+LAMMPS (3 Aug 2022)
+# initialisation
+
+units             metal
+dimension         3
+boundary          p p s
+atom_style        full
+special_bonds     lj 1 1 1
+neigh_modify      every 5 delay 0 check yes
+newton            on
+
+read_data         data.film_mesocnt
+Reading data file ...
+  orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  79596 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  79200 bonds
+  reading angles ...
+  78804 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    1        1        1       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.012 seconds
+  read_data CPU = 0.160 seconds
+
+# force field
+
+bond_style        mesocnt
+bond_coeff        1 C 10 10 10
+
+angle_style       mesocnt
+angle_coeff       1 buckling C 10 10 10
+
+pair_style        mesocnt 40 chain
+pair_coeff        * * C_10_10.mesocnt 1
+Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
+
+# output
+
+compute         epair all pe pair
+compute         ebond all pe bond
+compute         eangle all pe angle
+
+compute         epair_atom all pe/atom pair
+compute         ebond_atom all pe/atom bond
+compute         eangle_atom all pe/atom angle
+
+fix             angle_mesocnt_buckled all property/atom i_buckled ghost yes
+
+thermo_style    custom step temp etotal ke pe c_ebond c_eangle c_epair
+thermo 10
+#dump            custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
+
+# simulation setup
+
+velocity        all create 600.0 2022 loop geom
+timestep        0.01
+fix             nvt all nvt temp 300.0 300.0 1
+
+run             100
+Neighbor list info ...
+  update: every = 5 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 42
+  ghost atom cutoff = 42
+  binsize = 21, bins = 239 239 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair mesocnt, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 49.89 | 49.89 | 49.89 Mbytes
+   Step          Temp          TotEng         KinEng         PotEng        c_ebond        c_eangle       c_epair    
+         0   600            1355.8735      6173.0767     -4817.2032      28.668731      21.29199      -4867.1639    
+        10   389.92732      1373.1839      4011.7521     -2638.5683      848.77485      1387.6166     -4874.9597    
+        20   311.7468       1388.0161      3207.3949     -1819.3788      1211.534       1868.6817     -4899.5945    
+        30   291.75586      1385.2114      3001.7189     -1616.5075      1184.1423      2133.2088     -4933.8586    
+        40   320.42607      1364.2644      3296.6912     -1932.4267      951.62534      2088.33       -4972.382     
+        50   341.37701      1346.0547      3512.2441     -2166.1894      956.59158      1891.9196     -5014.7005    
+        60   333.15461      1337.5518      3427.6483     -2090.0965      1137.7331      1825.9946     -5053.8242    
+        70   324.47061      1328.7153      3338.3033     -2009.588       1133.3639      1953.8288     -5096.7807    
+        80   324.39487      1315.4948      3337.5241     -2022.0293      979.16213      2141.4697     -5142.6611    
+        90   323.39973      1302.3471      3327.2856     -2024.9385      972.70286      2185.7686     -5183.41      
+       100   322.73067      1289.0538      3320.402      -2031.3482      1100.1024      2088.3804     -5219.831     
+Loop time of 4.1637 on 1 procs for 100 steps with 79596 atoms
+
+Performance: 20.751 ns/day, 1.157 hours/ns, 24.017 timesteps/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.705      | 3.705      | 3.705      |   0.0 | 88.98
+Bond    | 0.29317    | 0.29317    | 0.29317    |   0.0 |  7.04
+Neigh   | 0.078491   | 0.078491   | 0.078491   |   0.0 |  1.89
+Comm    | 0.0019462  | 0.0019462  | 0.0019462  |   0.0 |  0.05
+Output  | 0.00099817 | 0.00099817 | 0.00099817 |   0.0 |  0.02
+Modify  | 0.079874   | 0.079874   | 0.079874   |   0.0 |  1.92
+Other   |            | 0.004224   |            |       |  0.10
+
+Nlocal:          79596 ave       79596 max       79596 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           2567 ave        2567 max        2567 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:   1.1337e+06 ave  1.1337e+06 max  1.1337e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1133696
+Ave neighs/atom = 14.243128
+Ave special neighs/atom = 5.9402985
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:05

examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.4

@@ -0,0 +1,126 @@
+LAMMPS (3 Aug 2022)
+# initialisation
+
+units             metal
+dimension         3
+boundary          p p s
+atom_style        full
+special_bonds     lj 1 1 1
+neigh_modify      every 5 delay 0 check yes
+newton            on
+
+read_data         data.film_mesocnt
+Reading data file ...
+  orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  79596 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  79200 bonds
+  reading angles ...
+  78804 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    1        1        1       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.005 seconds
+  read_data CPU = 0.156 seconds
+
+# force field
+
+bond_style        mesocnt
+bond_coeff        1 C 10 10 10
+
+angle_style       mesocnt
+angle_coeff       1 buckling C 10 10 10
+
+pair_style        mesocnt 40 chain
+pair_coeff        * * C_10_10.mesocnt 1
+Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
+
+# output
+
+compute         epair all pe pair
+compute         ebond all pe bond
+compute         eangle all pe angle
+
+compute         epair_atom all pe/atom pair
+compute         ebond_atom all pe/atom bond
+compute         eangle_atom all pe/atom angle
+
+fix             angle_mesocnt_buckled all property/atom i_buckled ghost yes
+
+thermo_style    custom step temp etotal ke pe c_ebond c_eangle c_epair
+thermo 10
+#dump            custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
+
+# simulation setup
+
+velocity        all create 600.0 2022 loop geom
+timestep        0.01
+fix             nvt all nvt temp 300.0 300.0 1
+
+run             100
+Neighbor list info ...
+  update: every = 5 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 42
+  ghost atom cutoff = 42
+  binsize = 21, bins = 239 239 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair mesocnt, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 16.47 | 16.58 | 16.89 Mbytes
+   Step          Temp          TotEng         KinEng         PotEng        c_ebond        c_eangle       c_epair    
+         0   600            1355.8735      6173.0767     -4817.2032      28.668731      21.29199      -4867.1639    
+        10   389.92732      1373.1839      4011.7521     -2638.5683      848.77485      1387.6166     -4874.9597    
+        20   311.7468       1388.0161      3207.3949     -1819.3788      1211.534       1868.6817     -4899.5945    
+        30   291.75586      1385.2114      3001.7189     -1616.5075      1184.1423      2133.2088     -4933.8586    
+        40   320.42607      1364.2644      3296.6912     -1932.4267      951.62534      2088.33       -4972.382     
+        50   341.37701      1346.0547      3512.2441     -2166.1894      956.59158      1891.9196     -5014.7005    
+        60   333.15461      1337.5518      3427.6483     -2090.0965      1137.7331      1825.9946     -5053.8242    
+        70   324.47061      1328.7153      3338.3033     -2009.588       1133.3639      1953.8288     -5096.7807    
+        80   324.39487      1315.4948      3337.5241     -2022.0293      979.16213      2141.4697     -5142.6611    
+        90   323.39973      1302.3471      3327.2856     -2024.9385      972.70286      2185.7686     -5183.41      
+       100   322.73067      1289.0538      3320.402      -2031.3482      1100.1024      2088.3804     -5219.831     
+Loop time of 1.25052 on 4 procs for 100 steps with 79596 atoms
+
+Performance: 69.091 ns/day, 0.347 hours/ns, 79.967 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.87036    | 0.97558    | 1.1135     |   9.0 | 78.01
+Bond    | 0.071751   | 0.076357   | 0.084244   |   1.7 |  6.11
+Neigh   | 0.023232   | 0.023239   | 0.023244   |   0.0 |  1.86
+Comm    | 0.0046002  | 0.15227    | 0.26319    |  24.1 | 12.18
+Output  | 0.00032696 | 0.00037811 | 0.00045537 |   0.0 |  0.03
+Modify  | 0.019263   | 0.020646   | 0.023155   |   1.1 |  1.65
+Other   |            | 0.00204    |            |       |  0.16
+
+Nlocal:          19899 ave       21951 max       18670 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Nghost:         1323.5 ave        1412 max        1255 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:       283424 ave      325466 max      258171 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+
+Total # of neighbors = 1133696
+Ave neighs/atom = 14.243128
+Ave special neighs/atom = 5.9402985
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/PACKAGES/mesont/log.9Jan20.cnt.g++.1

@@ -1,126 +0,0 @@
-LAMMPS (09 Jan 2020)
-#Initialisation
-
-units             nano
-dimension         3
-boundary          p p p
-atom_style        full
-comm_modify       cutoff 11.0
-neighbor          7.80 bin
-newton            on
-
-#Read data
-
-read_data           cnt.data
-  orthogonal box = (0 0 0) to (600 600 60)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  500 atoms
-  scanning bonds ...
-  1 = max bonds/atom
-  scanning angles ...
-  1 = max angles/atom
-  reading bonds ...
-  498 bonds
-  reading angles ...
-  496 angles
-  2 = max # of 1-2 neighbors
-  2 = max # of 1-3 neighbors
-  4 = max # of 1-4 neighbors
-  6 = max # of special neighbors
-  special bonds CPU = 0.000180006 secs
-  read_data CPU = 0.00125766 secs
-replicate 1 2 2
-  orthogonal box = (0 0 0) to (600 1200 120)
-  1 by 1 by 1 MPI processor grid
-  2000 atoms
-  1992 bonds
-  1984 angles
-  2 = max # of 1-2 neighbors
-  2 = max # of 1-3 neighbors
-  4 = max # of 1-4 neighbors
-  6 = max # of special neighbors
-  special bonds CPU = 0.00054121 secs
-  replicate CPU = 0.000902414 secs
-
-#Force field
-
-bond_style        harmonic
-bond_coeff        1 268896.77 2.0
-
-angle_style       harmonic
-angle_coeff       1 46562.17 180.0
-
-pair_style        mesocnt
-pair_coeff      * * 10_10.cnt
-Reading potential file 10_10.cnt with DATE: 2020-01-13
-
-#Output
-
-thermo          1000
-dump            xyz all xyz 1000 cnt.xyz
-
-#Simulation setup
-
-timestep        1.0e-05
-
-#Nose-Hoover thermostat
-fix             nvt all nvt temp 300 300 0.001
-run             10000
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 10.177
-  ghost atom cutoff = 11
-  binsize = 5.0885, bins = 118 236 24
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair mesocnt, perpetual
-      attributes: full, newton on
-      pair build: full/bin
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 11.21 | 11.21 | 11.21 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -4632.0136 5.7939238e-17   -4632.0136 -0.00015032304 
-    1000    298.82235   -19950.274    13208.089    5628.7024 -0.0056205182 
-    2000    300.43933   -28320.212    11980.296   -3902.0877 -0.0045324757 
-    3000     300.4263   -36049.855    11338.405   -12274.161 -0.0018833539 
-    4000    299.13368    -43471.21    11926.882   -19160.553 -0.00043030866 
-    5000    293.77858   -50083.893    12334.927   -25586.884 -0.0015653738 
-    6000     296.4851   -56330.135     12325.63   -31730.376 -0.0012795986 
-    7000    298.20879   -62120.359    12582.297   -37192.574 -0.0013845796 
-    8000    299.45547   -67881.692    13058.926   -42425.669 -0.00021100885 
-    9000    301.82622   -73333.698    13598.257   -47240.197 -0.0006009197 
-   10000    307.16873   -78292.306    13818.929    -51756.96 -0.0005609903 
-Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms
-
-Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.5955     | 2.5955     | 2.5955     |   0.0 | 64.38
-Bond    | 1.1516     | 1.1516     | 1.1516     |   0.0 | 28.57
-Neigh   | 0.001163   | 0.001163   | 0.001163   |   0.0 |  0.03
-Comm    | 0.0019577  | 0.0019577  | 0.0019577  |   0.0 |  0.05
-Output  | 0.020854   | 0.020854   | 0.020854   |   0.0 |  0.52
-Modify  | 0.21637    | 0.21637    | 0.21637    |   0.0 |  5.37
-Other   |            | 0.04409    |            |       |  1.09
-
-Nlocal:    2000 ave 2000 max 2000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  13320 ave 13320 max 13320 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 13320
-Ave neighs/atom = 6.66
-Ave special neighs/atom = 5.952
-Neighbor list builds = 1
-Dangerous builds = 0
-Total wall time: 0:00:05

examples/PACKAGES/mesont/log.9Jan20.cnt.g++.4

@@ -1,126 +0,0 @@
-LAMMPS (09 Jan 2020)
-#Initialisation
-
-units             nano
-dimension         3
-boundary          p p p
-atom_style        full
-comm_modify       cutoff 11.0
-neighbor          7.80 bin
-newton            on
-
-#Read data
-
-read_data           cnt.data
-  orthogonal box = (0 0 0) to (600 600 60)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  500 atoms
-  scanning bonds ...
-  1 = max bonds/atom
-  scanning angles ...
-  1 = max angles/atom
-  reading bonds ...
-  498 bonds
-  reading angles ...
-  496 angles
-  2 = max # of 1-2 neighbors
-  2 = max # of 1-3 neighbors
-  4 = max # of 1-4 neighbors
-  6 = max # of special neighbors
-  special bonds CPU = 0.000354767 secs
-  read_data CPU = 0.00286365 secs
-replicate 1 2 2
-  orthogonal box = (0 0 0) to (600 1200 120)
-  1 by 4 by 1 MPI processor grid
-  2000 atoms
-  1992 bonds
-  1984 angles
-  2 = max # of 1-2 neighbors
-  2 = max # of 1-3 neighbors
-  4 = max # of 1-4 neighbors
-  6 = max # of special neighbors
-  special bonds CPU = 0.00019598 secs
-  replicate CPU = 0.00055337 secs
-
-#Force field
-
-bond_style        harmonic
-bond_coeff        1 268896.77 2.0
-
-angle_style       harmonic
-angle_coeff       1 46562.17 180.0
-
-pair_style        mesocnt
-pair_coeff      * * 10_10.cnt
-Reading potential file 10_10.cnt with DATE: 2020-01-13
-
-#Output
-
-thermo          1000
-dump            xyz all xyz 1000 cnt.xyz
-
-#Simulation setup
-
-timestep        1.0e-05
-
-#Nose-Hoover thermostat
-fix             nvt all nvt temp 300 300 0.001
-run             10000
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 10.177
-  ghost atom cutoff = 11
-  binsize = 5.0885, bins = 118 236 24
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair mesocnt, perpetual
-      attributes: full, newton on
-      pair build: full/bin
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 2.725 | 2.725 | 2.725 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -4632.0136 5.7939238e-17   -4632.0136 -0.00015032304 
-    1000    298.82235   -19950.274    13208.089    5628.7024 -0.0056205182 
-    2000    300.43861   -28320.205    11980.287   -3902.1202 -0.0045324738 
-    3000    300.41076   -36049.308    11339.149   -12273.513 -0.0018848513 
-    4000    299.13326   -43471.424    11927.668   -19159.998 -0.00042845101 
-    5000    293.78857   -50083.216    12333.969   -25586.752 -0.0015664633 
-    6000    296.45482   -56329.621    12326.419   -31730.328 -0.0012773686 
-    7000    298.19097   -62119.086      12581.4   -37192.937 -0.0013862831 
-    8000    299.46424   -67880.989     13057.62   -42425.908 -0.00020874264 
-    9000    301.80677   -73332.208    13597.237   -47240.532 -0.00060074773 
-   10000    307.17104   -78292.912    13818.889    -51757.51 -0.00056148282 
-Loop time of 1.23665 on 4 procs for 10000 steps with 2000 atoms
-
-Performance: 6986.607 ns/day, 0.003 hours/ns, 8086.351 timesteps/s
-96.1% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.66321    | 0.68439    | 0.71413    |   2.5 | 55.34
-Bond    | 0.28561    | 0.29434    | 0.30976    |   1.7 | 23.80
-Neigh   | 0.00043321 | 0.00043637 | 0.00043917 |   0.0 |  0.04
-Comm    | 0.026656   | 0.05346    | 0.097228   |  12.7 |  4.32
-Output  | 0.0070224  | 0.0073031  | 0.0081415  |   0.6 |  0.59
-Modify  | 0.12769    | 0.15394    | 0.18743    |   6.5 | 12.45
-Other   |            | 0.04279    |            |       |  3.46
-
-Nlocal:    500 ave 504 max 496 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    22 ave 24 max 20 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  3330 ave 3368 max 3292 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 13320
-Ave neighs/atom = 6.66
-Ave special neighs/atom = 5.952
-Neighbor list builds = 1
-Dangerous builds = 0
-Total wall time: 0:00:02

examples/QM/LATTE/2uo2.lmp

@@ -0,0 +1,24 @@
+ LAMMPS Description
+ 
+           6 atoms
+ 
+           2 atom types
+ 
+   0.0000000000000000        10.800000000000001      xlo xhi
+   0.0000000000000000        5.4000000000000004      ylo yhi
+   0.0000000000000000        5.4000000000000004      zlo zhi
+   3.3065463576978537E-016   3.3065463576978537E-016   3.3065463576978537E-016 xy xz yz
+ 
+ Masses
+ 
+              1   238.05078125000000     
+              2   15.994915008544922     
+ 
+ Atoms
+ 
+    1    1    1   0.0   2.70000   8.10000   0.00000
+    2    1    2   0.0   1.35000   9.45000   1.35000
+    3    1    2   0.0   4.05000   9.45000   1.35000
+    4    1    1   0.0   2.70000  10.80000   2.70000
+    5    1    2   0.0   1.35000  12.15000   4.05000
+    6    1    2   0.0   4.05000  12.15000   4.05000

examples/QM/LATTE/3uo2.lmp

@@ -0,0 +1,27 @@
+ LAMMPS Description
+ 
+           9 atoms
+ 
+           2 atom types
+ 
+   0.0000000000000000        16.199999999999999      xlo xhi
+   0.0000000000000000        5.4000000000000004      ylo yhi
+   0.0000000000000000        5.4000000000000004      zlo zhi
+   3.3065463576978537E-016   3.3065463576978537E-016   3.3065463576978537E-016 xy xz yz
+ 
+ Masses
+ 
+              1   238.05078125000000     
+              2   15.994915008544922     
+ 
+ Atoms
+ 
+    1    1    1   0.0   2.70000   8.10000   0.00000
+    2    1    2   0.0   1.35000   9.45000   1.35000
+    3    1    2   0.0   4.05000   9.45000   1.35000
+    4    1    1   0.0   2.70000  10.80000   2.70000
+    5    1    2   0.0   1.35000  12.15000   4.05000
+    6    1    2   0.0   4.05000  12.15000   4.05000
+    7    1    1   0.0   2.70000  13.50000   5.40000
+    8    1    2   0.0   1.35000  14.85000   6.75000
+    9    1    2   0.0   4.05000  14.85000   6.75000

examples/QM/LATTE/4uo2.lmp

@@ -0,0 +1,30 @@
+ LAMMPS Description
+ 
+          12 atoms
+ 
+           2 atom types
+ 
+   0.0000000000000000        10.800000000000001      xlo xhi
+   0.0000000000000000        10.800000000000001      ylo yhi
+   0.0000000000000000        5.4000000000000004      zlo zhi
+   6.6130927153957075E-016   3.3065463576978537E-016   3.3065463576978537E-016 xy xz yz
+ 
+ Masses
+ 
+              1   238.05078125000000     
+              2   15.994915008544922     
+ 
+ Atoms
+ 
+    1    1    1   0.0   2.70000   8.10000   0.00000
+    2    1    2   0.0   1.35000   9.45000   1.35000
+    3    1    2   0.0   4.05000   9.45000   1.35000
+    4    1    1   0.0   5.40000   8.10000   2.70000
+    5    1    2   0.0   4.05000   9.45000   4.05000
+    6    1    2   0.0   6.75000   9.45000   4.05000
+    7    1    1   0.0   2.70000  10.80000   2.70000
+    8    1    2   0.0   1.35000  12.15000   4.05000
+    9    1    2   0.0   4.05000  12.15000   4.05000
+   10    1    1   0.0   5.40000  10.80000   5.40000
+   11    1    2   0.0   4.05000  12.15000   6.75000
+   12    1    2   0.0   6.75000  12.15000   6.75000

examples/QM/LATTE/README

@@ -0,0 +1,161 @@
+LATTE is a semi-empirical tight-binding quantum code, developed
+primarily at Los Alamos National Labs.
+
+See these links:
+
+  https://www.osti.gov/biblio/1526907-los-alamos-transferable-tight-binding-energetics-latte-version
+  https://github.com/lanl/LATTE
+
+LAMMPS has 2 ways of working with LATTE:
+
+(1) Via its LATTE package and the fix latte command
+    must run LAMMPS on a single processor, it calls LATTE as a library
+
+(2) Via its MDI package and the code-coupling MDI library
+    (a) can run LAMMPS and LATTE as stand-alone codes
+        LAMMPS can be run on any number of procs
+        LATTE must run on a single proc, but can use OpenMP
+    (b) can run LAMMPS with LATTE as a plug-in library
+        must run LAMMPS on a single processor
+
+Examples for use case (1) are in the examples/latte dir.  Use case (2)
+is illustrated in this dir.
+
+NOTE: If you compare MDI runs in this dir to similar fix latte runs in
+examples/latte, the answers for energy and virial will be differnt.
+This is b/c the version of LATTE used by the fix latte command within
+the LATTE package is older than the version of LATTE used here.
+
+------------------
+Building 3 codes needed to run these examples
+
+(1) Download and build MDI
+
+% git clone git@github.com:MolSSI-MDI/MDI_Library.git mdi
+% cd mdi
+% mkdir build; cd build
+% cmake ..           # includes support for all langauges (incl Fortran, Python)
+% make
+
+(2) Download and build LATTE with MDI support
+
+% git clone git@github.com:lanl/LATTE.git latte
+% cd latte
+% git checkout skimLATTE-progress    # goto branch with MDI support
+% cp makefiles/makefile.CHOICES.mdi makefile.CHOICES    # so can now edit
+% edit makefile.CHOICES settings to have these settings:
+  MAKELIB = OFF, SHARED = ON, MDI = ON
+  MDI_PATH must point to CMake build of MDI in (1), 
+    e.g. /home/sjplimp/mdi/build/MDI_Library
+  comment out 2 LIB lines with CUDA-CUDART_LIBRARY
+% make clean
+% make        # creates liblatte.so and LATTE_DOUBLE with support for MDI
+
+(3) Build LAMMPS with its MDI package
+    also with the MOLECULE package for these example scripts
+
+Build with traditional make
+
+% cd lammps/lib/mdi
+% python Install.py -m mpi     # downloads and builds MDI
+% cd ../../src
+% make yes-mdi yes-molecule
+$ make mpi                     # creates lmp_mpi
+
+% mkdir build; cd build
+% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
+% make                         # creates lmp
+
+Build with CMake
+
+% cd lammps
+% mkdir build; cd build
+% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
+% make                         # creates lmp
+
+(4) Copy LAMMPS and LATTE executables into this dir
+
+Copy the LAMMPS executable (lmp_mpi or lmp) into this dir as lmp_mpi.
+Copy the LATTE executable LATTE_DOUBLE into this dir.
+The run commands below assume you have done this.
+
+(5) Insure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
+with its libmdi.so file, e.g. mdi/build/MDI_Library.  This is needed
+so when LATTE_DOUBLE runs as an executable it will able to find
+libmdi.so.
+
+------------------
+Notes on LATTE usage
+
+You must run this version of LATTE on a single MPI processor.
+However, you can use OpenMP with LATTE.  To do this you need to build
+LATTE with OpenMP support by editing the makefile.CHOICES file to
+include -fopenmp with FFLAGS and LINKFLAGS.  Also -lapack and -lblas
+need to be added to LIB, and those libraries must be available on your
+system.  For best performance you should also build LATTE with its
+PROGRESS and BML libraries.  Building those libs is more complex,
+see details here:
+
+https://github.com/lanl/LATTE_SUPER/tree/allMachines/Laptop
+
+At run time, you need to also first set an environment variable for
+the number of OpenMP threads to use, e.g.
+
+% export OMP_NUM_THREADS=12 
+
+By default LATTE reads the latte.in file for its parameters.  That
+file specifies other files LATTE will read.  With MDI, the driver code
+(e.g. LAMMPS) can use the >FNAME command to specify an alternate
+filename to use instead of latte.in.
+
+By default LATTE writes out a log.latte file with info about its
+calculations.  An "OUTFILE= logfile" setting in latte.in can rename
+this file.
+
+---------
+Run example #1: AIMD
+
+* Run with MPI: 1 proc each
+
+mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
+  -in in.aimd -log log.aimd.lammps.mpi : \
+  -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
+
+* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
+
+mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
+  -in in.aimd -log log.aimd.lammps.mpi : \
+  -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
+
+* Run in plugin mode: 1 proc
+
+lmp_mpi -mdi \
+  "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
+  -in in.aimd.plugin -log log.aimd.lammps.plugin
+
+NOTE: The -plugin_path needs to point to where LATTE was built in step
+(2).
+
+---------
+Run example #2: sequence of configurations
+
+* Run with MPI: 1 proc each
+
+mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
+  -in in.series -log log.series.lammps.mpi : \
+  -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
+
+* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
+
+mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
+  -in in.series -log log.series.lammps.mpi : \
+  -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
+
+* Run in plugin mode: 1 proc
+
+lmp_mpi -mdi \
+  "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
+   -in in.series.plugin -log log.series.lammps.plugin
+
+NOTE: The -plugin_path needs to point to where LATTE was built in step
+(2).

examples/QM/LATTE/dump.8Sep22.aimd.mpi.1

@@ -0,0 +1,315 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.7 2.7 0 -0.601491 0.335597 -0.87242 -2.27066e-14 -1.33391e-14 2.31141e-14
+2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
+3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
+4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
+5 2 1.35 1.35 4.05 2.42711 -1.49109 -2.41596 2.35473 5.79901e-15 -1.19594e-14
+6 2 4.05 1.35 4.05 1.30688 0.784281 -1.73922 -2.35473 -1.38761e-14 1.09382e-14
+ITEM: TIMESTEP
+1
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69985 2.70008 -0.000218105 -0.601467 0.335616 -0.872428 0.00470101 0.00380515 -0.00141625
+2 2 1.35212 4.05114 1.35149 8.64389 4.55886 5.97363 2.34251 -0.00209926 -0.00172976
+3 2 4.0504 4.05163 1.3501 1.41949 6.51866 0.385561 -2.34936 -0.00247497 0.00051716
+4 1 2.69992 -0.00025811 2.70018 -0.325581 -1.03243 0.724334 0.00481137 0.00249244 0.00195665
+5 2 1.35065 1.34963 4.0494 2.78199 -1.49112 -2.4159 2.3517 -0.00043711 0.000874754
+6 2 4.05028 1.3502 4.04957 0.951796 0.784184 -1.73923 -2.35436 -0.00128625 -0.00020256
+ITEM: TIMESTEP
+2
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6997 2.70017 -0.000436214 -0.601396 0.335673 -0.872449 0.00939888 0.00756163 -0.00288164
+2 2 1.35432 4.05228 1.35299 8.99615 4.55837 5.97323 2.32921 -0.00431846 -0.00355855
+3 2 4.05071 4.05326 1.35019 1.06567 6.5181 0.385678 -2.34304 -0.00494314 0.00103532
+4 1 2.69984 -0.000516214 2.70036 -0.325507 -1.03239 0.724364 0.00976944 0.00512657 0.00403686
+5 2 1.35139 1.34925 4.04879 3.13634 -1.49122 -2.4157 2.34776 -0.000851489 0.00177498
+6 2 4.05048 1.35039 4.04913 0.596838 0.783892 -1.73928 -2.3531 -0.00257512 -0.000406965
+ITEM: TIMESTEP
+3
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69955 2.70025 -0.00065433 -0.601277 0.335769 -0.872486 0.0141006 0.0112702 -0.00439552
+2 2 1.35661 4.05342 1.35448 9.34633 4.55754 5.97255 2.31482 -0.00666433 -0.00549143
+3 2 4.05093 4.05489 1.35029 0.712875 6.51717 0.385873 -2.33577 -0.00740896 0.00154764
+4 1 2.69976 -0.000774304 2.70054 -0.325382 -1.03232 0.724417 0.0148831 0.00790884 0.00624833
+5 2 1.35222 1.34888 4.04819 3.49003 -1.49137 -2.41536 2.3429 -0.0012407 0.00270313
+6 2 4.05058 1.35059 4.0487 0.242138 0.783407 -1.73935 -2.35094 -0.00386511 -0.000612161
+ITEM: TIMESTEP
+4
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6994 2.70034 -0.000872457 -0.60111 0.335902 -0.872539 0.0188131 0.0149318 -0.00595718
+2 2 1.359 4.05456 1.35597 9.69425 4.55635 5.97156 2.29933 -0.00914346 -0.00753331
+3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
+4 1 2.69967 -0.00103238 2.70072 -0.325204 -1.03223 0.724492 0.020161 0.0108455 0.00859866
+5 2 1.35314 1.34851 4.04758 3.84292 -1.49159 -2.41488 2.33711 -0.00160232 0.00366164
+6 2 4.0506 1.35078 4.04826 -0.112168 0.782727 -1.73946 -2.34789 -0.00515472 -0.000817084
+ITEM: TIMESTEP
+5
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69925 2.70042 -0.0010906 -0.600896 0.336071 -0.872607 0.0235434 0.0185473 -0.00756588
+2 2 1.36146 4.0557 1.35747 10.0397 4.55478 5.97026 2.2827 -0.0117623 -0.00968894
+3 2 4.05111 4.05815 1.35048 0.0109366 6.51419 0.386489 -2.31832 -0.0123511 0.00252727
+4 1 2.69959 -0.00129042 2.70091 -0.324972 -1.0321 0.724592 0.0256115 0.0139425 0.0110953
+5 2 1.35414 1.34814 4.04698 4.19487 -1.49186 -2.41425 2.33039 -0.00193394 0.0046529
+6 2 4.05052 1.35098 4.04783 -0.465946 0.781852 -1.7396 -2.34393 -0.00644244 -0.00102066
+ITEM: TIMESTEP
+6
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6991 2.7005 -0.00130876 -0.600633 0.336277 -0.872692 0.0282985 0.0221175 -0.00922083
+2 2 1.36401 4.05684 1.35896 10.3827 4.55279 5.96863 2.26494 -0.0145272 -0.0119629
+3 2 4.05107 4.05978 1.35058 -0.337913 6.51214 0.386904 -2.30814 -0.0148362 0.00298071
+4 1 2.69951 -0.00154843 2.70109 -0.324684 -1.03194 0.724717 0.0312427 0.0172058 0.0137455
+5 2 1.35523 1.34776 4.04638 4.54573 -1.49217 -2.41347 2.32273 -0.00223319 0.00567932
+6 2 4.05036 1.35117 4.04739 -0.819058 0.780784 -1.73977 -2.33906 -0.00772673 -0.00122181
+ITEM: TIMESTEP
+7
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69895 2.70059 -0.00152695 -0.600322 0.336519 -0.872794 0.0330853 0.0256435 -0.0109212
+2 2 1.36665 4.05797 1.36045 10.7228 4.55038 5.96665 2.24601 -0.0174443 -0.0143597
+3 2 4.05094 4.0614 1.35068 -0.685154 6.50971 0.387385 -2.29698 -0.0173365 0.00340068
+4 1 2.69943 -0.00180639 2.70127 -0.324338 -1.03175 0.724871 0.0370626 0.020641 0.0165564
+5 2 1.35641 1.34739 4.04577 4.89536 -1.49253 -2.41254 2.31411 -0.0024977 0.00674323
+6 2 4.05012 1.35137 4.04696 -1.17137 0.779522 -1.73997 -2.33329 -0.00900604 -0.00141944
+ITEM: TIMESTEP
+8
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6988 2.70067 -0.00174516 -0.599962 0.336797 -0.872914 0.0379108 0.0291262 -0.0126661
+2 2 1.36938 4.05911 1.36194 11.06 4.54752 5.96429 2.2259 -0.0205196 -0.0168834
+3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
+4 1 2.69935 -0.0020643 2.70145 -0.323932 -1.03153 0.725054 0.0430788 0.0242538 0.0195348
+5 2 1.35768 1.34702 4.04517 5.24362 -1.49292 -2.41144 2.30452 -0.0027252 0.00784692
+6 2 4.04978 1.35156 4.04652 -1.52274 0.778068 -1.7402 -2.32659 -0.0102788 -0.00161245
+ITEM: TIMESTEP
+9
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69865 2.70076 -0.0019634 -0.599553 0.337109 -0.873051 0.0427817 0.0325667 -0.0144547
+2 2 1.37218 4.06025 1.36343 11.3941 4.54418 5.96155 2.20459 -0.023759 -0.019538
+3 2 4.05043 4.06466 1.35087 -1.37421 6.50372 0.388522 -2.27166 -0.0224003 0.00411244
+4 1 2.69927 -0.00232215 2.70163 -0.323464 -1.03126 0.725268 0.0492987 0.0280495 0.0226874
+5 2 1.35904 1.34664 4.04457 5.59036 -1.49335 -2.41017 2.29396 -0.00291347 0.00899259
+6 2 4.04935 1.35176 4.04609 -1.87303 0.776422 -1.74045 -2.31898 -0.0115434 -0.00179972
+ITEM: TIMESTEP
+10
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6985 2.70084 -0.00218168 -0.599095 0.337456 -0.873207 0.0477049 0.0359661 -0.0162858
+2 2 1.37507 4.06138 1.36492 11.7248 4.54034 5.95839 2.18206 -0.0271682 -0.0223275
+3 2 4.05004 4.06628 1.35097 -1.71572 6.50015 0.389163 -2.25748 -0.0249726 0.0043903
+4 1 2.69919 -0.00257993 2.70181 -0.322932 -1.03096 0.725515 0.0557294 0.0320331 0.0260207
+5 2 1.36048 1.34627 4.04397 5.93543 -1.4938 -2.40872 2.2824 -0.00306026 0.0101825
+6 2 4.04884 1.35195 4.04565 -2.2221 0.774587 -1.74074 -2.31042 -0.0127983 -0.00198013
+ITEM: TIMESTEP
+11
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69835 2.70092 -0.00240001 -0.598586 0.337838 -0.873382 0.0526872 0.0393256 -0.0181586
+2 2 1.37805 4.06252 1.36641 12.0521 4.53597 5.9548 2.15829 -0.0307526 -0.0252554
+3 2 4.04957 4.06791 1.35106 -2.05501 6.49619 0.389841 -2.24228 -0.0275775 0.00460683
+4 1 2.69911 -0.00283763 2.70199 -0.322334 -1.03061 0.725796 0.0623777 0.0362096 0.0295409
+5 2 1.362 1.3459 4.04336 6.27868 -1.49427 -2.40709 2.26985 -0.00316333 0.0114188
+6 2 4.04824 1.35215 4.04522 -2.56981 0.772563 -1.74105 -2.30093 -0.0140417 -0.00215255
+ITEM: TIMESTEP
+12
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6982 2.70101 -0.00261837 -0.598027 0.338253 -0.873575 0.0577351 0.0426463 -0.0200718
+2 2 1.3811 4.06365 1.3679 12.3757 4.53105 5.95076 2.13326 -0.0345179 -0.0283253
+3 2 4.04901 4.06953 1.35116 -2.39194 6.49183 0.390547 -2.22604 -0.0302194 0.00475506
+4 1 2.69903 -0.00309524 2.70217 -0.321667 -1.03022 0.726114 0.06925 0.0405836 0.0332542
+5 2 1.36362 1.34552 4.04276 6.61997 -1.49475 -2.40527 2.25627 -0.00322051 0.0127037
+6 2 4.04756 1.35234 4.04478 -2.91602 0.770353 -1.74139 -2.29048 -0.0152721 -0.00231583
+ITEM: TIMESTEP
+13
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69805 2.70109 -0.00283679 -0.597416 0.338702 -0.873788 0.0628554 0.0459295 -0.0220243
+2 2 1.38423 4.06478 1.36939 12.6954 4.52555 5.94625 2.10694 -0.0384688 -0.0315401
+3 2 4.04837 4.07115 1.35126 -2.72634 6.48707 0.39127 -2.20874 -0.0329024 0.00482793
+4 1 2.69895 -0.00335274 2.70236 -0.320929 -1.02979 0.726471 0.0763523 0.0451591 0.0371659
+5 2 1.36531 1.34515 4.04216 6.95912 -1.49523 -2.40326 2.24165 -0.00322965 0.0140393
+6 2 4.04678 1.35253 4.04434 -3.26057 0.767958 -1.74175 -2.27906 -0.0164877 -0.0024688
+ITEM: TIMESTEP
+14
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6979 2.70118 -0.00305527 -0.596753 0.339184 -0.874022 0.0680546 0.0491768 -0.0240145
+2 2 1.38745 4.06591 1.37087 13.0111 4.51944 5.94124 2.07932 -0.0426096 -0.0349018
+3 2 4.04765 4.07277 1.35136 -3.05804 6.4819 0.391997 -2.19038 -0.035631 0.00481829
+4 1 2.69887 -0.00361013 2.70254 -0.320118 -1.0293 0.726868 0.0836894 0.0499393 0.0412807
+5 2 1.3671 1.34478 4.04156 7.296 -1.49572 -2.40103 2.22598 -0.00318867 0.0154277
+6 2 4.04593 1.35272 4.04391 -3.60334 0.765381 -1.74213 -2.26667 -0.0176868 -0.00261028
+ITEM: TIMESTEP
+15
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69775 2.70126 -0.0032738 -0.596036 0.339698 -0.874275 0.0733392 0.0523895 -0.0260413
+2 2 1.39074 4.06704 1.37236 13.3225 4.51268 5.93571 2.05037 -0.0469451 -0.0384133
+3 2 4.04685 4.07439 1.35146 -3.3869 6.47632 0.392716 -2.17093 -0.038409 0.00471919
+4 1 2.69879 -0.00386739 2.70272 -0.319232 -1.02877 0.727309 0.0912666 0.0549279 0.0456036
+5 2 1.36896 1.3444 4.04096 7.63043 -1.49619 -2.3986 2.20924 -0.00309551 0.0168709
+6 2 4.04498 1.35291 4.04347 -3.94416 0.762625 -1.74253 -2.25329 -0.0188678 -0.0027391
+ITEM: TIMESTEP
+16
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6976 2.70135 -0.00349241 -0.595266 0.340245 -0.87455 0.0787153 0.055569 -0.0281032
+2 2 1.39411 4.06817 1.37384 13.6294 4.50526 5.92964 2.02007 -0.0514799 -0.042077
+3 2 4.04596 4.07601 1.35155 -3.71274 6.47031 0.393413 -2.15039 -0.0412405 0.00452364
+4 1 2.69871 -0.00412452 2.7029 -0.318268 -1.02819 0.727794 0.0990893 0.0601283 0.0501398
+5 2 1.37091 1.34403 4.04036 7.96225 -1.49665 -2.39594 2.19142 -0.00294819 0.0183708
+6 2 4.04395 1.3531 4.04304 -4.28288 0.759692 -1.74296 -2.2389 -0.0200287 -0.00285406
+ITEM: TIMESTEP
+17
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69745 2.70143 -0.00371108 -0.594441 0.340824 -0.874845 0.0841889 0.0587168 -0.0301987
+2 2 1.39755 4.0693 1.37532 13.9317 4.49714 5.92301 1.9884 -0.0562187 -0.0458954
+3 2 4.04499 4.07763 1.35165 -4.0354 6.46388 0.394073 -2.12872 -0.0441293 0.0042247
+4 1 2.69863 -0.00438149 2.70308 -0.317223 -1.02755 0.728326 0.107162 0.0655439 0.054894
+5 2 1.37294 1.34365 4.03976 8.2913 -1.49708 -2.39305 2.17248 -0.00274479 0.0199293
+6 2 4.04284 1.35329 4.0426 -4.61936 0.756586 -1.74339 -2.2235 -0.0211679 -0.00295392
+ITEM: TIMESTEP
+18
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69731 2.70152 -0.00392983 -0.593559 0.341435 -0.875162 0.0897661 0.0618346 -0.0323262
+2 2 1.40107 4.07042 1.3768 14.229 4.48829 5.91578 1.95532 -0.0611659 -0.0498706
+3 2 4.04394 4.07924 1.35175 -4.3547 6.457 0.394679 -2.10593 -0.0470792 0.0038154
+4 1 2.69855 -0.00463829 2.70327 -0.316095 -1.02686 0.728907 0.11549 0.0711775 0.0598705
+5 2 1.37506 1.34328 4.03916 8.61741 -1.49747 -2.38993 2.15241 -0.00248344 0.0215483
+6 2 4.04164 1.35348 4.04217 -4.95344 0.753309 -1.74385 -2.20706 -0.0222835 -0.00303744
+ITEM: TIMESTEP
+19
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69716 2.7016 -0.00414866 -0.592621 0.342077 -0.8755 0.0954526 0.0649239 -0.0344841
+2 2 1.40467 4.07154 1.37828 14.5213 4.47868 5.90795 1.92083 -0.0663258 -0.0540045
+3 2 4.04281 4.08086 1.35185 -4.67049 6.44967 0.395215 -2.08198 -0.050094 0.00328881
+4 1 2.69847 -0.00489492 2.70345 -0.314881 -1.02611 0.72954 0.124076 0.0770317 0.0650736
+5 2 1.37725 1.3429 4.03857 8.94041 -1.49782 -2.38655 2.13119 -0.00216234 0.0232295
+6 2 4.04036 1.35367 4.04173 -5.28496 0.749867 -1.74431 -2.18956 -0.0233735 -0.00310338
+ITEM: TIMESTEP
+20
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69701 2.70169 -0.00436758 -0.591624 0.342751 -0.875861 0.101254 0.0679866 -0.0366705
+2 2 1.40833 4.07266 1.37976 14.8083 4.46827 5.89948 1.88489 -0.0717024 -0.0582989
+3 2 4.0416 4.08247 1.35195 -4.98257 6.44189 0.395662 -2.05686 -0.0531772 0.00263798
+4 1 2.69839 -0.00515135 2.70363 -0.313579 -1.0253 0.730227 0.132925 0.0831089 0.0705072
+5 2 1.37953 1.34253 4.03797 9.26012 -1.49812 -2.38291 2.1088 -0.00177977 0.0249746
+6 2 4.039 1.35386 4.04129 -5.61376 0.746262 -1.74478 -2.171 -0.0244362 -0.00315046

examples/QM/LATTE/dump.8Sep22.aimd.mpi.2

@@ -0,0 +1,315 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.7 2.7 0 -0.601491 0.335597 -0.87242 -2.27066e-14 -1.33391e-14 2.31141e-14
+2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
+3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
+4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
+5 2 1.35 1.35 4.05 2.42711 -1.49109 -2.41596 2.35473 5.79901e-15 -1.19594e-14
+6 2 4.05 1.35 4.05 1.30688 0.784281 -1.73922 -2.35473 -1.38761e-14 1.09382e-14
+ITEM: TIMESTEP
+1
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69985 2.70008 -0.000218105 -0.601467 0.335616 -0.872428 0.00470101 0.00380515 -0.00141625
+2 2 1.35212 4.05114 1.35149 8.64389 4.55886 5.97363 2.34251 -0.00209926 -0.00172976
+3 2 4.0504 4.05163 1.3501 1.41949 6.51866 0.385561 -2.34936 -0.00247497 0.00051716
+4 1 2.69992 -0.00025811 2.70018 -0.325581 -1.03243 0.724334 0.00481137 0.00249244 0.00195665
+5 2 1.35065 1.34963 4.0494 2.78199 -1.49112 -2.4159 2.3517 -0.00043711 0.000874754
+6 2 4.05028 1.3502 4.04957 0.951796 0.784184 -1.73923 -2.35436 -0.00128625 -0.00020256
+ITEM: TIMESTEP
+2
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6997 2.70017 -0.000436214 -0.601396 0.335673 -0.872449 0.00939888 0.00756163 -0.00288164
+2 2 1.35432 4.05228 1.35299 8.99615 4.55837 5.97323 2.32921 -0.00431846 -0.00355855
+3 2 4.05071 4.05326 1.35019 1.06567 6.5181 0.385678 -2.34304 -0.00494314 0.00103532
+4 1 2.69984 -0.000516214 2.70036 -0.325507 -1.03239 0.724364 0.00976944 0.00512657 0.00403686
+5 2 1.35139 1.34925 4.04879 3.13634 -1.49122 -2.4157 2.34776 -0.000851489 0.00177498
+6 2 4.05048 1.35039 4.04913 0.596838 0.783892 -1.73928 -2.3531 -0.00257512 -0.000406965
+ITEM: TIMESTEP
+3
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69955 2.70025 -0.00065433 -0.601277 0.335769 -0.872486 0.0141006 0.0112702 -0.00439552
+2 2 1.35661 4.05342 1.35448 9.34633 4.55754 5.97255 2.31482 -0.00666433 -0.00549143
+3 2 4.05093 4.05489 1.35029 0.712875 6.51717 0.385873 -2.33577 -0.00740896 0.00154764
+4 1 2.69976 -0.000774304 2.70054 -0.325382 -1.03232 0.724417 0.0148831 0.00790884 0.00624833
+5 2 1.35222 1.34888 4.04819 3.49003 -1.49137 -2.41536 2.3429 -0.0012407 0.00270313
+6 2 4.05058 1.35059 4.0487 0.242138 0.783407 -1.73935 -2.35094 -0.00386511 -0.000612161
+ITEM: TIMESTEP
+4
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6994 2.70034 -0.000872457 -0.60111 0.335902 -0.872539 0.0188131 0.0149318 -0.00595718
+2 2 1.359 4.05456 1.35597 9.69425 4.55635 5.97156 2.29933 -0.00914346 -0.00753331
+3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
+4 1 2.69967 -0.00103238 2.70072 -0.325204 -1.03223 0.724492 0.020161 0.0108455 0.00859866
+5 2 1.35314 1.34851 4.04758 3.84292 -1.49159 -2.41488 2.33711 -0.00160232 0.00366164
+6 2 4.0506 1.35078 4.04826 -0.112168 0.782727 -1.73946 -2.34789 -0.00515472 -0.000817084
+ITEM: TIMESTEP
+5
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69925 2.70042 -0.0010906 -0.600896 0.336071 -0.872607 0.0235434 0.0185473 -0.00756588
+2 2 1.36146 4.0557 1.35747 10.0397 4.55478 5.97026 2.2827 -0.0117623 -0.00968894
+3 2 4.05111 4.05815 1.35048 0.0109366 6.51419 0.386489 -2.31832 -0.0123511 0.00252727
+4 1 2.69959 -0.00129042 2.70091 -0.324972 -1.0321 0.724592 0.0256115 0.0139425 0.0110953
+5 2 1.35414 1.34814 4.04698 4.19487 -1.49186 -2.41425 2.33039 -0.00193394 0.0046529
+6 2 4.05052 1.35098 4.04783 -0.465946 0.781852 -1.7396 -2.34393 -0.00644244 -0.00102066
+ITEM: TIMESTEP
+6
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6991 2.7005 -0.00130876 -0.600633 0.336277 -0.872692 0.0282985 0.0221175 -0.00922083
+2 2 1.36401 4.05684 1.35896 10.3827 4.55279 5.96863 2.26494 -0.0145272 -0.0119629
+3 2 4.05107 4.05978 1.35058 -0.337913 6.51214 0.386904 -2.30814 -0.0148362 0.00298071
+4 1 2.69951 -0.00154843 2.70109 -0.324684 -1.03194 0.724717 0.0312427 0.0172058 0.0137455
+5 2 1.35523 1.34776 4.04638 4.54573 -1.49217 -2.41347 2.32273 -0.00223319 0.00567932
+6 2 4.05036 1.35117 4.04739 -0.819058 0.780784 -1.73977 -2.33906 -0.00772673 -0.00122181
+ITEM: TIMESTEP
+7
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69895 2.70059 -0.00152695 -0.600322 0.336519 -0.872794 0.0330853 0.0256435 -0.0109212
+2 2 1.36665 4.05797 1.36045 10.7228 4.55038 5.96665 2.24601 -0.0174443 -0.0143597
+3 2 4.05094 4.0614 1.35068 -0.685154 6.50971 0.387385 -2.29698 -0.0173365 0.00340068
+4 1 2.69943 -0.00180639 2.70127 -0.324338 -1.03175 0.724871 0.0370626 0.020641 0.0165564
+5 2 1.35641 1.34739 4.04577 4.89536 -1.49253 -2.41254 2.31411 -0.0024977 0.00674323
+6 2 4.05012 1.35137 4.04696 -1.17137 0.779522 -1.73997 -2.33329 -0.00900604 -0.00141944
+ITEM: TIMESTEP
+8
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6988 2.70067 -0.00174516 -0.599962 0.336797 -0.872914 0.0379108 0.0291262 -0.0126661
+2 2 1.36938 4.05911 1.36194 11.06 4.54752 5.96429 2.2259 -0.0205196 -0.0168834
+3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
+4 1 2.69935 -0.0020643 2.70145 -0.323932 -1.03153 0.725054 0.0430788 0.0242538 0.0195348
+5 2 1.35768 1.34702 4.04517 5.24362 -1.49292 -2.41144 2.30452 -0.0027252 0.00784692
+6 2 4.04978 1.35156 4.04652 -1.52274 0.778068 -1.7402 -2.32659 -0.0102788 -0.00161245
+ITEM: TIMESTEP
+9
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69865 2.70076 -0.0019634 -0.599553 0.337109 -0.873051 0.0427817 0.0325667 -0.0144547
+2 2 1.37218 4.06025 1.36343 11.3941 4.54418 5.96155 2.20459 -0.023759 -0.019538
+3 2 4.05043 4.06466 1.35087 -1.37421 6.50372 0.388522 -2.27166 -0.0224003 0.00411244
+4 1 2.69927 -0.00232215 2.70163 -0.323464 -1.03126 0.725268 0.0492987 0.0280495 0.0226874
+5 2 1.35904 1.34664 4.04457 5.59036 -1.49335 -2.41017 2.29396 -0.00291347 0.00899259
+6 2 4.04935 1.35176 4.04609 -1.87303 0.776422 -1.74045 -2.31898 -0.0115434 -0.00179972
+ITEM: TIMESTEP
+10
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6985 2.70084 -0.00218168 -0.599095 0.337456 -0.873207 0.0477049 0.0359661 -0.0162858
+2 2 1.37507 4.06138 1.36492 11.7248 4.54034 5.95839 2.18206 -0.0271682 -0.0223275
+3 2 4.05004 4.06628 1.35097 -1.71572 6.50015 0.389163 -2.25748 -0.0249726 0.0043903
+4 1 2.69919 -0.00257993 2.70181 -0.322932 -1.03096 0.725515 0.0557294 0.0320331 0.0260207
+5 2 1.36048 1.34627 4.04397 5.93543 -1.4938 -2.40872 2.2824 -0.00306026 0.0101825
+6 2 4.04884 1.35195 4.04565 -2.2221 0.774587 -1.74074 -2.31042 -0.0127983 -0.00198013
+ITEM: TIMESTEP
+11
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69835 2.70092 -0.00240001 -0.598586 0.337838 -0.873382 0.0526872 0.0393256 -0.0181586
+2 2 1.37805 4.06252 1.36641 12.0521 4.53597 5.9548 2.15829 -0.0307526 -0.0252554
+3 2 4.04957 4.06791 1.35106 -2.05501 6.49619 0.389841 -2.24228 -0.0275775 0.00460683
+4 1 2.69911 -0.00283763 2.70199 -0.322334 -1.03061 0.725796 0.0623777 0.0362096 0.0295409
+5 2 1.362 1.3459 4.04336 6.27868 -1.49427 -2.40709 2.26985 -0.00316333 0.0114188
+6 2 4.04824 1.35215 4.04522 -2.56981 0.772563 -1.74105 -2.30093 -0.0140417 -0.00215255
+ITEM: TIMESTEP
+12
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6982 2.70101 -0.00261837 -0.598027 0.338253 -0.873575 0.0577351 0.0426463 -0.0200718
+2 2 1.3811 4.06365 1.3679 12.3757 4.53105 5.95076 2.13326 -0.0345179 -0.0283253
+3 2 4.04901 4.06953 1.35116 -2.39194 6.49183 0.390547 -2.22604 -0.0302194 0.00475506
+4 1 2.69903 -0.00309524 2.70217 -0.321667 -1.03022 0.726114 0.06925 0.0405836 0.0332542
+5 2 1.36362 1.34552 4.04276 6.61997 -1.49475 -2.40527 2.25627 -0.00322051 0.0127037
+6 2 4.04756 1.35234 4.04478 -2.91602 0.770353 -1.74139 -2.29048 -0.0152721 -0.00231583
+ITEM: TIMESTEP
+13
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69805 2.70109 -0.00283679 -0.597416 0.338702 -0.873788 0.0628554 0.0459295 -0.0220243
+2 2 1.38423 4.06478 1.36939 12.6954 4.52555 5.94625 2.10694 -0.0384688 -0.0315401
+3 2 4.04837 4.07115 1.35126 -2.72634 6.48707 0.39127 -2.20874 -0.0329024 0.00482793
+4 1 2.69895 -0.00335274 2.70236 -0.320929 -1.02979 0.726471 0.0763523 0.0451591 0.0371659
+5 2 1.36531 1.34515 4.04216 6.95912 -1.49523 -2.40326 2.24165 -0.00322965 0.0140393
+6 2 4.04678 1.35253 4.04434 -3.26057 0.767958 -1.74175 -2.27906 -0.0164877 -0.0024688
+ITEM: TIMESTEP
+14
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6979 2.70118 -0.00305527 -0.596753 0.339184 -0.874022 0.0680546 0.0491768 -0.0240145
+2 2 1.38745 4.06591 1.37087 13.0111 4.51944 5.94124 2.07932 -0.0426096 -0.0349018
+3 2 4.04765 4.07277 1.35136 -3.05804 6.4819 0.391997 -2.19038 -0.035631 0.00481829
+4 1 2.69887 -0.00361013 2.70254 -0.320118 -1.0293 0.726868 0.0836894 0.0499393 0.0412807
+5 2 1.3671 1.34478 4.04156 7.296 -1.49572 -2.40103 2.22598 -0.00318867 0.0154277
+6 2 4.04593 1.35272 4.04391 -3.60334 0.765381 -1.74213 -2.26667 -0.0176868 -0.00261028
+ITEM: TIMESTEP
+15
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69775 2.70126 -0.0032738 -0.596036 0.339698 -0.874275 0.0733392 0.0523895 -0.0260413
+2 2 1.39074 4.06704 1.37236 13.3225 4.51268 5.93571 2.05037 -0.0469451 -0.0384133
+3 2 4.04685 4.07439 1.35146 -3.3869 6.47632 0.392716 -2.17093 -0.038409 0.00471919
+4 1 2.69879 -0.00386739 2.70272 -0.319232 -1.02877 0.727309 0.0912666 0.0549279 0.0456036
+5 2 1.36896 1.3444 4.04096 7.63043 -1.49619 -2.3986 2.20924 -0.00309551 0.0168709
+6 2 4.04498 1.35291 4.04347 -3.94416 0.762625 -1.74253 -2.25329 -0.0188678 -0.0027391
+ITEM: TIMESTEP
+16
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6976 2.70135 -0.00349241 -0.595266 0.340245 -0.87455 0.0787153 0.055569 -0.0281032
+2 2 1.39411 4.06817 1.37384 13.6294 4.50526 5.92964 2.02007 -0.0514799 -0.042077
+3 2 4.04596 4.07601 1.35155 -3.71274 6.47031 0.393413 -2.15039 -0.0412405 0.00452364
+4 1 2.69871 -0.00412452 2.7029 -0.318268 -1.02819 0.727794 0.0990893 0.0601283 0.0501398
+5 2 1.37091 1.34403 4.04036 7.96225 -1.49665 -2.39594 2.19142 -0.00294819 0.0183708
+6 2 4.04395 1.3531 4.04304 -4.28288 0.759692 -1.74296 -2.2389 -0.0200287 -0.00285406
+ITEM: TIMESTEP
+17
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69745 2.70143 -0.00371108 -0.594441 0.340824 -0.874845 0.0841889 0.0587168 -0.0301987
+2 2 1.39755 4.0693 1.37532 13.9317 4.49714 5.92301 1.9884 -0.0562187 -0.0458954
+3 2 4.04499 4.07763 1.35165 -4.0354 6.46388 0.394073 -2.12872 -0.0441293 0.0042247
+4 1 2.69863 -0.00438149 2.70308 -0.317223 -1.02755 0.728326 0.107162 0.0655439 0.054894
+5 2 1.37294 1.34365 4.03976 8.2913 -1.49708 -2.39305 2.17248 -0.00274479 0.0199293
+6 2 4.04284 1.35329 4.0426 -4.61936 0.756586 -1.74339 -2.2235 -0.0211679 -0.00295392
+ITEM: TIMESTEP
+18
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69731 2.70152 -0.00392983 -0.593559 0.341435 -0.875162 0.0897661 0.0618346 -0.0323262
+2 2 1.40107 4.07042 1.3768 14.229 4.48829 5.91578 1.95532 -0.0611659 -0.0498706
+3 2 4.04394 4.07924 1.35175 -4.3547 6.457 0.394679 -2.10593 -0.0470792 0.0038154
+4 1 2.69855 -0.00463829 2.70327 -0.316095 -1.02686 0.728907 0.11549 0.0711775 0.0598705
+5 2 1.37506 1.34328 4.03916 8.61741 -1.49747 -2.38993 2.15241 -0.00248344 0.0215483
+6 2 4.04164 1.35348 4.04217 -4.95344 0.753309 -1.74385 -2.20706 -0.0222835 -0.00303744
+ITEM: TIMESTEP
+19
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69716 2.7016 -0.00414866 -0.592621 0.342077 -0.8755 0.0954526 0.0649239 -0.0344841
+2 2 1.40467 4.07154 1.37828 14.5213 4.47868 5.90795 1.92083 -0.0663258 -0.0540045
+3 2 4.04281 4.08086 1.35185 -4.67049 6.44967 0.395215 -2.08198 -0.050094 0.00328881
+4 1 2.69847 -0.00489492 2.70345 -0.314881 -1.02611 0.72954 0.124076 0.0770317 0.0650736
+5 2 1.37725 1.3429 4.03857 8.94041 -1.49782 -2.38655 2.13119 -0.00216234 0.0232295
+6 2 4.04036 1.35367 4.04173 -5.28496 0.749867 -1.74431 -2.18956 -0.0233735 -0.00310338
+ITEM: TIMESTEP
+20
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69701 2.70169 -0.00436758 -0.591624 0.342751 -0.875861 0.101254 0.0679866 -0.0366705
+2 2 1.40833 4.07266 1.37976 14.8083 4.46827 5.89948 1.88489 -0.0717024 -0.0582989
+3 2 4.0416 4.08247 1.35195 -4.98257 6.44189 0.395662 -2.05686 -0.0531772 0.00263798
+4 1 2.69839 -0.00515135 2.70363 -0.313579 -1.0253 0.730227 0.132925 0.0831089 0.0705072
+5 2 1.37953 1.34253 4.03797 9.26012 -1.49812 -2.38291 2.1088 -0.00177977 0.0249746
+6 2 4.039 1.35386 4.04129 -5.61376 0.746262 -1.74478 -2.171 -0.0244362 -0.00315046

examples/QM/LATTE/dump.8Sep22.aimd.plugin

@@ -0,0 +1,315 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.7 2.7 0 -0.601491 0.335597 -0.87242 -2.27066e-14 -1.33391e-14 2.31141e-14
+2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
+3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
+4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
+5 2 1.35 1.35 4.05 2.42711 -1.49109 -2.41596 2.35473 5.79901e-15 -1.19594e-14
+6 2 4.05 1.35 4.05 1.30688 0.784281 -1.73922 -2.35473 -1.38761e-14 1.09382e-14
+ITEM: TIMESTEP
+1
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69985 2.70008 -0.000218105 -0.601467 0.335616 -0.872428 0.00470101 0.00380515 -0.00141625
+2 2 1.35212 4.05114 1.35149 8.64389 4.55886 5.97363 2.34251 -0.00209926 -0.00172976
+3 2 4.0504 4.05163 1.3501 1.41949 6.51866 0.385561 -2.34936 -0.00247497 0.00051716
+4 1 2.69992 -0.00025811 2.70018 -0.325581 -1.03243 0.724334 0.00481137 0.00249244 0.00195665
+5 2 1.35065 1.34963 4.0494 2.78199 -1.49112 -2.4159 2.3517 -0.00043711 0.000874754
+6 2 4.05028 1.3502 4.04957 0.951796 0.784184 -1.73923 -2.35436 -0.00128625 -0.00020256
+ITEM: TIMESTEP
+2
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6997 2.70017 -0.000436214 -0.601396 0.335673 -0.872449 0.00939888 0.00756163 -0.00288164
+2 2 1.35432 4.05228 1.35299 8.99615 4.55837 5.97323 2.32921 -0.00431846 -0.00355855
+3 2 4.05071 4.05326 1.35019 1.06567 6.5181 0.385678 -2.34304 -0.00494314 0.00103532
+4 1 2.69984 -0.000516214 2.70036 -0.325507 -1.03239 0.724364 0.00976944 0.00512657 0.00403686
+5 2 1.35139 1.34925 4.04879 3.13634 -1.49122 -2.4157 2.34776 -0.000851489 0.00177498
+6 2 4.05048 1.35039 4.04913 0.596838 0.783892 -1.73928 -2.3531 -0.00257512 -0.000406965
+ITEM: TIMESTEP
+3
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69955 2.70025 -0.00065433 -0.601277 0.335769 -0.872486 0.0141006 0.0112702 -0.00439552
+2 2 1.35661 4.05342 1.35448 9.34633 4.55754 5.97255 2.31482 -0.00666433 -0.00549143
+3 2 4.05093 4.05489 1.35029 0.712875 6.51717 0.385873 -2.33577 -0.00740896 0.00154764
+4 1 2.69976 -0.000774304 2.70054 -0.325382 -1.03232 0.724417 0.0148831 0.00790884 0.00624833
+5 2 1.35222 1.34888 4.04819 3.49003 -1.49137 -2.41536 2.3429 -0.0012407 0.00270313
+6 2 4.05058 1.35059 4.0487 0.242138 0.783407 -1.73935 -2.35094 -0.00386511 -0.000612161
+ITEM: TIMESTEP
+4
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6994 2.70034 -0.000872457 -0.60111 0.335902 -0.872539 0.0188131 0.0149318 -0.00595718
+2 2 1.359 4.05456 1.35597 9.69425 4.55635 5.97156 2.29933 -0.00914346 -0.00753331
+3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
+4 1 2.69967 -0.00103238 2.70072 -0.325204 -1.03223 0.724492 0.020161 0.0108455 0.00859866
+5 2 1.35314 1.34851 4.04758 3.84292 -1.49159 -2.41488 2.33711 -0.00160232 0.00366164
+6 2 4.0506 1.35078 4.04826 -0.112168 0.782727 -1.73946 -2.34789 -0.00515472 -0.000817084
+ITEM: TIMESTEP
+5
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69925 2.70042 -0.0010906 -0.600896 0.336071 -0.872607 0.0235434 0.0185473 -0.00756588
+2 2 1.36146 4.0557 1.35747 10.0397 4.55478 5.97026 2.2827 -0.0117623 -0.00968894
+3 2 4.05111 4.05815 1.35048 0.0109366 6.51419 0.386489 -2.31832 -0.0123511 0.00252727
+4 1 2.69959 -0.00129042 2.70091 -0.324972 -1.0321 0.724592 0.0256115 0.0139425 0.0110953
+5 2 1.35414 1.34814 4.04698 4.19487 -1.49186 -2.41425 2.33039 -0.00193394 0.0046529
+6 2 4.05052 1.35098 4.04783 -0.465946 0.781852 -1.7396 -2.34393 -0.00644244 -0.00102066
+ITEM: TIMESTEP
+6
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6991 2.7005 -0.00130876 -0.600633 0.336277 -0.872692 0.0282985 0.0221175 -0.00922083
+2 2 1.36401 4.05684 1.35896 10.3827 4.55279 5.96863 2.26494 -0.0145272 -0.0119629
+3 2 4.05107 4.05978 1.35058 -0.337913 6.51214 0.386904 -2.30814 -0.0148362 0.00298071
+4 1 2.69951 -0.00154843 2.70109 -0.324684 -1.03194 0.724717 0.0312427 0.0172058 0.0137455
+5 2 1.35523 1.34776 4.04638 4.54573 -1.49217 -2.41347 2.32273 -0.00223319 0.00567932
+6 2 4.05036 1.35117 4.04739 -0.819058 0.780784 -1.73977 -2.33906 -0.00772673 -0.00122181
+ITEM: TIMESTEP
+7
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69895 2.70059 -0.00152695 -0.600322 0.336519 -0.872794 0.0330853 0.0256435 -0.0109212
+2 2 1.36665 4.05797 1.36045 10.7228 4.55038 5.96665 2.24601 -0.0174443 -0.0143597
+3 2 4.05094 4.0614 1.35068 -0.685154 6.50971 0.387385 -2.29698 -0.0173365 0.00340068
+4 1 2.69943 -0.00180639 2.70127 -0.324338 -1.03175 0.724871 0.0370626 0.020641 0.0165564
+5 2 1.35641 1.34739 4.04577 4.89536 -1.49253 -2.41254 2.31411 -0.0024977 0.00674323
+6 2 4.05012 1.35137 4.04696 -1.17137 0.779522 -1.73997 -2.33329 -0.00900604 -0.00141944
+ITEM: TIMESTEP
+8
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6988 2.70067 -0.00174516 -0.599962 0.336797 -0.872914 0.0379108 0.0291262 -0.0126661
+2 2 1.36938 4.05911 1.36194 11.06 4.54752 5.96429 2.2259 -0.0205196 -0.0168834
+3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
+4 1 2.69935 -0.0020643 2.70145 -0.323932 -1.03153 0.725054 0.0430788 0.0242538 0.0195348
+5 2 1.35768 1.34702 4.04517 5.24362 -1.49292 -2.41144 2.30452 -0.0027252 0.00784692
+6 2 4.04978 1.35156 4.04652 -1.52274 0.778068 -1.7402 -2.32659 -0.0102788 -0.00161245
+ITEM: TIMESTEP
+9
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69865 2.70076 -0.0019634 -0.599553 0.337109 -0.873051 0.0427817 0.0325667 -0.0144547
+2 2 1.37218 4.06025 1.36343 11.3941 4.54418 5.96155 2.20459 -0.023759 -0.019538
+3 2 4.05043 4.06466 1.35087 -1.37421 6.50372 0.388522 -2.27166 -0.0224003 0.00411244
+4 1 2.69927 -0.00232215 2.70163 -0.323464 -1.03126 0.725268 0.0492987 0.0280495 0.0226874
+5 2 1.35904 1.34664 4.04457 5.59036 -1.49335 -2.41017 2.29396 -0.00291347 0.00899259
+6 2 4.04935 1.35176 4.04609 -1.87303 0.776422 -1.74045 -2.31898 -0.0115434 -0.00179972
+ITEM: TIMESTEP
+10
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6985 2.70084 -0.00218168 -0.599095 0.337456 -0.873207 0.0477049 0.0359661 -0.0162858
+2 2 1.37507 4.06138 1.36492 11.7248 4.54034 5.95839 2.18206 -0.0271682 -0.0223275
+3 2 4.05004 4.06628 1.35097 -1.71572 6.50015 0.389163 -2.25748 -0.0249726 0.0043903
+4 1 2.69919 -0.00257993 2.70181 -0.322932 -1.03096 0.725515 0.0557294 0.0320331 0.0260207
+5 2 1.36048 1.34627 4.04397 5.93543 -1.4938 -2.40872 2.2824 -0.00306026 0.0101825
+6 2 4.04884 1.35195 4.04565 -2.2221 0.774587 -1.74074 -2.31042 -0.0127983 -0.00198013
+ITEM: TIMESTEP
+11
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69835 2.70092 -0.00240001 -0.598586 0.337838 -0.873382 0.0526872 0.0393256 -0.0181586
+2 2 1.37805 4.06252 1.36641 12.0521 4.53597 5.9548 2.15829 -0.0307526 -0.0252554
+3 2 4.04957 4.06791 1.35106 -2.05501 6.49619 0.389841 -2.24228 -0.0275775 0.00460683
+4 1 2.69911 -0.00283763 2.70199 -0.322334 -1.03061 0.725796 0.0623777 0.0362096 0.0295409
+5 2 1.362 1.3459 4.04336 6.27868 -1.49427 -2.40709 2.26985 -0.00316333 0.0114188
+6 2 4.04824 1.35215 4.04522 -2.56981 0.772563 -1.74105 -2.30093 -0.0140417 -0.00215255
+ITEM: TIMESTEP
+12
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6982 2.70101 -0.00261837 -0.598027 0.338253 -0.873575 0.0577351 0.0426463 -0.0200718
+2 2 1.3811 4.06365 1.3679 12.3757 4.53105 5.95076 2.13326 -0.0345179 -0.0283253
+3 2 4.04901 4.06953 1.35116 -2.39194 6.49183 0.390547 -2.22604 -0.0302194 0.00475506
+4 1 2.69903 -0.00309524 2.70217 -0.321667 -1.03022 0.726114 0.06925 0.0405836 0.0332542
+5 2 1.36362 1.34552 4.04276 6.61997 -1.49475 -2.40527 2.25627 -0.00322051 0.0127037
+6 2 4.04756 1.35234 4.04478 -2.91602 0.770353 -1.74139 -2.29048 -0.0152721 -0.00231583
+ITEM: TIMESTEP
+13
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69805 2.70109 -0.00283679 -0.597416 0.338702 -0.873788 0.0628554 0.0459295 -0.0220243
+2 2 1.38423 4.06478 1.36939 12.6954 4.52555 5.94625 2.10694 -0.0384688 -0.0315401
+3 2 4.04837 4.07115 1.35126 -2.72634 6.48707 0.39127 -2.20874 -0.0329024 0.00482793
+4 1 2.69895 -0.00335274 2.70236 -0.320929 -1.02979 0.726471 0.0763523 0.0451591 0.0371659
+5 2 1.36531 1.34515 4.04216 6.95912 -1.49523 -2.40326 2.24165 -0.00322965 0.0140393
+6 2 4.04678 1.35253 4.04434 -3.26057 0.767958 -1.74175 -2.27906 -0.0164877 -0.0024688
+ITEM: TIMESTEP
+14
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6979 2.70118 -0.00305527 -0.596753 0.339184 -0.874022 0.0680546 0.0491768 -0.0240145
+2 2 1.38745 4.06591 1.37087 13.0111 4.51944 5.94124 2.07932 -0.0426096 -0.0349018
+3 2 4.04765 4.07277 1.35136 -3.05804 6.4819 0.391997 -2.19038 -0.035631 0.00481829
+4 1 2.69887 -0.00361013 2.70254 -0.320118 -1.0293 0.726868 0.0836894 0.0499393 0.0412807
+5 2 1.3671 1.34478 4.04156 7.296 -1.49572 -2.40103 2.22598 -0.00318867 0.0154277
+6 2 4.04593 1.35272 4.04391 -3.60334 0.765381 -1.74213 -2.26667 -0.0176868 -0.00261028
+ITEM: TIMESTEP
+15
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69775 2.70126 -0.0032738 -0.596036 0.339698 -0.874275 0.0733392 0.0523895 -0.0260413
+2 2 1.39074 4.06704 1.37236 13.3225 4.51268 5.93571 2.05037 -0.0469451 -0.0384133
+3 2 4.04685 4.07439 1.35146 -3.3869 6.47632 0.392716 -2.17093 -0.038409 0.00471919
+4 1 2.69879 -0.00386739 2.70272 -0.319232 -1.02877 0.727309 0.0912666 0.0549279 0.0456036
+5 2 1.36896 1.3444 4.04096 7.63043 -1.49619 -2.3986 2.20924 -0.00309551 0.0168709
+6 2 4.04498 1.35291 4.04347 -3.94416 0.762625 -1.74253 -2.25329 -0.0188678 -0.0027391
+ITEM: TIMESTEP
+16
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.6976 2.70135 -0.00349241 -0.595266 0.340245 -0.87455 0.0787153 0.055569 -0.0281032
+2 2 1.39411 4.06817 1.37384 13.6294 4.50526 5.92964 2.02007 -0.0514799 -0.042077
+3 2 4.04596 4.07601 1.35155 -3.71274 6.47031 0.393413 -2.15039 -0.0412405 0.00452364
+4 1 2.69871 -0.00412452 2.7029 -0.318268 -1.02819 0.727794 0.0990893 0.0601283 0.0501398
+5 2 1.37091 1.34403 4.04036 7.96225 -1.49665 -2.39594 2.19142 -0.00294819 0.0183708
+6 2 4.04395 1.3531 4.04304 -4.28288 0.759692 -1.74296 -2.2389 -0.0200287 -0.00285406
+ITEM: TIMESTEP
+17
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69745 2.70143 -0.00371108 -0.594441 0.340824 -0.874845 0.0841889 0.0587168 -0.0301987
+2 2 1.39755 4.0693 1.37532 13.9317 4.49714 5.92301 1.9884 -0.0562187 -0.0458954
+3 2 4.04499 4.07763 1.35165 -4.0354 6.46388 0.394073 -2.12872 -0.0441293 0.0042247
+4 1 2.69863 -0.00438149 2.70308 -0.317223 -1.02755 0.728326 0.107162 0.0655439 0.054894
+5 2 1.37294 1.34365 4.03976 8.2913 -1.49708 -2.39305 2.17248 -0.00274479 0.0199293
+6 2 4.04284 1.35329 4.0426 -4.61936 0.756586 -1.74339 -2.2235 -0.0211679 -0.00295392
+ITEM: TIMESTEP
+18
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69731 2.70152 -0.00392983 -0.593559 0.341435 -0.875162 0.0897661 0.0618346 -0.0323262
+2 2 1.40107 4.07042 1.3768 14.229 4.48829 5.91578 1.95532 -0.0611659 -0.0498706
+3 2 4.04394 4.07924 1.35175 -4.3547 6.457 0.394679 -2.10593 -0.0470792 0.0038154
+4 1 2.69855 -0.00463829 2.70327 -0.316095 -1.02686 0.728907 0.11549 0.0711775 0.0598705
+5 2 1.37506 1.34328 4.03916 8.61741 -1.49747 -2.38993 2.15241 -0.00248344 0.0215483
+6 2 4.04164 1.35348 4.04217 -4.95344 0.753309 -1.74385 -2.20706 -0.0222835 -0.00303744
+ITEM: TIMESTEP
+19
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69716 2.7016 -0.00414866 -0.592621 0.342077 -0.8755 0.0954526 0.0649239 -0.0344841
+2 2 1.40467 4.07154 1.37828 14.5213 4.47868 5.90795 1.92083 -0.0663258 -0.0540045
+3 2 4.04281 4.08086 1.35185 -4.67049 6.44967 0.395215 -2.08198 -0.050094 0.00328881
+4 1 2.69847 -0.00489492 2.70345 -0.314881 -1.02611 0.72954 0.124076 0.0770317 0.0650736
+5 2 1.37725 1.3429 4.03857 8.94041 -1.49782 -2.38655 2.13119 -0.00216234 0.0232295
+6 2 4.04036 1.35367 4.04173 -5.28496 0.749867 -1.74431 -2.18956 -0.0233735 -0.00310338
+ITEM: TIMESTEP
+20
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z vx vy vz fx fy fz
+1 1 2.69701 2.70169 -0.00436758 -0.591624 0.342751 -0.875861 0.101254 0.0679866 -0.0366705
+2 2 1.40833 4.07266 1.37976 14.8083 4.46827 5.89948 1.88489 -0.0717024 -0.0582989
+3 2 4.0416 4.08247 1.35195 -4.98257 6.44189 0.395662 -2.05686 -0.0531772 0.00263798
+4 1 2.69839 -0.00515135 2.70363 -0.313579 -1.0253 0.730227 0.132925 0.0831089 0.0705072
+5 2 1.37953 1.34253 4.03797 9.26012 -1.49812 -2.38291 2.1088 -0.00177977 0.0249746
+6 2 4.039 1.35386 4.04129 -5.61376 0.746262 -1.74478 -2.171 -0.0244362 -0.00315046

examples/QM/LATTE/dump.8Sep22.series.mpi.1.2uo2

@@ -0,0 +1,15 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
+2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
+3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
+4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
+5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
+6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14

examples/QM/LATTE/dump.8Sep22.series.mpi.1.3uo2

@@ -0,0 +1,18 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+9
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 2.7 0 -1.27436e-13 0.760572 0.760572
+2 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
+3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
+4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
+5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
+6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
+7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
+8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
+9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

examples/QM/LATTE/dump.8Sep22.series.mpi.1.4uo2

@@ -0,0 +1,21 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+12
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
+2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
+3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
+4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
+5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
+6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
+7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
+8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
+9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
+10 1 5.4 0 0 0.211437 1.63064 -0.0728897
+11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
+12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

examples/QM/LATTE/dump.8Sep22.series.mpi.2.2uo2

@@ -0,0 +1,15 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
+2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
+3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
+4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
+5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
+6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14

examples/QM/LATTE/dump.8Sep22.series.mpi.2.3uo2

@@ -0,0 +1,18 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+9
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 2.7 0 -1.27436e-13 0.760572 0.760572
+2 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
+3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
+4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
+5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
+6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
+7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
+8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
+9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

examples/QM/LATTE/dump.8Sep22.series.mpi.2.4uo2

@@ -0,0 +1,21 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+12
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
+2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
+3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
+4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
+5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
+6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
+7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
+8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
+9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
+10 1 5.4 0 0 0.211437 1.63064 -0.0728897
+11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
+12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

examples/QM/LATTE/dump.8Sep22.series.plugin.2uo2

@@ -0,0 +1,15 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+6
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
+2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
+3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
+4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
+5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
+6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14

examples/QM/LATTE/dump.8Sep22.series.plugin.3uo2

@@ -0,0 +1,18 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+9
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 2.7 0 -1.27436e-13 0.760572 0.760572
+2 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
+3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
+4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
+5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
+6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
+7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
+8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
+9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

examples/QM/LATTE/dump.8Sep22.series.plugin.4uo2

@@ -0,0 +1,21 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+12
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
+0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
+0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
+ITEM: ATOMS id type x y z fx fy fz
+1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
+2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
+3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
+4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
+5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
+6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
+7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
+8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
+9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
+10 1 5.4 0 0 0.211437 1.63064 -0.0728897
+11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
+12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

examples/QM/LATTE/electrons.dat

@@ -0,0 +1,15 @@
+Noelem=  2
+Element   basis    Numel   Es          Ep        Ed          Ef    Mass     HubbardU  Wss        Wpp      Wdd        Wff
+U sdf 6.0 -4.08 0.0 0.816 -0.586 238.05078 9.0 0.0 0.0 0.0 0.0
+O sp 6.0 -23.77 -8.85 0.0 0.0 15.994915 12.2 0.0 0.0 0.0 0.0
+
+
+W spd 6.0 -4.52 0.53 -2.91 0.0 183.84 7.048 0.0 0.0 0.0 0.0
+Mo sd  6.0 -3.29 0.0 -1.98 0.0 95.95 6.48 0.0 0.0 0.0 0.0
+S sp  6.0 -14.00 -3.97 0.0 0.0 32.06 8.28 0.0 -0.4278 0.0 0.0
+
+
+N sp 5.000000 -18.543798 -7.862407 0.000000 0.000000 14.006700 17.053958 0.000000 -0.6934 0.000000 0.000000 
+H s 1.000000 -6.237968 0.000000 0.000000 0.000000 1.007900 13.684855 -2.23400 0.000000 0.000000 0.000000 
+C sp 4.000000 -13.736556 -4.748938 0.000000 0.000000 12.010000 10.522540 0.000000 -0.618100 0.000000 0.000000 
+O sp 6.000000 -23.833752 -9.645001 0.000000 0.000000 15.999400 14.443874 0.000000 -0.757650 0.000000 0.000000 

examples/QM/LATTE/in.aimd

@@ -0,0 +1,26 @@
+# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
+
+units           metal
+atom_style      full
+atom_modify     sort 0 0.0
+
+read_data       2uo2.lmp
+
+velocity        all create 300.0 87287 loop geom
+
+neighbor        1.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+timestep        0.00025
+
+fix             1 all nve
+
+fix             2 all mdi/qm virial yes elements 92 8
+
+thermo_style    custom step temp pe etotal press
+thermo          1
+
+dump            1 all custom 1 dump.aimd.mpi &
+                id type x y z vx vy vz fx fy fz
+
+run             20

examples/QM/LATTE/in.aimd.plugin

@@ -0,0 +1,27 @@
+# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
+
+units           metal
+atom_style      full
+atom_modify     sort 0 0.0
+
+read_data       2uo2.lmp
+
+velocity        all create 300.0 87287 loop geom
+
+neighbor        1.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+timestep        0.00025
+
+fix             1 all nve
+
+fix             2 all mdi/qm virial yes elements 92 8
+
+thermo_style    custom step temp pe etotal press
+thermo          1
+
+dump            1 all custom 1 dump.aimd.plugin &
+                id type x y z vx vy vz fx fy fz
+
+mdi             plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
+                command "run 20"

examples/QM/LATTE/in.series

@@ -0,0 +1,37 @@
+# Series of single-point calcs of 2,3,4 UO2 molecules
+# with LATTE in MDI stand-alone mode
+
+variable        files index 2uo2 3uo2 4uo2
+
+mdi             connect
+
+label LOOP
+
+  units           metal
+  atom_style      full
+  atom_modify     sort 0 0.0
+
+  read_data       ${files}.lmp
+
+  neighbor        0.3 bin
+  neigh_modify    every 1 delay 0 check yes
+
+  timestep        0.001
+
+  fix             1 all mdi/qm virial yes elements 92 8 connect no
+
+  thermo_style    custom step temp pe etotal press
+  thermo          1
+
+  run             0
+
+  write_dump      all custom dump.series.mpi.${files} &
+                  id type x y z fx fy fz modify sort id
+
+  clear
+
+next            files
+
+jump            SELF LOOP
+
+mdi             exit

examples/QM/LATTE/in.series.plugin

@@ -0,0 +1,32 @@
+# Series of single-point calcs of 2,3,4 UO2 molecules
+# with LATTE in MDI plugin mode
+
+variable        files index 2uo2 3uo2 4uo2
+
+label LOOP
+
+  units           metal
+  atom_style      full
+  atom_modify     sort 0 0.0
+
+  read_data       ${files}.lmp
+
+  neighbor        0.3 bin
+  neigh_modify    every 1 delay 0 check yes
+
+  fix             1 all mdi/qm virial yes elements 92 8
+
+  thermo_style    custom step temp pe etotal press
+  thermo          1
+
+  mdi             plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
+                  command "run 0"
+
+  write_dump      all custom dump.series.plugin.${files} &
+                  id type x y z fx fy fz modify sort id
+
+  clear
+
+next            files
+
+jump            SELF LOOP

examples/QM/LATTE/latte.in

@@ -0,0 +1,67 @@
+#General controls
+CONTROL{
+  XCONTROL= 1
+  BASISTYPE= NONORTHO
+  PARAMPATH= './'
+  SCLTYPE= TABLE
+  DEBUGON= 0
+  FERMIM= 6
+  CGORLIB= 1 CGTOL= 1.0e-6
+  KBT= 1.0
+  NORECS= 5
+  ENTROPYKIND= 1
+  PPOTON= 2 VDWON= 0
+  SPINON= 0 SPINTOL= 1.0e-4
+  ELECTRO= 1 ELECMETH= 0 ELEC_ETOL= 0.001 ELEC_QTOL= 1.0e-12
+  COULACC= 1.0e-6 COULCUT= -500.0 COULR1= 500.0
+  MAXSCF= 250
+  BREAKTOL= 1.0E-12 MINSP2ITER= 22 SP2CONV= REL
+  FULLQCONV= 1 QITER= 0
+  QMIX= 0.05 SPINMIX= 0.05 MDMIX= 0.05
+  #QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25
+  ORDERNMOL= 0
+  SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4
+  MSPARSE= 3000
+  LCNON= 0 LCNITER= 4 CHTOL= 0.01
+  SKIN= 1.0
+  RELAX= 0 RELAXTYPE= SD MAXITER= 100 RLXFTOL= 0.001
+  MDON= 1
+  PBCON= 1
+  RESTART= 0
+  CHARGE= 0
+  XBO= 1
+  XBODISON= 1
+  XBODISORDER= 5
+  NGPU= 2
+  KON= 0
+  COMPFORCE= 1
+  DOSFIT= 0 INTS2FIT= 1 BETA= 1000.0 NFITSTEP= 5000 QFIT= 0 MCSIGMA= 0.2
+  PPFITON=  0
+  ALLFITON= 0
+  PPSTEP= 500 BISTEP= 500 PP2FIT= 2 BINT2FIT= 6 
+  PPBETA= 1000.0 PPSIGMA= 0.01 PPNMOL= 10 PPNGEOM= 200
+  PARREP= 0
+  ER= 1.0
+  #DOKERNEL= T
+}
+
+MDCONTROL{
+MAXITER= 2000
+UDNEIGH= 1
+DT= 0.5
+TEMPERATURE= 1.0e-10 RNDIST= GAUSSIAN SEEDINIT= UNIFORM
+DUMPFREQ= 250
+RSFREQ= 500
+WRTFREQ= 1
+TOINITTEMP5= 1
+THERMPER= 500
+THERMRUN= 50000
+NVTON= 0 NPTON= 0 AVEPER= 1000  FRICTION= 1000.0 SEED= 54
+PTARGET= 0.0 NPTTYPE= ISO
+SHOCKON= 0
+SHOCKSTART= 100000
+SHOCKDIR= 1
+UPARTICLE= 500.0 USHOCK= -4590.0 C0= 1300.0
+MDADAPT= 0
+GETHUG= 0 E0= -795.725  V0= 896.984864 P0= 0.083149
+}

examples/QM/LATTE/log.8Sep22.aimd.lammps.mpi.1

@@ -0,0 +1,102 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
+
+units           metal
+atom_style      full
+atom_modify     sort 0 0.0
+
+read_data       2uo2.lmp
+Reading data file ...
+  triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  6 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+velocity        all create 300.0 87287 loop geom
+
+neighbor        1.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+timestep        0.00025
+
+fix             1 all nve
+
+fix             2 all mdi/qm virial yes elements 92 8
+
+thermo_style    custom step temp pe etotal press
+thermo          1
+
+dump            1 all custom 1 dump.aimd.mpi                 id type x y z vx vy vz fx fy fz
+
+run             20
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0
+  ghost atom cutoff = 0
+  binsize = 10.8, bins = 1 1 1
+  0 neighbor lists, perpetual/occasional/extra = 0 0 0
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
+Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
+   Step          Temp          PotEng         TotEng         Press     
+         0   300           -50.539035     -50.345145     -120197.6     
+         1   307.57345     -50.544722     -50.345937     -120123.27    
+         2   316.3757      -50.551342     -50.346868     -120035.12    
+         3   326.39203     -50.558885     -50.347938     -119933.11    
+         4   337.60559     -50.567341     -50.349146     -119817.17    
+         5   349.99734     -50.576697     -50.350493     -119687.24    
+         6   363.54606     -50.586939     -50.351979     -119543.23    
+         7   378.22834     -50.598054     -50.353605     -119385.07    
+         8   394.0186      -50.610024     -50.355369     -119212.67    
+         9   410.88903     -50.622831     -50.357273     -119025.94    
+        10   428.80963     -50.636457     -50.359317     -118824.77    
+        11   447.74819     -50.65088      -50.3615       -118609.06    
+        12   467.67027     -50.666079     -50.363823     -118378.7     
+        13   488.53922     -50.68203      -50.366287     -118133.58    
+        14   510.31617     -50.698708     -50.36889      -117873.58    
+        15   532.96002     -50.716086     -50.371633     -117598.57    
+        16   556.42747     -50.734137     -50.374517     -117308.44    
+        17   580.67298     -50.75283      -50.377541     -117003.05    
+        18   605.64879     -50.772136     -50.380705     -116682.27    
+        19   631.30497     -50.792023     -50.38401      -116345.95    
+        20   657.58937     -50.812455     -50.387454     -115993.97    
+Loop time of 3.40001 on 1 procs for 20 steps with 6 atoms
+
+Performance: 0.127 ns/day, 188.889 hours/ns, 5.882 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Bond    | 1.2223e-05 | 1.2223e-05 | 1.2223e-05 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 6.0971e-05 | 6.0971e-05 | 6.0971e-05 |   0.0 |  0.00
+Output  | 0.0009257  | 0.0009257  | 0.0009257  |   0.0 |  0.03
+Modify  | 3.3989     | 3.3989     | 3.3989     |   0.0 | 99.97
+Other   |            | 6.824e-05  |            |       |  0.00
+
+Nlocal:              6 ave           6 max           6 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              2 ave           2 max           2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:03