diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 0f15bf02be..08522c6d15 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -73,7 +73,7 @@ Here is a checklist of steps you need to follow to submit a single file or user
 * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
 * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
-* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). As appropriate, the text files can include mathematical expressions in MathJAX markup or links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
+* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
 * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
 * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
 
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 13e1d1539f..faba3a5ce0 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -2,7 +2,7 @@
 # CMake build system
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
-cmake_minimum_required(VERSION 2.8.12)
+cmake_minimum_required(VERSION 3.10)
 
 project(lammps CXX)
 set(SOVERSION 0)
@@ -52,16 +52,19 @@ include(CheckCCompilerFlag)
 include(CheckIncludeFileCXX)
 
 if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
-  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
 endif()
 
-option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
-if(DISABLE_CXX11_REQUIREMENT)
-  add_definitions(-DLAMMPS_CXX98)
-# else()
-#  set(CMAKE_CXX_STANDARD 11)
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  if(NOT ("${CMAKE_BUILD_TYPE}" STREQUAL "Debug"))
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ffast-math -ftree-vectorize -fexpensive-optimizations")
+  endif()
 endif()
 
+# we require C++11
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 # GNU compiler features
 if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
   option(ENABLE_COVERAGE "Enable code coverage" OFF)
@@ -131,9 +134,9 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
   USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS
   USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
   USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
-  USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC
-  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
-  USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
+  USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
+  USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+  USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
@@ -178,6 +181,7 @@ option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 if(BUILD_MPI)
   find_package(MPI REQUIRED)
   include_directories(${MPI_CXX_INCLUDE_PATH})
+  add_definitions(-DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1)
   list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
   option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
   if(LAMMPS_LONGLONG_TO_LONG)
@@ -355,9 +359,6 @@ endforeach(HEADER)
 set(MATH_LIBRARIES "m" CACHE STRING "math library")
 mark_as_advanced( MATH_LIBRARIES )
 include(CheckLibraryExists)
-if (CMAKE_VERSION VERSION_LESS "3.4")
-  enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
-endif()
 # RB: disabled this check because it breaks with KOKKOS CUDA enabled
 #foreach(FUNC sin cos)
 #  check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake
index dab9d51a3f..200d8fb51e 100644
--- a/cmake/Modules/Packages/GPU.cmake
+++ b/cmake/Modules/Packages/GPU.cmake
@@ -1,7 +1,4 @@
 if(PKG_GPU)
-    if (CMAKE_VERSION VERSION_LESS "3.1")
-      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
-    endif()
     set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
     set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                     ${GPU_SOURCES_DIR}/fix_gpu.h
diff --git a/cmake/Modules/Packages/LATTE.cmake b/cmake/Modules/Packages/LATTE.cmake
index de7116780b..8bcda84cdc 100644
--- a/cmake/Modules/Packages/LATTE.cmake
+++ b/cmake/Modules/Packages/LATTE.cmake
@@ -8,9 +8,6 @@ if(PKG_LATTE)
   endif()
   option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
   if(DOWNLOAD_LATTE)
-    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
-      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
-    endif()
     if(CMAKE_GENERATOR STREQUAL "Ninja")
       message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
     endif()
diff --git a/cmake/Modules/Packages/MSCG.cmake b/cmake/Modules/Packages/MSCG.cmake
index b442580583..99d98659ee 100644
--- a/cmake/Modules/Packages/MSCG.cmake
+++ b/cmake/Modules/Packages/MSCG.cmake
@@ -8,9 +8,6 @@ if(PKG_MSCG)
   endif()
   option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
   if(DOWNLOAD_MSCG)
-    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
-      message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
-    endif()
     if(CMAKE_GENERATOR STREQUAL "Ninja")
       message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
     endif()
diff --git a/cmake/Modules/Packages/USER-MOLFILE.cmake b/cmake/Modules/Packages/USER-MOLFILE.cmake
index b8c4234d26..16ffc34994 100644
--- a/cmake/Modules/Packages/USER-MOLFILE.cmake
+++ b/cmake/Modules/Packages/USER-MOLFILE.cmake
@@ -1,8 +1,4 @@
 if(PKG_USER-MOLFILE)
-  if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library
-    message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later")
-  endif()
-
   set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
diff --git a/doc/lammps.1 b/doc/lammps.1
index 08a282aac9..1368679d3c 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -1,4 +1,4 @@
-.TH LAMMPS "27 February 2020" "2020-02-27"
+.TH LAMMPS "3 March 2020" "2020-03-03"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst
index 8314afaa0e..939431c6b3 100644
--- a/doc/src/Build_cmake.rst
+++ b/doc/src/Build_cmake.rst
@@ -95,10 +95,8 @@ this directory or sub-directories within it that CMake creates.
    directory to un-install all packages.  The purge removes all the \*.h
    files auto-generated by make.
 
-You must have CMake version 2.8 or later on your system to build
-LAMMPS.  A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
-later version.  CMake will print a message telling you if a later
-version is required.  Installation instructions for CMake are below.
+You must have CMake version 3.10 or later on your system to build
+LAMMPS.  Installation instructions for CMake are below.
 
 After the initial build, if you edit LAMMPS source files, or add your
 own new files to the source directory, you can just re-type make from
diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst
index 74c4e71dbd..a4064ee812 100644
--- a/doc/src/Build_extras.rst
+++ b/doc/src/Build_extras.rst
@@ -287,22 +287,29 @@ KOKKOS\_ARCH settings described below.  Note that for CMake, these are
 really Kokkos variables, not LAMMPS variables.  Hence you must use
 case-sensitive values, e.g. BDW, not bdw.
 
+* AMDAVX = AMD 64-bit x86 CPUs
+* EPYC   = AMD EPYC Zen class CPUs
 * ARMv80 = ARMv8.0 Compatible CPU
 * ARMv81 = ARMv8.1 Compatible CPU
 * ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
-* BGQ = IBM Blue Gene/Q CPUs
-* Power8 = IBM POWER8 CPUs
-* Power9 = IBM POWER9 CPUs
+* ARMv8-TX2 = ARMv8 Cavium ThunderX2 CPU
+* WSM = Intel Westmere CPUs
 * SNB = Intel Sandy/Ivy Bridge CPUs
 * HSW = Intel Haswell CPUs
 * BDW = Intel Broadwell Xeon E-class CPUs
 * SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
 * KNC = Intel Knights Corner Xeon Phi
 * KNL = Intel Knights Landing Xeon Phi
+* BGQ = IBM Blue Gene/Q CPUs
+* Power7 = IBM POWER8 CPUs
+* Power8 = IBM POWER8 CPUs
+* Power9 = IBM POWER9 CPUs
+* Kepler = NVIDIA Kepler default (generation CC 3.5)
 * Kepler30 = NVIDIA Kepler generation CC 3.0
 * Kepler32 = NVIDIA Kepler generation CC 3.2
 * Kepler35 = NVIDIA Kepler generation CC 3.5
 * Kepler37 = NVIDIA Kepler generation CC 3.7
+* Maxwell = NVIDIA Maxwell default (generation CC 5.0)
 * Maxwell50 = NVIDIA Maxwell generation CC 5.0
 * Maxwell52 = NVIDIA Maxwell generation CC 5.2
 * Maxwell53 = NVIDIA Maxwell generation CC 5.3
diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst
index 1e668ee95d..5f835f76a0 100644
--- a/doc/src/Build_settings.rst
+++ b/doc/src/Build_settings.rst
@@ -23,11 +23,11 @@ explain how to do this for building both with CMake and make.
 C++11 standard compliance
 ------------------------------------------
 
-The LAMMPS developers plan to transition to make the C++11 standard the
-minimum requirement for compiling LAMMPS.  Currently this only applies to
-some packages like KOKKOS while the rest aims to be compatible with the C++98
-standard.  Most currently used compilers are compatible with C++11; some need
-to set extra flags to enable C++11 compliance.  Example for GNU c++:
+A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
+LAMMPS version 3 March 2020 is the last version compatible with the previous
+C++98 standard for the core code and most packages. Most currently used
+C++ compilers are compatible with C++11, but some older ones may need extra
+flags to enable C++11 compliance.  Example for GNU c++ 4.8.x:
 
 .. code-block:: make
 
diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst
index 721c5ece37..36ae112527 100644
--- a/doc/src/Commands_all.rst
+++ b/doc/src/Commands_all.rst
@@ -17,7 +17,7 @@ General commands
 An alphabetic list of all general LAMMPS commands.
 
 .. table_from_list::
-   :columns: 6
+   :columns: 5
 
    * :doc:`angle_coeff <angle_coeff>`
    * :doc:`angle_style <angle_style>`
diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst
index 00d06fed47..da40ada999 100644
--- a/doc/src/Commands_category.rst
+++ b/doc/src/Commands_category.rst
@@ -9,133 +9,161 @@ have their own pages where they are listed alphabetically.
 Initialization:
 ------------------------------
 
-* :doc:`newton <newton>`,
-* :doc:`package <package>`,
-* :doc:`processors <processors>`,
-* :doc:`suffix <suffix>`,
-* :doc:`units <units>`
+.. table_from_list::
+   :columns: 5
+
+   * :doc:`newton <newton>`
+   * :doc:`package <package>`
+   * :doc:`processors <processors>`
+   * :doc:`suffix <suffix>`
+   * :doc:`units <units>`
 
 Setup simulation box:
 ------------------------------
 
-* :doc:`boundary <boundary>`,
-* :doc:`box <box>`,
-* :doc:`change_box <change_box>`,
-* :doc:`create_box <create_box>`,
-* :doc:`dimension <dimension>`,
-* :doc:`lattice <lattice>`,
-* :doc:`region <region>`
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`boundary <boundary>`
+   * :doc:`box <box>`
+   * :doc:`change_box <change_box>`
+   * :doc:`create_box <create_box>`
+   * :doc:`dimension <dimension>`
+   * :doc:`lattice <lattice>`
+   * :doc:`region <region>`
 
 Setup atoms:
 ------------------------------
 
-* :doc:`atom_modify <atom_modify>`,
-* :doc:`atom_style <atom_style>`,
-* :doc:`balance <balance>`,
-* :doc:`create_atoms <create_atoms>`,
-* :doc:`create_bonds <create_bonds>`,
-* :doc:`delete_atoms <delete_atoms>`,
-* :doc:`delete_bonds <delete_bonds>`,
-* :doc:`displace_atoms <displace_atoms>`,
-* :doc:`group <group>`,
-* :doc:`mass <mass>`,
-* :doc:`molecule <molecule>`,
-* :doc:`read_data <read_data>`,
-* :doc:`read_dump <read_dump>`,
-* :doc:`read_restart <read_restart>`,
-* :doc:`replicate <replicate>`,
-* :doc:`set <set>`,
-* :doc:`velocity <velocity>`
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`atom_modify <atom_modify>`
+   * :doc:`atom_style <atom_style>`
+   * :doc:`balance <balance>`
+   * :doc:`create_atoms <create_atoms>`
+   * :doc:`create_bonds <create_bonds>`
+   * :doc:`delete_atoms <delete_atoms>`
+   * :doc:`delete_bonds <delete_bonds>`
+   * :doc:`displace_atoms <displace_atoms>`
+   * :doc:`group <group>`
+   * :doc:`mass <mass>`
+   * :doc:`molecule <molecule>`
+   * :doc:`read_data <read_data>`
+   * :doc:`read_dump <read_dump>`
+   * :doc:`read_restart <read_restart>`
+   * :doc:`replicate <replicate>`
+   * :doc:`set <set>`
+   * :doc:`velocity <velocity>`
 
 Force fields:
 ------------------------------
 
-* :doc:`angle_coeff <angle_coeff>`,
-* :doc:`angle_style <angle_style>`,
-* :doc:`bond_coeff <bond_coeff>`,
-* :doc:`bond_style <bond_style>`,
-* :doc:`bond_write <bond_write>`,
-* :doc:`dielectric <dielectric>`,
-* :doc:`dihedral_coeff <dihedral_coeff>`,
-* :doc:`dihedral_style <dihedral_style>`,
-* :doc:`improper_coeff <improper_coeff>`,
-* :doc:`improper_style <improper_style>`,
-* :doc:`kspace_modify <kspace_modify>`,
-* :doc:`kspace_style <kspace_style>`,
-* :doc:`pair_coeff <pair_coeff>`,
-* :doc:`pair_modify <pair_modify>`,
-* :doc:`pair_style <pair_style>`,
-* :doc:`pair_write <pair_write>`,
-* :doc:`special_bonds <special_bonds>`
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`angle_coeff <angle_coeff>`
+   * :doc:`angle_style <angle_style>`
+   * :doc:`bond_coeff <bond_coeff>`
+   * :doc:`bond_style <bond_style>`
+   * :doc:`bond_write <bond_write>`
+   * :doc:`dielectric <dielectric>`
+   * :doc:`dihedral_coeff <dihedral_coeff>`
+   * :doc:`dihedral_style <dihedral_style>`
+   * :doc:`improper_coeff <improper_coeff>`
+   * :doc:`improper_style <improper_style>`
+   * :doc:`kspace_modify <kspace_modify>`
+   * :doc:`kspace_style <kspace_style>`
+   * :doc:`pair_coeff <pair_coeff>`
+   * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_style <pair_style>`
+   * :doc:`pair_write <pair_write>`
+   * :doc:`special_bonds <special_bonds>`
 
 Settings:
 ------------------------------
 
-* :doc:`comm_modify <comm_modify>`,
-* :doc:`comm_style <comm_style>`,
-* :doc:`info <info>`,
-* :doc:`min_modify <min_modify>`,
-* :doc:`min_style <min_style>`,
-* :doc:`neigh_modify <neigh_modify>`,
-* :doc:`neighbor <neighbor>`,
-* :doc:`partition <partition>`,
-* :doc:`reset_timestep <reset_timestep>`,
-* :doc:`run_style <run_style>`,
-* :doc:`timer <timer>`,
-* :doc:`timestep <timestep>`
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`comm_modify <comm_modify>`
+   * :doc:`comm_style <comm_style>`
+   * :doc:`info <info>`
+   * :doc:`min_modify <min_modify>`
+   * :doc:`min_style <min_style>`
+   * :doc:`neigh_modify <neigh_modify>`
+   * :doc:`neighbor <neighbor>`
+   * :doc:`partition <partition>`
+   * :doc:`reset_timestep <reset_timestep>`
+   * :doc:`run_style <run_style>`
+   * :doc:`timer <timer>`
+   * :doc:`timestep <timestep>`
 
 Operations within timestepping (fixes) and diagnostics (computes):
 ------------------------------------------------------------------------------------------
 
-* :doc:`compute <compute>`,
-* :doc:`compute_modify <compute_modify>`,
-* :doc:`fix <fix>`,
-* :doc:`fix_modify <fix_modify>`,
-* :doc:`uncompute <uncompute>`,
-* :doc:`unfix <unfix>`
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`compute <compute>`
+   * :doc:`compute_modify <compute_modify>`
+   * :doc:`fix <fix>`
+   * :doc:`fix_modify <fix_modify>`
+   * :doc:`uncompute <uncompute>`
+   * :doc:`unfix <unfix>`
 
 Output:
 ------------------------------
 
-* :doc:`dump image <dump_image>`,
-* :doc:`dump movie <dump_image>`,
-* :doc:`dump <dump>`,
-* :doc:`dump_modify <dump_modify>`,
-* :doc:`restart <restart>`,
-* :doc:`thermo <thermo>`,
-* :doc:`thermo_modify <thermo_modify>`,
-* :doc:`thermo_style <thermo_style>`,
-* :doc:`undump <undump>`,
-* :doc:`write_coeff <write_coeff>`,
-* :doc:`write_data <write_data>`,
-* :doc:`write_dump <write_dump>`,
-* :doc:`write_restart <write_restart>`
+.. table_from_list::
+   :columns: 4
+
+   * :doc:`dump image <dump_image>`
+   * :doc:`dump movie <dump_image>`
+   * :doc:`dump <dump>`
+   * :doc:`dump_modify <dump_modify>`
+   * :doc:`restart <restart>`
+   * :doc:`thermo <thermo>`
+   * :doc:`thermo_modify <thermo_modify>`
+   * :doc:`thermo_style <thermo_style>`
+   * :doc:`undump <undump>`
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`
 
 Actions:
 ------------------------------
 
-* :doc:`minimize <minimize>`,
-* :doc:`neb <neb>`,
-* :doc:`neb_spin <neb_spin>`,
-* :doc:`prd <prd>`,
-* :doc:`rerun <rerun>`,
-* :doc:`run <run>`,
-* :doc:`tad <tad>`,
-* :doc:`temper <temper>`
+.. table_from_list::
+   :columns: 6
+
+   * :doc:`minimize <minimize>`
+   * :doc:`neb <neb>`
+   * :doc:`neb_spin <neb_spin>`
+   * :doc:`prd <prd>`
+   * :doc:`rerun <rerun>`
+   * :doc:`run <run>`
+   * :doc:`tad <tad>`
+   * :doc:`temper <temper>`
 
 Input script control:
 ------------------------------
 
-* :doc:`clear <clear>`,
-* :doc:`echo <echo>`,
-* :doc:`if <if>`,
-* :doc:`include <include>`,
-* :doc:`jump <jump>`,
-* :doc:`label <label>`,
-* :doc:`log <log>`,
-* :doc:`next <next>`,
-* :doc:`print <print>`,
-* :doc:`python <python>`,
-* :doc:`quit <quit>`,
-* :doc:`shell <shell>`,
-* :doc:`variable <variable>`
+.. table_from_list::
+   :columns: 7
+
+   * :doc:`clear <clear>`
+   * :doc:`echo <echo>`
+   * :doc:`if <if>`
+   * :doc:`include <include>`
+   * :doc:`info <info>`
+   * :doc:`jump <jump>`
+   * :doc:`label <label>`
+   * :doc:`log <log>`
+   * :doc:`next <next>`
+   * :doc:`print <print>`
+   * :doc:`python <python>`
+   * :doc:`quit <quit>`
+   * :doc:`shell <shell>`
+   * :doc:`variable <variable>`
diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index ad5e4f10bf..13336fa89b 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -20,7 +20,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
 .. table_from_list::
-   :columns: 6
+   :columns: 5
 
    * :doc:`ackland/atom <compute_ackland_atom>`
    * :doc:`adf <compute_adf>`
diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index 0b6b892b9d..0ee7381617 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -20,7 +20,7 @@ parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 6
+   :columns: 5
 
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index 28f50bfd8e..10873f1203 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -26,6 +26,10 @@ OPT.
    * :doc:`zero <pair_zero>`
    * :doc:`hybrid (k) <pair_hybrid>`
    * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   * :doc:`kim <pair_kim>`
+   * :doc:`list <pair_list>`
+   *
+   *
    *
    *
    *
@@ -108,14 +112,12 @@ OPT.
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
    * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
-   * :doc:`kim <pair_kim>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
    * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
    * :doc:`lcbop <pair_lcbop>`
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
    * :doc:`line/lj <pair_line_lj>`
-   * :doc:`list <pair_list>`
    * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
    * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst
index da2260bcbf..4866de31c6 100644
--- a/doc/src/Errors_messages.rst
+++ b/doc/src/Errors_messages.rst
@@ -509,14 +509,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 
 *Bond/react: Atom affected by reaction too close to template edge*
    This means an atom which changes type or connectivity during the
-   reaction is too close to an 'edge' atom defined in the superimpose
+   reaction is too close to an 'edge' atom defined in the map
    file. This could cause incorrect assignment of bonds, angle, etc.
    Generally, this means you must include more atoms in your templates,
    such that there are at least two atoms between each atom involved in
    the reaction and an edge atom.
 
 *Bond/react: Fix bond/react needs ghost atoms from farther away*
-   This is because a processor needs to superimpose the entire unreacted
+   This is because a processor needs to map the entire unreacted
    molecule template onto simulation atoms it knows about. The
    comm\_modify cutoff command can be used to extend the communication
    range.
diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst
index 1009eb5089..fb99077137 100644
--- a/doc/src/Howto_drude2.rst
+++ b/doc/src/Howto_drude2.rst
@@ -181,7 +181,7 @@ include Coulomb interactions, for instance *lj/cut/coul/long* with
 
 As compared to the non-polarizable input file, *pair\_coeff* lines need
 to be added for the DPs.  Since the DPs have no Lennard-Jones
-interactions, their *epsilon* is 0. so the only *pair\_coeff* line
+interactions, their :math:`\epsilon` is 0. so the only *pair\_coeff* line
 that needs to be added is
 
 
diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst
index e0501dfaaa..0e642a4883 100644
--- a/doc/src/Howto_triclinic.rst
+++ b/doc/src/Howto_triclinic.rst
@@ -55,7 +55,7 @@ rotation of **A**\ , **B**\ , and **C** and can be computed as follows:
   c_z = & |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2}
 
 where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^)
-indicates the corresponding unit vector. *beta* and *gamma* are angles
+indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles
 between the vectors described below. Note that by construction,
 **a**\ , **b**\ , and **c** have strictly positive x, y, and z components, respectively.
 If it should happen that
diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst
index cda5df21c2..238f53d5a3 100644
--- a/doc/src/Install_git.rst
+++ b/doc/src/Install_git.rst
@@ -11,16 +11,20 @@ has several advantages:
 * You can submit your new features back to GitHub for inclusion in
   LAMMPS.
 
-You must have `git <git_>`_ installed on your system to communicate with
-the public git server for LAMMPS.
+You must have `git <git_>`_ installed on your system to use the
+commands explained below to communicate with the git servers on
+GitHub.  For people still using subversion (svn), GitHub also
+provides `limited support for subversion clients <svn_>`_.
+
 
 .. warning::
 
    As of October 2016, the official home of public LAMMPS development is
    on GitHub.  The previously advertised LAMMPS git repositories on
-   git.lammps.org and bitbucket.org are now deprecated, and may go away at any time.
+   git.lammps.org and bitbucket.org are now deprecated or offline.
 
 .. _git: https://git-scm.com
+.. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github
 
 You can follow LAMMPS development on 3 different git branches:
 
diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst
index e74f0d9a6d..08cfa862ab 100644
--- a/doc/src/Manual.rst
+++ b/doc/src/Manual.rst
@@ -78,7 +78,3 @@ Indices and tables
 
 * :ref:`genindex`
 * :ref:`search`
-
-.. raw:: html
-
-   </BODY>
diff --git a/doc/src/Manual_build.rst b/doc/src/Manual_build.rst
index 26c32c0ccb..b401a65ac9 100644
--- a/doc/src/Manual_build.rst
+++ b/doc/src/Manual_build.rst
@@ -1,22 +1,28 @@
 Building the LAMMPS manual
 **************************
 
-Depending on how you obtained LAMMPS, the doc directory has 2 or 3
-sub-directories and optionally 2 PDF files and 2 e-book format files:
+Depending on how you obtained LAMMPS, the doc directory has up
+to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
+plus 2 e-book format files:
 
 
 .. parsed-literal::
 
    src             # content files for LAMMPS documentation
    html            # HTML version of the LAMMPS manual (see html/Manual.html)
-   tools           # tools and settings for building the documentation
+   utils           # tools and settings for building the documentation
+   docenv          # virtualenv for processing the manual sources
+   doctrees        # temporary data from processing the manual
+   mathjax         # code and fonts for rendering math in html
    Manual.pdf      # large PDF version of entire manual
    Developer.pdf   # small PDF with info about how LAMMPS is structured
    LAMMPS.epub     # Manual in ePUB e-book format
    LAMMPS.mobi     # Manual in MOBI e-book format
+   lammps.1        # man page for the lammps command
+   msi2lmp.1       # man page for the msi2lmp command
 
-If you downloaded LAMMPS as a tarball from the web site, all these
-directories and files should be included.
+If you downloaded LAMMPS as a tarball from the web site, the html folder
+and the PDF files should be included.
 
 If you downloaded LAMMPS from the public git repository, then the HTML
 and PDF files are not included.  Instead you need to create them, in one
diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst
index 0fd333b568..4a1377bcf0 100644
--- a/doc/src/Modify_contribute.rst
+++ b/doc/src/Modify_contribute.rst
@@ -140,8 +140,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
   and your name and email address at the top, like other
   user-contributed LAMMPS source files.  They need to create a class
   that is inside the LAMMPS namespace.  If the file is for one of the
-
-* USER packages, including USER-MISC, then we are not as picky about the
+  USER packages, including USER-MISC, then we are not as picky about the
   coding style (see above).  I.e. the files do not need to be in the
   same stylistic format and syntax as other LAMMPS files, though that
   would be nice for developers as well as users who try to read your
diff --git a/doc/src/Modify_overview.rst b/doc/src/Modify_overview.rst
index 495dc0fae8..6b5b07e538 100644
--- a/doc/src/Modify_overview.rst
+++ b/doc/src/Modify_overview.rst
@@ -4,7 +4,7 @@ Overview
 The best way to add a new feature to LAMMPS is to find a similar
 feature and look at the corresponding source and header files to figure
 out what it does.  You will need some knowledge of C++ to be able to
-understand the hi-level structure of LAMMPS and its class
+understand the high-level structure of LAMMPS and its class
 organization, but functions (class methods) that do actual
 computations are written in vanilla C-style code and operate on simple
 C-style data structures (vectors and arrays).
diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf
index dd028ae65e..c9a67d6a1d 100644
Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ
diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst
index 89157ece6d..26b9026fb0 100644
--- a/doc/src/Packages_details.rst
+++ b/doc/src/Packages_details.rst
@@ -94,6 +94,7 @@ page gives those details.
    * :ref:`USER-QMMM <PKG-USER-QMMM>`
    * :ref:`USER-QTB <PKG-USER-QTB>`
    * :ref:`USER-QUIP <PKG-USER-QUIP>`
+   * :ref:`USER-REACTION <PKG-USER-REACTION>`
    * :ref:`USER-REAXC <PKG-USER-REAXC>`
    * :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`
    * :ref:`USER-SDPD <PKG-USER-SDPD>`
@@ -2180,6 +2181,39 @@ This package has :ref:`specific installation instructions <user-quip>` on the :d
 ----------
 
 
+.. _PKG-USER-REACTION:
+
+USER-REACTION package
+---------------------
+
+**Contents:**
+
+This package allows for complex bond topology changes (reactions)
+during a running MD simulation, when using classical force fields.
+Topology changes are defined in pre- and post-reaction molecule
+templates and can include creation and deletion of bonds, angles,
+dihedrals, impropers, atom types, bond types, angle types, dihedral
+types, improper types, and/or atomic charges. Other options currently
+available include reaction constraints (e.g. angle and Arrhenius
+constraints), deletion of reaction byproducts or other small
+molecules, and chiral-sensitive reactions.
+
+**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center.
+
+**Supporting info:**
+
+* src/USER-REACTION: filenames -> commands
+* src/USER-REACTION/README
+* :doc:`fix bond/react <fix_bond_react>`
+* examples/USER/reaction
+* `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
+* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
+* disarmmd.org
+
+
+----------
+
+
 .. _PKG-USER-REAXC:
 
 USER-REAXC package
diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst
index e3f0dba469..0e3a5e3f33 100644
--- a/doc/src/Packages_user.rst
+++ b/doc/src/Packages_user.rst
@@ -91,6 +91,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
 | :ref:`USER-QUIP <PKG-USER-QUIP>`               | QUIP/libatoms interface                                         | :doc:`pair_style quip <pair_quip>`                                            | USER/quip                                           | ext     |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+| :ref:`USER-REACTION <PKG-USER-REACTION>`       | chemical reactions in classical MD                              | :doc:`fix bond/react <fix_bond_react>`                                        | USER/reaction                                       | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
 | :ref:`USER-REAXC <PKG-USER-REAXC>`             | ReaxFF potential (C/C++)                                        | :doc:`pair_style reaxc <pair_reaxc>`                                          | reax                                                | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
 | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`       | wrapper on ScaFaCoS solver                                      | :doc:`kspace_style scafacos <kspace_style>`                                   | USER/scafacos                                       | ext     |
diff --git a/doc/src/Python_mpi.rst b/doc/src/Python_mpi.rst
index 9ecd876bcf..d1c9ab0ca0 100644
--- a/doc/src/Python_mpi.rst
+++ b/doc/src/Python_mpi.rst
@@ -66,7 +66,7 @@ and see one line of output for each processor you run on.
    insure both are using the same version of MPI.  If you only have one
    MPI installed on your system, this is not an issue, but it can be if
    you have multiple MPIs.  Your LAMMPS build is explicit about which MPI
-   it is using, since you specify the details in your lo-level
+   it is using, since you specify the details in your low-level
    src/MAKE/Makefile.foo file.  Mpi4py uses the "mpicc" command to find
    information about the MPI it uses to build against.  And it tries to
    load "libmpi.so" from the LD\_LIBRARY\_PATH.  This may or may not find
diff --git a/doc/src/Python_test.rst b/doc/src/Python_test.rst
index 3368041935..13d0a1ab27 100644
--- a/doc/src/Python_test.rst
+++ b/doc/src/Python_test.rst
@@ -38,7 +38,7 @@ If an error occurs, carefully go through the steps on the
 library and the :doc:`Python\_install <Python_install>` doc page about
 insuring Python can find the necessary two files it needs.
 
-**Test LAMMPS and Python in serial:**
+Test LAMMPS and Python in serial:
 -------------------------------------
 
 To run a LAMMPS test in serial, type these lines into Python
@@ -67,7 +67,7 @@ typed something like:
 
    lmp_g++ -in in.lj
 
-**Test LAMMPS and Python in parallel:**
+Test LAMMPS and Python in parallel:
 ---------------------------------------
 
 To run LAMMPS in parallel, assuming you have installed the
@@ -128,7 +128,7 @@ described in the PyPar documentation.  The last line of your Python
 script should be pypar.finalize(), to insure MPI is shut down
 correctly.
 
-**Running Python scripts:**
+Running Python scripts:
 ---------------------------
 
 Note that any Python script (not just for LAMMPS) can be invoked in
diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst
index 8ae558df24..e2b385b243 100644
--- a/doc/src/Run_options.rst
+++ b/doc/src/Run_options.rst
@@ -196,9 +196,9 @@ Specify a log file for LAMMPS to write status information to.  In
 one-partition mode, if the switch is not used, LAMMPS writes to the
 file log.lammps.  If this switch is used, LAMMPS writes to the
 specified file.  In multi-partition mode, if the switch is not used, a
-log.lammps file is created with hi-level status information.  Each
+log.lammps file is created with high-level status information.  Each
 partition also writes to a log.lammps.N file where N is the partition
-ID.  If the switch is specified in multi-partition mode, the hi-level
+ID.  If the switch is specified in multi-partition mode, the high-level
 logfile is named "file" and each partition also logs information to a
 file.N.  For both one-partition and multi-partition mode, if the
 specified file is "none", then no log files are created.  Using a
@@ -529,10 +529,10 @@ Specify a file for LAMMPS to write its screen information to.  In
 one-partition mode, if the switch is not used, LAMMPS writes to the
 screen.  If this switch is used, LAMMPS writes to the specified file
 instead and you will see no screen output.  In multi-partition mode,
-if the switch is not used, hi-level status information is written to
+if the switch is not used, high-level status information is written to
 the screen.  Each partition also writes to a screen.N file where N is
 the partition ID.  If the switch is specified in multi-partition mode,
-the hi-level screen dump is named "file" and each partition also
+the high-level screen dump is named "file" and each partition also
 writes screen information to a file.N.  For both one-partition and
 multi-partition mode, if the specified file is "none", then no screen
 output is performed. Option -pscreen will override the name of the
diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst
index 9f9b1ee532..c15fd635b7 100644
--- a/doc/src/angle_sdk.rst
+++ b/doc/src/angle_sdk.rst
@@ -35,13 +35,14 @@ The *sdk* angle style is a combination of the harmonic angle potential,
    E = K (\theta - \theta_0)^2 
 
 
-where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor,
-with the *repulsive* part of the non-bonded *lj/sdk* pair style
-between the atoms 1 and 3.  This angle potential is intended for
-coarse grained MD simulations with the CMM parameterization using the
-:doc:`pair_style lj/sdk <pair_sdk>`.  Relative to the pair\_style
-*lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden
-jumps.  Note that the usual 1/2 factor is included in :math:`K`.
+where :math:`\theta_0` is the equilibrium value of the angle and
+:math:`K` a prefactor, with the *repulsive* part of the non-bonded
+*lj/sdk* pair style between the atoms 1 and 3.  This angle potential is
+intended for coarse grained MD simulations with the CMM parameterization
+using the :doc:`pair_style lj/sdk <pair_sdk>`.  Relative to the
+pair\_style *lj/sdk*\ , however, the energy is shifted by
+:math:`\epsilon`, to avoid sudden jumps.  Note that the usual 1/2 factor
+is included in :math:`K`.
 
 The following coefficients must be defined for each angle type via the
 :doc:`angle_coeff <angle_coeff>` command as in the example above:
diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst
index 8ec1e8e817..e93d493b97 100644
--- a/doc/src/compute_ke.rst
+++ b/doc/src/compute_ke.rst
@@ -28,8 +28,8 @@ Description
 Define a computation that calculates the translational kinetic energy
 of a group of particles.
 
-The kinetic energy of each particle is computed as 1/2 m v\^2, where m
-and v are the mass and velocity of the particle.
+The kinetic energy of each particle is computed as :math:`\frac{1}{2} m
+v^2`, where *m* and *v* are the mass and velocity of the particle.
 
 There is a subtle difference between the quantity calculated by this
 compute and the kinetic energy calculated by the *ke* or *etotal*
@@ -37,12 +37,13 @@ keyword used in thermodynamic output, as specified by the
 :doc:`thermo_style <thermo_style>` command.  For this compute, kinetic
 energy is "translational" kinetic energy, calculated by the simple
 formula above.  For thermodynamic output, the *ke* keyword infers
-kinetic energy from the temperature of the system with 1/2 Kb T of
-energy for each degree of freedom.  For the default temperature
-computation via the :doc:`compute temp <compute_temp>` command, these
-are the same.  But different computes that calculate temperature can
-subtract out different non-thermal components of velocity and/or
-include different degrees of freedom (translational, rotational, etc).
+kinetic energy from the temperature of the system with
+:math:`\frac{1}{2} k_B T` of energy for each degree of freedom.  For the
+default temperature computation via the :doc:`compute temp
+<compute_temp>` command, these are the same.  But different computes
+that calculate temperature can subtract out different non-thermal
+components of velocity and/or include different degrees of freedom
+(translational, rotational, etc).
 
 **Output info:**
 
diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst
index 85b5756182..d9cfbf8c94 100644
--- a/doc/src/compute_ke_atom_eff.rst
+++ b/doc/src/compute_ke_atom_eff.rst
@@ -18,7 +18,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute 1 all ke/atom/eff
 
@@ -30,11 +30,12 @@ Define a computation that calculates the per-atom translational
 group.  The particles are assumed to be nuclei and electrons modeled
 with the :doc:`electronic force field <pair_eff>`.
 
-The kinetic energy for each nucleus is computed as 1/2 m v\^2, where m
-corresponds to the corresponding nuclear mass, and the kinetic energy
-for each electron is computed as 1/2 (me v\^2 + 3/4 me s\^2), where me
-and v correspond to the mass and translational velocity of each
-electron, and s to its radial velocity, respectively.
+The kinetic energy for each nucleus is computed as :math:`\frac{1}{2} m
+v^2`, where *m* corresponds to the corresponding nuclear mass, and the
+kinetic energy for each electron is computed as :math:`\frac{1}{2} (m_e
+v^2 + \frac{3}{4} m_e s^2)`, where :math:`m_e` and *v* correspond to the mass
+and translational velocity of each electron, and *s* to its radial
+velocity, respectively.
 
 There is a subtle difference between the quantity calculated by this
 compute and the kinetic energy calculated by the *ke* or *etotal*
@@ -43,8 +44,8 @@ keyword used in thermodynamic output, as specified by the
 energy is "translational" plus electronic "radial" kinetic energy,
 calculated by the simple formula above. For thermodynamic output, the
 *ke* keyword infers kinetic energy from the temperature of the system
-with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
-eFF.
+with :math:`\frac{1}{2} k_B T` of energy for each (nuclear-only) degree
+of freedom in eFF.
 
 .. note::
 
@@ -53,7 +54,7 @@ eFF.
    command, as shown in the following example:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute         effTemp all temp/eff
    thermo_style    custom step etotal pe ke temp press
diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst
index 5819bb6220..ab3f37ef81 100644
--- a/doc/src/compute_ke_eff.rst
+++ b/doc/src/compute_ke_eff.rst
@@ -29,11 +29,12 @@ Define a computation that calculates the kinetic energy of motion of a
 group of eFF particles (nuclei and electrons), as modeled with the
 :doc:`electronic force field <pair_eff>`.
 
-The kinetic energy for each nucleus is computed as 1/2 m v\^2 and the
-kinetic energy for each electron is computed as 1/2(me v\^2 + 3/4 me
-s\^2), where m corresponds to the nuclear mass, me to the electron
-mass, v to the translational velocity of each particle, and s to the
-radial velocity of the electron, respectively.
+The kinetic energy for each nucleus is computed as :math:`\frac{1}{2} m
+v^2` and the kinetic energy for each electron is computed as
+:math:`\frac{1}{2}(m_e v^2 + \frac{3}{4} m_e s^2)`, where *m*
+corresponds to the nuclear mass, :math:`m_e` to the electron mass, *v*
+to the translational velocity of each particle, and *s* to the radial
+velocity of the electron, respectively.
 
 There is a subtle difference between the quantity calculated by this
 compute and the kinetic energy calculated by the *ke* or *etotal*
@@ -42,18 +43,20 @@ keyword used in thermodynamic output, as specified by the
 energy is "translational" and "radial" (only for electrons) kinetic
 energy, calculated by the simple formula above.  For thermodynamic
 output, the *ke* keyword infers kinetic energy from the temperature of
-the system with 1/2 Kb T of energy for each degree of freedom.  For
-the eFF temperature computation via the :doc:`compute temp\_eff <compute_temp_eff>` command, these are the same.  But
-different computes that calculate temperature can subtract out
-different non-thermal components of velocity and/or include other
-degrees of freedom.
+the system with :math:`\frac{1}{2} k_B T` of energy for each degree of
+freedom.  For the eFF temperature computation via the :doc:`compute
+temp\_eff <compute_temp_eff>` command, these are the same.  But
+different computes that calculate temperature can subtract out different
+non-thermal components of velocity and/or include other degrees of
+freedom.
 
-IMPRORTANT NOTE: The temperature in eFF models should be monitored via
-the :doc:`compute temp/eff <compute_temp_eff>` command, which can be
-printed with thermodynamic output by using the
-:doc:`thermo_modify <thermo_modify>` command, as shown in the following
-example:
+.. warning::
 
+   The temperature in eFF models should be monitored via
+   the :doc:`compute temp/eff <compute_temp_eff>` command, which can be
+   printed with thermodynamic output by using the
+   :doc:`thermo_modify <thermo_modify>` command, as shown in the following
+   example:
 
 .. parsed-literal::
 
diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst
index ed3b90c8e1..ea7b238db0 100644
--- a/doc/src/compute_pressure.rst
+++ b/doc/src/compute_pressure.rst
@@ -21,7 +21,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute 1 all pressure thermo_temp
    compute 1 all pressure NULL pair bond
@@ -42,20 +42,20 @@ The pressure is computed by the formula
    P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
 
 
-where N is the number of atoms in the system (see discussion of DOF
-below), Kb is the Boltzmann constant, T is the temperature, d is the
-dimensionality of the system (2 or 3 for 2d/3d), and V is the system
-volume (or area in 2d).  The second term is the virial, equal to
+where *N* is the number of atoms in the system (see discussion of DOF
+below), :math:`k_B` is the Boltzmann constant, *T* is the temperature, d
+is the dimensionality of the system (2 or 3 for 2d/3d), and *V* is the
+system volume (or area in 2d).  The second term is the virial, equal to
 -dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
-many-body, and long-range interactions, where r\_i and f\_i are the
-position and force vector of atom i, and the black dot indicates a dot
-product.  When periodic boundary conditions are used, N' necessarily
-includes periodic image (ghost) atoms outside the central box, and the
-position and force vectors of ghost atoms are thus included in the
-summation.  When periodic boundary conditions are not used, N' = N =
-the number of atoms in the system.  :doc:`Fixes <fix>` that impose
-constraints (e.g. the :doc:`fix shake <fix_shake>` command) also
-contribute to the virial term.
+many-body, and long-range interactions, where :math:`r_i` and
+:math:`f_i` are the position and force vector of atom *i*, and the black
+dot indicates a dot product.  When periodic boundary conditions are
+used, N' necessarily includes periodic image (ghost) atoms outside the
+central box, and the position and force vectors of ghost atoms are thus
+included in the summation.  When periodic boundary conditions are not
+used, N' = N = the number of atoms in the system.  :doc:`Fixes <fix>`
+that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command)
+also contribute to the virial term.
 
 A symmetric pressure tensor, stored as a 6-element vector, is also
 calculated by this compute.  The 6 components of the vector are
@@ -108,7 +108,7 @@ A compute of this style with the ID of "thermo\_press" is created when
 LAMMPS starts up, as if this command were in the input script:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute thermo_press all pressure thermo_temp
 
diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst
index 60e6bf52ea..e7e6f0ee44 100644
--- a/doc/src/dump_image.rst
+++ b/doc/src/dump_image.rst
@@ -89,7 +89,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump d0 all image 100 dump.\*.jpg type type
    dump d1 mobile image 500 snap.\*.png element element ssao yes 4539 0.6
@@ -121,19 +121,12 @@ script to generate the images/movie.
 Here are two sample images, rendered as 1024x1024 JPEG files.  Click
 to see the full-size images:
 
-.. raw:: html
-
-   <DIV ALIGN=center>
-
 .. image:: JPG/dump1_small.jpg
    :target: JPG/dump1.jpg
-
+   :width: 48%
 .. image:: JPG/dump2_small.jpg
    :target: JPG/dump2.jpg
-
-.. raw:: html
-
-   </DIV>
+   :width: 48%
 
 Only atoms in the specified group are rendered in the image.  The
 :doc:`dump_modify region and thresh <dump_modify>` commands can also
@@ -235,8 +228,6 @@ the `AtomEye <atomeye_>`_ visualization package.
 
 .. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
 
-
-
 If other atom attributes are used for the *color* or *diameter*
 settings, they are interpreted in the following way.
 
@@ -258,20 +249,16 @@ drawn.  Note that finite-size spherical particles, as defined by
 :doc:`atom_style sphere <atom_style>` define a per-particle radius or
 diameter, which can be used as the *diameter* setting.
 
-
 ----------
 
-
 The various keywords listed above control how the image is rendered.
 As listed below, all of the keywords have defaults, most of which you
 will likely not need to change.  The :doc:`dump modify <dump_modify>`
 also has options specific to the dump image style, particularly for
 assigning colors to atoms, bonds, and other image features.
 
-
 ----------
 
-
 The *atom* keyword allow you to turn off the drawing of all atoms, if
 the specified value is *no*\ .  Note that this will not turn off the
 drawing of particles that are represented as lines, triangles, or
@@ -283,10 +270,8 @@ set a single numeric *size*\ .  All atoms will be drawn with that
 diameter, e.g. 1.5, which is in whatever distance :doc:`units <units>`
 the input script defines, e.g. Angstroms.
 
-
 ----------
 
-
 The *bond* keyword allows to you to alter how bonds are drawn.  A bond
 is only drawn if both atoms in the bond are being drawn due to being
 in the specified group and due to other selection criteria
@@ -329,10 +314,8 @@ If *type* is specified for the *width* value then the diameter of each
 bond is determined by its bond type.  By default all types have
 diameter 0.5.  This mapping can be changed by the :doc:`dump_modify bdiam <dump_modify>` command.
 
-
 ----------
 
-
 The *line* keyword can be used when :doc:`atom_style line <atom_style>`
 is used to define particles as line segments, and will draw them as
 lines.  If this keyword is not used, such particles will be drawn as
@@ -586,10 +569,10 @@ MPEG or other movie file you can use:
 
 * a) Use the ImageMagick convert program.
   
-  .. parsed-literal::
+  .. code-block:: bash
   
-     % convert \*.jpg foo.gif
-     % convert -loop 1 \*.ppm foo.mpg
+     % convert *.jpg foo.gif
+     % convert -loop 1 *.ppm foo.mpg
 
 
   Animated GIF files from ImageMagick are not optimized. You can use
@@ -614,18 +597,15 @@ MPEG or other movie file you can use:
   allows extremely flexible encoding and decoding of movies.
 
   
-  .. parsed-literal::
+  .. code-block:: bash
   
-     cat snap.\*.jpg \| ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
-     cat snap.\*.ppm \| ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
+     cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
+     cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
 
 
   Front ends for FFmpeg exist for multiple platforms. For more
   information see the `FFmpeg homepage <http://www.ffmpeg.org/>`_
 
-
-
-
 ----------
 
 
@@ -640,7 +620,7 @@ Play the movie:
   movie. Both are available for multiple OSes and support a large
   variety of file formats and decoders.
   
-  .. parsed-literal::
+  .. code-block:: bash
   
      % mplayer foo.mpg
      % ffplay bar.avi
@@ -649,9 +629,9 @@ Play the movie:
   `animate tool <http://www.sandia.gov/~sjplimp/pizza/doc/animate.html>`_,
   which works directly on a series of image files.
   
-  .. parsed-literal::
+  .. code-block:: python
   
-     a = animate("foo\*.jpg")
+     a = animate("foo*.jpg")
 
 * d) QuickTime and other Windows- or MacOS-based media players can
   obviously play movie files directly. Similarly for corresponding tools
@@ -660,11 +640,8 @@ Play the movie:
   additional libraries, purchasing a license, or may not be
   supported.
 
-
-
 ----------
 
-
 See the :doc:`Modify <Modify>` doc page for information on how to add
 new compute and fix styles to LAMMPS to calculate per-atom quantities
 which could then be output into dump files.
diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst
index 14d04009e7..1206177ba1 100644
--- a/doc/src/fix_bond_react.rst
+++ b/doc/src/fix_bond_react.rst
@@ -60,7 +60,7 @@ Syntax
 Examples
 """"""""
 
-For unabridged example scripts and files, see examples/USER/misc/bond\_react.
+For unabridged example scripts and files, see examples/USER/reaction.
 
 
 .. parsed-literal::
@@ -149,10 +149,9 @@ constant-topology parts of your system separately. The dynamic group
 contains only atoms not involved in a reaction at a given timestep,
 and therefore should be used by a subsequent system-wide time
 integrator such as nvt, npt, or nve, as shown in the second example
-above (full examples can be found at examples/USER/misc/bond\_react).
-The time integration command should be placed after the fix bond/react
-command due to the internal dynamic grouping performed by fix
-bond/react.
+above (full examples can be found at examples/USER/reaction). The time
+integration command should be placed after the fix bond/react command
+due to the internal dynamic grouping performed by fix bond/react.
 
 .. note::
 
@@ -295,7 +294,7 @@ either 'none' or 'charges.' Further details are provided in the
 discussion of the 'update\_edges' keyword. The fifth optional section
 begins with the keyword 'Constraints' and lists additional criteria
 that must be satisfied in order for the reaction to occur. Currently,
-there are three types of constraints available, as discussed below.
+there are four types of constraints available, as discussed below.
 
 A sample map file is given below:
 
@@ -371,6 +370,24 @@ the central atom). Angles must be specified in degrees. This
 constraint can be used to enforce a certain orientation between
 reacting molecules.
 
+The constraint of type 'dihedral' has the following syntax:
+
+
+.. parsed-literal::
+
+   dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2*
+
+where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3*
+and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in
+the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>`
+documentation for further details on convention. If *amin* is less
+than *amax*, these four atoms must form a dihedral angle greater than
+*amin* **and** less than *amax* for the reaction to occur. If *amin*
+is greater than *amax*, these four atoms must form a dihedral angle
+greater than *amin* **or** less than *amax* for the reaction to occur.
+Angles must be specified in degrees. Optionally, a second range of
+permissible angles *amin2*-*amax2* can be specified.
+
 The constraint of type 'arrhenius' imposes an additional reaction
 probability according to the temperature-dependent Arrhenius equation:
 
@@ -516,7 +533,7 @@ Restrictions
 """"""""""""
 
 
-This fix is part of the USER-MISC package.  It is only enabled if
+This fix is part of the USER-REACTION package.  It is only enabled if
 LAMMPS was built with that package.  See the
 :doc:`Build package <Build_package>` doc page for more info.
 
diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst
index d7d0f012b6..7512f34ab7 100644
--- a/doc/src/fix_hyper_local.rst
+++ b/doc/src/fix_hyper_local.rst
@@ -155,17 +155,15 @@ simulation domain.
 
 To accomplish this, if :math:`B_{ij} < B_{target}`, the :math:`C_{ij}`
 prefactor for bond *ij* is incremented on the current timestep by an
-amount proportional to the inverse of the specified *alpha* and the
-difference (:math:`B_{ij} - B_{target}`).
-Conversely if :math:`B_{ij} > B_{target}`, :math:`C_{ij}` is decremented
-by the same amount.
-This procedure is termed "boostostatting" in :ref:`(Voter2013) <Voter2013lhd>`.
-It drives all of the individual :math:`C_{ij}` to
-values such that when :math:`V^{max}_{ij}` is applied as a bias to
-bond *ij*, the resulting boost factor :math:`B_{ij}` will be close
-to :math:`B_{target}` on average.
-Thus the LHD time acceleration factor for the overall system is
-effectively *Btarget*\ .
+amount proportional to the inverse of the specified :math:`\alpha` and
+the difference (:math:`B_{ij} - B_{target}`).  Conversely if
+:math:`B_{ij} > B_{target}`, :math:`C_{ij}` is decremented by the same
+amount.  This procedure is termed "boostostatting" in :ref:`(Voter2013)
+<Voter2013lhd>`.  It drives all of the individual :math:`C_{ij}` to
+values such that when :math:`V^{max}_{ij}` is applied as a bias to bond
+*ij*, the resulting boost factor :math:`B_{ij}` will be close to
+:math:`B_{target}` on average.  Thus the LHD time acceleration factor
+for the overall system is effectively *Btarget*\ .
 
 Note that in LHD, the boost factor :math:`B_{target}` is specified by the user.
 This is in contrast to global hyperdynamics (GHD) where the boost
diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst
index 45b900b298..2b764ef908 100644
--- a/doc/src/fix_langevin.rst
+++ b/doc/src/fix_langevin.rst
@@ -51,7 +51,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 3 boundary langevin 1.0 1.0 1000.0 699483
    fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5
@@ -67,35 +67,35 @@ performs Brownian dynamics (BD), since the total force on each atom
 will have the form:
 
 
-.. parsed-literal::
+.. math::
 
-   F = Fc + Ff + Fr
-   Ff = - (m / damp) v
-   Fr is proportional to sqrt(Kb T m / (dt damp))
+   F = & F_c + F_f + F_r \\
+   F_f = & - \frac{m}{\mathrm{damp}} v \\
+   F_r \propto & \sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}
 
-Fc is the conservative force computed via the usual inter-particle
-interactions (:doc:`pair_style <pair_style>`,
-:doc:`bond_style <bond_style>`, etc).
+:math:`F_c` is the conservative force computed via the usual
+inter-particle interactions (:doc:`pair_style <pair_style>`,
+:doc:`bond_style <bond_style>`, etc).  The :math:`F_f` and :math:`F_r`
+terms are added by this fix on a per-particle basis.  See the
+:doc:`pair_style dpd/tstat <pair_dpd>` command for a thermostatting
+option that adds similar terms on a pairwise basis to pairs of
+interacting particles.
 
-The Ff and Fr terms are added by this fix on a per-particle basis.
-See the :doc:`pair_style dpd/tstat <pair_dpd>` command for a
-thermostatting option that adds similar terms on a pairwise basis to
-pairs of interacting particles.
+:math:`F_f` is a frictional drag or viscous damping term proportional to
+the particle's velocity.  The proportionality constant for each atom is
+computed as :math:`\frac{m}{\mathrm{damp}}`, where *m* is the mass of the
+particle and damp is the damping factor specified by the user.
 
-Ff is a frictional drag or viscous damping term proportional to the
-particle's velocity.  The proportionality constant for each atom is
-computed as m/damp, where m is the mass of the particle and damp is
-the damping factor specified by the user.
-
-Fr is a force due to solvent atoms at a temperature T randomly bumping
-into the particle.  As derived from the fluctuation/dissipation
-theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
-dt damp), where Kb is the Boltzmann constant, T is the desired
-temperature, m is the mass of the particle, dt is the timestep size,
-and damp is the damping factor.  Random numbers are used to randomize
-the direction and magnitude of this force as described in
-:ref:`(Dunweg) <Dunweg1>`, where a uniform random number is used (instead of
-a Gaussian random number) for speed.
+:math:`F_r` is a force due to solvent atoms at a temperature *T*
+randomly bumping into the particle.  As derived from the
+fluctuation/dissipation theorem, its magnitude as shown above is
+proportional to :math:`\sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}`, where
+:math:`k_B` is the Boltzmann constant, *T* is the desired temperature,
+*m* is the mass of the particle, *dt* is the timestep size, and damp is
+the damping factor.  Random numbers are used to randomize the direction
+and magnitude of this force as described in :ref:`(Dunweg) <Dunweg1>`,
+where a uniform random number is used (instead of a Gaussian random
+number) for speed.
 
 Note that unless you use the *omega* or *angmom* keywords, the
 thermostat effect of this fix is applied to only the translational
@@ -107,14 +107,15 @@ thermostatting takes place; see the description below.
 
 .. note::
 
-   Unlike the :doc:`fix nvt <fix_nh>` command which performs
-   Nose/Hoover thermostatting AND time integration, this fix does NOT
-   perform time integration.  It only modifies forces to effect
-   thermostatting.  Thus you must use a separate time integration fix,
-   like :doc:`fix nve <fix_nve>` to actually update the velocities and
-   positions of atoms using the modified forces.  Likewise, this fix
-   should not normally be used on atoms that also have their temperature
-   controlled by another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>` commands.
+   Unlike the :doc:`fix nvt <fix_nh>` command which performs Nose/Hoover
+   thermostatting AND time integration, this fix does NOT perform time
+   integration.  It only modifies forces to effect thermostatting.  Thus
+   you must use a separate time integration fix, like :doc:`fix nve
+   <fix_nve>` to actually update the velocities and positions of atoms
+   using the modified forces.  Likewise, this fix should not normally be
+   used on atoms that also have their temperature controlled by another
+   fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale
+   <fix_temp_rescale>` commands.
 
 See the :doc:`Howto thermostat <Howto_thermostat>` doc page for
 a discussion of different ways to compute temperature and perform
@@ -154,13 +155,14 @@ the remaining thermal degrees of freedom, and the bias is added back
 in.
 
 The *damp* parameter is specified in time units and determines how
-rapidly the temperature is relaxed.  For example, a value of 100.0
-means to relax the temperature in a timespan of (roughly) 100 time
-units (tau or fmsec or psec - see the :doc:`units <units>` command).
-The damp factor can be thought of as inversely related to the
-viscosity of the solvent.  I.e. a small relaxation time implies a
-hi-viscosity solvent and vice versa.  See the discussion about gamma
-and viscosity in the documentation for the :doc:`fix viscous <fix_viscous>` command for more details.
+rapidly the temperature is relaxed.  For example, a value of 100.0 means
+to relax the temperature in a timespan of (roughly) 100 time units
+(:math:`\tau` or fs or ps - see the :doc:`units <units>` command).  The
+damp factor can be thought of as inversely related to the viscosity of
+the solvent.  I.e. a small relaxation time implies a high-viscosity
+solvent and vice versa.  See the discussion about :math:`\gamma` and
+viscosity in the documentation for the :doc:`fix viscous <fix_viscous>`
+command for more details.
 
 The random # *seed* must be a positive integer.  A Marsaglia random
 number generator is used.  Each processor uses the input seed to
@@ -191,39 +193,40 @@ The rotational temperature of the particles can be monitored by the
 :doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute temp/asphere <compute_temp_asphere>` commands with their rotate
 options.
 
-For the *omega* keyword there is also a scale factor of 10.0/3.0 that
-is applied as a multiplier on the Ff (damping) term in the equation
-above and of sqrt(10.0/3.0) as a multiplier on the Fr term.  This does
-not affect the thermostatting behavior of the Langevin formalism but
-insures that the randomized rotational diffusivity of spherical
-particles is correct.
+For the *omega* keyword there is also a scale factor of
+:math:`\frac{10.0}{3.0}` that is applied as a multiplier on the
+:math:`F_f` (damping) term in the equation above and of
+:math:`\sqrt{\frac{10.0}{3.0}}` as a multiplier on the :math:`F_r` term.
+This does not affect the thermostatting behavior of the Langevin
+formalism but insures that the randomized rotational diffusivity of
+spherical particles is correct.
 
 For the *angmom* keyword a similar scale factor is needed which is
-10.0/3.0 for spherical particles, but is anisotropic for aspherical
-particles (e.g. ellipsoids).  Currently LAMMPS only applies an
-isotropic scale factor, and you can choose its magnitude as the
+:math:`\frac{10.0}{3.0}` for spherical particles, but is anisotropic for
+aspherical particles (e.g. ellipsoids).  Currently LAMMPS only applies
+an isotropic scale factor, and you can choose its magnitude as the
 specified value of the *angmom* keyword.  If your aspherical particles
-are (nearly) spherical than a value of 10.0/3.0 = 3.333 is a good
-choice.  If they are highly aspherical, a value of 1.0 is as good a
-choice as any, since the effects on rotational diffusivity of the
-particles will be incorrect regardless.  Note that for any reasonable
-scale factor, the thermostatting effect of the *angmom* keyword on the
-rotational temperature of the aspherical particles should still be
-valid.
+are (nearly) spherical than a value of :math:`\frac{10.0}{3.0} =
+3.\overline{3}` is a good choice.  If they are highly aspherical, a
+value of 1.0 is as good a choice as any, since the effects on rotational
+diffusivity of the particles will be incorrect regardless.  Note that
+for any reasonable scale factor, the thermostatting effect of the
+*angmom* keyword on the rotational temperature of the aspherical
+particles should still be valid.
 
 The keyword *scale* allows the damp factor to be scaled up or down by
 the specified factor for atoms of that type.  This can be useful when
 different atom types have different sizes or masses.  It can be used
 multiple times to adjust damp for several atom types.  Note that
 specifying a ratio of 2 increases the relaxation time which is
-equivalent to the solvent's viscosity acting on particles with 1/2 the
-diameter.  This is the opposite effect of scale factors used by the
-:doc:`fix viscous <fix_viscous>` command, since the damp factor in fix
-*langevin* is inversely related to the gamma factor in fix *viscous*\ .
-Also note that the damping factor in fix *langevin* includes the
-particle mass in Ff, unlike fix *viscous*\ .  Thus the mass and size of
-different atom types should be accounted for in the choice of ratio
-values.
+equivalent to the solvent's viscosity acting on particles with
+:math:`\frac{1}{2}` the diameter.  This is the opposite effect of scale
+factors used by the :doc:`fix viscous <fix_viscous>` command, since the
+damp factor in fix *langevin* is inversely related to the :math:`\gamma`
+factor in fix *viscous*\ .  Also note that the damping factor in fix
+*langevin* includes the particle mass in Ff, unlike fix *viscous*\ .
+Thus the mass and size of different atom types should be accounted for
+in the choice of ratio values.
 
 The keyword *tally* enables the calculation of the cumulative energy
 added/subtracted to the atoms as they are thermostatted.  Effectively
diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst
index 2fa055e380..5057ea1e8a 100644
--- a/doc/src/fix_langevin_eff.rst
+++ b/doc/src/fix_langevin_eff.rst
@@ -41,7 +41,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
    fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5
@@ -55,28 +55,31 @@ this command performs Brownian dynamics (BD), since the total force on
 each atom will have the form:
 
 
-.. parsed-literal::
+.. math::
 
-   F = Fc + Ff + Fr
-   Ff = - (m / damp) v
-   Fr is proportional to sqrt(Kb T m / (dt damp))
+   F   = & F_c + F_f + F_r \\
+   F_f = & - \frac{m}{\mathrm{damp}} v \\
+   F_r \propto &  \sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}
 
-Fc is the conservative force computed via the usual inter-particle
-interactions (:doc:`pair_style <pair_style>`).
 
-The Ff and Fr terms are added by this fix on a per-particle basis.
+:math:`F_c` is the conservative force computed via the usual
+inter-particle interactions (:doc:`pair_style <pair_style>`).
+The :math:`F_f` and :math:`F_r` terms are added by this fix on a
+per-particle basis.
 
-The operation of this fix is exactly like that described by the :doc:`fix langevin <fix_langevin>` command, except that the thermostatting
-is also applied to the radial electron velocity for electron
-particles.
+The operation of this fix is exactly like that described by the
+:doc:`fix langevin <fix_langevin>` command, except that the
+thermostatting is also applied to the radial electron velocity for
+electron particles.
 
 **Restart, fix\_modify, output, run start/stop, minimize info:**
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  Because the state of the random number generator
-is not saved in restart files, this means you cannot do "exact"
-restarts with this fix, where the simulation continues on the same as
-if no restart had taken place.  However, in a statistical sense, a
-restarted simulation should produce the same behavior.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  Because the state of the random number generator is not
+saved in restart files, this means you cannot do "exact" restarts with
+this fix, where the simulation continues on the same as if no restart
+had taken place.  However, in a statistical sense, a restarted
+simulation should produce the same behavior.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a temperature :doc:`compute <compute>`
diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst
index 0c923d923b..5f487906bd 100644
--- a/doc/src/fix_lb_fluid.rst
+++ b/doc/src/fix_lb_fluid.rst
@@ -125,9 +125,9 @@ functions,
 Full details of the lattice-Boltzmann algorithm used can be found in
 :ref:`Mackay et al. <fluid-Mackay>`.
 
-The fluid is coupled to the MD particles described by *group-ID*
-through a velocity dependent force.  The contribution to the fluid
-force on a given lattice mesh site j due to MD particle alpha is
+The fluid is coupled to the MD particles described by *group-ID* through
+a velocity dependent force.  The contribution to the fluid force on a
+given lattice mesh site j due to MD particle :math:`\alpha` is
 calculated as:
 
 .. math::
@@ -137,7 +137,7 @@ calculated as:
 
 where :math:`\mathbf{v}_n` is the velocity of the MD particle,
 :math:`\mathbf{u}_f` is the fluid
-velocity interpolated to the particle location, and gamma is the force
+velocity interpolated to the particle location, and :math:`\gamma` is the force
 coupling constant.  :math:`\zeta` is a weight assigned to the grid point,
 obtained by distributing the particle to the nearest lattice sites.
 For this, the user has the choice between a trilinear stencil, which
@@ -163,10 +163,10 @@ t_{collision}` is a collision time, chosen such that
 :math:`\frac{\tau}{\Delta t_{collision}} = 1` (see :ref:`Mackay and
 Denniston <Mackay2>` for full details).  In order to calculate :math:`m_u`,
 the fluid density is interpolated to the MD particle location, and
-multiplied by a volume, node\_area\*dx\_lb, where node\_area
+multiplied by a volume, node\_area * :math:`dx_{LB}`, where node\_area
 represents the portion of the surface area of the composite object
 associated with a given MD particle.  By default, node\_area is set
-equal to dx\_lb\*dx\_lb; however specific values for given atom types
+equal to :math:`dx_{LB}^2`; however specific values for given atom types
 can be set using the *setArea* keyword.
 
 The user also has the option of specifying their own value for the
@@ -174,7 +174,7 @@ force coupling constant, for all the MD particles associated with the
 fix, through the use of the *setGamma* keyword.  This may be useful
 when modelling porous particles.  See :ref:`Mackay et al. <fluid-Mackay>` for a
 detailed description of the method by which the user can choose an
-appropriate gamma value.
+appropriate :math:`\gamma` value.
 
 .. note::
 
@@ -188,7 +188,9 @@ appropriate gamma value.
    used to integrate the particle motion.  However, if the user specifies
    their own value for the force coupling constant, as mentioned in
    :ref:`Mackay et al. <fluid-Mackay>`, the built-in LAMMPS integrators may prove to
-   be unstable.  Therefore, we have included our own integrators :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and :doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
+   be unstable.  Therefore, we have included our own integrators
+   :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and
+   :doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
    cases.  These integrators should not be used with the
    :doc:`lb/viscous <fix_lb_viscous>` fix, as they add hydrodynamic forces
    to the particles directly.  In addition, they can not be used if the
@@ -207,28 +209,29 @@ appropriate gamma value.
    location, in order to approximate an infinitely massive particle (see
    the dragforce test run for an example).
 
-
 ----------
 
-
 Inside the fix, parameters are scaled by the lattice-Boltzmann
-timestep, dt, grid spacing, dx, and mass unit, dm.  dt is set equal to
-(nevery\*dt\_MD), where dt\_MD is the MD timestep.  By default, dm is set
-equal to 1.0, and dx is chosen so that tau/(dt) =
-(3\*eta\*dt)/(rho\*dx\^2) is approximately equal to 1.  However, the user
-has the option of specifying their own values for dm, and dx, by using
+timestep, :math:`dt_{LB}`, grid spacing, :math:`dx_{LB}`, and mass unit,
+:math:`dm_{LB}`.  :math:`dt_{LB}` is set equal to
+:math:`\mathrm{nevery}\cdot dt_{MD}`, where :math:`dt_{MD}` is the MD timestep.
+By default,
+:math:`dm_{LB}` is set equal to 1.0, and :math:`dx_{LB}` is chosen so that
+:math:`\frac{\tau}{dt} = \frac{3\eta dt}{\rho dx^2}` is approximately equal to 1.
+However, the user has the option of specifying their own values for
+:math:`dm_{LB}`, and :math:`dx_{LB}`, by using
 the optional keywords *dm*\ , and *dx* respectively.
 
 .. note::
 
-   Care must be taken when choosing both a value for dx, and a
-   simulation domain size.  This fix uses the same subdivision of the
-   simulation domain among processors as the main LAMMPS program.  In
+   Care must be taken when choosing both a value for :math:`dx_{LB}`,
+   and a simulation domain size.  This fix uses the same subdivision of
+   the simulation domain among processors as the main LAMMPS program.  In
    order to uniformly cover the simulation domain with lattice sites, the
    lengths of the individual LAMMPS sub-domains must all be evenly
-   divisible by dx.  If the simulation domain size is cubic, with equal
-   lengths in all dimensions, and the default value for dx is used, this
-   will automatically be satisfied.
+   divisible by :math:`dx_{LB}`.  If the simulation domain size is cubic,
+   with equal lengths in all dimensions, and the default value for
+   :math:`dx_{LB}` is used, this will automatically be satisfied.
 
 Physical parameters describing the fluid are specified through
 *viscosity*\ , *density*\ , and *a0*\ . If the force coupling constant is
@@ -240,27 +243,25 @@ the mass, distance, and time units chosen for the main LAMMPS run, as
 they are scaled by the LB timestep, lattice spacing, and mass unit,
 inside the fix.
 
-
 ----------
 
-
 The *setArea* keyword allows the user to associate a surface area with
 a given atom type.  For example if a spherical composite object of
 radius R is represented as a spherical shell of N evenly distributed
 MD particles, all of the same type, the surface area per particle
-associated with that atom type should be set equal to 4\*pi\*R\^2/N.
+associated with that atom type should be set equal to :math:`\frac{4\pi R^2}{N}`.
 This keyword should only be used if the force coupling constant,
-gamma, is set the default way.
+:math:`\gamma`, is set the default way.
 
 The *setGamma* keyword allows the user to specify their own value for
-the force coupling constant, gamma, instead of using the default
+the force coupling constant, :math:`\gamma`, instead of using the default
 value.
 
 The *scaleGamma* keyword should be used in conjunction with the
-*setGamma* keyword, when the user wishes to specify different gamma
+*setGamma* keyword, when the user wishes to specify different :math:`\gamma`
 values for different atom types.  This keyword allows the user to
-scale the *setGamma* gamma value by a factor, gammaFactor, for a given
-atom type.
+scale the *setGamma* :math:`\gamma` value by a factor, gammaFactor,
+for a given atom type.
 
 The *dx* keyword allows the user to specify a value for the LB grid
 spacing.
@@ -269,9 +270,10 @@ The *dm* keyword allows the user to specify the LB mass unit.
 
 If the *a0* keyword is used, the value specified is used for the
 square of the speed of sound in the fluid.  If this keyword is not
-present, the speed of sound squared is set equal to (1/3)\*(dx/dt)\^2.
-Setting a0 > (dx/dt)\^2 is not allowed, as this may lead to
-instabilities.
+present, the speed of sound squared is set equal to
+:math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
+Setting :math:`a0 > (\frac{dx_{LB}}{dt_{LB}})^2` is not allowed,
+as this may lead to instabilities.
 
 If the *noise* keyword is used, followed by a positive temperature
 value, and a positive integer random number seed, a thermal
@@ -388,13 +390,13 @@ By default, the force coupling constant is set according to
    \gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
 
 
-and an area of dx\_lb\^2 per node, used to calculate the fluid mass at
+and an area of :math:`dx_{LB}^2` per node, used to calculate the fluid mass at
 the particle node location, is assumed.
 
-dx is chosen such that tau/(delta t\_LB) =
-(3 eta dt\_LB)/(rho dx\_lb\^2) is approximately equal to 1.
-dm is set equal to 1.0.
-a0 is set equal to (1/3)\*(dx\_lb/dt\_lb)\^2.
+*dx* is chosen such that :math:`\frac{\tau}{dt_{LB}} =
+\frac{3\eta dt_{LB}}{\rho dx_{LB}^2}` is approximately equal to 1.
+*dm* is set equal to 1.0.
+*a0* is set equal to :math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
 The Peskin stencil is used as the default interpolation method.
 The D3Q15 lattice is used for the lattice-Boltzmann algorithm.
 If walls are present, they are assumed to be stationary.
diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst
index 36f2bd2ae0..80bfaf24bd 100644
--- a/doc/src/fix_msst.rst
+++ b/doc/src/fix_msst.rst
@@ -35,7 +35,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
    fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4  v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01
@@ -101,16 +101,17 @@ timestep. To do this, the fix creates its own computes of style "temp"
 "pressure", and "pe", as if these commands had been issued:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute fix-ID_MSST_temp all temp
    compute fix-ID_MSST_press all pressure fix-ID_MSST_temp
 
    compute fix-ID_MSST_pe all pe
 
-See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>` commands for details.  Note that the
-IDs of the new computes are the fix-ID + "_MSST\_temp`or <MSST_press">`_
-or "_MSST\_pe".  The group for the new computes is "all".
+See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure
+<compute_pressure>` commands for details.  Note that the IDs of the
+new computes are the fix-ID + "_MSST\_temp" or "MSST\_press" or
+"_MSST\_pe".  The group for the new computes is "all".
 
 
 ----------
@@ -132,9 +133,10 @@ timestepping.  DFTB+ will communicate its info to LAMMPS via that fix.
 
 **Restart, fix\_modify, output, run start/stop, minimize info:**
 
-This fix writes the state of all internal variables to :doc:`binary restart files <restart>`.  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
+This fix writes the state of all internal variables to :doc:`binary
+restart files <restart>`.  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.
 
 The progress of the MSST can be monitored by printing the global
@@ -161,7 +163,7 @@ To print these quantities to the log file with descriptive column
 headers, the following LAMMPS commands are suggested:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix              msst all msst z
    fix_modify       msst energy yes
@@ -172,15 +174,17 @@ headers, the following LAMMPS commands are suggested:
    thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
 
 These fixes compute a global scalar and a global vector of 4
-quantities, which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar values calculated by this fix
-are "extensive"; the vector values are "intensive".
+quantities, which can be accessed by various :doc:`output commands
+<Howto_output>`.  The scalar values calculated by this fix are
+"extensive"; the vector values are "intensive".
 
 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>` doc page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 All cell dimensions must be periodic. This fix can not be used with a
 triclinic cell.  The MSST fix has been tested only for the group-ID
diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst
index 5704966827..e360e70c23 100644
--- a/doc/src/fix_nve_dotc_langevin.rst
+++ b/doc/src/fix_nve_dotc_langevin.rst
@@ -29,7 +29,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
    fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10
@@ -61,33 +61,33 @@ over the standard integrator, permitting slightly larger timestep sizes.
 The total force on each atom will have the form:
 
 
-.. parsed-literal::
+.. math::
 
-   F = Fc + Ff + Fr
-   Ff = - (m / damp) v
-   Fr is proportional to sqrt(Kb T m / (dt damp))
+   F =   & F_c + F_f + F_r \\
+   F_f = & - \frac{m}{\mathrm{damp}} v \\
+   F_r \propto & \sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}
 
-Fc is the conservative force computed via the usual inter-particle
-interactions (:doc:`pair_style <pair_style>`,
-:doc:`bond_style <bond_style>`, etc).
+:math:`F_c` is the conservative force computed via the usual
+inter-particle interactions (:doc:`pair_style <pair_style>`,
+:doc:`bond_style <bond_style>`, etc). The :math:`F_f` and :math:`F_r`
+terms are implicitly taken into account by this fix on a per-particle
+basis.
 
-The Ff and Fr terms are implicitly taken into account by this fix
-on a per-particle basis.
+:math:`F_f` is a frictional drag or viscous damping term proportional to
+the particle's velocity.  The proportionality constant for each atom is
+computed as :math:`\frac{m}{\mathrm{damp}}`, where *m* is the mass of
+the particle and damp is the damping factor specified by the user.
 
-Ff is a frictional drag or viscous damping term proportional to the
-particle's velocity.  The proportionality constant for each atom is
-computed as m/damp, where m is the mass of the particle and damp is
-the damping factor specified by the user.
-
-Fr is a force due to solvent atoms at a temperature T randomly bumping
-into the particle.  As derived from the fluctuation/dissipation
-theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
-dt damp), where Kb is the Boltzmann constant, T is the desired
-temperature, m is the mass of the particle, dt is the timestep size,
-and damp is the damping factor.  Random numbers are used to randomize
-the direction and magnitude of this force as described in
-:ref:`(Dunweg) <Dunweg5>`, where a uniform random number is used (instead of
-a Gaussian random number) for speed.
+:math:`F_r` is a force due to solvent atoms at a temperature *T*
+randomly bumping into the particle.  As derived from the
+fluctuation/dissipation theorem, its magnitude as shown above is
+proportional to :math:`\sqrt{\frac{k_B T m}{dt~\mathrm{damp}}}`, where
+:math:`k_B` is the Boltzmann constant, *T* is the desired temperature,
+*m* is the mass of the particle, *dt* is the timestep size, and damp is
+the damping factor.  Random numbers are used to randomize the direction
+and magnitude of this force as described in :ref:`(Dunweg) <Dunweg5>`,
+where a uniform random number is used (instead of a Gaussian random
+number) for speed.
 
 
 ----------
@@ -104,7 +104,7 @@ means to relax the temperature in a timespan of (roughly) 0.03 time
 units tau (see the :doc:`units <units>` command).
 The damp factor can be thought of as inversely related to the
 viscosity of the solvent, i.e. a small relaxation time implies a
-hi-viscosity solvent and vice versa.  See the discussion about gamma
+high-viscosity solvent and vice versa.  See the discussion about gamma
 and viscosity in the documentation for the :doc:`fix viscous <fix_viscous>` command for more details.
 Note that the value 78.9375 in the second example above corresponds
 to a diffusion constant, which is about an order of magnitude larger
@@ -124,10 +124,10 @@ particles are always considered to have a finite size.
 The keyword *angmom* enables thermostatting of the rotational degrees of
 freedom in addition to the usual translational degrees of freedom.
 
-The scale factor after the *angmom* keyword gives the ratio of the rotational to
-the translational friction coefficient.
+The scale factor after the *angmom* keyword gives the ratio of the
+rotational to the translational friction coefficient.
 
-An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
+An example input file can be found in examples/USER/cgdna/examples/duplex2/.
 Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
 The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
 
diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst
index 94a4294e8b..984c0ca793 100644
--- a/doc/src/fix_qbmsst.rst
+++ b/doc/src/fix_qbmsst.rst
@@ -26,7 +26,7 @@ Syntax
        *v0* value = initial simulation cell volume in the shock equations (distance\^3 units)
        *e0* value = initial total energy (energy units)
        *tscale* value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
-       *damp* value = damping parameter (time units) inverse of friction <i>&gamma;</i>
+       *damp* value = damping parameter (time units) inverse of friction *gamma*
        *seed* value = random number seed (positive integer)
        *f_max* value = upper cutoff frequency of the vibration spectrum (1/time units)
        *N_f* value = number of frequency bins (positive integer)
@@ -40,44 +40,47 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
-   fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
+   # (liquid methane modeled with the REAX force field, real units)
+   fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110
+   # (quartz modeled with the BKS force field, metal units)
+   fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300
 
-Two example input scripts are given, including shocked alpha quartz
-and shocked liquid methane. The input script first equilibrate an
-initial state with the quantum thermal bath at the target temperature
-and then apply the qbmsst to simulate shock compression with quantum
-nuclear correction.  The following two figures plot related quantities
-for shocked alpha quartz.
+Two example input scripts are given, including shocked
+:math:`\alpha\textrm{-quartz}` and shocked liquid methane.  The input
+script first equilibrates an initial state with the quantum thermal
+bath at the target temperature and then applies *fix qbmsst* to simulate
+shock compression with quantum nuclear correction.  The following two
+figures plot relevant quantities for shocked
+:math:`\alpha\textrm{-quartz}`.
 
 .. image:: JPG/qbmsst_init.jpg
    :align: center
 
-Figure 1. Classical temperature <i>T</i><sup>cl</sup> = &sum;
-<i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub> vs. time
-for coupling the alpha quartz initial state with the quantum thermal
-bath at target quantum temperature <i>T</i><sup>qm</sup> = 300 K. The
-NpH ensemble is used for time integration while QTB provides the
-colored random force. <i>T</i><sup>cl</sup> converges at the timescale
-of *damp* which is set to be 1 ps.
+Figure 1. Classical temperature
+:math:`T_{cl} = \sum \frac{m_iv_i^2}{3Nk_B}` vs. time for coupling the
+:math:`\alpha\textrm{-quartz}` initial state with the quantum thermal
+bath at target quantum temperature :math:`T^{qm} = 300 K`. The NpH
+ensemble is used for time integration while QTB provides the colored
+random force. :math:`T^{cl}` converges at the timescale of *damp*
+which is set to be 1 ps.
 
 .. image:: JPG/qbmsst_shock.jpg
    :align: center
 
 Figure 2. Quantum temperature and pressure vs. time for simulating
-shocked alpha quartz with the QBMSST. The shock propagates along the z
-direction. Restart of the QBMSST command is demonstrated in the
-example input script. Thermodynamic quantities stay continuous before
-and after the restart.
+shocked :math:`\alpha\textrm{-quartz}` with *fix qbmsst*\. The shock
+propagates along the z direction. Restart of the *fix qbmsst* command
+is demonstrated in the example input script. Thermodynamic quantities
+stay continuous before and after the restart.
 
 Description
 """""""""""
 
 This command performs the Quantum-Bath coupled Multi-Scale Shock
 Technique (QBMSST) integration. See :ref:`(Qi) <Qi>` for a detailed
-description of this method.  The QBMSST provides description of the
+description of this method.  QBMSST provides description of the
 thermodynamics and kinetics of shock processes while incorporating
 quantum nuclear effects.  The *shockvel* setting determines the steady
 shock velocity that will be simulated along direction *dir*\ .
@@ -107,37 +110,34 @@ in the command :doc:`fix msst <fix_msst>`. The values of *e0*\ , *p0*\ , or
 parameter of *damp*\ , *f\_max*, and *N\_f* are described in the command
 :doc:`fix qtb <fix_qtb>`.
 
-The fix qbmsst command couples the shock system to a quantum thermal
+The *fix qbmsst* command couples the shock system to a quantum thermal
 bath with a rate that is proportional to the change of the total
-energy of the shock system, <i>etot</i> - <i>etot</i><sub>0</sub>.
-Here <i>etot</i> consists of both the system energy and a thermal
-term, see :ref:`(Qi) <Qi>`, and <i>etot</i><sub>0</sub> = *e0* is the
+energy of the shock system, :math:`E^{tot} - E^{tot}_0`.
+Here :math:`E^{etot}` consists of both the system energy and a thermal
+term, see :ref:`(Qi) <Qi>`, and :math:`E^{tot}_0 = e0` is the
 initial total energy.
 
-The *eta* (<i>&eta;</i>) parameter is a unitless coupling constant
-between the shock system and the quantum thermal bath. A small *eta*
+The *eta* (:math:`\eta`) parameter is a unitless coupling constant
+between the shock system and the quantum thermal bath. A small :math:`\eta`
 value cannot adjust the quantum temperature fast enough during the
-temperature ramping period of shock compression while large *eta*
-leads to big temperature oscillation. A value of *eta* between 0.3 and
+temperature ramping period of shock compression while large :math:`\eta`
+leads to big temperature oscillation. A value of :math:`\eta` between 0.3 and
 1 is usually appropriate for simulating most systems under shock
-compression. We observe that different values of *eta* lead to almost
+compression. We observe that different values of :math:`\eta` lead to almost
 the same final thermodynamic state behind the shock, as expected.
 
-The quantum temperature is updated every *beta* (<i>&beta;</i>) steps
-with an integration time interval *beta* times longer than the
-simulation time step. In that case, <i>etot</i> is taken as its
-average over the past *beta* steps. The temperature of the quantum
-thermal bath <i>T</i><sup>qm</sup> changes dynamically according to
-the following equation where &Delta;<i>t</i> is the MD time step and
-<i>&gamma;</i> is the friction constant which is equal to the inverse
+The quantum temperature is updated every *beta* (:math:`\beta`) steps
+with an integration time interval :math:`\beta` times longer than the
+simulation time step. In that case, :math:`E^{tot}` is taken as its
+average over the past :math:`\beta` steps. The temperature of the quantum
+thermal bath :math:`T^{qm}` changes dynamically according to
+the following equation where :math:`\Delta_t` is the MD time step and
+:math:`\gamma` is the friction constant which is equal to the inverse
 of the *damp* parameter.
 
-.. raw:: html
+.. math::
 
-   <center><font size="4"> <i>dT</i><sup>qm</sup>/<i>dt =
-   &gamma;&eta;</i>&sum;<i><sup>&beta;</sup><sub>l =
-   1</sub></i>[<i>etot</i>(<i>t-l</i>&Delta;<i>t</i>)-<i>etot</i><sub>0</sub>]/<i>3&beta;Nk</i><sub>B</sub>
-   </font></center>
+   \frac{dT^{qm}}{dt} = \gamma\eta\sum^\beta_{l=1}\frac{E^{tot}(t-l\Delta t) - E^{tot}_0}{3\beta N k_B}
 
 The parameter *T\_init* is the initial temperature of the quantum
 thermal bath and the system before shock loading.
@@ -172,12 +172,12 @@ vector contains five values in this order:
 2. *drayleigh* is the departure from the Rayleigh line (pressure units).
 3. *lagrangian\_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
 4. *lagrangian\_position* is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front.
-5. *quantum\_temperature* is the temperature of the quantum thermal bath <i>T</i><sup>qm</sup>.
+5. *quantum\_temperature* is the temperature of the quantum thermal bath :math:`T^{qm}`.
 
 To print these quantities to the log file with descriptive column
 headers, the following LAMMPS commands are suggested. Here the
 :doc:`fix_modify <fix_modify>` energy command is also enabled to allow
-the thermo keyword *etotal* to print the quantity <i>etot</i>.  See
+the thermo keyword *etotal* to print the quantity :math:`E^{tot}`.  See
 also the :doc:`thermo_style <thermo_style>` command.
 
 
@@ -193,10 +193,11 @@ also the :doc:`thermo_style <thermo_style>` command.
    thermo_style    custom  step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
 
 The global scalar under the entry f\_fix\_id is the quantity of thermo
-energy as an extra part of <i>etot</i>. This global scalar and the
-vector of 5 quantities can be accessed by various :doc:`output commands <Howto_output>`. It is worth noting that the temp keyword
+energy as an extra part of :math:`E^{tot}`. This global scalar and the
+vector of 5 quantities can be accessed by various :doc:`output commands <Howto_output>`.
+It is worth noting that the temp keyword
 under the :doc:`thermo_style <thermo_style>` command print the
-instantaneous classical temperature <i>T</i><sup>cl</sup> as described
+instantaneous classical temperature :math:`T^{cl}` as described
 in the command :doc:`fix qtb <fix_qtb>`.
 
 
diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst
index 235c28ca19..7242d0739b 100644
--- a/doc/src/fix_qtb.rst
+++ b/doc/src/fix_qtb.rst
@@ -19,7 +19,7 @@ Syntax
   .. parsed-literal::
   
        *temp* value = target quantum temperature (temperature units)
-       *damp* value = damping parameter (time units) inverse of friction <i>&gamma</i>;
+       *damp* value = damping parameter (time units) inverse of friction *gamma*
        *seed* value = random number seed (positive integer)
        *f_max* value = upper cutoff frequency of the vibration spectrum (1/time units)
        *N_f* value = number of frequency bins (positive integer)
@@ -30,12 +30,14 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
+   # (liquid methane modeled with the REAX force field, real units)
    fix 1 all nve
-   fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
+   fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100
+   # (quartz modeled with the BKS force field, metal units)
    fix 2 all nph iso 1.01325 1.01325 1
-   fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
+   fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100
 
 Description
 """""""""""
@@ -56,61 +58,54 @@ atoms and thus higher classical limits.
 The equation of motion implemented by this command follows a Langevin
 form:
 
-.. raw:: html
+.. math::
 
-   <center><font size="4"><i> m<sub>i</sub>a<sub>i</sub> = f<sub>i</sub>
-   + R<sub>i</sub> -
-   m<sub>i</sub>&gamma;v<sub>i</sub>. </i></font></center>
+   m_i a_i = f_i + R_i - m_i\gamma v_i
 
-Here <i>m<sub>i</sub></i>, <i>a<sub>i</sub></i>, <i>f<sub>i</sub>
-</i>, <i>R<sub>i</sub></i>, <i>&gamma;</i> and <i>v<sub>i</sub> </i>
-represent mass, acceleration, force exerted by all other atoms, random
+Here :math:`m_i, a_i, f_i, R_i, \gamma, \textrm{and} v_i`
+represent in this order mass, acceleration, force exerted by all other atoms, random
 force, frictional coefficient (the inverse of damping parameter damp),
-and velocity. The random force <i>R<sub>i</sub></i> is "colored" so
-that any vibrational mode with frequency <i>&omega;</i> will have a
-temperature-sensitive energy <i>&theta;</i>(<i>&omega;,T</i>) which
+and velocity. The random force :math:`R_i` is "colored" so
+that any vibrational mode with frequency :math:`\omega` will have a
+temperature-sensitive energy :math:`\theta(\omega,T)` which
 resembles the energy expectation for a quantum harmonic oscillator
 with the same natural frequency:
 
-.. raw:: html
 
-   <center><font size="4"> <i>&theta;</i>(<i>&omega;,T</i>) =
-   &#8463;&omega;/2 +
-   &#8463;&omega;[</i>exp(<i>&#8463;&omega;/k</i><sub>B</sub><i>T</i>)<i>-1</i>]<i><sup>-1</sup></i>
-   </font></center>
+.. math::
+
+   \theta(\omega T) = \frac{\hbar}{2} + \hbar\omega \left[\exp(\frac{\hbar\omega}{k_B T})-1 \right]^{-1}
 
 To efficiently generate the random forces, we employ the method
 of :ref:`(Barrat) <Barrat>`, that circumvents the need to generate all
 random forces for all times before the simulation. The memory
 requirement of this approach is less demanding and independent
-of the simulation duration. Since the total random force <i>R</i><sub>tot</sub>
+of the simulation duration. Since the total random force :math:`R_{tot}`
 does not necessarily vanish for a finite number of atoms,
-<i>R<sub>i</sub></i> is replaced by <i>R<sub>i</sub></i> - <i>R</i><sub>tot</sub>/<i>N</i><sub>tot</sub>
+:math:`R_i` is replaced by :math:`R_i - \frac{R_{tot}}{N_{tot}}`
 to avoid collective motion of the system.
 
 The *temp* parameter sets the target quantum temperature. LAMMPS will
 still have an output temperature in its thermo style. That is the
-instantaneous classical temperature <i>T</i><sup>cl</sup> derived from
+instantaneous classical temperature :math:`T^{cl}` derived from
 the atom velocities at thermal equilibrium. A non-zero
-<i>T</i><sup>cl</sup> will be present even when the quantum
+:math:`T^{cl}` will be present even when the quantum
 temperature approaches zero. This is associated with zero-point energy
 at low temperatures.
 
-.. raw:: html
+.. math::
 
-   <center><font size="4"> <i>T</i><sup>cl</sup> = &sum;
-   <i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub>
-   </font></center>
+   T^{cl} = \sum \frac{m_i v_i^2}{3 N k_B}
 
 The *damp* parameter is specified in time units, and it equals the
-inverse of the frictional coefficient <i>&gamma;</i>. <i>&gamma;</i>
+inverse of the frictional coefficient :math:`\gamma`. :math:`\gamma`
 should be as small as possible but slightly larger than the timescale
 of anharmonic coupling in the system which is about 10 ps to 100
-ps. When <i>&gamma;</i> is too large, it gives an energy spectrum that
-differs from the desired Bose-Einstein spectrum. When <i>&gamma;</i>
+ps. When :math:`\gamma` is too large, it gives an energy spectrum that
+differs from the desired Bose-Einstein spectrum. When :math:`\gamma`
 is too small, the quantum thermal bath coupling to the system will be
 less significant than anharmonic effects, reducing to a classical
-limit. We find that setting <i>&gamma;</i> between 5 THz and 1 THz
+limit. We find that setting :math:`\gamma` between 5 THz and 1 THz
 could be appropriate depending on the system.
 
 The random number *seed* is a positive integer used to initiate a
@@ -121,23 +116,22 @@ runs on different numbers of processors.
 
 The *f\_max* parameter truncate the noise frequency domain so that
 vibrational modes with frequencies higher than *f\_max* will not be
-modulated. If we denote &Delta;<i>t</i> as the time interval for the
+modulated. If we denote :math:`\Delta t` as the time interval for the
 MD integration, *f\_max* is always reset by the code to make
-<i>&alpha;</i> = (int)(2*f\_max*&Delta;<i>t</i>)<sup><i>-1</i></sup> a
+:math:`\alpha = (int)(2` *f\_max* :math:`\Delta t)^{-1}` a
 positive integer and print out relative information. An appropriate
-value for the cutoff frequency *f\_max* would be around 2~3
-<i>f</i><sub>D</sub>, where <i>f</i><sub>D</sub> is the Debye
-frequency.
+value for the cutoff frequency *f\_max* would be around 2~3 :math:`f_D`,
+where :math:`f_D` is the Debye frequency.
 
 The *N\_f* parameter is the frequency grid size, the number of points
 from 0 to *f\_max* in the frequency domain that will be
-sampled. <i>3&times;2</i> *N\_f* per-atom random numbers are required
+sampled. 3*2\ *N\_f* per-atom random numbers are required
 in the random force generation and there could be as many atoms as in
 the whole simulation that can migrate into every individual
 processor. A larger *N\_f* provides a more accurate sampling of the
 spectrum while consumes more memory.  With fixed *f\_max* and
-<i>&gamma;</i>, *N\_f* should be big enough to converge the classical
-temperature <i>T</i><sup>cl</sup> as a function of target quantum bath
+:math:`\gamma`, *N\_f* should be big enough to converge the classical
+temperature :math:`T^{cl}` as a function of target quantum bath
 temperature. Memory usage per processor could be from 10 to 100
 Mbytes.
 
@@ -147,10 +141,12 @@ Mbytes.
    Nose/Hoover thermostatting AND time integration, this fix does NOT
    perform time integration. It only modifies forces to a colored
    thermostat. Thus you must use a separate time integration fix, like
-   :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>` to actually update the
-   velocities and positions of atoms (as shown in the
-   examples). Likewise, this fix should not normally be used with other
-   fixes or commands that also specify system temperatures , e.g. :doc:`fix nvt <fix_nh>` and :doc:`fix temp/rescale <fix_temp_rescale>`.
+   :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>` to actually
+   update the velocities and positions of atoms (as shown in the
+   examples). Likewise, this fix should not normally be used with
+   other fixes or commands that also specify system temperatures ,
+   e.g. :doc:`fix nvt <fix_nh>` and :doc:`fix temp/rescale
+   <fix_temp_rescale>`.
 
 
 ----------
@@ -158,10 +154,11 @@ Mbytes.
 
 **Restart, fix\_modify, output, run start/stop, minimizie info:**
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  Because the state of the random number generator
-is not saved in restart files, this means you cannot do "exact"
-restarts with this fix. However, in a statistical sense, a restarted
-simulation should produce similar behaviors of the system.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  Because the state of the random number generator is not
+saved in restart files, this means you cannot do "exact" restarts with
+this fix. However, in a statistical sense, a restarted simulation
+should produce similar behaviors of the system.
 
 This fix is not invoked during :doc:`energy minimization <minimize>`.
 
@@ -174,7 +171,8 @@ Restrictions
 
 
 This fix style is part of the USER-QTB package.  It is only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 
 ----------
@@ -183,7 +181,8 @@ LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
 Related commands
 """"""""""""""""
 
-:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix qbmsst <fix_qbmsst>`
+:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`,
+:doc:`fix langevin <fix_langevin>`, :doc:`fix qbmsst <fix_qbmsst>`
 
 
 ----------
diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst
index 92ae085ff1..63d93a1c48 100644
--- a/doc/src/fix_srd.rst
+++ b/doc/src/fix_srd.rst
@@ -84,36 +84,37 @@ the implementation and usage of mixture systems (solute particles in
 an SRD fluid).  See the examples/srd directory for sample input
 scripts using SRD particles in both settings.
 
-This fix does 2 things:
+This fix does two things:
 
-(1) It advects the SRD particles, performing collisions between SRD
-and big particles or walls every timestep, imparting force and torque
-to the big particles.  Collisions also change the position and
-velocity of SRD particles.
+  1. It advects the SRD particles, performing collisions between SRD
+     and big particles or walls every timestep, imparting force and torque
+     to the big particles.  Collisions also change the position and
+     velocity of SRD particles.
 
-(2) It resets the velocity distribution of SRD particles via random
-rotations every N timesteps.
+  2. It resets the velocity distribution of SRD particles via random
+     rotations every N timesteps.
 
 SRD particles have a mass, temperature, characteristic timestep
-dt\_SRD, and mean free path between collisions (lamda).  The
-fundamental equation relating these 4 quantities is
+:math:`dt_{SRD}`, and mean free path between collisions
+(:math:`\lambda`).  The fundamental equation relating these 4 quantities
+is
 
 
-.. parsed-literal::
+.. math::
 
-   lamda = dt_SRD \* sqrt(Kboltz \* Tsrd / mass)
+   \lambda = dt_{SRD} \sqrt{\frac{k_B T_{SRD}}{m}}
 
-The mass of SRD particles is set by the :doc:`mass <mass>` command
-elsewhere in the input script.  The SRD timestep dt\_SRD is N times the
-step dt defined by the :doc:`timestep <timestep>` command.  Big
-particles move in the normal way via a time integration :doc:`fix <fix>`
-with a short timestep dt.  SRD particles advect with a large timestep
-dt\_SRD >= dt.
+The mass *m* of SRD particles is set by the :doc:`mass <mass>` command
+elsewhere in the input script.  The SRD timestep :math:`dt_{SRD}` is N
+times the step *dt* defined by the :doc:`timestep <timestep>` command.
+Big particles move in the normal way via a time integration :doc:`fix
+<fix>` with a short timestep dt.  SRD particles advect with a large
+timestep :math:`dt_{SRD} \ge dt`.
 
 If the *lamda* keyword is not specified, the SRD temperature
-*Tsrd* is used in the above formula to compute lamda.  If the *lamda*
-keyword is specified, then the *Tsrd* setting is ignored and the above
-equation is used to compute the SRD temperature.
+:math:`T_{SRD}` is used in the above formula to compute :math:`\lambda`.
+If the *lamda* keyword is specified, then the *Tsrd* setting is ignored
+and the above equation is used to compute the SRD temperature.
 
 The characteristic length scale for the SRD fluid is set by *hgrid*
 which is used to bin SRD particles for purposes of resetting their
@@ -121,13 +122,14 @@ velocities.  Normally hgrid is set to be 1/4 of the big particle
 diameter or smaller, to adequately resolve fluid properties around the
 big particles.
 
-Lamda cannot be smaller than 0.6 \* hgrid, else an error is generated
-(unless the *shift* keyword is used, see below).  The velocities of
-SRD particles are bounded by Vmax, which is set so that an SRD
-particle will not advect further than Dmax = 4\*lamda in dt\_SRD.  This
-means that roughly speaking, Dmax should not be larger than a big
-particle diameter, else SRDs may pass through big particles without
-colliding.  A warning is generated if this is the case.
+:math:`\lambda` cannot be smaller than 0.6 \* hgrid, else an error is
+generated (unless the *shift* keyword is used, see below).  The
+velocities of SRD particles are bounded by Vmax, which is set so that an
+SRD particle will not advect further than :math:`D_{max} = 4 \lambda` in
+:math:`dt_{SRD}`.  This means that roughly speaking, :math:`D_{max}`
+should not be larger than a big particle diameter, else SRDs may pass
+through big particles without colliding.  A warning is generated if this
+is the case.
 
 Collisions between SRD particles and big particles or walls are
 modeled as a lightweight SRD point particle hitting a heavy big
@@ -160,11 +162,12 @@ the big particles appropriately should be used.
 The *overlap* keyword should be set to *yes* if two (or more) big
 particles can ever overlap.  This depends on the pair potential
 interaction used for big-big interactions, or could be the case if
-multiple big particles are held together as rigid bodies via the :doc:`fix rigid <fix_rigid>` command.  If the *overlap* keyword is *no* and
-big particles do in fact overlap, then SRD/big collisions can generate
-an error if an SRD ends up inside two (or more) big particles at once.
-How this error is treated is determined by the *inside* keyword.
-Running with *overlap* set to *no* allows for faster collision
+multiple big particles are held together as rigid bodies via the
+:doc:`fix rigid <fix_rigid>` command.  If the *overlap* keyword is *no*
+and big particles do in fact overlap, then SRD/big collisions can
+generate an error if an SRD ends up inside two (or more) big particles
+at once.  How this error is treated is determined by the *inside*
+keyword.  Running with *overlap* set to *no* allows for faster collision
 checking, so it should only be set to *yes* if needed.
 
 The *inside* keyword determines how a collision is treated if the
@@ -258,30 +261,30 @@ warning is generated.
    reneighboring.  Note that changing the SRD bin size may alter the
    properties of the SRD fluid, such as its viscosity.
 
-The *shift* keyword determines whether the coordinates of SRD
-particles are randomly shifted when binned for purposes of rotating
-their velocities.  When no shifting is performed, SRD particles are
-binned and the velocity distribution of the set of SRD particles in
-each bin is adjusted via a rotation operator.  This is a statistically
-valid operation if SRD particles move sufficiently far between
-successive rotations.  This is determined by their mean-free path
-lamda.  If lamda is less than 0.6 of the SRD bin size, then shifting
-is required.  A shift means that all of the SRD particles are shifted
-by a vector whose coordinates are chosen randomly in the range [-1/2
-bin size, 1/2 bin size].  Note that all particles are shifted by the
-same vector.  The specified random number *shiftseed* is used to
-generate these vectors.  This operation sufficiently randomizes which
-SRD particles are in the same bin, even if lamda is small.
+The *shift* keyword determines whether the coordinates of SRD particles
+are randomly shifted when binned for purposes of rotating their
+velocities.  When no shifting is performed, SRD particles are binned and
+the velocity distribution of the set of SRD particles in each bin is
+adjusted via a rotation operator.  This is a statistically valid
+operation if SRD particles move sufficiently far between successive
+rotations.  This is determined by their mean-free path :math:`\lambda`.
+If :math:`\lambda` is less than 0.6 of the SRD bin size, then shifting
+is required.  A shift means that all of the SRD particles are shifted by
+a vector whose coordinates are chosen randomly in the range [-1/2 bin
+size, 1/2 bin size].  Note that all particles are shifted by the same
+vector.  The specified random number *shiftseed* is used to generate
+these vectors.  This operation sufficiently randomizes which SRD
+particles are in the same bin, even if :math:`lambda` is small.
 
 If the *shift* flag is set to *no*\ , then no shifting is performed, but
-bin data will be communicated if bins overlap processor boundaries.
-An error will be generated if lamda < 0.6 of the SRD bin size.  If the
-*shift* flag is set to *possible*\ , then shifting is performed only if
-lamda < 0.6 of the SRD bin size.  A warning is generated to let you
-know this is occurring.  If the *shift* flag is set to *yes* then
-shifting is performed regardless of the magnitude of lamda.  Note that
-the *shiftseed* is not used if the *shift* flag is set to *no*\ , but
-must still be specified.
+bin data will be communicated if bins overlap processor boundaries.  An
+error will be generated if :math:`\lambda < 0.6` of the SRD bin size.
+If the *shift* flag is set to *possible*\ , then shifting is performed
+only if :math:`\lambda < 0.6` of the SRD bin size.  A warning is
+generated to let you know this is occurring.  If the *shift* flag is set
+to *yes* then shifting is performed regardless of the magnitude of
+:math:`\lambda`.  Note that the *shiftseed* is not used if the *shift*
+flag is set to *no*\ , but must still be specified.
 
 Note that shifting of SRD coordinates requires extra communication,
 hence it should not normally be enabled unless required.
@@ -398,10 +401,10 @@ Related commands
 Default
 """""""
 
-The option defaults are lamda inferred from Tsrd, collision = noslip,
-overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
-search = hgrid, cubic = error 0.01, shift = no, tstat = no, and
-rescale = yes.
+The option defaults are: *lamda* (:math:`\lambda`) is inferred from *Tsrd*,
+collision = noslip, overlap = no, inside = error, exact = yes, radius =
+1.0, bounce = 0, search = hgrid, cubic = error 0.01, shift = no, tstat =
+no, and rescale = yes.
 
 
 ----------
diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst
index 026a850b46..427ff06cfd 100644
--- a/doc/src/fix_viscous.rst
+++ b/doc/src/fix_viscous.rst
@@ -47,11 +47,11 @@ energy to the system), it has the effect of slowly (or rapidly)
 freezing the system; hence it can also be used as a simple energy
 minimization technique.
 
-The damping force F is given by F = - gamma \* velocity.  The larger
-the coefficient, the faster the kinetic energy is reduced.  If the
-optional keyword *scale* is used, gamma can scaled up or down by the
-specified factor for atoms of that type.  It can be used multiple
-times to adjust gamma for several atom types.
+The damping force :math:`F_i` is given by :math:`F_i = - \gamma v_i`.
+The larger the coefficient, the faster the kinetic energy is reduced.
+If the optional keyword *scale* is used, :math:`\gamma` can scaled up or
+down by the specified factor for atoms of that type.  It can be used
+multiple times to adjust :math:`\gamma` for several atom types.
 
 .. note::
 
@@ -60,38 +60,40 @@ times to adjust gamma for several atom types.
    :doc:`units <units>` options like "real" or "metal" that are not
    self-consistent.
 
-In a Brownian dynamics context, gamma = Kb T / D, where Kb =
-Boltzmann's constant, T = temperature, and D = particle diffusion
-coefficient.  D can be written as Kb T / (3 pi eta d), where eta =
-dynamic viscosity of the frictional fluid and d = diameter of
-particle.  This means gamma = 3 pi eta d, and thus is proportional to
-the viscosity of the fluid and the particle diameter.
+In a Brownian dynamics context, :math:`\gamma = \frac{k_B T}{D}`, where
+:math:`k_B =` Boltzmann's constant, *T* = temperature, and *D* = particle
+diffusion coefficient.  *D* can be written as :math:`\frac{k_B T}{3 \pi
+\eta d}`, where :math:`\eta =` dynamic viscosity of the frictional fluid
+and d = diameter of particle.  This means :math:`\gamma = 3 \pi \eta d`,
+and thus is proportional to the viscosity of the fluid and the particle
+diameter.
 
 In the current implementation, rather than have the user specify a
-viscosity, gamma is specified directly in force/velocity units.  If
-needed, gamma can be adjusted for atoms of different sizes
-(i.e. sigma) by using the *scale* keyword.
+viscosity, :math:`\gamma` is specified directly in force/velocity units.
+If needed, :math:`\gamma` can be adjusted for atoms of different sizes
+(i.e. :math:`\sigma`) by using the *scale* keyword.
 
 Note that Brownian dynamics models also typically include a randomized
-force term to thermostat the system at a chosen temperature.  The :doc:`fix langevin <fix_langevin>` command does this.  It has the same
+force term to thermostat the system at a chosen temperature.  The
+:doc:`fix langevin <fix_langevin>` command does this.  It has the same
 viscous damping term as fix viscous and adds a random force to each
-atom.  The random force term is proportional to the sqrt of the chosen
-thermostatting temperature.  Thus if you use fix langevin with a
-target T = 0, its random force term is zero, and you are essentially
-performing the same operation as fix viscous.  Also note that the
-gamma of fix viscous is related to the damping parameter of :doc:`fix langevin <fix_langevin>`, however the former is specified in units
-of force/velocity and the latter in units of time, so that it can more
-easily be used as a thermostat.
-
+atom.  The random force term is proportional to the square root of the
+chosen thermostatting temperature.  Thus if you use fix langevin with a
+target :math:`T = 0`, its random force term is zero, and you are
+essentially performing the same operation as fix viscous.  Also note
+that the gamma of fix viscous is related to the damping parameter of
+:doc:`fix langevin <fix_langevin>`, however the former is specified in
+units of force/velocity and the latter in units of time, so that it can
+more easily be used as a thermostat.
 
 ----------
 
-
 **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
-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 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.
 
diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst
index 600c880f20..c76b0c8905 100644
--- a/doc/src/fix_wall.rst
+++ b/doc/src/fix_wall.rst
@@ -158,7 +158,7 @@ For style *wall/morse*\ , the energy E is given by a Morse potential:
 
 
 In all cases, *r* is the distance from the particle to the wall at
-position *coord*\ , and Rc is the *cutoff* distance at which the
+position *coord*\ , and :math:`r_c` is the *cutoff* distance at which the
 particle and wall no longer interact.  The energy of the wall
 potential is shifted so that the wall-particle interaction energy is
 0.0 at the cutoff distance.
@@ -185,10 +185,10 @@ box parameters and timestep and elapsed time.  Thus it is easy to
 specify a time-dependent wall position.  See examples below.
 
 For the *wall/lj93* and *wall/lj126* and *wall/lj1043* styles,
-*epsilon* and *sigma* are the usual Lennard-Jones parameters, which
+:math:`\epsilon` and :math:`\sigma` are the usual Lennard-Jones parameters, which
 determine the strength and size of the particle as it interacts with
-the wall.  Epsilon has energy units.  Note that this *epsilon* and
-*sigma* may be different than any *epsilon* or *sigma* values defined
+the wall.  Epsilon has energy units.  Note that this :math:`\epsilon` and
+:math:`\sigma` may be different than any :math:`\epsilon` or :math:`\sigma` values defined
 for a pair style that computes particle-particle interactions.
 
 The *wall/lj93* interaction is derived by integrating over a 3d
@@ -197,39 +197,39 @@ interaction is effectively a harder, more repulsive wall interaction.
 The *wall/lj1043* interaction is yet a different form of wall
 interaction, described in Magda et al in :ref:`(Magda) <Magda>`.
 
-For the *wall/colloid* style, *R* is the radius of the colloid
-particle, *D* is the distance from the surface of the colloid particle
-to the wall (r-R), and *sigma* is the size of a constituent LJ
-particle inside the colloid particle and wall.  Note that the cutoff
-distance Rc in this case is the distance from the colloid particle
-center to the wall.  The prefactor *epsilon* can be thought of as an
-effective Hamaker constant with energy units for the strength of the
-colloid-wall interaction.  More specifically, the *epsilon* pre-factor
-= 4 \* pi\^2 \* rho\_wall \* rho\_colloid \* epsilon \* sigma\^6, where epsilon
-and sigma are the LJ parameters for the constituent LJ
-particles. Rho\_wall and rho\_colloid are the number density of the
-constituent particles, in the wall and colloid respectively, in units
-of 1/volume.
+For the *wall/colloid* style, *R* is the radius of the colloid particle,
+*D* is the distance from the surface of the colloid particle to the wall
+(r-R), and :math:`\sigma` is the size of a constituent LJ particle
+inside the colloid particle and wall.  Note that the cutoff distance Rc
+in this case is the distance from the colloid particle center to the
+wall.  The prefactor :math:`\epsilon` can be thought of as an effective
+Hamaker constant with energy units for the strength of the colloid-wall
+interaction.  More specifically, the :math:`\epsilon` pre-factor is
+:math:`4\pi^2 \rho_{wall} \rho_{colloid} \epsilon \sigma^6`, where
+:math:`\epsilon` and :math:`\sigma` are the LJ parameters for the
+constituent LJ particles. :math:`\rho_{wall}` and :math:`\rho_{colloid}`
+are the number density of the constituent particles, in the wall and
+colloid respectively, in units of 1/volume.
 
 The *wall/colloid* interaction is derived by integrating over
-constituent LJ particles of size *sigma* within the colloid particle
-and a 3d half-lattice of Lennard-Jones 12/6 particles of size *sigma*
+constituent LJ particles of size :math:`\sigma` within the colloid particle
+and a 3d half-lattice of Lennard-Jones 12/6 particles of size :math:`\sigma`
 in the wall.  As mentioned in the preceding paragraph, the density of
 particles in the wall and colloid can be different, as specified by
-the *epsilon* pre-factor.
+the :math:`\epsilon` pre-factor.
 
-For the *wall/harmonic* style, *epsilon* is effectively the spring
+For the *wall/harmonic* style, :math:`\epsilon` is effectively the spring
 constant K, and has units (energy/distance\^2).  The input parameter
-*sigma* is ignored.  The minimum energy position of the harmonic
+:math:`\sigma` is ignored.  The minimum energy position of the harmonic
 spring is at the *cutoff*\ .  This is a repulsive-only spring since the
 interaction is truncated at the *cutoff*
 
 For the *wall/morse* style, the three parameters are in this order:
-*D\_0* the depth of the potential, *alpha* the width parameter, and
-*r\_0* the location of the minimum.  *D\_0* has energy units, *alpha*
-inverse distance units, and *r\_0* distance units.
+:math:`D_0` the depth of the potential, :math:`\alpha` the width parameter, and
+:math:`r_0` the location of the minimum.  :math:`D_0` has energy units, :math:`\alpha`
+inverse distance units, and :math:`r_0` distance units.
 
-For any wall, the *epsilon* and/or *sigma* and/or *alpha* parameter can
+For any wall, the :math:`\epsilon` and/or :math:`\sigma` and/or :math:`\alpha` parameter can
 be specified
 as an :doc:`equal-style variable <variable>`, in which case it should be
 specified as v\_name, where name is the variable name.  As with a
@@ -253,7 +253,7 @@ time.  Thus it is easy to specify a time-dependent wall interaction.
    the finite-size particles of radius R must be a distance larger than R
    from the wall position *coord*\ .  The *harmonic* style is a softer
    potential and does not blow up as r -> 0, but you must use a large
-   enough *epsilon* that particles always reamin on the correct side of
+   enough :math:`\epsilon` that particles always reamin on the correct side of
    the wall (r > 0).
 
 The *units* keyword determines the meaning of the distance units used
diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst
index 921600a3e8..ce2b988256 100644
--- a/doc/src/kspace_style.rst
+++ b/doc/src/kspace_style.rst
@@ -229,7 +229,7 @@ parameters and how to choose them is described in
 
    All of the PPPM styles can be used with single-precision FFTs by
    using the compiler switch -DFFT\_SINGLE for the FFT\_INC setting in your
-   lo-level Makefile.  This setting also changes some of the PPPM
+   low-level Makefile.  This setting also changes some of the PPPM
    operations (e.g. mapping charge to mesh and interpolating electric
    fields to particles) to be performed in single precision.  This option
    can speed-up long-range calculations, particularly in parallel or on
@@ -397,7 +397,7 @@ produce the same results, except for round-off and precision issues.
 More specifically, the *pppm/gpu* style performs charge assignment and
 force interpolation calculations on the GPU.  These processes are
 performed either in single or double precision, depending on whether
-the -DFFT\_SINGLE setting was specified in your lo-level Makefile, as
+the -DFFT\_SINGLE setting was specified in your low-level Makefile, as
 discussed above.  The FFTs themselves are still calculated on the CPU.
 If *pppm/gpu* is used with a GPU-enabled pair style, part of the PPPM
 calculation can be performed concurrently on the GPU while other
diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst
index 797f2a8cec..6b38c7f570 100644
--- a/doc/src/pair_buck6d_coul_gauss.rst
+++ b/doc/src/pair_buck6d_coul_gauss.rst
@@ -87,9 +87,9 @@ is thus evaluated as:
 
 where C is an energy-conversion constant, :math:`q_i` and :math:`q_j`
 are the charges on the 2 atoms, epsilon is the dielectric constant which
-can be set by the :doc:`dielectric <dielectric>` command, alpha is ion
-pair dependent damping parameter and erf() is the error-function.  The
-cutoff Rc truncates the interaction distance.
+can be set by the :doc:`dielectric <dielectric>` command, :math:`\alpha`
+is the ion pair dependent damping parameter and erf() is the
+error-function.  The cutoff :math:`r_c` truncates the interaction distance.
 
 The style *buck6d/coul/gauss/dsf* computes the Coulomb interaction
 via the damped shifted force model described in :ref:`(Fennell) <Fennell>`
diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst
index f7fe3dc55a..b893f56502 100644
--- a/doc/src/pair_comb.rst
+++ b/doc/src/pair_comb.rst
@@ -45,8 +45,8 @@ Description
 Style *comb* computes the second-generation variable charge COMB
 (Charge-Optimized Many-Body) potential.  Style *comb3* computes the
 third-generation COMB potential.  These COMB potentials are described
-in :ref:`(COMB) <COMB>` and :ref:`(COMB3) <COMB3>`.  Briefly, the total energy
-*E<sub>T</sub>* of a system of atoms is given by
+in :ref:`(COMB) <COMB>` and :ref:`(COMB3) <COMB3>`.  Briefly, the
+total energy :math:`E_T` of a system of atoms is given by
 
 .. math::
 
diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst
index a5d0a0f42f..ac4aa4e8d5 100644
--- a/doc/src/pair_coul.rst
+++ b/doc/src/pair_coul.rst
@@ -207,7 +207,7 @@ manipulation of adding and subtracting a self term (for i = j) to the
 first and second term on the right-hand-side, respectively, and a
 small enough :math:`\alpha` damping parameter, the second term shrinks and
 the potential becomes a rapidly-converging real-space summation.  With
-a long enough cutoff and small enough alpha parameter, the energy and
+a long enough cutoff and small enough :math:`\alpha` parameter, the energy and
 forces calculated by the Wolf summation method approach those of the
 Ewald sum.  So it is a means of getting effective long-range
 interactions with a short-range potential.
diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst
index 5a054621ef..24f1aebd74 100644
--- a/doc/src/pair_edip.rst
+++ b/doc/src/pair_edip.rst
@@ -88,14 +88,14 @@ and three-body coefficients in the formula above:
 * B (distance units)
 * cutoffA (distance units)
 * cutoffC (distance units)
-* alpha
-* beta
-* eta
-* gamma (distance units)
-* lambda (energy units)
-* mu
-* tho
-* sigma (distance units)
+* :math:`\alpha`
+* :math:`\beta`
+* :math:`\eta`
+* :math:`\gamma` (distance units)
+* :math:`lambda` (energy units)
+* :math:`\mu`
+* :math:`\tau`
+* :math:`\sigma` (distance units)
 * Q0
 * u1
 * u2
diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst
index 3840158fbc..8320d1701c 100644
--- a/doc/src/pair_line_lj.rst
+++ b/doc/src/pair_line_lj.rst
@@ -28,13 +28,13 @@ Description
 """""""""""
 
 Style *line/lj* treats particles which are line segments as a set of
-small spherical particles that tile the line segment length as
-explained below.  Interactions between two line segments, each with N1
-and N2 spherical particles, are calculated as the pairwise sum of
-N1\*N2 Lennard-Jones interactions.  Interactions between a line segment
-with N spherical particles and a point particle are treated as the
-pairwise sum of N Lennard-Jones interactions.  See the :doc:`pair_style lj/cut <pair_lj>` doc page for the definition of Lennard-Jones
-interactions.
+small spherical particles that tile the line segment length as explained
+below.  Interactions between two line segments, each with N1 and N2
+spherical particles, are calculated as the pairwise sum of N1\*N2
+Lennard-Jones interactions.  Interactions between a line segment with N
+spherical particles and a point particle are treated as the pairwise sum
+of N Lennard-Jones interactions.  See the :doc:`pair_style lj/cut
+<pair_lj>` doc page for the definition of Lennard-Jones interactions.
 
 The set of non-overlapping spherical sub-particles that represent a
 line segment are generated in the following manner.  Their size is a
@@ -50,10 +50,10 @@ each pair of points.
 
 The LJ interaction between 2 spheres on different line segments (or a
 sphere on a line segment and a point particles) is computed with
-sub-particle epsilon, sigma, and cutoff values that are set by the
-pair\_coeff command, as described below.  If the distance between the 2
-spheres is greater than the sub-particle cutoff, there is no
-interaction.  This means that some pairs of sub-particles on 2 line
+sub-particle :math:`\epsilon`, :math:`\sigma`, and *cutoff* values that
+are set by the pair\_coeff command, as described below.  If the distance
+between the 2 spheres is greater than the sub-particle cutoff, there is
+no interaction.  This means that some pairs of sub-particles on 2 line
 segments may interact, but others may not.
 
 For purposes of creating the neighbor list for pairs of interacting
@@ -86,8 +86,8 @@ commands:
 
 * sizeI (distance units)
 * sizeJ (distance units)
-* epsilon (energy units)
-* sigma (distance units)
+* :math:`\epsilon` (energy units)
+* :math:`\sigma` (distance units)
 * subcutoff (distance units)
 * cutoff (distance units)
 
@@ -102,11 +102,11 @@ sizeI will apply to all segments of type I.  If typeI or typeJ refers
 to point particles, the corresponding sizeI or sizeJ is ignored; it
 can be set to 0.0.
 
-The *epsilon*\ , *sigma*\ , and *subcutoff* coefficients are used to
-compute an LJ interactions between a pair of sub-particles on 2 line
-segments (of type I and J), or between a sub particle/point particle
-pair.  As discussed above, the *subcutoff* and *cutoff* params are
-different.  The latter is only used for building the neighbor list
+The :math:`\epsilon`, :math:`\sigma`, and *subcutoff* coefficients are
+used to compute an LJ interactions between a pair of sub-particles on 2
+line segments (of type I and J), or between a sub particle/point
+particle pair.  As discussed above, the *subcutoff* and *cutoff* params
+are different.  The latter is only used for building the neighbor list
 when the distance between centers of two line segments or one segment
 and a point particle is calculated.
 
diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst
index ff1b841223..7f97913be6 100644
--- a/doc/src/pair_lj.rst
+++ b/doc/src/pair_lj.rst
@@ -295,7 +295,7 @@ a self term (for i = j) to the first and second term on the
 right-hand-side, respectively, and a small enough :math:`\alpha` damping
 parameter, the second term shrinks and the potential becomes a
 rapidly-converging real-space summation.  With a long enough cutoff and
-small enough alpha parameter, the energy and forces calculated by the
+small enough :math:`\alpha` parameter, the energy and forces calculated by the
 Wolf summation method approach those of the Ewald sum.  So it is a means
 of getting effective long-range interactions with a short-range
 potential.
diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst
index ed99d03c6f..af317ac99c 100644
--- a/doc/src/pair_local_density.rst
+++ b/doc/src/pair_local_density.rst
@@ -128,7 +128,7 @@ where :math:`\alpha` gives the type of atom *i*\ , :math:`\beta` the
 type of atom *j*\ , and the coefficients *a* and *b* filter for atom
 types as specified by the user. *a* is called the central atom filter as
 it determines to which atoms the potential applies; :math:`a_{\alpha} =
-1` if the LD potential applies to atom type alpha else zero. On the
+1` if the LD potential applies to atom type :math:`\alpha` else zero. On the
 other hand, *b* is called the neighbor atom filter because it specifies
 which atom types to use in the calculation of the LD; :math:`b_{\beta} =
 1` if atom type :math:`\beta` contributes to the LD and zero otherwise.
@@ -210,12 +210,15 @@ and potential.  In general, blank lines anywhere are ignored.
 ----------
 
 **Mixing, shift, table, tail correction, restart, info**\ :
-This pair style does not support automatic mixing. For atom type pairs alpha,
-beta and alpha != beta, even if LD potentials of type (alpha, alpha) and 
-(beta, beta) are provided, you will need to explicitly provide LD potential 
-types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha,
-beta) means that alpha is the central atom to which the LD potential is applied
-and beta is the neighbor atom which contributes to the LD potential on alpha).
+This pair style does not support automatic mixing. For atom type pairs
+:math:`\alpha`, :math:`\beta` and :math:`\alpha` != :math:`\beta`, even
+if LD potentials of type (:math:`\alpha`, :math:`\alpha`) and
+(:math:`\beta`, :math:`\beta`) are provided, you will need to explicitly
+provide LD potential types (:math:`\alpha`, :math:`\beta`) and
+(:math:`\beta`, :math:`\alpha`) if need be (Here, the notation
+(:math:`\alpha`, :math:`\beta`) means that :math:`\alpha` is the central
+atom to which the LD potential is applied and :math:`\beta` is the
+neighbor atom which contributes to the LD potential on :math:`\alpha`).
 
 This pair style does not support the :doc:`pair_modify <pair_modify>`
 shift, table, and tail options.
diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst
index 7a7923c0cc..5c78b93716 100644
--- a/doc/src/pair_modify.rst
+++ b/doc/src/pair_modify.rst
@@ -90,30 +90,29 @@ See the doc page for individual pair styles for those restrictions.  Note also t
 coefficients for a specific I != J pairing, in which case no mixing is
 performed.
 
-mix *geometric*
+- mix *geometric*
 
 
-.. parsed-literal::
+  .. math::
 
-   epsilon_ij = sqrt(epsilon_i \* epsilon_j)
-   sigma_ij = sqrt(sigma_i \* sigma_j)
+     \epsilon_{ij} = & \sqrt{\epsilon_i  \epsilon_j} \\
+     \sigma_{ij}   = & \sqrt{\sigma_i  \sigma_j}
 
-mix *arithmetic*
+- mix *arithmetic*
 
 
-.. parsed-literal::
+  .. math::
 
-   epsilon_ij = sqrt(epsilon_i \* epsilon_j)
-   sigma_ij = (sigma_i + sigma_j) / 2
+    \epsilon_{ij} = & \sqrt{\epsilon_i  \epsilon_j} \\
+    \sigma_{ij}   = & \frac{1}{2} (\sigma_i + \sigma_j)
 
-mix *sixthpower*
+- mix *sixthpower*
 
 
-.. parsed-literal::
+  .. math::
 
-   epsilon_ij = (2 \* sqrt(epsilon_i\*epsilon_j) \* sigma_i\^3 \* sigma_j\^3) /
-                (sigma_i\^6 + sigma_j\^6)
-   sigma_ij = ((sigma_i\*\*6 + sigma_j\*\*6) / 2) \^ (1/6)
+    \epsilon_{ij} = & \frac{2 \sqrt{\epsilon_i \epsilon_j} \sigma_i^3 \sigma_j^3}{\sigma_i^6 + \sigma_j^6} \\
+    \sigma_{ij} =   & \left(\frac{1}{2} (\sigma_i^6 + \sigma_j^6) \right)^{\frac{1}{6}}
 
 The *shift* keyword determines whether a Lennard-Jones potential is
 shifted at its cutoff to 0.0.  If so, this adds an energy term to each
diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst
index eb0666d3cb..121d4fbc76 100644
--- a/doc/src/pair_morse.rst
+++ b/doc/src/pair_morse.rst
@@ -70,9 +70,9 @@ above, or in the data file or restart files read by the
 :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands:
 
-* D0 (energy units)
-* alpha (1/distance units)
-* r0 (distance units)
+* :math:`D_0` (energy units)
+* :math:`\alpha` (1/distance units)
+* :math:`r_0` (distance units)
 * cutoff (distance units)
 
 The last coefficient is optional.  If not specified, the global morse
diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst
index 5f74f98554..d08da012f2 100644
--- a/doc/src/pair_peri.rst
+++ b/doc/src/pair_peri.rst
@@ -91,11 +91,11 @@ For the *peri/pmb* style:
 * c (energy/distance/volume\^2 units)
 * horizon (distance units)
 * s00 (unitless)
-* alpha (unitless)
+* :math:`\alpha` (unitless)
 
 C is the effectively a spring constant for Peridynamic bonds, the
 horizon is a cutoff distance for truncating interactions, and s00 and
-alpha are used as a bond breaking criteria.  The units of c are such
+:math:`\alpha` are used as a bond breaking criteria.  The units of c are such
 that c/distance = stiffness/volume\^2, where stiffness is
 energy/distance\^2 and volume is distance\^3.  See the users guide for
 more details.
@@ -106,10 +106,10 @@ For the *peri/lps* style:
 * G (force/area units)
 * horizon (distance units)
 * s00 (unitless)
-* alpha (unitless)
+* :math:`\alpha` (unitless)
 
 K is the bulk modulus and G is the shear modulus.  The horizon is a
-cutoff distance for truncating interactions, and s00 and alpha are
+cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
 used as a bond breaking criteria. See the users guide for more
 details.
 
@@ -119,12 +119,12 @@ For the *peri/ves* style:
 * G (force/area units)
 * horizon (distance units)
 * s00 (unitless)
-* alpha (unitless)
+* :math:`\alpha` (unitless)
 * m\_lambdai (unitless)
 * m\_taubi (unitless)
 
 K is the bulk modulus and G is the shear modulus. The horizon is a
-cutoff distance for truncating interactions, and s00 and alpha are
+cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
 used as a bond breaking criteria. m\_lambdai and m\_taubi are the
 viscoelastic relaxation parameter and time constant,
 respectively. m\_lambdai varies within zero to one. For very small
@@ -138,11 +138,11 @@ For the *peri/eps* style:
 * G (force/area units)
 * horizon (distance units)
 * s00 (unitless)
-* alpha (unitless)
+* :math:`\alpha` (unitless)
 * m\_yield\_stress (force/area units)
 
 K is the bulk modulus and G is the shear modulus. The horizon is a
-cutoff distance and s00 and alpha are used as a bond breaking
+cutoff distance and s00 and :math:`\alpha` are used as a bond breaking
 criteria.  m\_yield\_stress is the yield stress of the material. For
 details please see the description in "(Mtchell2011a)".
 
diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst
index 843e8ce2ca..b3ce8d7c5d 100644
--- a/doc/src/pair_smtbq.rst
+++ b/doc/src/pair_smtbq.rst
@@ -47,13 +47,13 @@ smooth convergence to zero interaction.
 
 The parameters appearing in the upper expressions are set in the
 ffield.SMTBQ.Syst file where Syst corresponds to the selected system
-(e.g. field.SMTBQ.Al2O3). Examples for TiO2,
-Al2O3 are provided.  A single pair\_coeff command
+(e.g. field.SMTBQ.Al2O3). Examples for :math:`\mathrm{TiO_2}`,
+:math:`\mathrm{Al_2O_3}` are provided.  A single pair\_coeff command
 is used with the SMTBQ styles which provides the path to the potential
 file with parameters for needed elements. These are mapped to LAMMPS
 atom types by specifying additional arguments after the potential
 filename in the pair\_coeff command. Note that atom type 1 must always
-correspond to oxygen atoms. As an example, to simulate a TiO2 system,
+correspond to oxygen atoms. As an example, to simulate a :math:`\mathrm{TiO_2}` system,
 atom type 1 has to be oxygen and atom type 2 Ti. The following
 pair\_coeff command should then be used:
 
@@ -76,7 +76,7 @@ Interaction between oxygen, :math:`E_{OO}`, consists of two parts,
 an attractive and a repulsive part. The attractive part is effective
 only at short range (< :math:`r_2^{OO}`). The attractive
 contribution was optimized to study surfaces reconstruction
-(e.g. :ref:`SMTB-Q\_2 <SMTB-Q_2>` in TiO2) and is not necessary
+(e.g. :ref:`SMTB-Q\_2 <SMTB-Q_2>` in :math:`\mathrm{TiO_2}`) and is not necessary
 for oxide bulk modeling. The repulsive part is the Pauli interaction
 between the electron clouds of oxygen. The Pauli repulsion and the
 coulombic electrostatic interaction have same cut off value. In the
@@ -99,7 +99,7 @@ ffield.SMTBQ.Syst. The energy band term is given by:
    \delta Q_i & =  | Q_i^{F} | - | Q_i |
 
 
-where :math:\eta_i` is the stoichiometry of atom *i*\ ,
+where :math:`\eta_i` is the stoichiometry of atom *i*\ ,
 :math:`\delta Q_i` is the charge delocalization of atom *i*\ ,
 compared to its formal charge
 :math:`Q^F_i`. :math:`n_0`, the number of hybridized
@@ -118,7 +118,7 @@ two visions is explained in appendix A of the article in the
 SrTiO3 :ref:`SMTB-Q\_3 <SMTB-Q_3>` (parameter :math:`\beta` shown in
 this article is in fact the :math:`\beta_O`). To summarize the
 relationship between the hopping integral :math:`\xi^O`  and the
-others, we have in an oxide CnOm the following
+others, we have in an oxide :math:`\mathrm{C_n O_m}` the following
 relationship:
 
 .. math::
@@ -127,7 +127,7 @@ relationship:
    \frac{\beta_O}{\sqrt{m}} & = \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2}
 
 
-Thus parameter :math:`\mu`, indicated above, is given by :math:`\mu = (\sqrt{n} + \sqrt{m}) / 2`
+Thus parameter :math:`\mu`, indicated above, is given by :math:`\mu = \frac{1}{2}(\sqrt{n}+\sqrt{m})`
 
 The potential offers the possibility to consider the polarizability of
 the electron clouds of oxygen by changing the slater radius of the
@@ -158,7 +158,7 @@ quotation marks ('').
 1) Number of different element in the oxide:
 
 * N_elem= 2 or 3
-* Dividing line
+* Divider line
 
 2) Atomic parameters
 
@@ -166,68 +166,111 @@ For the anion (oxygen)
 
 * Name of element (char) and stoichiometry in oxide
 * Formal charge and mass of element
-* Principal quantum number of outer orbital n), electronegativity (:math:`\xi^0_i`) and hardness (:math:`J^0_i`)
+* Principal quantum number of outer orbital n), electronegativity (:math:`\chi^0_i`) and hardness (:math:`J^0_i`)
 * Ionic radius parameters  : max coordination number (\ *coordBB* = 6 by default), bulk coordination number *(coordB)*\ , surface coordination number  *(coordS)* and *rBB, rB and rS*  the slater radius for each coordination number. (**note : If you don't want to change the slater radius, use three identical radius values**)
 * Number of orbital shared by the element in the oxide (:math:`d_i`)
-* Dividing line
+* Divider line
 
 For each cations (metal):
 
 * Name of element (char) and stoichiometry in oxide
 * Formal charge and mass of element
-* Number of electron in outer orbital *(ne)*\ , electronegativity (\ *&#967<sup>0</sup><sub>i</simulationub>*\ ), hardness (\ *J<sup>0</sup><sub>i</sub>*\ ) and *r<sub>Salter</sub>* the slater radius for the cation.
-* Number of orbitals shared by the elements in the oxide (\ *d<sub>i</sub>*\ )
-* Dividing line
+* Number of electron in outer orbital *(ne)*\ , electronegativity (:math:`\chi^0_i`), hardness (:math:`J^0_i`) and :math:`r_{Slater}` the slater radius for the cation.
+* Number of orbitals shared by the elements in the oxide (:math:`d_i`)
+* Divider line
 
 3) Potential parameters:
 
-* Keyword for element1, element2 and interaction potential ('second\_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2.  If the potential is 'second\_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
-* Potential parameter: <pre><br/> If type of potential is 'second\_moment' : *A (eV)*\ , *p*\ , *&#958<sup>0</sup>* (eV) and *q* <br/> *r<sub>c1</sub>* (&#197), *r<sub>c2</sub>* (&#197) and *r<sub>0</sub>* (&#197) <br/> If type of potential is 'buck' : *C* (eV) and *&#961* (&#197) <br/> If type of potential is 'buckPlusAttr' : *C* (eV) and *&#961* (&#197) <br/> *D* (eV), *B* (&#197<sup>-1</sup>), *r<sub>1</sub><sup>OO</sup>* (&#197) and *r<sub>2</sub><sup>OO</sup>* (&#197) </pre>
-* Dividing line
+* Keyword for element1, element2 and interaction potential
+  ('second\_moment' or 'buck' or 'buckPlusAttr') between element 1
+  and 2.  If the potential is 'second\_moment', specify 'oxide' or
+  'metal' for metal-oxygen or metal-metal interactions respectively.
+* Potential parameter:
+
+  - If type of potential is 'second\_moment' : A (eV), *p*,
+    :math:`\zeta^0` (eV) and *q*, :math:`r_{c1} (\mathrm{\mathring{A}})`, :math:`r_{c2}
+    (\mathrm{\mathring{A}})` and :math:`r_0 (\mathrm{\mathring{A}})`
+  - If type of potential is 'buck' : *C* (eV) and :math:`\rho (\mathrm{\mathring{A}})`
+  - If type of potential is 'buckPlusAttr' : *C* (eV) and :math:`\rho
+    (\mathrm{\mathring{A}})` *D* (eV), *B* :math:`(\mathrm{\mathring{A}}^{-1})`, :math:`r^{OO}_1 (\mathrm{\mathring{A}})` and
+    :math:`r^{OO}_2 (\mathrm{\mathring{A}})`
+* Divider line
 
 4) Tables parameters:
 
-* Cutoff radius for the Coulomb interaction (\ *R<sub>coul</sub>*\ )
-* Starting radius  (\ *r<sub>min</sub>* = 1,18845 &#197) and increments (\ *dr* = 0,001 &#197) for creating the potential table.
-* Dividing line
+* Cutoff radius for the Coulomb interaction (:math:`R_{coul}`)
+* Starting radius (:math:`r_{min} = 1,18845 \mathrm{\mathring{A}}`) and increments
+  (:math:`dr = 0.001 \mathrm{\mathring{A}}`) for creating the potential table.
+* Divider line
 
 5) Rick model parameter:
 
-* *Nevery* : parameter to set the frequency (\ *1/Nevery*\ ) of the charge resolution. The charges are evaluated each *Nevery* time steps.
-* Max number of iterative loop (\ *loopmax*\ ) and precision criterion (\ *prec*\ ) in eV of the charge resolution
-* Dividing line
+* *Nevery* : parameter to set the frequency of the charge
+  resolution. The charges are evaluated each *Nevery* time steps.
+* Max number of iterative loop (\ *loopmax*\ ) and convergence criterion
+  (\ *prec*\ ) in eV of the charge resolution
+* Divider line
 
 6) Coordination parameter:
 
-* First (\ *r<sub>1n</sub>*\ ) and second (\ *r<sub>2n</sub>*\ ) neighbor distances in &#197
-* Dividing line
+* First (:math:`r_{1n}`) and second (:math:`r_{2n}`) neighbor distances
+  in angstrom
+* Divider line
 
 7) Charge initialization mode:
 
-* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Q<sub>init</sub>*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Q<sub>init</sub>*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create\_atom"#create\_atom command or the charge specified in the file structure using :doc:`read_data <read_data>` command.
-* Dividing line
+* Keyword (\ *QInitMode*\ ) and initial oxygen charge
+  (:math:`Q_{init}`). If keyword = 'true', all oxygen charges are
+  initially set equal to :math:`Q_{init}`. The charges on the cations
+  are initially set in order to respect the neutrality of the box. If
+  keyword = 'false', all atom charges are initially set equal to 0 if
+  you use the :doc:`create_atoms <create_atoms>` command or the charge
+  specified in the file structure using :doc:`read_data <read_data>`
+  command.
+* Divider line
 
-8) Mode for the electronegativity equalization (Qeq) 
+8) Mode for the electronegativity equalization (Qeq)
+
+* Keyword (\ *mode*\ ) followed by:
+
+  - QEqAll  (one QEq group) \|   no parameters
+  - QEqAllParallel (several QEq groups) \|   no parameters
+  - Surface \|   zlim   (QEq only for z>zlim)
 
-* Keyword mode: <pre> <br/> QEqAll  (one QEq group) \|   no parameters <br/> QEqAllParallel (several QEq groups) \|   no parameters <br/> Surface \|   zlim   (QEq only for z>zlim)   </pre>
 * Parameter if necessary
-* Dividing line
+* Divider line
 
 9) Verbose 
 
 * If you want the code to work in verbose mode or not : 'true' or 'false'
-* If you want to print or not in file 'Energy\_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and *N<sub>Energy</sub>*\ . This option writes in file every *N<sub>Energy</sub>* time step. If the value is 'false' then *N<sub>Energy</sub>* = 0. The file take into account the possibility to have several QEq group *g* then it writes: time step, number of atoms in group *g*\ , electrostatic part of energy, *E<sub>ES</sub>*\ , the interaction between oxygen, *E<sub>OO</sub>*\ , and short range metal-oxygen interaction, *E<sub>MO</sub>*\ .
-* If you want to print in file 'Electroneg\_component.txt' the electronegativity component (\ *&#8706E<sub>tot</sub> &#8260&#8706Q<sub>i</sub>*\ ) or not: 'true' or 'false' and *N<sub>Electroneg</sub>*\ .This option writes in file every *N<sub>Electroneg</sub>* time step. If the value is 'false' then *N<sub>Electroneg</sub>* = 0.  The file consist in atom number *i*\ , atom type (1 for oxygen and # higher than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge of atom *i*\ , electrostatic part of atom *i* electronegativity, covalent part of atom *i* electronegativity, the hopping integral of atom *i* *(Z&#946<sup>2</sup>)<sub>i<sub>* and box electronegativity.
+* If you want to print or not in the file 'Energy\_component.txt' the
+  three main contributions to the energy of the system according to the
+  description presented above : 'true' or 'false' and
+  :math:`N_{Energy}`. This option writes to the file every
+  :math:`N_{Energy}` time steps. If the value is 'false' then
+  :math:`N_{Energy} = 0`. The file takes into account the possibility to
+  have several QEq groups *g* then it writes: time step, number of atoms
+  in group *g*\ , electrostatic part of energy, :math:`E_{ES}`, the
+  interaction between oxygen, :math:`E_{OO}`, and short range
+  metal-oxygen interaction, :math:`E_{MO}`.
+* If you want to print to the file 'Electroneg\_component.txt' the
+  electronegativity component (:math:`\frac{\partial E_{tot}}{\partial
+  Q_i}`) or not: 'true' or 'false' and :math:`N_{Electroneg}`. This
+  option writes to the file every :math:`N_{Electroneg}` time steps. If
+  the value is 'false' then :math:`N_{Electroneg} = 0`.  The file
+  consist of atom number *i*\ , atom type (1 for oxygen and # higher
+  than 1 for metal), atom position: *x*\ , *y* and *z*\ , atomic charge
+  of atom *i*\ , electrostatic part of atom *i* electronegativity,
+  covalent part of atom *i* electronegativity, the hopping integral of
+  atom *i* :math:`(Z\beta^2)_i` and box electronegativity.
 
 .. note::
 
    This last option slows down the calculation dramatically.  Use
    only with a single processor simulation.
 
-
 ----------
 
-
 **Mixing, shift, table, tail correction, restart, rRESPA info:**
 
 This pair style does not support the :doc:`pair_modify <pair_modify>`
@@ -241,10 +284,8 @@ This pair style can only be used via the *pair* keyword of the
 :doc:`run_style respa <run_style>` command.  It does not support the
 *inner*\ , *middle*\ , *outer* keywords.
 
-
 ----------
 
-
 **Restriction:**
 
 This pair style is part of the USER-SMTBQ package and is only enabled
@@ -259,50 +300,36 @@ for pair interactions.
 The SMTB-Q potential files provided with LAMMPS (see the potentials
 directory) are parameterized for metal :doc:`units <units>`.
 
-
 ----------
 
-
 **Citing this work:**
 
 Please cite related publication: N. Salles, O. Politano, E. Amzallag
 and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
 
-
 ----------
 
-
 .. _SMTB-Q\_1:
 
-
-
 **(SMTB-Q\_1)** N. Salles, O. Politano, E. Amzallag, R. Tetot,
 Comput. Mater. Sci. 111 (2016) 181-189
 
 .. _SMTB-Q\_2:
 
-
-
 **(SMTB-Q\_2)** E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
 H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399
 
 .. _SMTB-Q\_3:
 
-
-
 **(SMTB-Q\_3)** R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
 Science 616, 19-8722 28 (2013)
 
 .. _Wolf2:
 
-
-
 **(Wolf)** D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
 Phys, 110, 8254 (1999).
 
 .. _Rick3:
 
-
-
 **(Rick)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
 (1994).
diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst
index 4f3734aab7..32c092ee69 100644
--- a/doc/src/pair_snap.rst
+++ b/doc/src/pair_snap.rst
@@ -113,9 +113,9 @@ by the following commands:
    variable zblz equal 73
    pair_style hybrid/overlay &
    zbl ${zblcutinner} ${zblcutouter} snap
-   pair_coeff \* \* zbl 0.0
+   pair_coeff * * zbl 0.0
    pair_coeff 1 1 zbl ${zblz}
-   pair_coeff \* \* snap Ta06A.snapcoeff Ta06A.snapparam Ta
+   pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
 
 It is convenient to keep these commands in a separate file that can
 be inserted in any LAMMPS input script using the :doc:`include <include>`
@@ -164,8 +164,7 @@ into two passes.
 Detailed definitions for all the other keywords 
 are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page. 
 
-If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term,
-0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
+If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term, 0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
 The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
 for each element, the upper-triangular elements of alpha.
 
diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst
index 68dc270500..b3d33f6036 100644
--- a/doc/src/pair_thole.rst
+++ b/doc/src/pair_thole.rst
@@ -113,7 +113,7 @@ For pair\_style *thole*\ , the following coefficients must be defined for
 each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command
 as in the example above.
 
-* alpha (distance units\^3)
+* :math:`\alpha` (distance units\^3)
 * damp
 * cutoff (distance units)
 
@@ -126,10 +126,10 @@ For pair style *lj/cut/thole/long*\ , the following coefficients must be
 defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>`
 command.
 
-* epsilon (energy units)
-* sigma (length units)
-* alpha (distance units\^3)
-* damps
+* :math:`\epsilon` (energy units)
+* :math:`\sigma` (length units)
+* :math:`\alpha` (distance units\^3)
+* damp
 * LJ cutoff (distance units)
 
 The last two coefficients are optional and default to the global values from
@@ -168,12 +168,9 @@ are defined using
 
 .. math::
 
-   \alpha_{ij} = \sqrt{\alpha_i\alpha_j}
-
-
-.. math::
-
-   a_{ij} = \frac 1 2 (a_i + a_j)
+   \alpha_{ij} = & \sqrt{\alpha_i\alpha_j} \\
+   & \\
+   a_{ij} = & \frac 1 2 (a_i + a_j)
 
 Restrictions
 """"""""""""
diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst
index bb549cadf1..b093160611 100644
--- a/doc/src/thermo_style.rst
+++ b/doc/src/thermo_style.rst
@@ -50,7 +50,7 @@ Syntax
            ke = kinetic energy
            etotal = total energy (pe + ke)
            enthalpy = enthalpy (etotal + press\*vol)
-           evdwl = VanderWaal pairwise energy (includes etail)
+           evdwl = van der Waals pairwise energy (includes etail)
            ecoul = Coulombic pairwise energy
            epair = pairwise energy (evdwl + ecoul + elong)
            ebond = bond energy
@@ -59,7 +59,7 @@ Syntax
            eimp = improper energy
            emol = molecular energy (ebond + eangle + edihed + eimp)
            elong = long-range kspace energy
-           etail = VanderWaal energy long-range tail correction
+           etail = van der Waals energy long-range tail correction
            vol = volume
            density = mass density of system
            lx,ly,lz = box lengths in x,y,z
@@ -205,13 +205,13 @@ change the attributes of this potential energy via the
 
 
 The kinetic energy of the system *ke* is inferred from the temperature
-of the system with 1/2 Kb T of energy for each degree of freedom.
-Thus, using different :doc:`compute commands <compute>` for calculating
-temperature, via the :doc:`thermo_modify temp <thermo_modify>` command,
-may yield different kinetic energies, since different computes that
-calculate temperature can subtract out different non-thermal
-components of velocity and/or include different degrees of freedom
-(translational, rotational, etc).
+of the system with :math:`\frac{1}{2} k_B T` of energy for each degree
+of freedom.  Thus, using different :doc:`compute commands <compute>` for
+calculating temperature, via the :doc:`thermo_modify temp
+<thermo_modify>` command, may yield different kinetic energies, since
+different computes that calculate temperature can subtract out different
+non-thermal components of velocity and/or include different degrees of
+freedom (translational, rotational, etc).
 
 The potential energy of the system *pe* will include contributions
 from fixes if the :doc:`fix_modify thermo <fix_modify>` option is set
@@ -219,7 +219,7 @@ for a fix that calculates such a contribution.  For example, the :doc:`fix wall/
 interacting with the wall.  See the doc pages for "individual fixes"
 to see which ones contribute.
 
-A long-range tail correction *etail* for the VanderWaal pairwise
+A long-range tail correction *etail* for the van der Waals pairwise
 energy will be non-zero only if the :doc:`pair_modify tail <pair_modify>` option is turned on.  The *etail* contribution
 is included in *evdwl*\ , *epair*\ , *pe*\ , and *etotal*\ , and the
 corresponding tail correction to the pressure is included in *press*
diff --git a/doc/src/units.rst b/doc/src/units.rst
index 5527208831..4104b428ce 100644
--- a/doc/src/units.rst
+++ b/doc/src/units.rst
@@ -17,7 +17,7 @@ Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    units metal
    units lj
@@ -56,28 +56,29 @@ is often not simple to do.
 
 
 For style *lj*\ , all quantities are unitless.  Without loss of
-generality, LAMMPS sets the fundamental quantities mass, sigma,
-epsilon, and the Boltzmann constant = 1.  The masses, distances,
-energies you specify are multiples of these fundamental values.  The
-formulas relating the reduced or unitless quantity (with an asterisk)
-to the same quantity with units is also given.  Thus you can use the
-mass & sigma & epsilon values for a specific material and convert the
-results from a unitless LJ simulation into physical quantities.
+generality, LAMMPS sets the fundamental quantities mass, :math:`\sigma`,
+:math:`\epsilon`, and the Boltzmann constant :math:`k_B = 1`.  The
+masses, distances, energies you specify are multiples of these
+fundamental values.  The formulas relating the reduced or unitless
+quantity (with an asterisk) to the same quantity with units is also
+given.  Thus you can use the mass & :math:`\sigma` & :math:`\epsilon`
+values for a specific material and convert the results from a unitless
+LJ simulation into physical quantities.
 
-* mass = mass or m
-* distance = sigma, where x\* = x / sigma
-* time = tau, where t\* = t (epsilon / m / sigma\^2)\^1/2
-* energy = epsilon, where E\* = E / epsilon
-* velocity = sigma/tau, where v\* = v tau / sigma
-* force = epsilon/sigma, where f\* = f sigma / epsilon
-* torque = epsilon, where t\* = t / epsilon
-* temperature = reduced LJ temperature, where T\* = T Kb / epsilon
-* pressure = reduced LJ pressure, where P\* = P sigma\^3 / epsilon
-* dynamic viscosity = reduced LJ viscosity, where eta\* = eta sigma\^3 / epsilon / tau
-* charge = reduced LJ charge, where q\* = q / (4 pi perm0 sigma epsilon)\^1/2
-* dipole = reduced LJ dipole, moment where \*mu = mu / (4 pi perm0 sigma\^3 epsilon)\^1/2
-* electric field = force/charge, where E\* = E (4 pi perm0 sigma epsilon)\^1/2 sigma / epsilon
-* density = mass/volume, where rho\* = rho sigma\^dim
+* mass = mass or *m*
+* distance = :math:`\sigma`, where :math:`x^* = \frac{x}{\sigma}`
+* time = :math:`\tau`, where :math:`\tau^* = \tau \sqrt{\frac{\epsilon}{m \sigma^2}}`
+* energy = :math:`\epsilon`, where :math:`E^* = \frac{E}{\epsilon}`
+* velocity = :math:`\frac{\sigma}{\tau}`, where :math:`v^* = v \frac{\tau}{\sigma}`
+* force = :math:`\frac{\epsilon}{\sigma}`, where :math:`f^* = f \frac{\sigma}{\epsilon}`
+* torque = :math:`\epsilon`, where :math:`t^* = \frac{t}{\epsilon}`
+* temperature = reduced LJ temperature, where :math:`T^* = \frac{T k_B}{\epsilon}`
+* pressure = reduced LJ pressure, where :math:`p^* = p \frac{\sigma^3}{\epsilon}`
+* dynamic viscosity = reduced LJ viscosity, where :math:`\eta^* = \eta \frac{\sigma^3}{\epsilon\tau}`
+* charge = reduced LJ charge, where :math:`q^* = q \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon}}`
+* dipole = reduced LJ dipole, moment where :math:`\mu^* = \mu \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma^3 \epsilon}}`
+* electric field = force/charge, where :math:`E^* = E \frac{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon} \sigma}{\epsilon}`
+* density = mass/volume, where :math:`\rho^* = \rho \sigma^{dim}`
 
 Note that for LJ units, the default mode of thermodynamic output via
 the :doc:`thermo_style <thermo_style>` command is to normalize all
@@ -228,6 +229,6 @@ Default
 """""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    units lj
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index a0a0535c71..1de0e66ecc 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -615,6 +615,7 @@ dipolar
 dir
 Direc
 dirname
+disarmmd
 discoverable
 discretization
 discretized
@@ -2017,6 +2018,7 @@ Nrecompute
 Nrepeat
 nreset
 Nrho
+Nroff
 nrun
 Ns
 Nsample
@@ -3129,6 +3131,7 @@ webpage
 Weckner
 WeinanE
 Wennberg
+Westmere
 Westview
 wget
 Whelan
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz
deleted file mode 100644
index c620b879a8..0000000000
Binary files a/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz and /dev/null differ
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt b/examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
rename to examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
rename to examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
rename to examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map
rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template
rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map
rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template
rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
similarity index 100%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
rename to examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
diff --git a/examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized
new file mode 100644
index 0000000000..0e6e97cd46
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized
@@ -0,0 +1,49 @@
+# two molecules DGEBA (diepoxy) and one DETA (linker)
+# two crosslinking reactions
+
+units real
+
+boundary p p p
+
+atom_style full
+
+pair_style lj/class2 8
+
+angle_style class2 
+
+bond_style class2 
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_epoxy.data
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_pre.data_template
+molecule mol2 rxn1_stp1_post.data_template
+molecule mol3 rxn1_stp2_post.data_template
+molecule mol4 rxn2_stp1_pre.data_template
+molecule mol5 rxn2_stp1_post.data_template
+molecule mol6 rxn2_stp2_post.data_template
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix rxns all bond/react stabilization yes statted_grp .03 &
+  react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map &
+  react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map &
+  react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map &
+  react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
+
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
+
+run 2000
+
+# write_restart restart_longrun
+# write_data restart_longrun.data nofix
diff --git a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 b/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1
new file mode 100644
index 0000000000..6ca0361513
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1
@@ -0,0 +1,172 @@
+LAMMPS (20 Nov 2019)
+
+WARNING-WARNING-WARNING-WARNING-WARNING
+This LAMMPS executable was compiled using C++98 compatibility.
+Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
+GNU C++ 4.8.5
+WARNING-WARNING-WARNING-WARNING-WARNING
+
+Reading data file ...
+  orthogonal box = (10 -10 -15) to (30 20 10)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  118 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  4 = max impropers/atom
+  reading bonds ...
+  123 bonds
+  reading angles ...
+  221 angles
+  reading dihedrals ...
+  302 dihedrals
+  reading impropers ...
+  115 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  19 = max # of 1-4 neighbors
+  22 = max # of special neighbors
+  special bonds CPU = 0.000286808 secs
+  read_data CPU = 0.00724107 secs
+Read molecule mol1:
+  31 atoms with max type 10
+  30 bonds with max type 15
+  53 angles with max type 29
+  66 dihedrals with max type 39
+  31 impropers with max type 5
+Read molecule mol2:
+  31 atoms with max type 10
+  30 bonds with max type 17
+  55 angles with max type 36
+  75 dihedrals with max type 51
+  34 impropers with max type 5
+Read molecule mol3:
+  31 atoms with max type 11
+  30 bonds with max type 18
+  53 angles with max type 37
+  72 dihedrals with max type 53
+  31 impropers with max type 5
+Read molecule mol4:
+  42 atoms with max type 11
+  41 bonds with max type 18
+  73 angles with max type 41
+  96 dihedrals with max type 54
+  43 impropers with max type 5
+Read molecule mol5:
+  42 atoms with max type 11
+  41 bonds with max type 18
+  75 angles with max type 37
+  108 dihedrals with max type 53
+  46 impropers with max type 5
+Read molecule mol6:
+  42 atoms with max type 11
+  41 bonds with max type 19
+  73 angles with max type 50
+  102 dihedrals with max type 66
+  43 impropers with max type 22
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 4 6 5
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 17.28 | 17.28 | 17.28 Mbytes
+Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] 
+       0          300            0            0            0            0 
+      50    391.52956            1            0            0            0 
+     100    475.26826            1            1            0            0 
+     150    605.26215            1            1            1            0 
+     200     545.7485            1            1            1            0 
+     250    461.64929            1            1            1            1 
+     300    452.10611            1            1            1            1 
+     350    379.61671            1            1            1            1 
+     400    331.22444            1            1            1            1 
+     450    275.63969            1            1            1            1 
+     500    316.63407            1            1            1            1 
+     550    261.39841            1            1            1            1 
+     600    313.70928            1            1            1            1 
+     650    294.24011            1            1            1            1 
+     700    285.81736            1            1            1            1 
+     750    340.37496            1            1            1            1 
+     800     333.2496            1            1            1            1 
+     850    307.40826            1            1            1            1 
+     900    304.68718            1            1            1            1 
+     950     328.0289            1            1            1            1 
+    1000    290.22808            1            1            1            1 
+    1050    272.78518            1            1            1            1 
+    1100    291.30546            1            1            1            1 
+    1150    320.33992            1            1            1            1 
+    1200    330.57057            1            1            1            1 
+    1250    300.51008            1            1            1            1 
+    1300     293.6209            1            1            1            1 
+    1350    324.36604            1            1            1            1 
+    1400    331.15408            1            1            1            1 
+    1450    302.23396            1            1            1            1 
+    1500    297.55562            1            1            1            1 
+    1550     277.3187            1            1            1            1 
+    1600    289.66052            1            1            1            1 
+    1650    281.85404            1            1            1            1 
+    1700     293.4999            1            1            1            1 
+    1750    306.21866            1            1            1            1 
+    1800    283.22696            1            1            1            1 
+    1850    295.10473            1            1            1            1 
+    1900     317.3843            1            1            1            1 
+    1950    305.14825            1            1            1            1 
+    2000    289.00911            1            1            1            1 
+Loop time of 1.87066 on 1 procs for 2000 steps with 118 atoms
+
+Performance: 92.374 ns/day, 0.260 hours/ns, 1069.141 timesteps/s
+98.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.12832    | 0.12832    | 0.12832    |   0.0 |  6.86
+Bond    | 0.77458    | 0.77458    | 0.77458    |   0.0 | 41.41
+Neigh   | 0.45068    | 0.45068    | 0.45068    |   0.0 | 24.09
+Comm    | 0.029785   | 0.029785   | 0.029785   |   0.0 |  1.59
+Output  | 0.31635    | 0.31635    | 0.31635    |   0.0 | 16.91
+Modify  | 0.16657    | 0.16657    | 0.16657    |   0.0 |  8.90
+Other   |            | 0.004368   |            |       |  0.23
+
+Nlocal:    118 ave 118 max 118 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    332 ave 332 max 332 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4338 ave 4338 max 4338 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4338
+Ave neighs/atom = 36.7627
+Ave special neighs/atom = 10.5763
+Neighbor list builds = 2000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:02
diff --git a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 b/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4
new file mode 100644
index 0000000000..4673ba3980
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4
@@ -0,0 +1,172 @@
+LAMMPS (20 Nov 2019)
+
+WARNING-WARNING-WARNING-WARNING-WARNING
+This LAMMPS executable was compiled using C++98 compatibility.
+Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
+GNU C++ 4.8.5
+WARNING-WARNING-WARNING-WARNING-WARNING
+
+Reading data file ...
+  orthogonal box = (10 -10 -15) to (30 20 10)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  118 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  4 = max impropers/atom
+  reading bonds ...
+  123 bonds
+  reading angles ...
+  221 angles
+  reading dihedrals ...
+  302 dihedrals
+  reading impropers ...
+  115 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  19 = max # of 1-4 neighbors
+  22 = max # of special neighbors
+  special bonds CPU = 0.000239905 secs
+  read_data CPU = 0.0080783 secs
+Read molecule mol1:
+  31 atoms with max type 10
+  30 bonds with max type 15
+  53 angles with max type 29
+  66 dihedrals with max type 39
+  31 impropers with max type 5
+Read molecule mol2:
+  31 atoms with max type 10
+  30 bonds with max type 17
+  55 angles with max type 36
+  75 dihedrals with max type 51
+  34 impropers with max type 5
+Read molecule mol3:
+  31 atoms with max type 11
+  30 bonds with max type 18
+  53 angles with max type 37
+  72 dihedrals with max type 53
+  31 impropers with max type 5
+Read molecule mol4:
+  42 atoms with max type 11
+  41 bonds with max type 18
+  73 angles with max type 41
+  96 dihedrals with max type 54
+  43 impropers with max type 5
+Read molecule mol5:
+  42 atoms with max type 11
+  41 bonds with max type 18
+  75 angles with max type 37
+  108 dihedrals with max type 53
+  46 impropers with max type 5
+Read molecule mol6:
+  42 atoms with max type 11
+  41 bonds with max type 19
+  73 angles with max type 50
+  102 dihedrals with max type 66
+  43 impropers with max type 22
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 4 6 5
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 16.26 | 16.45 | 16.63 Mbytes
+Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] 
+       0          300            0            0            0            0 
+      50    391.52956            1            0            0            0 
+     100    475.26826            1            1            0            0 
+     150    605.26215            1            1            1            0 
+     200     545.7485            1            1            1            0 
+     250    461.64929            1            1            1            1 
+     300    452.10611            1            1            1            1 
+     350    379.61671            1            1            1            1 
+     400    331.22444            1            1            1            1 
+     450    275.63969            1            1            1            1 
+     500    316.63407            1            1            1            1 
+     550    261.39841            1            1            1            1 
+     600    313.70928            1            1            1            1 
+     650    294.24011            1            1            1            1 
+     700    285.81736            1            1            1            1 
+     750    340.37496            1            1            1            1 
+     800     333.2496            1            1            1            1 
+     850    307.40826            1            1            1            1 
+     900    304.68718            1            1            1            1 
+     950     328.0289            1            1            1            1 
+    1000    290.22808            1            1            1            1 
+    1050    272.78518            1            1            1            1 
+    1100    291.30546            1            1            1            1 
+    1150    320.33992            1            1            1            1 
+    1200    330.57057            1            1            1            1 
+    1250    300.51008            1            1            1            1 
+    1300     293.6209            1            1            1            1 
+    1350    324.36604            1            1            1            1 
+    1400    331.15408            1            1            1            1 
+    1450    302.23396            1            1            1            1 
+    1500    297.55562            1            1            1            1 
+    1550     277.3187            1            1            1            1 
+    1600    289.66052            1            1            1            1 
+    1650    281.85404            1            1            1            1 
+    1700     293.4999            1            1            1            1 
+    1750    306.21866            1            1            1            1 
+    1800    283.22695            1            1            1            1 
+    1850    295.10472            1            1            1            1 
+    1900    317.38431            1            1            1            1 
+    1950    305.14824            1            1            1            1 
+    2000    289.00909            1            1            1            1 
+Loop time of 0.689125 on 4 procs for 2000 steps with 118 atoms
+
+Performance: 250.753 ns/day, 0.096 hours/ns, 2902.231 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.02002    | 0.030617   | 0.053133   |   7.7 |  4.44
+Bond    | 0.10356    | 0.18908    | 0.22691    |  11.6 | 27.44
+Neigh   | 0.16721    | 0.17002    | 0.17247    |   0.5 | 24.67
+Comm    | 0.057286   | 0.12002    | 0.21612    |  17.0 | 17.42
+Output  | 0.00028991 | 0.00034121 | 0.00049323 |   0.0 |  0.05
+Modify  | 0.17626    | 0.17675    | 0.17721    |   0.1 | 25.65
+Other   |            | 0.002287   |            |       |  0.33
+
+Nlocal:    29.5 ave 41 max 18 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    306 ave 349 max 269 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs:    1084.5 ave 2154 max 397 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 4338
+Ave neighs/atom = 36.7627
+Ave special neighs/atom = 10.5763
+Neighbor list builds = 2000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map b/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map
new file mode 100644
index 0000000000..fb8720be63
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map
@@ -0,0 +1,47 @@
+this is a map file
+
+1 edgeIDs
+31 equivalences
+
+BondingIDs
+
+15
+1
+
+EdgeIDs
+
+5
+
+Equivalences
+
+1	1
+2	2
+3	3
+4	4
+5	5
+6	6
+7	7
+8	8
+9	9
+10	10
+11	11
+12	12
+13	13
+14	14
+15	15
+16	16
+17	17
+18	18
+19	19
+20	20
+21  21
+22  22
+23  23
+24  24
+25  25
+26  26
+27  27
+28  28
+29  29
+30	30
+31  31
diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template b/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template
new file mode 100644
index 0000000000..e510883432
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template
@@ -0,0 +1,315 @@
+rxn1_stp1_post
+
+31 atoms           
+30 bonds           
+55 angles           
+75 dihedrals           
+34 impropers           
+
+Types
+
+1 1
+2 6
+3 1
+4 7
+5 4
+6 7
+7 8
+8 8
+9 8
+10 8
+11 8
+12 9
+13 1
+14 1
+15 9
+16 9
+17 1
+18 1
+19 10
+20 8
+21 8
+22 8
+23 8
+24 10
+25 10
+26 10
+27 10
+28 8
+29 8
+30 8
+31 8
+
+Charges
+
+1 0.000000
+2 0.000000
+3 0.000000
+4 0.100000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.000000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 -0.025000
+16 -0.025000
+17 0.000000
+18 0.000000
+19 0.000000
+20 0.000000
+21 0.000000
+22 0.000000
+23 0.000000
+24 0.000000
+25 0.000000
+26 0.000000
+27 0.000000
+28 0.000000
+29 0.000000
+30 0.000000
+31 0.000000
+
+Coords
+
+1 22.582573 10.988183 -5.014054
+2 23.904713 10.750493 -4.202215
+3 23.989172 9.487042 -3.323374
+4 24.067001 11.723383 -4.037435
+5 24.627851 7.325302 -3.319944
+6 24.554632 8.418972 -4.080365
+7 22.667763 11.445703 -5.999605
+8 21.787441 10.247643 -4.916974
+9 24.964962 10.712683 -4.449374
+10 24.616703 9.689913 -2.456034
+11 22.989313 9.208153 -2.991455
+12 18.808882 13.758042 -3.958724
+13 19.293213 12.549683 -3.196594
+14 20.810543 12.417832 -3.417504
+15 21.090193 12.251203 -4.891234
+16 17.657042 16.437199 -3.985224
+17 19.126713 16.210239 -4.245154
+18 19.589151 14.957593 -3.479565
+19 19.000433 13.609432 -5.041715
+20 18.761223 11.614392 -3.573184
+21 19.082903 12.688992 -2.085145
+22 21.202852 11.511562 -2.848624
+23 21.328482 13.360252 -3.038924
+24 19.949852 12.199403 -5.680355
+25 21.477343 13.247442 -5.445915
+26 17.080341 15.555528 -4.334374
+27 17.319832 17.341927 -4.532204
+28 19.720472 17.115158 -3.887564
+29 19.298622 16.058659 -5.361685
+30 19.410772 15.105113 -2.363724
+31 20.700163 14.782252 -3.666344
+
+Bonds
+
+1 1 1 8
+2 16 1 2
+3 1 1 7
+4 13 1 15
+5 16 3 2
+6 12 2 9
+7 17 2 4
+8 3 3 6
+9 1 3 10
+10 1 3 11
+11 8 6 5
+12 13 13 12
+13 13 18 12
+14 14 12 19
+15 15 13 14
+16 1 13 20
+17 1 13 21
+18 13 14 15
+19 1 14 22
+20 1 14 23
+21 14 15 24
+22 14 15 25
+23 13 17 16
+24 14 16 26
+25 14 16 27
+26 15 17 18
+27 1 17 28
+28 1 17 29
+29 1 18 30
+30 1 18 31
+
+Angles
+
+1 30 2 1 8
+2 2 8 1 7
+3 26 8 1 15
+4 30 2 1 7
+5 31 2 1 15
+6 26 7 1 15
+7 32 1 2 3
+8 33 1 2 9
+9 34 1 2 4
+10 33 3 2 9
+11 34 3 2 4
+12 35 4 2 9
+13 36 2 3 6
+14 30 2 3 10
+15 30 2 3 11
+16 3 6 3 10
+17 3 6 3 11
+18 2 10 3 11
+19 22 3 6 5
+20 23 13 12 18
+21 24 13 12 19
+22 24 18 12 19
+23 25 14 13 12
+24 26 20 13 12
+25 26 21 13 12
+26 27 14 13 20
+27 27 14 13 21
+28 2 20 13 21
+29 25 13 14 15
+30 27 13 14 22
+31 27 13 14 23
+32 26 22 14 15
+33 26 23 14 15
+34 2 22 14 23
+35 23 1 15 14
+36 24 1 15 24
+37 24 1 15 25
+38 24 14 15 24
+39 24 14 15 25
+40 28 24 15 25
+41 24 17 16 26
+42 24 17 16 27
+43 28 26 16 27
+44 25 18 17 16
+45 26 28 17 16
+46 26 29 17 16
+47 27 18 17 28
+48 27 18 17 29
+49 2 28 17 29
+50 25 17 18 12
+51 26 30 18 12
+52 26 31 18 12
+53 27 17 18 30
+54 27 17 18 31
+55 2 30 18 31
+
+Dihedrals
+
+1 40 8 1 2 3
+2 41 8 1 2 9
+3 42 8 1 2 4
+4 40 7 1 2 3
+5 41 7 1 2 9
+6 42 7 1 2 4
+7 43 15 1 2 3
+8 44 15 1 2 9
+9 45 15 1 2 4
+10 28 8 1 15 14
+11 30 8 1 15 24
+12 30 8 1 15 25
+13 46 2 1 15 14
+14 47 2 1 15 24
+15 47 2 1 15 25
+16 28 7 1 15 14
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diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1_pre.data_template b/examples/USER/reaction/tiny_epoxy/rxn1_stp1_pre.data_template
new file mode 100644
index 0000000000..dd767a4cba
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp1_pre.data_template
@@ -0,0 +1,301 @@
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diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp2.map b/examples/USER/reaction/tiny_epoxy/rxn1_stp2.map
new file mode 100644
index 0000000000..9e39e57310
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp2.map
@@ -0,0 +1,47 @@
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diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template b/examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template
new file mode 100644
index 0000000000..cbb66a3151
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template
@@ -0,0 +1,307 @@
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diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1.map b/examples/USER/reaction/tiny_epoxy/rxn2_stp1.map
new file mode 100644
index 0000000000..cbe2a44f36
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn2_stp1.map
@@ -0,0 +1,59 @@
+this is a map file
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diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1_post.data_template b/examples/USER/reaction/tiny_epoxy/rxn2_stp1_post.data_template
new file mode 100644
index 0000000000..0600abdc0c
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn2_stp1_post.data_template
@@ -0,0 +1,424 @@
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diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1_pre.data_template b/examples/USER/reaction/tiny_epoxy/rxn2_stp1_pre.data_template
new file mode 100644
index 0000000000..9ee4ffb2de
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn2_stp1_pre.data_template
@@ -0,0 +1,407 @@
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diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp2.map b/examples/USER/reaction/tiny_epoxy/rxn2_stp2.map
new file mode 100644
index 0000000000..f90915a54f
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn2_stp2.map
@@ -0,0 +1,59 @@
+this is a map file
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diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp2_post.data_template b/examples/USER/reaction/tiny_epoxy/rxn2_stp2_post.data_template
new file mode 100644
index 0000000000..2b37ecff03
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/rxn2_stp2_post.data_template
@@ -0,0 +1,413 @@
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+27 14.583670 15.922830 -0.748110
+28 16.984310 15.696060 -0.103470
+29 16.562460 14.639560 -1.577590
+30 16.674610 13.686010 1.420370
+31 17.964001 13.363150 0.117750
+32 18.680189 9.134390 -4.183100
+33 18.099751 8.263650 -5.343000
+34 19.081829 7.609610 -6.334180
+35 17.971729 9.827680 -5.367080
+36 20.263880 5.733600 -6.736780
+37 19.414030 6.299980 -5.878960
+38 18.194740 9.091640 -3.210950
+39 19.788940 9.208560 -4.119640
+40 17.399309 7.432220 -5.407800
+41 18.616249 7.545570 -7.316910
+42 19.987049 8.212500 -6.399400
+
+Bonds
+
+1 1 1 8
+2 2 1 2
+3 1 1 7
+4 13 1 15
+5 2 3 2
+6 6 2 9
+7 19 2 4
+8 3 3 6
+9 1 3 10
+10 1 3 11
+11 18 4 25
+12 8 6 5
+13 13 13 12
+14 13 18 12
+15 14 12 19
+16 15 13 14
+17 1 13 20
+18 1 13 21
+19 13 14 15
+20 1 14 22
+21 1 14 23
+22 13 32 15
+23 13 17 16
+24 14 16 26
+25 14 16 27
+26 15 17 18
+27 1 17 28
+28 1 17 29
+29 1 18 30
+30 1 18 31
+31 18 35 24
+32 1 32 39
+33 16 32 33
+34 1 32 38
+35 17 35 33
+36 16 34 33
+37 12 40 33
+38 3 34 37
+39 1 34 41
+40 1 34 42
+41 8 37 36
+
+Angles
+
+1 1 2 1 8
+2 2 8 1 7
+3 26 8 1 15
+4 1 2 1 7
+5 42 2 1 15
+6 26 7 1 15
+7 43 1 2 3
+8 7 1 2 9
+9 44 1 2 4
+10 7 3 2 9
+11 44 3 2 4
+12 45 4 2 9
+13 4 2 3 6
+14 1 2 3 10
+15 1 2 3 11
+16 3 6 3 10
+17 3 6 3 11
+18 2 10 3 11
+19 46 2 4 25
+20 22 3 6 5
+21 23 13 12 18
+22 24 13 12 19
+23 24 18 12 19
+24 25 14 13 12
+25 26 20 13 12
+26 26 21 13 12
+27 27 14 13 20
+28 27 14 13 21
+29 2 20 13 21
+30 25 13 14 15
+31 27 13 14 22
+32 27 13 14 23
+33 26 22 14 15
+34 26 23 14 15
+35 2 22 14 23
+36 23 1 15 14
+37 23 1 15 32
+38 23 14 15 32
+39 24 17 16 26
+40 24 17 16 27
+41 28 26 16 27
+42 25 18 17 16
+43 26 28 17 16
+44 26 29 17 16
+45 27 18 17 28
+46 27 18 17 29
+47 2 28 17 29
+48 25 17 18 12
+49 26 30 18 12
+50 26 31 18 12
+51 27 17 18 30
+52 27 17 18 31
+53 2 30 18 31
+54 26 39 32 15
+55 47 15 32 33
+56 26 38 32 15
+57 48 39 32 33
+58 2 39 32 38
+59 48 38 32 33
+60 34 32 33 35
+61 32 32 33 34
+62 33 32 33 40
+63 34 34 33 35
+64 35 35 33 40
+65 33 34 33 40
+66 49 37 34 33
+67 48 41 34 33
+68 48 42 34 33
+69 3 37 34 41
+70 3 37 34 42
+71 2 41 34 42
+72 50 24 35 33
+73 22 34 37 36
+
+Dihedrals
+
+1 55 8 1 2 3
+2 3 8 1 2 9
+3 56 8 1 2 4
+4 55 7 1 2 3
+5 3 7 1 2 9
+6 56 7 1 2 4
+7 57 15 1 2 3
+8 58 15 1 2 9
+9 59 15 1 2 4
+10 28 8 1 15 14
+11 28 8 1 15 32
+12 60 2 1 15 14
+13 60 2 1 15 32
+14 28 7 1 15 14
+15 28 7 1 15 32
+16 61 6 3 2 1
+17 55 10 3 2 1
+18 55 11 3 2 1
+19 6 6 3 2 9
+20 3 10 3 2 9
+21 3 11 3 2 9
+22 62 6 3 2 4
+23 56 10 3 2 4
+24 56 11 3 2 4
+25 63 1 2 4 25
+26 63 3 2 4 25
+27 64 9 2 4 25
+28 8 2 3 6 5
+29 7 10 3 6 5
+30 7 11 3 6 5
+31 27 14 13 12 18
+32 28 20 13 12 18
+33 28 21 13 12 18
+34 29 14 13 12 19
+35 30 20 13 12 19
+36 30 21 13 12 19
+37 27 17 18 12 13
+38 28 30 18 12 13
+39 28 31 18 12 13
+40 29 17 18 12 19
+41 30 30 18 12 19
+42 30 31 18 12 19
+43 31 12 13 14 15
+44 32 22 14 13 12
+45 32 23 14 13 12
+46 32 20 13 14 15
+47 33 20 13 14 22
+48 33 20 13 14 23
+49 32 21 13 14 15
+50 33 21 13 14 22
+51 33 21 13 14 23
+52 27 13 14 15 1
+53 27 13 14 15 32
+54 28 22 14 15 1
+55 28 22 14 15 32
+56 28 23 14 15 1
+57 28 23 14 15 32
+58 28 39 32 15 1
+59 46 33 32 15 1
+60 28 38 32 15 1
+61 28 39 32 15 14
+62 46 33 32 15 14
+63 28 38 32 15 14
+64 29 18 17 16 26
+65 30 28 17 16 26
+66 30 29 17 16 26
+67 29 18 17 16 27
+68 30 28 17 16 27
+69 30 29 17 16 27
+70 31 16 17 18 12
+71 32 30 18 17 16
+72 32 31 18 17 16
+73 32 28 17 18 12
+74 33 28 17 18 30
+75 33 28 17 18 31
+76 32 29 17 18 12
+77 33 29 17 18 30
+78 33 29 17 18 31
+79 45 15 32 33 35
+80 43 15 32 33 34
+81 44 15 32 33 40
+82 42 39 32 33 35
+83 40 39 32 33 34
+84 41 39 32 33 40
+85 42 38 32 33 35
+86 40 38 32 33 34
+87 41 38 32 33 40
+88 65 24 35 33 32
+89 65 24 35 33 34
+90 66 24 35 33 40
+91 48 37 34 33 32
+92 40 41 34 33 32
+93 40 42 34 33 32
+94 50 37 34 33 35
+95 42 41 34 33 35
+96 42 42 34 33 35
+97 49 37 34 33 40
+98 41 41 34 33 40
+99 41 42 34 33 40
+100 51 33 34 37 36
+101 7 41 34 37 36
+102 7 42 34 37 36
+
+Impropers
+
+1 4 13 12 18 19
+2 22 1 15 14 32
+3 5 17 16 26 27
+4 1 2 1 8 7
+5 1 2 1 8 15
+6 1 8 1 7 15
+7 1 2 1 7 15
+8 1 1 2 3 9
+9 1 1 2 3 4
+10 1 1 2 4 9
+11 1 3 2 4 9
+12 1 2 3 6 10
+13 1 2 3 6 11
+14 1 2 3 10 11
+15 1 6 3 10 11
+16 1 14 13 20 12
+17 1 14 13 21 12
+18 1 20 13 21 12
+19 1 14 13 20 21
+20 1 13 14 22 15
+21 1 13 14 23 15
+22 1 13 14 22 23
+23 1 22 14 23 15
+24 1 18 17 28 16
+25 1 18 17 29 16
+26 1 28 17 29 16
+27 1 18 17 28 29
+28 1 17 18 30 12
+29 1 17 18 31 12
+30 1 30 18 31 12
+31 1 17 18 30 31
+32 1 39 32 15 33
+33 1 39 32 38 15
+34 1 38 32 15 33
+35 1 39 32 38 33
+36 1 32 33 34 35
+37 1 32 33 35 40
+38 1 32 33 34 40
+39 1 34 33 35 40
+40 1 37 34 41 33
+41 1 37 34 42 33
+42 1 41 34 42 33
+43 1 37 34 41 42
diff --git a/examples/USER/reaction/tiny_epoxy/tiny_epoxy.data b/examples/USER/reaction/tiny_epoxy/tiny_epoxy.data
new file mode 100644
index 0000000000..d98006b107
--- /dev/null
+++ b/examples/USER/reaction/tiny_epoxy/tiny_epoxy.data
@@ -0,0 +1,1582 @@
+# two molecules DGEBA (diepoxy) and one DETA (linker)
+
+118 atoms           
+123 bonds           
+221 angles           
+302 dihedrals           
+115 impropers           
+11 atom types          
+19 bond types          
+50 angle types          
+66 dihedral types          
+22 improper types          
+10 30 xlo xhi
+-10 20 ylo yhi
+-15 10 zlo zhi
+
+Masses            
+
+1 12.011150 # c2         
+2 12.011150 # c3m         
+3 15.999400 # o3e         
+4 12.011150 # cp         
+5 12.011150 # c         
+6 12.011150 # c3         
+7 15.999400 # oc         
+8 1.007970 # hc         
+9 14.006700 # na         
+10 1.007970 # hn         
+11 1.007970 # ho         
+
+Pair Coeffs # lj/class2/coul/long         
+
+1 0.0540000000 4.0100000000 # c2        
+2 0.0540000000 4.0100000000 # c3m        
+3 0.2400000000 3.5350000000 # o3e        
+4 0.0640000000 4.0100000000 # cp        
+5 0.0540000000 4.0100000000 # c        
+6 0.0540000000 4.0100000000 # c3        
+7 0.2400000000 3.5350000000 # oc        
+8 0.0200000000 2.7000000000 # hc        
+9 0.0650000000 4.0700000000 # na        
+10 0.0130000000 1.0980000000 # hn        
+11 0.0130000000 1.0980000000 # ho        
+
+Bond Coeffs # class2         
+
+1 1.1010 345.0000 -691.8900 844.6000 # c2-hc      
+2 1.5300 299.6700 -501.7700 679.8100 # c2-c3m      
+3 1.4200 400.3954 -835.1951 1313.0142 # c2-oc      
+4 1.4200 400.3954 -835.1951 1313.0142 # c3m-o3e      
+5 1.5300 299.6700 -501.7700 679.8100 # c3m-c3m      
+6 1.1010 345.0000 -691.8900 844.6000 # c3m-hc      
+7 1.4170 470.8361 -627.6179 1327.6345 # cp-cp      
+8 1.3768 428.8798 -738.2351 1114.9655 # cp-oc      
+9 1.0982 372.8251 -803.4526 894.3173 # cp-hc      
+10 1.5010 321.9021 -521.8208 572.1628 # cp-c      
+11 1.5300 299.6700 -501.7700 679.8100 # c-c3      
+12 1.1010 345.0000 -691.8900 844.6000 # c3-hc      
+13 1.4570 365.8052 -699.6368 998.4842 # c2-na      
+14 1.0060 466.7400 -1073.6018 1251.1056 # na-hn      
+15 1.5300 299.6700 -501.7700 679.8100 # c2-c2      
+16 1.5300 299.6700 -501.7700 679.8100 # c2-c3      
+17 1.4200 400.3954 -835.1951 1313.0142 # c3-oc      
+18 0.9650 532.5062 -1282.9050 2004.7658 # oc-ho      
+19 1.4200 400.3954 -835.1951 1313.0142 # c3m-oc      
+
+Angle Coeffs # class2         
+
+1 110.7700 41.4530 -10.6040 5.1290 # c3m-c2-hc      
+2 107.6600 39.6410 -12.9210 -2.4318 # hc-c2-hc      
+3 108.7280 58.5446 -10.8088 -12.4006 # oc-c2-hc      
+4 111.2700 54.5381 -8.3642 -13.0838 # c3m-c2-oc      
+5 111.2700 54.5381 -8.3642 -13.0838 # c2-c3m-o3e      
+6 112.6700 39.5160 -7.4430 -9.5583 # c2-c3m-c3m      
+7 110.7700 41.4530 -10.6040 5.1290 # c2-c3m-hc      
+8 111.2700 54.5381 -8.3642 -13.0838 # c3m-c3m-o3e      
+9 108.7280 58.5446 -10.8088 -12.4006 # o3e-c3m-hc      
+10 110.7700 41.4530 -10.6040 5.1290 # c3m-c3m-hc      
+11 107.6600 39.6410 -12.9210 -2.4318 # hc-c3m-hc      
+12 104.5000 35.7454 -10.0067 -6.2729 # c3m-o3e-c3m      
+13 118.9000 61.0226 -34.9931 0.0000 # cp-cp-cp      
+14 123.4200 73.6781 -21.6787 0.0000 # cp-cp-oc      
+15 117.9400 35.1558 -12.4682 0.0000 # cp-cp-hc      
+16 120.0500 44.7148 -22.7352 0.0000 # cp-cp-c      
+17 108.4000 43.9594 -8.3924 -9.3379 # cp-c-c3      
+18 111.0000 44.3234 -9.4454 0.0000 # cp-c-cp      
+19 112.6700 39.5160 -7.4430 -9.5583 # c3-c-c3      
+20 110.7700 41.4530 -10.6040 5.1290 # c-c3-hc      
+21 107.6600 39.6410 -12.9210 -2.4318 # hc-c3-hc      
+22 102.9695 38.9739 -6.2595 -8.1710 # c2-oc-cp      
+23 112.4436 47.2337 -10.6612 -10.2062 # c2-na-c2      
+24 110.9538 50.8652 -4.4522 -10.0298 # c2-na-hn      
+25 111.9100 60.7147 -13.3366 -13.0785 # c2-c2-na      
+26 110.6204 51.3137 -6.7198 -2.6003 # hc-c2-na      
+27 110.7700 41.4530 -10.6040 5.1290 # c2-c2-hc      
+28 107.0671 45.2520 -7.5558 -9.5120 # hn-na-hn      
+29 112.6700 39.5160 -7.4430 -9.5583 # c3m-c3m-c2      
+30 110.7700 41.4530 -10.6040 5.1290 # c3-c2-hc      
+31 111.9100 60.7147 -13.3366 -13.0785 # c3-c2-na      
+32 112.6700 39.5160 -7.4430 -9.5583 # c2-c3-c2      
+33 110.7700 41.4530 -10.6040 5.1290 # c2-c3-hc      
+34 111.2700 54.5381 -8.3642 -13.0838 # c2-c3-oc      
+35 108.7280 58.5446 -10.8088 -12.4006 # oc-c3-hc      
+36 111.2700 54.5381 -8.3642 -13.0838 # c3-c2-oc      
+37 105.8000 52.7061 -12.1090 -9.8681 # c3-oc-ho      
+38 108.7280 58.5446 -10.8088 -12.4006 # hc-c3m-o3e      
+39 110.7700 41.4530 -10.6040 5.1290 # hc-c3m-c3m      
+40 111.2700 54.5381 -8.3642 -13.0838 # oc-c2-c3m      
+41 110.7700 41.4530 -10.6040 5.1290 # hc-c2-c3m      
+42 111.9100 60.7147 -13.3366 -13.0785 # c3m-c2-na      
+43 112.6700 39.5160 -7.4430 -9.5583 # c2-c3m-c2      
+44 111.2700 54.5381 -8.3642 -13.0838 # c2-c3m-oc      
+45 108.7280 58.5446 -10.8088 -12.4006 # oc-c3m-hc      
+46 105.8000 52.7061 -12.1090 -9.8681 # c3m-oc-ho      
+47 111.9100 60.7147 -13.3366 -13.0785 # na-c2-c3      
+48 110.7700 41.4530 -10.6040 5.1290 # hc-c2-c3      
+49 111.2700 54.5381 -8.3642 -13.0838 # oc-c2-c3      
+50 105.8000 52.7061 -12.1090 -9.8681 # ho-oc-c3      
+
+Dihedral Coeffs # class2         
+
+1 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3m-o3e     
+2 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3m-c3m     
+3 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c3m-hc     
+4 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3m-o3e     
+5 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3m-c3m     
+6 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# oc-c2-c3m-hc     
+7 0.9513 0.0000 0.1155 0.0000 0.0720 0.0000# hc-c2-oc-cp     
+8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# c3m-c2-oc-cp     
+9 -0.5203 0.0000 -0.3028 0.0000 -0.3450 0.0000# c2-c3m-o3e-c3m     
+10 0.5302 0.0000 0.0000 0.0000 -0.3966 0.0000# hc-c3m-o3e-c3m     
+11 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# c2-c3m-c3m-o3e     
+12 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c2-c3m-c3m-hc     
+13 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# o3e-c3m-c3m-hc     
+14 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c3m-c3m-hc     
+15 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000# cp-cp-cp-cp     
+16 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000# cp-cp-cp-hc     
+17 0.0000 0.0000 4.8498 0.0000 0.0000 0.0000# cp-cp-cp-oc     
+18 0.0000 0.0000 1.7234 0.0000 0.0000 0.0000# oc-cp-cp-hc     
+19 0.0000 0.0000 1.5000 0.0000 0.0000 0.0000# cp-cp-oc-c2     
+20 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000# hc-cp-cp-hc     
+21 0.0000 0.0000 4.4072 0.0000 0.0000 0.0000# cp-cp-cp-c     
+22 0.0000 0.0000 1.5590 0.0000 0.0000 0.0000# c-cp-cp-hc     
+23 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000# cp-cp-c-c3     
+24 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000# cp-cp-c-cp     
+25 -0.0228 0.0000 0.0280 0.0000 -0.1863 0.0000# cp-c-c3-hc     
+26 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c3-c-c3-hc     
+27 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c2-c2-na-c2     
+28 0.1904 0.0000 -0.1342 0.0000 -0.2460 0.0000# hc-c2-na-c2     
+29 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000# c2-c2-na-hn     
+30 -0.5187 0.0000 -0.4837 0.0000 -0.1692 0.0000# hc-c2-na-hn     
+31 0.3805 0.0000 0.3547 0.0000 -0.1102 0.0000# na-c2-c2-na     
+32 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# hc-c2-c2-na     
+33 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c2-hc     
+34 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# c3m-c3m-c2-oc     
+35 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c3m-c3m-c2-hc     
+36 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# o3e-c3m-c2-oc     
+37 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# o3e-c3m-c2-hc     
+38 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c3m-c2-oc     
+39 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c3m-c2-hc     
+40 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3-c2     
+41 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c3-hc     
+42 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3-oc     
+43 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000# na-c2-c3-c2     
+44 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# na-c2-c3-hc     
+45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# na-c2-c3-oc     
+46 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c3-c2-na-c2     
+47 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000# c3-c2-na-hn     
+48 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3-c2     
+49 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# oc-c2-c3-hc     
+50 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3-oc     
+51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# c3-c2-oc-cp     
+52 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# c2-c3-oc-ho     
+53 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# hc-c3-oc-ho     
+54 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c3m-c3m-o3e     
+55 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3m-c2     
+56 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3m-oc     
+57 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000# na-c2-c3m-c2     
+58 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# na-c2-c3m-hc     
+59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# na-c2-c3m-oc     
+60 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c3m-c2-na-c2     
+61 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3m-c2     
+62 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3m-oc     
+63 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# c2-c3m-oc-ho     
+64 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# hc-c3m-oc-ho     
+65 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# ho-oc-c3-c2     
+66 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# ho-oc-c3-hc     
+
+Improper Coeffs # class2         
+
+1 13.0421 0.0000 # cp-cp-cp-oc        
+2 4.8912 0.0000 # cp-cp-cp-hc        
+3 7.8153 0.0000 # cp-cp-cp-c        
+4 0.0000 0.0000 # c2-na-c2-hn        
+5 0.0000 0.0000 # c2-na-hn-hn        
+6 0.0000 0.0000          
+7 0.0000 0.0000          
+8 0.0000 0.0000          
+9 0.0000 0.0000          
+10 0.0000 0.0000          
+11 0.0000 0.0000          
+12 0.0000 0.0000          
+13 0.0000 0.0000          
+14 0.0000 0.0000          
+15 0.0000 0.0000          
+16 0.0000 0.0000          
+17 0.0000 0.0000          
+18 0.0000 0.0000          
+19 0.0000 0.0000          
+20 0.0000 0.0000          
+21 0.0000 0.0000          
+22 0.0000 0.0000 # c2-na-c2-c2        
+
+BondBond Coeffs           
+
+1 3.3872 1.5300 1.1010         
+2 5.3316 1.1010 1.1010         
+3 23.1979 1.4200 1.1010         
+4 11.4318 1.5300 1.4200         
+5 11.4318 1.5300 1.4200         
+6 0.0000 1.5300 1.5300         
+7 3.3872 1.5300 1.1010         
+8 11.4318 1.5300 1.4200         
+9 23.1979 1.4200 1.1010         
+10 3.3872 1.5300 1.1010         
+11 5.3316 1.1010 1.1010         
+12 -7.1131 1.4200 1.4200         
+13 68.2856 1.4170 1.4170         
+14 48.4754 1.4170 1.3768         
+15 1.0795 1.4170 1.0982         
+16 12.0676 1.4170 1.5010         
+17 0.0000 1.5010 1.5300         
+18 0.0000 1.5010 1.5010         
+19 0.0000 1.5300 1.5300         
+20 3.3872 1.5300 1.1010         
+21 5.3316 1.1010 1.1010         
+22 0.0000 1.4200 1.3768         
+23 -2.1113 1.4570 1.4570         
+24 -6.4168 1.4570 1.0060         
+25 4.6217 1.5300 1.4570         
+26 12.4260 1.1010 1.4570         
+27 3.3872 1.5300 1.1010         
+28 -1.8749 1.0060 1.0060         
+29 0.0000 1.5300 1.5300         
+30 3.3872 1.5300 1.1010         
+31 4.6217 1.5300 1.4570         
+32 0.0000 1.5300 1.5300         
+33 3.3872 1.5300 1.1010         
+34 11.4318 1.5300 1.4200         
+35 23.1979 1.4200 1.1010         
+36 11.4318 1.5300 1.4200         
+37 -9.6879 1.4200 0.9650         
+38 23.1979 1.1010 1.4200         
+39 3.3872 1.1010 1.5300         
+40 11.4318 1.4200 1.5300         
+41 3.3872 1.1010 1.5300         
+42 4.6217 1.5300 1.4570         
+43 0.0000 1.5300 1.5300         
+44 11.4318 1.5300 1.4200         
+45 23.1979 1.4200 1.1010         
+46 -9.6879 1.4200 0.9650         
+47 4.6217 1.4570 1.5300         
+48 3.3872 1.1010 1.5300         
+49 11.4318 1.4200 1.5300         
+50 -9.6879 0.9650 1.4200         
+
+BondAngle Coeffs           
+
+1 20.7540 11.4210 1.5300 1.1010        
+2 18.1030 18.1030 1.1010 1.1010        
+3 55.3270 4.6189 1.4200 1.1010        
+4 2.6868 20.4033 1.5300 1.4200        
+5 2.6868 20.4033 1.5300 1.4200        
+6 8.0160 8.0160 1.5300 1.5300        
+7 20.7540 11.4210 1.5300 1.1010        
+8 2.6868 20.4033 1.5300 1.4200        
+9 55.3270 4.6189 1.4200 1.1010        
+10 20.7540 11.4210 1.5300 1.1010        
+11 18.1030 18.1030 1.1010 1.1010        
+12 -2.8112 -2.8112 1.4200 1.4200        
+13 28.8708 28.8708 1.4170 1.4170        
+14 58.4790 107.6806 1.4170 1.3768        
+15 20.0033 24.2183 1.4170 1.0982        
+16 31.0771 47.0579 1.4170 1.5010        
+17 0.0000 0.0000 1.5010 1.5300        
+18 0.0000 0.0000 1.5010 1.5010        
+19 8.0160 8.0160 1.5300 1.5300        
+20 20.7540 11.4210 1.5300 1.1010        
+21 18.1030 18.1030 1.1010 1.1010        
+22 0.0000 0.0000 1.4200 1.3768        
+23 -7.2229 -7.2229 1.4570 1.4570        
+24 31.8096 20.5799 1.4570 1.0060        
+25 6.0876 16.5702 1.5300 1.4570        
+26 13.4582 42.4332 1.1010 1.4570        
+27 20.7540 11.4210 1.5300 1.1010        
+28 28.0322 28.0322 1.0060 1.0060        
+29 8.0160 8.0160 1.5300 1.5300        
+30 20.7540 11.4210 1.5300 1.1010        
+31 6.0876 16.5702 1.5300 1.4570        
+32 8.0160 8.0160 1.5300 1.5300        
+33 20.7540 11.4210 1.5300 1.1010        
+34 2.6868 20.4033 1.5300 1.4200        
+35 55.3270 4.6189 1.4200 1.1010        
+36 2.6868 20.4033 1.5300 1.4200        
+37 28.5800 18.9277 1.4200 0.9650        
+38 4.6189 55.3270 1.1010 1.4200        
+39 11.4210 20.7540 1.1010 1.5300        
+40 20.4033 2.6868 1.4200 1.5300        
+41 11.4210 20.7540 1.1010 1.5300        
+42 6.0876 16.5702 1.5300 1.4570        
+43 8.0160 8.0160 1.5300 1.5300        
+44 2.6868 20.4033 1.5300 1.4200        
+45 55.3270 4.6189 1.4200 1.1010        
+46 28.5800 18.9277 1.4200 0.9650        
+47 16.5702 6.0876 1.4570 1.5300        
+48 11.4210 20.7540 1.1010 1.5300        
+49 20.4033 2.6868 1.4200 1.5300        
+50 18.9277 28.5800 0.9650 1.4200        
+
+AngleAngle Coeffs           
+
+1 0.0000 0.0000 0.0000 118.9000 123.4200 123.4200      
+2 0.0000 0.0000 0.0000 118.9000 117.9400 117.9400      
+3 0.0000 0.0000 0.0000 118.9000 120.0500 120.0500      
+4 0.0000 0.0000 0.0000 112.4436 110.9538 110.9538      
+5 0.0000 0.0000 0.0000 110.9538 107.0671 110.9538      
+6 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700      
+7 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700      
+8 2.4259 2.1283 2.4259 108.7280 107.6600 108.7280      
+9 -0.8330 -0.8330 -3.5744 112.6700 111.2700 111.2700      
+10 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700      
+11 -1.3199 -1.3199 0.1184 112.6700 110.7700 110.7700      
+12 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700      
+13 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700      
+14 2.4259 2.1283 2.4259 108.7280 107.6600 108.7280      
+15 0.0000 0.0000 0.0000 108.4000 112.6700 108.4000      
+16 0.0000 0.0000 0.0000 111.0000 108.4000 108.4000      
+17 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700      
+18 -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600      
+19 2.4286 0.5381 -2.5301 110.7700 110.6204 111.9100      
+20 2.4321 2.4321 -3.5496 107.6600 110.6204 110.6204      
+21 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700      
+22 0.0000 0.0000 0.0000 112.4436 112.4436 112.4436      
+
+AngleAngleTorsion Coeffs           
+
+1 -20.2006 110.7700 111.2700         
+2 -16.1640 110.7700 112.6700         
+3 -12.5640 110.7700 110.7700         
+4 -14.0484 111.2700 111.2700         
+5 -29.0420 111.2700 112.6700         
+6 -20.2006 111.2700 110.7700         
+7 0.0000 108.7280 102.9695         
+8 0.0000 111.2700 102.9695         
+9 -19.0059 111.2700 104.5000         
+10 -16.4438 108.7280 104.5000         
+11 -29.0420 112.6700 111.2700         
+12 -16.1640 112.6700 110.7700         
+13 -20.2006 111.2700 110.7700         
+14 -12.5640 110.7700 110.7700         
+15 0.0000 118.9000 118.9000         
+16 -4.8141 118.9000 117.9400         
+17 -21.0247 118.9000 123.4200         
+18 4.2296 123.4200 117.9400         
+19 0.0000 123.4200 102.9695         
+20 0.3598 117.9400 117.9400         
+21 -14.4097 118.9000 120.0500         
+22 4.4444 120.0500 117.9400         
+23 0.0000 120.0500 108.4000         
+24 0.0000 120.0500 111.0000         
+25 0.0000 108.4000 110.7700         
+26 -16.1640 112.6700 110.7700         
+27 -24.3818 111.9100 112.4436         
+28 -12.5567 110.6204 112.4436         
+29 -7.5499 111.9100 110.9538         
+30 -10.4258 110.6204 110.9538         
+31 -11.2307 111.9100 111.9100         
+32 -15.7572 110.7700 111.9100         
+33 -12.5640 110.7700 110.7700         
+34 -29.0420 112.6700 111.2700         
+35 -16.1640 112.6700 110.7700         
+36 -14.0484 111.2700 111.2700         
+37 -20.2006 111.2700 110.7700         
+38 -20.2006 110.7700 111.2700         
+39 -12.5640 110.7700 110.7700         
+40 -16.1640 110.7700 112.6700         
+41 -12.5640 110.7700 110.7700         
+42 -20.2006 110.7700 111.2700         
+43 -27.3953 111.9100 112.6700         
+44 -15.7572 111.9100 110.7700         
+45 0.0000 111.9100 111.2700         
+46 -24.3818 111.9100 112.4436         
+47 -7.5499 111.9100 110.9538         
+48 -29.0420 111.2700 112.6700         
+49 -20.2006 111.2700 110.7700         
+50 -14.0484 111.2700 111.2700         
+51 0.0000 111.2700 102.9695         
+52 -12.1038 111.2700 105.8000         
+53 -10.5093 108.7280 105.8000         
+54 -20.2006 110.7700 111.2700         
+55 -16.1640 110.7700 112.6700         
+56 -20.2006 110.7700 111.2700         
+57 -27.3953 111.9100 112.6700         
+58 -15.7572 111.9100 110.7700         
+59 0.0000 111.9100 111.2700         
+60 -24.3818 111.9100 112.4436         
+61 -29.0420 111.2700 112.6700         
+62 -14.0484 111.2700 111.2700         
+63 -12.1038 111.2700 105.8000         
+64 -10.5093 108.7280 105.8000         
+65 -12.1038 105.8000 111.2700         
+66 -10.5093 105.8000 108.7280         
+
+EndBondTorsion Coeffs           
+
+1 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200    
+2 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300    
+3 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010    
+4 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200    
+5 1.1538 0.8409 -0.9138 -0.3190 0.4411 -0.7174 1.4200 1.5300    
+6 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010    
+7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.1010 1.3768    
+8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5300 1.3768    
+9 -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200    
+10 -0.6054 1.3339 0.9648 -0.1620 0.1564 -1.1408 1.1010 1.4200    
+11 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200    
+12 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010    
+13 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010    
+14 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010    
+15 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170    
+16 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 1.4170 1.0982    
+17 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768    
+18 0.0000 4.2641 0.0000 0.0000 -1.5867 0.0000 1.3768 1.0982    
+19 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.4200    
+20 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982    
+21 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 1.4170 1.5010    
+22 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 1.5010 1.0982    
+23 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5300    
+24 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5010    
+25 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5010 1.1010    
+26 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010    
+27 0.0997 -0.0046 -0.2657 -0.0128 -0.0495 -0.1079 1.5300 1.4570    
+28 -0.5892 0.7140 0.3505 0.0628 0.0873 -0.0882 1.1010 1.4570    
+29 -0.9466 0.9356 -0.5542 0.0570 0.0625 0.4112 1.5300 1.0060    
+30 -1.1685 0.9266 -0.0993 0.0850 0.3061 0.2104 1.1010 1.0060    
+31 0.0286 0.0566 -0.0493 0.0286 0.0566 -0.0493 1.4570 1.4570    
+32 0.1960 0.7056 0.1120 0.1022 0.2090 0.6433 1.1010 1.4570    
+33 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010    
+34 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200    
+35 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010    
+36 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200    
+37 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010    
+38 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200    
+39 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010    
+40 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300    
+41 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010    
+42 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200    
+43 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.4570 1.5300    
+44 0.1022 0.2090 0.6433 0.1960 0.7056 0.1120 1.4570 1.1010    
+45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4570 1.4200    
+46 0.0997 -0.0046 -0.2657 -0.0128 -0.0495 -0.1079 1.5300 1.4570    
+47 -0.9466 0.9356 -0.5542 0.0570 0.0625 0.4112 1.5300 1.0060    
+48 1.1538 0.8409 -0.9138 -0.3190 0.4411 -0.7174 1.4200 1.5300    
+49 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010    
+50 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200    
+51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5300 1.3768    
+52 -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 1.5300 0.9650    
+53 -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 1.1010 0.9650    
+54 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200    
+55 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300    
+56 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200    
+57 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.4570 1.5300    
+58 0.1022 0.2090 0.6433 0.1960 0.7056 0.1120 1.4570 1.1010    
+59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4570 1.4200    
+60 0.0997 -0.0046 -0.2657 -0.0128 -0.0495 -0.1079 1.5300 1.4570    
+61 1.1538 0.8409 -0.9138 -0.3190 0.4411 -0.7174 1.4200 1.5300    
+62 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200    
+63 -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 1.5300 0.9650    
+64 -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 1.1010 0.9650    
+65 0.0000 0.5343 0.9025 -0.5800 0.9004 0.0000 0.9650 1.5300    
+66 0.2493 0.6803 0.0000 -1.7554 1.3145 0.2263 0.9650 1.1010    
+
+MiddleBondTorsion Coeffs           
+
+1 -16.7975 -1.2296 -0.2750 1.5300        
+2 -14.8790 -3.6581 -0.3138 1.5300        
+3 -14.2610 -0.5322 -0.4864 1.5300        
+4 -17.2585 -3.6157 -0.8364 1.5300        
+5 -21.8842 -7.6764 -0.6868 1.5300        
+6 -16.7975 -1.2296 -0.2750 1.5300        
+7 0.0000 0.0000 0.0000 1.4200        
+8 0.0000 0.0000 0.0000 1.4200        
+9 -5.9288 -2.7007 -0.3175 1.4200        
+10 -6.8007 -4.6546 -1.4101 1.4200        
+11 -21.8842 -7.6764 -0.6868 1.5300        
+12 -14.8790 -3.6581 -0.3138 1.5300        
+13 -16.7975 -1.2296 -0.2750 1.5300        
+14 -14.2610 -0.5322 -0.4864 1.5300        
+15 27.5989 -2.3120 0.0000 1.4170        
+16 0.0000 -1.1521 0.0000 1.4170        
+17 0.0000 4.8255 0.0000 1.4170        
+18 0.0000 5.5432 0.0000 1.4170        
+19 0.0000 0.0000 0.0000 1.3768        
+20 0.0000 4.8228 0.0000 1.4170        
+21 0.0000 9.1792 0.0000 1.4170        
+22 0.0000 3.9421 0.0000 1.4170        
+23 0.0000 0.0000 0.0000 1.5010        
+24 0.0000 0.0000 0.0000 1.5010        
+25 0.0000 0.0000 0.0000 1.5300        
+26 -14.8790 -3.6581 -0.3138 1.5300        
+27 -8.0036 -7.7321 -3.0640 1.4570        
+28 -6.4529 -6.8122 -1.1632 1.4570        
+29 -2.2208 0.5479 -0.3527 1.4570        
+30 -3.4611 1.6996 -0.6007 1.4570        
+31 -3.3497 1.0143 -3.0062 1.5300        
+32 -10.4959 -0.7647 -0.0545 1.5300        
+33 -14.2610 -0.5322 -0.4864 1.5300        
+34 -21.8842 -7.6764 -0.6868 1.5300        
+35 -14.8790 -3.6581 -0.3138 1.5300        
+36 -17.2585 -3.6157 -0.8364 1.5300        
+37 -16.7975 -1.2296 -0.2750 1.5300        
+38 -16.7975 -1.2296 -0.2750 1.5300        
+39 -14.2610 -0.5322 -0.4864 1.5300        
+40 -14.8790 -3.6581 -0.3138 1.5300        
+41 -14.2610 -0.5322 -0.4864 1.5300        
+42 -16.7975 -1.2296 -0.2750 1.5300        
+43 -15.4174 -7.3055 -1.0749 1.5300        
+44 -10.4959 -0.7647 -0.0545 1.5300        
+45 0.0000 0.0000 0.0000 1.5300        
+46 -8.0036 -7.7321 -3.0640 1.4570        
+47 -2.2208 0.5479 -0.3527 1.4570        
+48 -21.8842 -7.6764 -0.6868 1.5300        
+49 -16.7975 -1.2296 -0.2750 1.5300        
+50 -17.2585 -3.6157 -0.8364 1.5300        
+51 0.0000 0.0000 0.0000 1.4200        
+52 1.2472 0.0000 0.7485 1.4200        
+53 0.0000 0.9241 -0.5889 1.4200        
+54 -16.7975 -1.2296 -0.2750 1.5300        
+55 -14.8790 -3.6581 -0.3138 1.5300        
+56 -16.7975 -1.2296 -0.2750 1.5300        
+57 -15.4174 -7.3055 -1.0749 1.5300        
+58 -10.4959 -0.7647 -0.0545 1.5300        
+59 0.0000 0.0000 0.0000 1.5300        
+60 -8.0036 -7.7321 -3.0640 1.4570        
+61 -21.8842 -7.6764 -0.6868 1.5300        
+62 -17.2585 -3.6157 -0.8364 1.5300        
+63 1.2472 0.0000 0.7485 1.4200        
+64 0.0000 0.9241 -0.5889 1.4200        
+65 1.2472 0.0000 0.7485 1.4200        
+66 0.0000 0.9241 -0.5889 1.4200        
+
+BondBond13 Coeffs           
+
+1 0.0000 1.1010 1.4200         
+2 0.0000 1.1010 1.5300         
+3 0.0000 1.1010 1.1010         
+4 0.0000 1.4200 1.4200         
+5 0.0000 1.4200 1.5300         
+6 0.0000 1.4200 1.1010         
+7 0.0000 1.1010 1.3768         
+8 0.0000 1.5300 1.3768         
+9 0.0000 1.5300 1.4200         
+10 0.0000 1.1010 1.4200         
+11 0.0000 1.5300 1.4200         
+12 0.0000 1.5300 1.1010         
+13 0.0000 1.4200 1.1010         
+14 0.0000 1.1010 1.1010         
+15 53.0000 1.4170 1.4170         
+16 -6.2741 1.4170 1.0982         
+17 -2.2436 1.4170 1.3768         
+18 2.0517 1.3768 1.0982         
+19 0.0000 1.4170 1.4200         
+20 -1.7077 1.0982 1.0982         
+21 2.5085 1.4170 1.5010         
+22 0.8743 1.5010 1.0982         
+23 0.0000 1.4170 1.5300         
+24 0.0000 1.4170 1.5010         
+25 0.0000 1.5010 1.1010         
+26 0.0000 1.5300 1.1010         
+27 0.0000 1.5300 1.4570         
+28 0.0000 1.1010 1.4570         
+29 0.0000 1.5300 1.0060         
+30 0.0000 1.1010 1.0060         
+31 0.0000 1.4570 1.4570         
+32 0.0000 1.1010 1.4570         
+33 0.0000 1.1010 1.1010         
+34 0.0000 1.5300 1.4200         
+35 0.0000 1.5300 1.1010         
+36 0.0000 1.4200 1.4200         
+37 0.0000 1.4200 1.1010         
+38 0.0000 1.1010 1.4200         
+39 0.0000 1.1010 1.1010         
+40 0.0000 1.1010 1.5300         
+41 0.0000 1.1010 1.1010         
+42 0.0000 1.1010 1.4200         
+43 0.0000 1.4570 1.5300         
+44 0.0000 1.4570 1.1010         
+45 0.0000 1.4570 1.4200         
+46 0.0000 1.5300 1.4570         
+47 0.0000 1.5300 1.0060         
+48 0.0000 1.4200 1.5300         
+49 0.0000 1.4200 1.1010         
+50 0.0000 1.4200 1.4200         
+51 0.0000 1.5300 1.3768         
+52 0.0000 1.5300 0.9650         
+53 0.0000 1.1010 0.9650         
+54 0.0000 1.1010 1.4200         
+55 0.0000 1.1010 1.5300         
+56 0.0000 1.1010 1.4200         
+57 0.0000 1.4570 1.5300         
+58 0.0000 1.4570 1.1010         
+59 0.0000 1.4570 1.4200         
+60 0.0000 1.5300 1.4570         
+61 0.0000 1.4200 1.5300         
+62 0.0000 1.4200 1.4200         
+63 0.0000 1.5300 0.9650         
+64 0.0000 1.1010 0.9650         
+65 0.0000 0.9650 1.5300         
+66 0.0000 0.9650 1.1010         
+
+AngleTorsion Coeffs           
+
+1 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700    
+2 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700    
+3 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700    
+4 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700    
+5 0.9672 -0.7566 -1.2331 0.5623 -0.3041 -0.4015 111.2700 112.6700    
+6 -0.1892 0.4918 0.7273 2.3668 2.4920 -1.0122 111.2700 110.7700    
+7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.7280 102.9695    
+8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 111.2700 102.9695    
+9 -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 111.2700 104.5000    
+10 -1.8234 1.6393 0.5144 -0.7777 0.4340 -0.6653 108.7280 104.5000    
+11 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700    
+12 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700    
+13 -0.1892 0.4918 0.7273 2.3668 2.4920 -1.0122 111.2700 110.7700    
+14 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700    
+15 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000    
+16 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 118.9000 117.9400    
+17 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200    
+18 0.0000 2.5706 0.0000 0.0000 1.8729 0.0000 123.4200 117.9400    
+19 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 123.4200 102.9695    
+20 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400    
+21 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 118.9000 120.0500    
+22 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 120.0500 117.9400    
+23 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 120.0500 108.4000    
+24 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 120.0500 111.0000    
+25 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.4000 110.7700    
+26 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700    
+27 -2.7883 1.5193 1.4796 1.2031 1.3645 -0.7071 111.9100 112.4436    
+28 -2.6321 0.9353 -0.8398 -1.3582 0.1465 -0.5729 110.6204 112.4436    
+29 -3.3430 4.4558 -0.0346 0.2873 -0.8072 -0.0960 111.9100 110.9538    
+30 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.6204 110.9538    
+31 1.3673 0.4528 -2.7700 1.3673 0.4528 -2.7700 111.9100 111.9100    
+32 0.5111 1.6328 -1.0155 -1.1075 0.2820 0.8318 110.7700 111.9100    
+33 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700    
+34 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700    
+35 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700    
+36 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700    
+37 -0.1892 0.4918 0.7273 2.3668 2.4920 -1.0122 111.2700 110.7700    
+38 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700    
+39 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700    
+40 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700    
+41 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700    
+42 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700    
+43 2.0125 0.9440 -2.7612 -1.9225 -1.3450 0.2210 111.9100 112.6700    
+44 -1.1075 0.2820 0.8318 0.5111 1.6328 -1.0155 111.9100 110.7700    
+45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 111.9100 111.2700    
+46 -2.7883 1.5193 1.4796 1.2031 1.3645 -0.7071 111.9100 112.4436    
+47 -3.3430 4.4558 -0.0346 0.2873 -0.8072 -0.0960 111.9100 110.9538    
+48 0.9672 -0.7566 -1.2331 0.5623 -0.3041 -0.4015 111.2700 112.6700    
+49 -0.1892 0.4918 0.7273 2.3668 2.4920 -1.0122 111.2700 110.7700    
+50 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700    
+51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 111.2700 102.9695    
+52 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.2700 105.8000    
+53 -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 108.7280 105.8000    
+54 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700    
+55 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700    
+56 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700    
+57 2.0125 0.9440 -2.7612 -1.9225 -1.3450 0.2210 111.9100 112.6700    
+58 -1.1075 0.2820 0.8318 0.5111 1.6328 -1.0155 111.9100 110.7700    
+59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 111.9100 111.2700    
+60 -2.7883 1.5193 1.4796 1.2031 1.3645 -0.7071 111.9100 112.4436    
+61 0.9672 -0.7566 -1.2331 0.5623 -0.3041 -0.4015 111.2700 112.6700    
+62 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700    
+63 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.2700 105.8000    
+64 -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 108.7280 105.8000    
+65 0.8726 -0.3577 0.3888 -3.5903 2.5225 0.4888 105.8000 111.2700    
+66 0.0000 -0.2810 -0.5944 -3.4060 1.6396 0.0737 105.8000 108.7280    
+
+Atoms # full          
+
+1 1 1 0.000000 25.246496201 -1.871744037 -8.651348114 0 0 0 # c2 
+2 1 2 0.000000 25.610639572 -3.288228035 -8.165973663 0 0 0 # c3m 
+3 1 2 0.000000 24.731319427 -4.483242989 -8.675741196 0 0 0 # c3m 
+4 1 2 0.000000 18.703355789 9.118826866 -4.174236774 0 0 0 # c3m 
+5 1 2 0.000000 18.099748611 8.263649940 -5.343001842 0 0 0 # c3m 
+6 1 1 0.000000 19.081827164 7.609607220 -6.334177017 0 0 0 # c2 
+7 1 3 0.100000 26.190139771 -4.295329094 -9.220970154 0 0 0 # o3e 
+8 1 3 0.100000 17.971729279 9.827675819 -5.367077827 0 0 0 # o3e 
+9 1 4 0.000000 20.263877869 5.733595848 -6.736782074 0 0 0 # cp 
+10 1 4 0.000000 19.777191162 4.983679771 -7.809411049 0 0 0 # cp 
+11 1 4 0.000000 20.667026520 4.390971184 -8.707633972 0 0 0 # cp 
+12 1 4 0.000000 22.043539047 4.548151016 -8.533248901 0 0 0 # cp 
+13 1 4 0.000000 22.530214310 5.298062801 -7.460619926 0 0 0 # cp 
+14 1 4 0.000000 21.640394211 5.890783787 -6.562390804 0 0 0 # cp 
+15 1 5 0.000000 23.005182266 3.906831026 -9.503917694 0 0 0 # c 
+16 1 6 0.000000 24.286390305 4.758069992 -9.590908051 0 0 0 # c3 
+17 1 6 0.000000 22.342786789 3.812531948 -10.891778946 0 0 0 # c3 
+18 1 4 0.000000 23.361906052 2.519830942 -9.029184341 0 0 0 # cp 
+19 1 4 0.000000 24.458705902 2.330889940 -8.185920715 0 0 0 # cp 
+20 1 4 0.000000 24.788816452 1.047963977 -7.745534897 0 0 0 # cp 
+21 1 4 0.000000 24.022008896 -0.046867002 -8.149927139 0 0 0 # cp 
+22 1 4 0.000000 22.925630569 0.140873000 -8.992565155 0 0 0 # cp 
+23 1 4 0.000000 22.595729828 1.424777985 -9.432847977 0 0 0 # cp 
+24 1 7 0.000000 19.414030075 6.299984932 -5.878956795 0 0 0 # oc 
+25 1 7 0.000000 24.338140488 -1.273216963 -7.729548931 0 0 0 # oc 
+26 1 8 0.000000 26.150024414 -1.266484976 -8.715751648 0 0 0 # hc 
+27 1 8 0.000000 24.778566360 -1.933199048 -9.633987427 0 0 0 # hc 
+28 1 8 0.000000 25.929294586 -2.927781105 -7.187973022 0 0 0 # hc 
+29 1 8 0.000000 24.549385071 -5.308847904 -7.987242222 0 0 0 # hc 
+30 1 8 0.000000 23.904827118 -4.254271030 -9.348136902 0 0 0 # hc 
+31 1 8 0.000000 18.194736481 9.091637611 -3.210949898 0 0 0 # hc 
+32 1 8 0.000000 19.788938522 9.208558083 -4.119643211 0 0 0 # hc 
+33 1 8 0.000000 17.399309158 7.432216167 -5.407801151 0 0 0 # hc 
+34 1 8 0.000000 18.616250992 7.545570850 -7.316913128 0 0 0 # hc 
+35 1 8 0.000000 19.987047195 8.212498665 -6.399401188 0 0 0 # hc 
+36 1 8 0.000000 18.713207245 4.862418175 -7.944396973 0 0 0 # hc 
+37 1 8 0.000000 20.290582657 3.811013937 -9.537291527 0 0 0 # hc 
+38 1 8 0.000000 23.594188690 5.419342995 -7.325634956 0 0 0 # hc 
+39 1 8 0.000000 22.016828537 6.470753193 -5.732734203 0 0 0 # hc 
+40 1 8 0.000000 24.982324600 4.297049999 -10.290958405 0 0 0 # hc 
+41 1 8 0.000000 24.034254074 5.760886192 -9.936174393 0 0 0 # hc 
+42 1 8 0.000000 24.749143600 4.819462776 -8.606439590 0 0 0 # hc 
+43 1 8 0.000000 23.034755707 3.349560976 -11.594371796 0 0 0 # hc 
+44 1 8 0.000000 21.438467026 3.207982063 -10.822364807 0 0 0 # hc 
+45 1 8 0.000000 22.084871292 4.811752796 -11.239845276 0 0 0 # hc 
+46 1 8 0.000000 25.050769806 3.177418947 -7.873311996 0 0 0 # hc 
+47 1 8 0.000000 25.636974335 0.901705027 -7.093626022 0 0 0 # hc 
+48 1 8 0.000000 22.333581924 -0.705653012 -9.305183411 0 0 0 # hc 
+49 1 8 0.000000 21.747369766 1.570054054 -10.084861755 0 0 0 # hc 
+50 1 1 0.000000 25.222612381 -4.200571060 0.463562995 0 0 0 # c2 
+51 1 2 0.000000 25.832977295 -5.360119820 -0.347983003 0 0 0 # c3m 
+52 1 2 0.000000 27.389345169 -5.551681042 -0.290704012 0 0 0 # c3m 
+53 1 2 0.000000 20.635538101 8.396902084 -1.535487056 0 0 0 # c3m 
+54 1 2 0.000000 21.957460403 8.158697128 -0.723941982 0 0 0 # c3m 
+55 1 1 0.000000 22.041673660 6.895174980 0.154822007 0 0 0 # c2 
+56 1 3 0.100000 26.447082520 -6.565405846 0.448491007 0 0 0 # o3e 
+57 1 3 0.100000 20.959102631 9.287891388 -0.285212994 0 0 0 # o3e 
+58 1 4 0.000000 22.680345535 4.733430862 0.158248007 0 0 0 # cp 
+59 1 4 0.000000 23.824728012 4.488029957 0.920358002 0 0 0 # cp 
+60 1 4 0.000000 23.901163101 3.343113899 1.716701984 0 0 0 # cp 
+61 1 4 0.000000 22.833225250 2.443607092 1.750934958 0 0 0 # cp 
+62 1 4 0.000000 21.688846588 2.689002037 0.988831997 0 0 0 # cp 
+63 1 4 0.000000 21.612403870 3.833913088 0.192488998 0 0 0 # cp 
+64 1 5 0.000000 22.916360855 1.205785036 2.611289978 0 0 0 # c 
+65 1 6 0.000000 21.501018524 0.810333014 3.075165987 0 0 0 # c3 
+66 1 6 0.000000 23.808341980 1.493147969 3.834667921 0 0 0 # c3 
+67 1 4 0.000000 23.514062881 0.070205003 1.817157984 0 0 0 # cp 
+68 1 4 0.000000 22.684833527 -0.782863975 1.085504055 0 0 0 # cp 
+69 1 4 0.000000 23.237234116 -1.833225965 0.349765003 0 0 0 # cp 
+70 1 4 0.000000 24.619955063 -2.031138897 0.346872985 0 0 0 # cp 
+71 1 4 0.000000 25.449554443 -1.179108977 1.077638030 0 0 0 # cp 
+72 1 4 0.000000 24.896312714 -0.128257006 1.813575983 0 0 0 # cp 
+73 1 7 0.000000 22.607131958 5.827101231 -0.602173984 0 0 0 # oc 
+74 1 7 0.000000 25.147769928 -3.035661936 -0.355791986 0 0 0 # oc 
+75 1 8 0.000000 24.221906662 -4.476489067 0.794990003 0 0 0 # hc 
+76 1 8 0.000000 25.849754333 -3.994390965 1.331357956 0 0 0 # hc 
+77 1 8 0.000000 25.097463608 -5.257826805 -1.146129966 0 0 0 # hc 
+78 1 8 0.000000 27.892013550 -5.893630028 -1.196079969 0 0 0 # hc 
+79 1 8 0.000000 27.964216232 -4.855231762 0.319745004 0 0 0 # hc 
+80 1 8 0.000000 20.720872879 8.854673386 -2.520912886 0 0 0 # hc 
+81 1 8 0.000000 19.840383530 7.656352043 -1.438712001 0 0 0 # hc 
+82 1 8 0.000000 23.017726898 8.120765686 -0.970986009 0 0 0 # hc 
+83 1 8 0.000000 22.669095993 7.097908974 1.022259951 0 0 0 # hc 
+84 1 8 0.000000 21.041725159 6.616360188 0.486577004 0 0 0 # hc 
+85 1 8 0.000000 24.650087357 5.183434963 0.894133985 0 0 0 # hc 
+86 1 8 0.000000 24.786277771 3.153367996 2.306194067 0 0 0 # hc 
+87 1 8 0.000000 20.863473892 1.993592978 1.015051961 0 0 0 # hc 
+88 1 8 0.000000 20.727291107 4.023673058 -0.397009999 0 0 0 # hc 
+89 1 8 0.000000 21.558345795 -0.083162002 3.696341038 0 0 0 # hc 
+90 1 8 0.000000 21.065618515 1.626867056 3.651936054 0 0 0 # hc 
+91 1 8 0.000000 20.876825333 0.608124971 2.205033064 0 0 0 # hc 
+92 1 8 0.000000 23.870355606 0.601037025 4.457283974 0 0 0 # hc 
+93 1 8 0.000000 24.807676315 1.770614982 3.498578072 0 0 0 # hc 
+94 1 8 0.000000 23.380037308 2.311306953 4.412462234 0 0 0 # hc 
+95 1 8 0.000000 21.616291046 -0.629218996 1.087699056 0 0 0 # hc 
+96 1 8 0.000000 22.596149445 -2.493021011 -0.215893999 0 0 0 # hc 
+97 1 8 0.000000 26.518102646 -1.332759023 1.075448036 0 0 0 # hc 
+98 1 8 0.000000 25.538236618 0.531040013 2.379035950 0 0 0 # hc 
+99 1 9 0.000000 16.072591782 12.338866234 -0.174325004 0 0 0 # na 
+100 1 1 0.000000 16.557256699 11.130316734 0.587288976 0 0 0 # c2 
+101 1 1 0.000000 18.074571609 10.998808861 0.366084993 0 0 0 # c2 
+102 1 9 -0.025000 18.353967667 10.832372665 -1.107717037 0 0 0 # na 
+103 1 9 -0.025000 14.920715332 15.017822266 -0.200534001 0 0 0 # na 
+104 1 1 0.000000 16.390434265 14.791102409 -0.460442007 0 0 0 # c2 
+105 1 1 0.000000 16.852983475 13.538317680 0.304865986 0 0 0 # c2 
+106 1 10 0.000000 16.263746262 12.190562248 -1.257431984 0 0 0 # hn 
+107 1 8 0.000000 16.025363922 10.195071220 0.210473999 0 0 0 # hc 
+108 1 8 0.000000 16.347120285 11.269214630 1.698830962 0 0 0 # hc 
+109 1 8 0.000000 18.467184067 10.092565536 0.934801996 0 0 0 # hc 
+110 1 8 0.000000 18.592388153 11.941304207 0.744638979 0 0 0 # hc 
+111 1 10 0.000000 17.843862534 9.919928551 -1.479779005 0 0 0 # hn 
+112 1 10 0.000000 19.448190689 10.736482620 -1.267521024 0 0 0 # hn 
+113 1 10 0.000000 14.344121933 14.136246681 -0.550131977 0 0 0 # hn 
+114 1 10 0.000000 14.583471298 15.922760963 -0.747138977 0 0 0 # hn 
+115 1 8 0.000000 16.984062195 15.696007729 -0.102596000 0 0 0 # hc 
+116 1 8 0.000000 16.562423706 14.639820099 -1.577000022 0 0 0 # hc 
+117 1 8 0.000000 16.674821854 13.685671806 1.420761943 0 0 0 # hc 
+118 1 8 0.000000 17.963953018 13.362975121 0.117853999 0 0 0 # hc 
+
+Bonds            
+
+1 1 1 26         
+2 2 1 2         
+3 1 1 27         
+4 3 1 25         
+5 4 2 7         
+6 5 2 3         
+7 6 2 28         
+8 4 3 7         
+9 6 3 29         
+10 6 3 30         
+11 6 4 32         
+12 4 4 8         
+13 5 4 5         
+14 6 4 31         
+15 4 5 8         
+16 2 6 5         
+17 6 5 33         
+18 3 6 24         
+19 1 6 34         
+20 1 6 35         
+21 7 9 14         
+22 7 9 10         
+23 8 9 24         
+24 7 10 11         
+25 9 10 36         
+26 7 11 12         
+27 9 11 37         
+28 7 12 13         
+29 10 12 15         
+30 7 13 14         
+31 9 13 38         
+32 9 14 39         
+33 11 15 16         
+34 11 15 17         
+35 10 18 15         
+36 12 16 40         
+37 12 16 41         
+38 12 16 42         
+39 12 17 43         
+40 12 17 44         
+41 12 17 45         
+42 7 18 23         
+43 7 18 19         
+44 7 19 20         
+45 9 19 46         
+46 7 20 21         
+47 9 20 47         
+48 7 21 22         
+49 8 21 25         
+50 7 22 23         
+51 9 22 48         
+52 9 23 49         
+53 1 50 75         
+54 2 50 51         
+55 1 50 76         
+56 3 50 74         
+57 4 51 56         
+58 5 51 52         
+59 6 51 77         
+60 4 52 56         
+61 6 52 78         
+62 6 52 79         
+63 6 53 81         
+64 4 53 57         
+65 5 53 54         
+66 6 53 80         
+67 4 54 57         
+68 2 55 54         
+69 6 54 82         
+70 3 55 73         
+71 1 55 83         
+72 1 55 84         
+73 7 58 63         
+74 7 58 59         
+75 8 58 73         
+76 7 59 60         
+77 9 59 85         
+78 7 60 61         
+79 9 60 86         
+80 7 61 62         
+81 10 61 64         
+82 7 62 63         
+83 9 62 87         
+84 9 63 88         
+85 11 64 65         
+86 11 64 66         
+87 10 67 64         
+88 12 65 89         
+89 12 65 90         
+90 12 65 91         
+91 12 66 92         
+92 12 66 93         
+93 12 66 94         
+94 7 67 72         
+95 7 67 68         
+96 7 68 69         
+97 9 68 95         
+98 7 69 70         
+99 9 69 96         
+100 7 70 71         
+101 8 70 74         
+102 7 71 72         
+103 9 71 97         
+104 9 72 98         
+105 13 100 99         
+106 13 105 99         
+107 14 99 106         
+108 15 100 101         
+109 1 100 107         
+110 1 100 108         
+111 13 101 102         
+112 1 101 109         
+113 1 101 110         
+114 14 102 111         
+115 14 102 112         
+116 13 104 103         
+117 14 103 113         
+118 14 103 114         
+119 15 104 105         
+120 1 104 115         
+121 1 104 116         
+122 1 105 117         
+123 1 105 118         
+
+Angles            
+
+1 1 2 1 26        
+2 2 26 1 27        
+3 3 25 1 26        
+4 1 2 1 27        
+5 4 2 1 25        
+6 3 25 1 27        
+7 5 1 2 7        
+8 6 1 2 3        
+9 7 1 2 28        
+10 8 3 2 7        
+11 9 7 2 28        
+12 10 3 2 28        
+13 8 2 3 7        
+14 10 2 3 29        
+15 10 2 3 30        
+16 9 7 3 29        
+17 9 7 3 30        
+18 11 29 3 30        
+19 9 8 4 32        
+20 10 5 4 32        
+21 11 32 4 31        
+22 8 5 4 8        
+23 9 8 4 31        
+24 10 5 4 31        
+25 8 4 5 8        
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diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized b/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized
rename to examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized
diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized b/examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized
rename to examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
rename to examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
rename to examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
rename to examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
rename to examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map b/examples/USER/reaction/tiny_nylon/rxn1_stp1_map
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map
rename to examples/USER/reaction/tiny_nylon/rxn1_stp1_map
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template
rename to examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template
rename to examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map b/examples/USER/reaction/tiny_nylon/rxn1_stp2_map
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map
rename to examples/USER/reaction/tiny_nylon/rxn1_stp2_map
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template
rename to examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template
rename to examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template
diff --git a/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data b/examples/USER/reaction/tiny_nylon/tiny_nylon.data
similarity index 100%
rename from examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data
rename to examples/USER/reaction/tiny_nylon/tiny_nylon.data
diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_map b/examples/USER/reaction/tiny_polystyrene/2styrene_map
new file mode 100644
index 0000000000..be2a789671
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/2styrene_map
@@ -0,0 +1,44 @@
+this is a map file
+
+0 edgeIDs
+32 equivalences
+
+BondingIDs
+
+4
+30
+
+Equivalences
+
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+2 2
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diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template b/examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template
new file mode 100644
index 0000000000..c4fa646e9f
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template
@@ -0,0 +1,312 @@
+2styrene_reacted
+
+32 atoms           
+33 bonds           
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diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template b/examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template
new file mode 100644
index 0000000000..fc0a893191
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template
@@ -0,0 +1,284 @@
+2styrene_unreacted
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diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_map b/examples/USER/reaction/tiny_polystyrene/chain_chain_map
new file mode 100644
index 0000000000..5a0fde6742
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/chain_chain_map
@@ -0,0 +1,67 @@
+this is a map file
+
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diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template b/examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template
new file mode 100644
index 0000000000..e01d42b7fb
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template
@@ -0,0 +1,497 @@
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diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_unreacted.data_template b/examples/USER/reaction/tiny_polystyrene/chain_chain_unreacted.data_template
new file mode 100644
index 0000000000..d8e0d977df
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/chain_chain_unreacted.data_template
@@ -0,0 +1,467 @@
+chain_chain_unreacted
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diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_map b/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_map
new file mode 100644
index 0000000000..56808b0962
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_map
@@ -0,0 +1,62 @@
+this is a map file
+
+1 edgeIDs
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+
+EdgeIDs
+
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+
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diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template b/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template
new file mode 100644
index 0000000000..352d88737d
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template
@@ -0,0 +1,451 @@
+chain_plus_styrene_reacted
+
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+13 23.766701 3.658900 -0.952300
+14 21.622700 3.802900 -1.871300
+15 21.672701 4.544900 -1.970300
+16 20.979700 2.979900 -2.165300
+17 13.465800 0.682500 -1.658900
+18 14.397800 1.221500 -1.658900
+19 12.235800 1.392500 -1.658900
+20 12.235800 2.892500 -1.658900
+21 11.005800 0.682500 -1.658900
+22 10.073800 1.221500 -1.658900
+23 11.005800 -0.737500 -1.658900
+24 10.073800 -1.276500 -1.658900
+25 12.235800 -1.447500 -1.658900
+26 12.235800 -2.524500 -1.658900
+27 13.465800 -0.737500 -1.658900
+28 14.397800 -1.276500 -1.658900
+29 13.101800 3.297500 -1.301900
+30 10.957800 3.441500 -2.220900
+31 18.663500 0.855500 -1.372100
+32 19.595501 1.394500 -1.372100
+33 17.433500 1.565500 -1.372100
+34 17.433500 3.065500 -1.372100
+35 16.203501 0.855500 -1.372100
+36 15.271500 1.394500 -1.372100
+37 16.203501 -0.564500 -1.372100
+38 15.271500 -1.103500 -1.372100
+39 17.433500 -1.274500 -1.372100
+40 17.433500 -2.351500 -1.372100
+41 18.663500 -0.564500 -1.372100
+42 19.595501 -1.103500 -1.372100
+43 18.299500 3.470500 -1.015100
+44 16.155500 3.614500 -1.934100
+45 16.205500 4.356500 -2.033100
+46 15.512500 2.791500 -2.228100
+
+Bonds
+
+1 1 1 2
+2 2 1 3
+3 2 1 11
+4 11 3 4
+5 2 3 5
+6 12 13 4
+7 13 4 14
+8 1 5 6
+9 2 5 7
+10 1 7 8
+11 2 7 9
+12 1 9 10
+13 2 9 11
+14 1 11 12
+15 10 15 14
+16 10 16 14
+17 9 14 34
+18 1 17 18
+19 2 17 19
+20 2 17 27
+21 7 19 20
+22 2 19 21
+23 8 29 20
+24 9 30 20
+25 9 44 20
+26 1 21 22
+27 2 21 23
+28 1 23 24
+29 2 23 25
+30 1 25 26
+31 2 25 27
+32 1 27 28
+33 1 31 32
+34 2 31 33
+35 2 31 41
+36 7 33 34
+37 2 33 35
+38 8 43 34
+39 9 44 34
+40 1 35 36
+41 2 35 37
+42 1 37 38
+43 2 37 39
+44 1 39 40
+45 2 39 41
+46 1 41 42
+47 10 45 44
+48 10 46 44
+
+Angles
+
+1 1 3 1 2
+2 1 11 1 2
+3 2 3 1 11
+4 17 1 3 4
+5 2 1 3 5
+6 17 5 3 4
+7 18 3 4 13
+8 19 3 4 14
+9 20 13 4 14
+10 1 3 5 6
+11 2 3 5 7
+12 1 7 5 6
+13 1 5 7 8
+14 2 5 7 9
+15 1 9 7 8
+16 1 7 9 10
+17 2 7 9 11
+18 1 11 9 10
+19 2 1 11 9
+20 1 1 11 12
+21 1 9 11 12
+22 21 15 14 4
+23 21 16 14 4
+24 22 4 14 34
+25 15 15 14 16
+26 14 15 14 34
+27 14 16 14 34
+28 1 19 17 18
+29 1 27 17 18
+30 2 19 17 27
+31 9 17 19 20
+32 2 17 19 21
+33 9 21 19 20
+34 10 19 20 29
+35 11 19 20 30
+36 11 19 20 44
+37 12 29 20 30
+38 12 29 20 44
+39 13 30 20 44
+40 1 19 21 22
+41 2 19 21 23
+42 1 23 21 22
+43 1 21 23 24
+44 2 21 23 25
+45 1 25 23 24
+46 1 23 25 26
+47 2 23 25 27
+48 1 27 25 26
+49 2 17 27 25
+50 1 17 27 28
+51 1 25 27 28
+52 1 33 31 32
+53 1 41 31 32
+54 2 33 31 41
+55 9 31 33 34
+56 2 31 33 35
+57 9 35 33 34
+58 11 33 34 14
+59 12 43 34 14
+60 13 14 34 44
+61 10 33 34 43
+62 11 33 34 44
+63 12 43 34 44
+64 1 33 35 36
+65 2 33 35 37
+66 1 37 35 36
+67 1 35 37 38
+68 2 35 37 39
+69 1 39 37 38
+70 1 37 39 40
+71 2 37 39 41
+72 1 41 39 40
+73 2 31 41 39
+74 1 31 41 42
+75 1 39 41 42
+76 16 20 44 34
+77 14 45 44 20
+78 14 46 44 20
+79 14 45 44 34
+80 14 46 44 34
+81 15 45 44 46
+
+Dihedrals
+
+1 20 2 1 3 4
+2 2 5 3 1 2
+3 21 11 1 3 4
+4 4 11 1 3 5
+5 2 9 11 1 2
+6 5 2 1 11 12
+7 4 3 1 11 9
+8 2 3 1 11 12
+9 22 1 3 4 13
+10 23 1 3 4 14
+11 22 5 3 4 13
+12 23 5 3 4 14
+13 2 1 3 5 6
+14 4 1 3 5 7
+15 20 6 5 3 4
+16 21 7 5 3 4
+17 24 3 4 14 15
+18 24 3 4 14 16
+19 25 3 4 14 34
+20 26 13 4 14 15
+21 26 13 4 14 16
+22 27 13 4 14 34
+23 2 3 5 7 8
+24 4 3 5 7 9
+25 5 6 5 7 8
+26 2 9 7 5 6
+27 2 5 7 9 10
+28 4 5 7 9 11
+29 5 8 7 9 10
+30 2 11 9 7 8
+31 4 7 9 11 1
+32 2 7 9 11 12
+33 2 1 11 9 10
+34 5 10 9 11 12
+35 28 4 14 34 33
+36 29 4 14 34 43
+37 30 4 14 34 44
+38 31 15 14 34 33
+39 32 15 14 34 43
+40 33 15 14 34 44
+41 31 16 14 34 33
+42 32 16 14 34 43
+43 33 16 14 34 44
+44 10 18 17 19 20
+45 2 21 19 17 18
+46 11 27 17 19 20
+47 4 27 17 19 21
+48 2 25 27 17 18
+49 5 18 17 27 28
+50 4 19 17 27 25
+51 2 19 17 27 28
+52 12 17 19 20 29
+53 13 17 19 20 30
+54 13 17 19 20 44
+55 12 21 19 20 29
+56 13 21 19 20 30
+57 13 21 19 20 44
+58 2 17 19 21 22
+59 4 17 19 21 23
+60 10 22 21 19 20
+61 11 23 21 19 20
+62 34 34 44 20 19
+63 31 45 44 20 19
+64 31 46 44 20 19
+65 35 34 44 20 29
+66 32 45 44 20 29
+67 32 46 44 20 29
+68 36 34 44 20 30
+69 33 45 44 20 30
+70 33 46 44 20 30
+71 2 19 21 23 24
+72 4 19 21 23 25
+73 5 22 21 23 24
+74 2 25 23 21 22
+75 2 21 23 25 26
+76 4 21 23 25 27
+77 5 24 23 25 26
+78 2 27 25 23 24
+79 4 23 25 27 17
+80 2 23 25 27 28
+81 2 17 27 25 26
+82 5 26 25 27 28
+83 10 32 31 33 34
+84 2 35 33 31 32
+85 11 41 31 33 34
+86 4 41 31 33 35
+87 2 39 41 31 32
+88 5 32 31 41 42
+89 4 33 31 41 39
+90 2 33 31 41 42
+91 13 31 33 34 14
+92 12 31 33 34 43
+93 13 31 33 34 44
+94 13 35 33 34 14
+95 12 35 33 34 43
+96 13 35 33 34 44
+97 2 31 33 35 36
+98 4 31 33 35 37
+99 10 36 35 33 34
+100 11 37 35 33 34
+101 36 20 44 34 14
+102 33 45 44 34 14
+103 33 46 44 34 14
+104 34 20 44 34 33
+105 31 45 44 34 33
+106 31 46 44 34 33
+107 35 20 44 34 43
+108 32 45 44 34 43
+109 32 46 44 34 43
+110 2 33 35 37 38
+111 4 33 35 37 39
+112 5 36 35 37 38
+113 2 39 37 35 36
+114 2 35 37 39 40
+115 4 35 37 39 41
+116 5 38 37 39 40
+117 2 41 39 37 38
+118 4 37 39 41 31
+119 2 37 39 41 42
+120 2 31 41 39 40
+121 5 40 39 41 42
+
+Impropers
+
+1 1 3 1 11 2
+2 8 1 3 5 4
+3 9 3 4 13 14
+4 1 3 5 7 6
+5 1 5 7 9 8
+6 1 7 9 11 10
+7 1 1 11 9 12
+8 1 19 17 27 18
+9 5 17 19 21 20
+10 1 19 21 23 22
+11 1 21 23 25 24
+12 1 23 25 27 26
+13 1 17 27 25 28
+14 1 33 31 41 32
+15 5 31 33 35 34
+16 1 33 35 37 36
+17 1 35 37 39 38
+18 1 37 39 41 40
+19 1 31 41 39 42
+20 1 15 14 16 4
+21 1 15 14 4 34
+22 1 16 14 4 34
+23 1 15 14 16 34
+24 1 19 20 29 30
+25 1 19 20 29 44
+26 1 19 20 30 44
+27 1 29 20 30 44
+28 1 33 34 43 14
+29 1 33 34 14 44
+30 1 43 34 14 44
+31 1 33 34 43 44
+32 1 45 44 34 20
+33 1 46 44 34 20
+34 1 45 44 46 20
+35 1 45 44 46 34
diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template b/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template
new file mode 100644
index 0000000000..f76aad50e6
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template
@@ -0,0 +1,422 @@
+chain_plus_styrene_unreacted
+
+46 atoms           
+47 bonds           
+75 angles           
+105 dihedrals           
+29 impropers           
+
+Types
+
+1 1
+2 2
+3 1
+4 3
+5 1
+6 2
+7 1
+8 2
+9 1
+10 2
+11 1
+12 2
+13 2
+14 4
+15 2
+16 2
+17 1
+18 2
+19 1
+20 5
+21 1
+22 2
+23 1
+24 2
+25 1
+26 2
+27 1
+28 2
+29 2
+30 6
+31 1
+32 2
+33 1
+34 5
+35 1
+36 2
+37 1
+38 2
+39 1
+40 2
+41 1
+42 2
+43 2
+44 6
+45 2
+46 2
+
+Charges
+
+1 -0.129000
+2 0.123700
+3 0.026600
+4 -0.018200
+5 -0.129000
+6 0.123700
+7 -0.173400
+8 0.140300
+9 -0.113400
+10 0.128800
+11 -0.173400
+12 0.140300
+13 0.051600
+14 -0.069600
+15 0.035400
+16 0.035400
+17 -0.129000
+18 0.123700
+19 0.026600
+20 -0.018200
+21 -0.129000
+22 0.123700
+23 -0.173400
+24 0.140300
+25 -0.113400
+26 0.128800
+27 -0.173400
+28 0.140300
+29 0.051600
+30 -0.069600
+31 -0.129000
+32 0.123700
+33 0.026600
+34 -0.018200
+35 -0.129000
+36 0.123700
+37 -0.173400
+38 0.140300
+39 -0.113400
+40 0.128800
+41 -0.173400
+42 0.140300
+43 0.051600
+44 -0.069600
+45 0.035400
+46 0.035400
+
+Coords
+
+1 24.130699 1.043900 -1.309300
+2 25.062700 1.582900 -1.309300
+3 22.900700 1.753900 -1.309300
+4 22.900700 3.253900 -1.309300
+5 21.670700 1.043900 -1.309300
+6 20.738701 1.582900 -1.309300
+7 21.670700 -0.376100 -1.309300
+8 20.738701 -0.915100 -1.309300
+9 22.900700 -1.086100 -1.309300
+10 22.900700 -2.163100 -1.309300
+11 24.130699 -0.376100 -1.309300
+12 25.062700 -0.915100 -1.309300
+13 23.766701 3.658900 -0.952300
+14 21.622700 3.802900 -1.871300
+15 21.672701 4.544900 -1.970300
+16 20.979700 2.979900 -2.165300
+17 13.465800 0.682500 -1.658900
+18 14.397800 1.221500 -1.658900
+19 12.235800 1.392500 -1.658900
+20 12.235800 2.892500 -1.658900
+21 11.005800 0.682500 -1.658900
+22 10.073800 1.221500 -1.658900
+23 11.005800 -0.737500 -1.658900
+24 10.073800 -1.276500 -1.658900
+25 12.235800 -1.447500 -1.658900
+26 12.235800 -2.524500 -1.658900
+27 13.465800 -0.737500 -1.658900
+28 14.397800 -1.276500 -1.658900
+29 13.101800 3.297500 -1.301900
+30 10.957800 3.441500 -2.220900
+31 18.663500 0.855500 -1.372100
+32 19.595501 1.394500 -1.372100
+33 17.433500 1.565500 -1.372100
+34 17.433500 3.065500 -1.372100
+35 16.203501 0.855500 -1.372100
+36 15.271500 1.394500 -1.372100
+37 16.203501 -0.564500 -1.372100
+38 15.271500 -1.103500 -1.372100
+39 17.433500 -1.274500 -1.372100
+40 17.433500 -2.351500 -1.372100
+41 18.663500 -0.564500 -1.372100
+42 19.595501 -1.103500 -1.372100
+43 18.299500 3.470500 -1.015100
+44 16.155500 3.614500 -1.934100
+45 16.205500 4.356500 -2.033100
+46 15.512500 2.791500 -2.228100
+
+Bonds
+
+1 1 1 2
+2 2 1 3
+3 2 1 11
+4 3 3 4
+5 2 3 5
+6 4 13 4
+7 5 4 14
+8 1 5 6
+9 2 5 7
+10 1 7 8
+11 2 7 9
+12 1 9 10
+13 2 9 11
+14 1 11 12
+15 6 15 14
+16 6 16 14
+17 1 17 18
+18 2 17 19
+19 2 17 27
+20 7 19 20
+21 2 19 21
+22 8 29 20
+23 9 20 30
+24 9 20 44
+25 1 21 22
+26 2 21 23
+27 1 23 24
+28 2 23 25
+29 1 25 26
+30 2 25 27
+31 1 27 28
+32 1 31 32
+33 2 31 33
+34 2 31 41
+35 7 33 34
+36 2 33 35
+37 8 43 34
+38 9 34 44
+39 1 35 36
+40 2 35 37
+41 1 37 38
+42 2 37 39
+43 1 39 40
+44 2 39 41
+45 1 41 42
+46 10 45 44
+47 10 46 44
+
+Angles
+
+1 1 3 1 2
+2 1 11 1 2
+3 2 3 1 11
+4 3 1 3 4
+5 2 1 3 5
+6 3 5 3 4
+7 4 3 4 13
+8 5 3 4 14
+9 6 13 4 14
+10 1 3 5 6
+11 2 3 5 7
+12 1 7 5 6
+13 1 5 7 8
+14 2 5 7 9
+15 1 9 7 8
+16 1 7 9 10
+17 2 7 9 11
+18 1 11 9 10
+19 2 1 11 9
+20 1 1 11 12
+21 1 9 11 12
+22 7 15 14 4
+23 7 16 14 4
+24 8 15 14 16
+25 1 19 17 18
+26 1 27 17 18
+27 2 19 17 27
+28 9 17 19 20
+29 2 17 19 21
+30 9 21 19 20
+31 10 19 20 29
+32 11 19 20 30
+33 11 19 20 44
+34 12 29 20 30
+35 12 29 20 44
+36 13 30 20 44
+37 1 19 21 22
+38 2 19 21 23
+39 1 23 21 22
+40 1 21 23 24
+41 2 21 23 25
+42 1 25 23 24
+43 1 23 25 26
+44 2 23 25 27
+45 1 27 25 26
+46 2 17 27 25
+47 1 17 27 28
+48 1 25 27 28
+49 1 33 31 32
+50 1 41 31 32
+51 2 33 31 41
+52 9 31 33 34
+53 2 31 33 35
+54 9 35 33 34
+55 10 33 34 43
+56 11 33 34 44
+57 12 43 34 44
+58 1 33 35 36
+59 2 33 35 37
+60 1 37 35 36
+61 1 35 37 38
+62 2 35 37 39
+63 1 39 37 38
+64 1 37 39 40
+65 2 37 39 41
+66 1 41 39 40
+67 2 31 41 39
+68 1 31 41 42
+69 1 39 41 42
+70 16 20 44 34
+71 14 45 44 20
+72 14 46 44 20
+73 14 45 44 34
+74 14 46 44 34
+75 15 45 44 46
+
+Dihedrals
+
+1 1 2 1 3 4
+2 2 5 3 1 2
+3 3 11 1 3 4
+4 4 11 1 3 5
+5 2 9 11 1 2
+6 5 2 1 11 12
+7 4 3 1 11 9
+8 2 3 1 11 12
+9 6 1 3 4 13
+10 7 1 3 4 14
+11 6 5 3 4 13
+12 7 5 3 4 14
+13 2 1 3 5 6
+14 4 1 3 5 7
+15 1 6 5 3 4
+16 3 7 5 3 4
+17 8 3 4 14 15
+18 8 3 4 14 16
+19 9 13 4 14 15
+20 9 13 4 14 16
+21 2 3 5 7 8
+22 4 3 5 7 9
+23 5 6 5 7 8
+24 2 9 7 5 6
+25 2 5 7 9 10
+26 4 5 7 9 11
+27 5 8 7 9 10
+28 2 11 9 7 8
+29 4 7 9 11 1
+30 2 7 9 11 12
+31 2 1 11 9 10
+32 5 10 9 11 12
+33 10 18 17 19 20
+34 2 21 19 17 18
+35 11 27 17 19 20
+36 4 27 17 19 21
+37 2 25 27 17 18
+38 5 18 17 27 28
+39 4 19 17 27 25
+40 2 19 17 27 28
+41 12 17 19 20 29
+42 13 17 19 20 30
+43 13 17 19 20 44
+44 12 21 19 20 29
+45 13 21 19 20 30
+46 13 21 19 20 44
+47 2 17 19 21 22
+48 4 17 19 21 23
+49 10 22 21 19 20
+50 11 23 21 19 20
+51 17 19 20 44 34
+52 14 19 20 44 45
+53 14 19 20 44 46
+54 18 29 20 44 34
+55 15 29 20 44 45
+56 15 29 20 44 46
+57 19 30 20 44 34
+58 16 30 20 44 45
+59 16 30 20 44 46
+60 2 19 21 23 24
+61 4 19 21 23 25
+62 5 22 21 23 24
+63 2 25 23 21 22
+64 2 21 23 25 26
+65 4 21 23 25 27
+66 5 24 23 25 26
+67 2 27 25 23 24
+68 4 23 25 27 17
+69 2 23 25 27 28
+70 2 17 27 25 26
+71 5 26 25 27 28
+72 10 32 31 33 34
+73 2 35 33 31 32
+74 11 41 31 33 34
+75 4 41 31 33 35
+76 2 39 41 31 32
+77 5 32 31 41 42
+78 4 33 31 41 39
+79 2 33 31 41 42
+80 12 31 33 34 43
+81 13 31 33 34 44
+82 12 35 33 34 43
+83 13 35 33 34 44
+84 2 31 33 35 36
+85 4 31 33 35 37
+86 10 36 35 33 34
+87 11 37 35 33 34
+88 17 33 34 44 20
+89 14 33 34 44 45
+90 14 33 34 44 46
+91 18 43 34 44 20
+92 15 43 34 44 45
+93 15 43 34 44 46
+94 2 33 35 37 38
+95 4 33 35 37 39
+96 5 36 35 37 38
+97 2 39 37 35 36
+98 2 35 37 39 40
+99 4 35 37 39 41
+100 5 38 37 39 40
+101 2 41 39 37 38
+102 4 37 39 41 31
+103 2 37 39 41 42
+104 2 31 41 39 40
+105 5 40 39 41 42
+
+Impropers
+
+1 1 3 1 11 2
+2 2 1 3 5 4
+3 3 3 4 13 14
+4 1 3 5 7 6
+5 1 5 7 9 8
+6 1 7 9 11 10
+7 1 1 11 9 12
+8 4 15 14 16 4
+9 1 19 17 27 18
+10 5 17 19 21 20
+11 1 19 21 23 22
+12 1 21 23 25 24
+13 1 23 25 27 26
+14 1 17 27 25 28
+15 1 33 31 41 32
+16 5 31 33 35 34
+17 7 33 34 43 44
+18 1 33 35 37 36
+19 1 35 37 39 38
+20 1 37 39 41 40
+21 1 31 41 39 42
+22 1 19 20 29 30
+23 1 19 20 29 44
+24 1 19 20 30 44
+25 1 29 20 30 44
+26 1 45 44 34 20
+27 1 46 44 34 20
+28 1 45 44 46 20
+29 1 45 44 46 34
diff --git a/examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized
new file mode 100644
index 0000000000..a711f3eaa9
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized
@@ -0,0 +1,56 @@
+# 20 styrene molecules
+# three reactions defined  
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2 
+
+bond_style class2 
+
+dihedral_style class2
+
+improper_style class2
+
+variable T equal 530
+
+read_data tiny_polystyrene.data  &
+  extra/bond/per/atom 5 &
+  extra/angle/per/atom 15 &
+  extra/dihedral/per/atom 15 &
+  extra/improper/per/atom 25 &
+  extra/special/per/atom 25
+
+molecule mol1 2styrene_unreacted.data_template
+molecule mol2 2styrene_reacted.data_template
+molecule mol3 chain_plus_styrene_unreacted.data_template
+molecule mol4 chain_plus_styrene_reacted.data_template
+molecule mol5 chain_chain_unreacted.data_template
+molecule mol6 chain_chain_reacted.data_template
+
+thermo 100
+
+# dump 1 all xyz 5 test_vis.xyz
+
+fix rxn1 all bond/react stabilization yes statted_grp .03 &
+ react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 &
+ react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 &
+ react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100
+
+fix 1 statted_grp_REACT nvt temp $T $T 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
+
+thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]
+
+run 10000
+
+# write_restart restart_longrun nofix
+# write_data restart_longrun.data 
diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 b/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1
new file mode 100644
index 0000000000..274c72ece9
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1
@@ -0,0 +1,245 @@
+LAMMPS (20 Nov 2019)
+
+WARNING-WARNING-WARNING-WARNING-WARNING
+This LAMMPS executable was compiled using C++98 compatibility.
+Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
+GNU C++ 4.8.5
+WARNING-WARNING-WARNING-WARNING-WARNING
+
+Reading data file ...
+  orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  320 atoms
+  reading velocities ...
+  320 velocities
+  scanning bonds ...
+  8 = max bonds/atom
+  scanning angles ...
+  18 = max angles/atom
+  scanning dihedrals ...
+  22 = max dihedrals/atom
+  scanning impropers ...
+  26 = max impropers/atom
+  reading bonds ...
+  320 bonds
+  reading angles ...
+  480 angles
+  reading dihedrals ...
+  640 dihedrals
+  reading impropers ...
+  160 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  3 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  39 = max # of special neighbors
+  special bonds CPU = 0.000929056 secs
+  read_data CPU = 0.00930568 secs
+Read molecule mol1:
+  32 atoms with max type 4
+  32 bonds with max type 6
+  48 angles with max type 8
+  64 dihedrals with max type 9
+  16 impropers with max type 4
+Read molecule mol2:
+  32 atoms with max type 6
+  33 bonds with max type 10
+  54 angles with max type 16
+  79 dihedrals with max type 19
+  22 impropers with max type 7
+Read molecule mol3:
+  46 atoms with max type 6
+  47 bonds with max type 10
+  75 angles with max type 16
+  105 dihedrals with max type 19
+  29 impropers with max type 7
+Read molecule mol4:
+  46 atoms with max type 6
+  48 bonds with max type 13
+  81 angles with max type 22
+  121 dihedrals with max type 36
+  35 impropers with max type 9
+Read molecule mol5:
+  50 atoms with max type 6
+  51 bonds with max type 10
+  84 angles with max type 16
+  118 dihedrals with max type 19
+  36 impropers with max type 7
+Read molecule mol6:
+  50 atoms with max type 6
+  52 bonds with max type 10
+  90 angles with max type 16
+  135 dihedrals with max type 19
+  42 impropers with max type 5
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304)
+  using 12-bit tables for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.255611
+  grid = 6 6 6
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00974692
+  estimated relative force accuracy = 2.93525e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 1331 216
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 4 4 4
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 31.14 | 31.14 | 31.14 Mbytes
+Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3] 
+       0    320.13638    -376.0844   0.76796752            0            0            0 
+     100    520.00782    3952.7008   0.76796752            8            0            0 
+     200     499.9174    2360.8219   0.76796752            8            3            1 
+     300    583.93895    2453.7374   0.76796752            8            3            2 
+     400    560.65536   -2243.3464   0.76796752            8            3            3 
+     500    556.27995    3598.7044   0.76796752            8            3            3 
+     600     570.8397   -3340.1826   0.76796752            8            4            4 
+     700    456.89894   -1087.8081   0.76796752            8            4            4 
+     800    572.91817   -776.19188   0.76796752            8            4            4 
+     900    530.13621   -246734.46   0.76796752            8            4            5 
+    1000    542.34698    1044.0793   0.76796752            8            4            5 
+    1100    562.86339    1207.1715   0.76796752            8            4            5 
+    1200     520.1559    2725.6523   0.76796752            8            4            5 
+    1300    534.01667     951.0972   0.76796752            8            4            5 
+    1400    478.68681    1184.9224   0.76796752            8            4            5 
+    1500    509.05445    2020.5224   0.76796752            8            4            5 
+    1600     549.5382    810.17577   0.76796752            8            4            5 
+    1700    549.46882   -6349.7751   0.76796752            8            4            5 
+    1800    496.77334    3953.1043   0.76796752            8            4            5 
+    1900    522.28719   -2271.7599   0.76796752            8            4            6 
+    2000    569.95975    5633.4352   0.76796752            8            4            6 
+    2100     590.8418    2355.8447   0.76796752            8            4            6 
+    2200    537.64787    6459.6743   0.76796752            8            4            6 
+    2300    548.38487   -1566.3528   0.76796752            8            4            6 
+    2400    533.50353     6755.664   0.76796752            8            4            6 
+    2500    512.57053    325.30968   0.76796752            8            4            6 
+    2600     498.4597   -2468.1165   0.76796752            8            4            6 
+    2700    559.03937    2428.3446   0.76796752            8            4            6 
+    2800    585.85721   -2896.3607   0.76796752            8            4            6 
+    2900    523.18635     1391.254   0.76796752            8            4            6 
+    3000    524.62076    375.02973   0.76796752            8            4            6 
+    3100    534.65688   -1522.7879   0.76796752            8            4            6 
+    3200    499.42665    3725.5476   0.76796752            8            4            6 
+    3300    514.36972    1725.8329   0.76796752            8            4            6 
+    3400    482.52662    4648.5013   0.76796752            8            4            6 
+    3500    495.36836     967.3482   0.76796752            8            4            6 
+    3600    583.28736    745.21794   0.76796752            8            4            6 
+    3700    531.99717   -804.39572   0.76796752            8            4            6 
+    3800    555.08359    -2381.363   0.76796752            8            4            6 
+    3900     520.1818   -547.34169   0.76796752            8            4            6 
+    4000    444.38804   -2488.7881   0.76796752            8            4            6 
+    4100    518.65622   -3135.9573   0.76796752            8            4            6 
+    4200    484.15227   -1040.2447   0.76796752            8            4            6 
+    4300    514.58006    550.14626   0.76796752            8            4            6 
+    4400    579.81405   -849.81454   0.76796752            8            4            6 
+    4500     522.8698     5222.654   0.76796752            8            4            6 
+    4600    490.78275    3251.2892   0.76796752            8            4            6 
+    4700    492.64299    3785.3482   0.76796752            8            4            6 
+    4800    500.11059    4441.8978   0.76796752            8            4            6 
+    4900    536.80009    965.33724   0.76796752            8            4            6 
+    5000    516.98575   -3794.4213   0.76796752            8            4            6 
+    5100    516.76648   -3593.9106   0.76796752            8            4            6 
+    5200     521.6379   -6532.7773   0.76796752            8            4            6 
+    5300    535.64798     2931.412   0.76796752            8            4            6 
+    5400    559.83266    7628.1659   0.76796752            8            4            6 
+    5500    538.91756    2841.6746   0.76796752            8            4            6 
+    5600    539.13999    10445.173   0.76796752            8            4            6 
+    5700    501.56603   -2106.3309   0.76796752            8            4            6 
+    5800    496.72952   -4831.0565   0.76796752            8            4            6 
+    5900    536.12979   -3916.8197   0.76796752            8            4            6 
+    6000    553.10092    3142.6871   0.76796752            8            4            6 
+    6100    558.09546     3154.584   0.76796752            8            4            6 
+    6200    523.48472    9807.0034   0.76796752            8            4            6 
+    6300    551.80343   -3608.2078   0.76796752            8            4            6 
+    6400    484.28359    2255.4675   0.76796752            8            4            6 
+    6500    560.68443   -4826.4868   0.76796752            8            4            6 
+    6600    604.50797    402.32183   0.76796752            8            4            6 
+    6700    538.84714   -7670.3312   0.76796752            8            4            6 
+    6800    528.82853   -380.32058   0.76796752            8            4            6 
+    6900    579.30919    4438.4574   0.76796752            8            4            6 
+    7000     540.3406    3738.0524   0.76796752            8            4            6 
+    7100    519.53645   -1825.5563   0.76796752            8            4            6 
+    7200      474.136    1657.3863   0.76796752            8            4            6 
+    7300    485.55159   -221.84939   0.76796752            8            4            6 
+    7400    527.38494    1037.1777   0.76796752            8            4            6 
+    7500    517.14767   -2313.5823   0.76796752            8            4            6 
+    7600    517.95967   -4763.4709   0.76796752            8            4            6 
+    7700    513.63507    4819.0253   0.76796752            8            4            6 
+    7800    503.56828    1295.1212   0.76796752            8            4            6 
+    7900    520.87804    1506.9417   0.76796752            8            4            6 
+    8000    509.46453   -5800.0971   0.76796752            8            4            6 
+    8100    566.67059    6065.4607   0.76796752            8            4            6 
+    8200    592.53068    1097.2277   0.76796752            8            4            6 
+    8300    529.55235   -580.81757   0.76796752            8            4            6 
+    8400    518.22587    560.45589   0.76796752            8            4            6 
+    8500    521.94561    5325.9459   0.76796752            8            4            6 
+    8600    510.54416   -1929.1967   0.76796752            8            4            6 
+    8700    562.71252   -629.90392   0.76796752            8            4            6 
+    8800    540.23123   -3484.3893   0.76796752            8            4            6 
+    8900    513.82411    -5227.152   0.76796752            8            4            6 
+    9000     534.3307    -3299.088   0.76796752            8            4            6 
+    9100    509.24467   -5676.2775   0.76796752            8            4            6 
+    9200     506.3216   -7043.8493   0.76796752            8            4            7 
+    9300    480.37682    2380.4696   0.76796752            8            4            7 
+    9400    546.15532    1831.0103   0.76796752            8            4            7 
+    9500    567.18341    3839.9843   0.76796752            8            4            7 
+    9600    536.14883    4258.5304   0.76796752            8            4            7 
+    9700    496.04153    3321.3561   0.76796752            8            4            7 
+    9800    531.78927    3124.9156   0.76796752            8            4            7 
+    9900    530.91395    38.987859   0.76796752            8            4            7 
+   10000    551.22761    1027.5706   0.76796752            8            4            7 
+Loop time of 57.7096 on 1 procs for 10000 steps with 320 atoms
+
+Performance: 14.972 ns/day, 1.603 hours/ns, 173.281 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    | 11.621     | 11.621     | 11.621     |   0.0 | 20.14
+Bond    | 11.151     | 11.151     | 11.151     |   0.0 | 19.32
+Kspace  | 2.2403     | 2.2403     | 2.2403     |   0.0 |  3.88
+Neigh   | 25.467     | 25.467     | 25.467     |   0.0 | 44.13
+Comm    | 0.90467    | 0.90467    | 0.90467    |   0.0 |  1.57
+Output  | 0.0017984  | 0.0017984  | 0.0017984  |   0.0 |  0.00
+Modify  | 6.2622     | 6.2622     | 6.2622     |   0.0 | 10.85
+Other   |            | 0.06192    |            |       |  0.11
+
+Nlocal:    320 ave 320 max 320 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    3240 ave 3240 max 3240 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    54336 ave 54336 max 54336 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 54336
+Ave neighs/atom = 169.8
+Ave special neighs/atom = 11.3063
+Neighbor list builds = 10000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:58
diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 b/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4
new file mode 100644
index 0000000000..29aae1cd0b
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4
@@ -0,0 +1,255 @@
+LAMMPS (20 Nov 2019)
+
+WARNING-WARNING-WARNING-WARNING-WARNING
+This LAMMPS executable was compiled using C++98 compatibility.
+Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
+GNU C++ 4.8.5
+WARNING-WARNING-WARNING-WARNING-WARNING
+
+Reading data file ...
+  orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  320 atoms
+  reading velocities ...
+  320 velocities
+  scanning bonds ...
+  8 = max bonds/atom
+  scanning angles ...
+  18 = max angles/atom
+  scanning dihedrals ...
+  22 = max dihedrals/atom
+  scanning impropers ...
+  26 = max impropers/atom
+  reading bonds ...
+  320 bonds
+  reading angles ...
+  480 angles
+  reading dihedrals ...
+  640 dihedrals
+  reading impropers ...
+  160 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  3 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  39 = max # of special neighbors
+  special bonds CPU = 0.000751222 secs
+  read_data CPU = 0.0268223 secs
+Read molecule mol1:
+  32 atoms with max type 4
+  32 bonds with max type 6
+  48 angles with max type 8
+  64 dihedrals with max type 9
+  16 impropers with max type 4
+Read molecule mol2:
+  32 atoms with max type 6
+  33 bonds with max type 10
+  54 angles with max type 16
+  79 dihedrals with max type 19
+  22 impropers with max type 7
+Read molecule mol3:
+  46 atoms with max type 6
+  47 bonds with max type 10
+  75 angles with max type 16
+  105 dihedrals with max type 19
+  29 impropers with max type 7
+Read molecule mol4:
+  46 atoms with max type 6
+  48 bonds with max type 13
+  81 angles with max type 22
+  121 dihedrals with max type 36
+  35 impropers with max type 9
+Read molecule mol5:
+  50 atoms with max type 6
+  51 bonds with max type 10
+  84 angles with max type 16
+  118 dihedrals with max type 19
+  36 impropers with max type 7
+Read molecule mol6:
+  50 atoms with max type 6
+  52 bonds with max type 10
+  90 angles with max type 16
+  135 dihedrals with max type 19
+  42 impropers with max type 5
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304)
+  using 12-bit tables for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.255611
+  grid = 6 6 6
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00974692
+  estimated relative force accuracy = 2.93525e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 704 72
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 4 4 4
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 30.66 | 30.68 | 30.69 Mbytes
+Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3] 
+       0    320.13638    -376.0844   0.76796752            0            0            0 
+     100    522.71544    6623.0579   0.76796752            8            0            0 
+     200    500.86716   -9439.5519   0.76796752            8            3            2 
+     300    594.60588    6714.1323   0.76796752            8            3            3 
+     400    598.68768    683.70457   0.76796752            8            3            3 
+     500     563.1011    3576.6857   0.76796752            8            3            4 
+     600    510.29713   -196148.37   0.76796752            8            3            5 
+     700    494.14346   -118517.45   0.76796752            8            3            6 
+     800    565.62849    7678.1235   0.76796752            8            3            6 
+     900    515.74468    554.84571   0.76796752            8            3            6 
+    1000    500.64636    450.15932   0.76796752            8            3            6 
+    1100    463.34973    6023.8346   0.76796752            8            3            6 
+    1200    529.88483     2748.185   0.76796752            8            3            6 
+    1300    546.84049    1353.4891   0.76796752            8            3            6 
+    1400    552.27356    1446.5807   0.76796752            8            3            6 
+    1500    557.70874   -2745.1523   0.76796752            8            3            6 
+    1600     572.0005    629.36722   0.76796752            8            3            6 
+    1700    503.96569    5937.0231   0.76796752            8            3            6 
+    1800    491.34262   -1175.8104   0.76796752            8            3            6 
+    1900    538.24798   -81.197397   0.76796752            8            3            6 
+    2000    523.89324    2857.2466   0.76796752            8            3            6 
+    2100     515.1424    2288.2405   0.76796752            8            3            6 
+    2200    546.80854    3807.1038   0.76796752            8            3            6 
+    2300    500.31231   -135.33933   0.76796752            8            4            6 
+    2400    497.16354     5516.857   0.76796752            8            4            6 
+    2500    545.34187    3485.5645   0.76796752            8            4            6 
+    2600    522.70122    3114.1284   0.76796752            8            4            6 
+    2700    531.76604    6633.5518   0.76796752            8            4            6 
+    2800    521.97643   -279.83682   0.76796752            8            4            6 
+    2900    497.29575    7052.9409   0.76796752            8            4            6 
+    3000     524.5942    2284.8918   0.76796752            8            4            6 
+    3100    567.61329   -3667.4557   0.76796752            8            4            6 
+    3200    506.82452   -2934.4936   0.76796752            8            4            6 
+    3300     510.8521    313.36263   0.76796752            8            4            6 
+    3400    516.70206    3671.1899   0.76796752            8            4            6 
+    3500    535.12788    2645.2564   0.76796752            8            4            6 
+    3600    580.14214    2604.3079   0.76796752            8            4            6 
+    3700    529.77869    2684.0812   0.76796752            8            4            6 
+    3800    502.93191    2838.6698   0.76796752            8            4            6 
+    3900    585.91492    5308.0828   0.76796752            8            4            6 
+    4000    548.89917    5262.5775   0.76796752            8            4            6 
+    4100     550.7662   -1066.6807   0.76796752            8            4            6 
+    4200    519.19198    2777.5276   0.76796752            8            4            6 
+    4300    521.46332   -3429.7171   0.76796752            8            4            6 
+    4400    532.64173    2301.3135   0.76796752            8            4            6 
+    4500    528.96107    1369.0991   0.76796752            8            4            6 
+    4600    564.66443    9687.2531   0.76796752            8            4            6 
+    4700    558.49446    2322.6085   0.76796752            8            4            6 
+    4800    497.78614   -442.45053   0.76796752            8            4            6 
+    4900    511.09435   -10251.159   0.76796752            8            4            6 
+    5000     525.6642   -1202.0584   0.76796752            8            4            6 
+    5100    521.76974    1821.7811   0.76796752            8            4            6 
+    5200     555.9859    7256.9632   0.76796752            8            4            6 
+    5300    551.51971   -122893.16   0.76796752            8            4            7 
+    5400    524.34705    2905.1033   0.76796752            8            4            7 
+    5500    567.09396    2896.4824   0.76796752            8            4            7 
+    5600    487.57746    1417.1715   0.76796752            8            4            7 
+    5700    547.37304    3900.8734   0.76796752            8            4            7 
+    5800    536.17647   -4048.7522   0.76796752            8            4            7 
+    5900    536.85051    4497.9847   0.76796752            8            4            7 
+    6000    548.58212   -4880.4979   0.76796752            8            4            7 
+    6100    500.94692    6004.2105   0.76796752            8            4            7 
+    6200    486.82494     402.5875   0.76796752            8            4            7 
+    6300    478.09381     6600.767   0.76796752            8            4            7 
+    6400    559.90398    2868.0805   0.76796752            8            4            7 
+    6500    526.01866   -3398.4788   0.76796752            8            4            7 
+    6600    539.68471   -1202.0012   0.76796752            8            4            7 
+    6700    507.51217   -378.71164   0.76796752            8            4            7 
+    6800    526.15958   -4536.9888   0.76796752            8            4            7 
+    6900    511.37134   -2522.3553   0.76796752            8            4            7 
+    7000    538.86918   -2028.0323   0.76796752            8            4            7 
+    7100    523.25566    2911.9962   0.76796752            8            4            7 
+    7200    513.28464   -1000.4758   0.76796752            8            4            7 
+    7300    510.19826    5181.7976   0.76796752            8            4            7 
+    7400    493.46528   -1166.3996   0.76796752            8            4            7 
+    7500    491.51305    5669.2213   0.76796752            8            4            7 
+    7600    506.72032    -2840.301   0.76796752            8            4            7 
+    7700     513.4319    2802.1719   0.76796752            8            4            7 
+    7800     543.7658   -7477.3623   0.76796752            8            4            7 
+    7900    527.35619   -3182.3155   0.76796752            8            4            7 
+    8000    533.50993    613.16561   0.76796752            8            4            7 
+    8100    512.44958   -5037.3414   0.76796752            8            4            7 
+    8200    494.88981    1799.3513   0.76796752            8            4            7 
+    8300    554.81474   -2436.0507   0.76796752            8            4            7 
+    8400    523.22917    364.30593   0.76796752            8            4            7 
+    8500    515.12395    525.24581   0.76796752            8            4            7 
+    8600     511.6321   -1679.8669   0.76796752            8            4            7 
+    8700     531.6327   -1168.1215   0.76796752            8            4            7 
+    8800    548.14438   -5222.7573   0.76796752            8            4            7 
+    8900    517.72579    2073.9695   0.76796752            8            4            7 
+    9000    543.11894   -5307.0759   0.76796752            8            4            7 
+    9100    521.13747   -5546.8552   0.76796752            8            4            7 
+    9200    509.66142    -1584.019   0.76796752            8            4            7 
+    9300    488.73821   -277.85847   0.76796752            8            4            7 
+    9400    513.67282    989.60653   0.76796752            8            4            7 
+    9500    509.98833   -1754.8786   0.76796752            8            4            7 
+    9600    558.72497    5616.6969   0.76796752            8            4            7 
+    9700    533.74988    811.48871   0.76796752            8            4            7 
+    9800    510.94641   -3136.5876   0.76796752            8            4            7 
+    9900    517.80127   -1962.0837   0.76796752            8            4            7 
+   10000    477.50428   -3768.1653   0.76796752            8            4            7 
+Loop time of 20.9963 on 4 procs for 10000 steps with 320 atoms
+
+Performance: 41.150 ns/day, 0.583 hours/ns, 476.276 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.4968     | 3.0329     | 3.3607     |  18.6 | 14.45
+Bond    | 2.3164     | 2.8835     | 3.456      |  26.0 | 13.73
+Kspace  | 1.3332     | 2.2082     | 3.285      |  48.0 | 10.52
+Neigh   | 7.4831     | 7.4922     | 7.5012     |   0.3 | 35.68
+Comm    | 1.2809     | 1.3121     | 1.3297     |   1.6 |  6.25
+Output  | 0.0012138  | 0.0013506  | 0.0017552  |   0.6 |  0.01
+Modify  | 4.0269     | 4.0301     | 4.0335     |   0.1 | 19.19
+Other   |            | 0.03583    |            |       |  0.17
+
+Nlocal:    80 ave 94 max 66 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    2243.75 ave 2260 max 2221 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs:    13658.5 ave 17096 max 9421 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 54634
+Ave neighs/atom = 170.731
+Ave special neighs/atom = 11.3063
+Neighbor list builds = 10000
+Dangerous builds = 0
+System init for write_data ...
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:323)
+  G vector (1/distance) = 0.255611
+  grid = 6 6 6
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00974692
+  estimated relative force accuracy = 2.93525e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 704 72
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:21
diff --git a/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data b/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data
new file mode 100644
index 0000000000..5f0ed4cfa6
--- /dev/null
+++ b/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data
@@ -0,0 +1,2643 @@
+LAMMPS data file via write_data, version 20 Nov 2019, timestep = 25000
+
+320 atoms
+7 atom types
+320 bonds
+13 bond types
+480 angles
+22 angle types
+640 dihedrals
+36 dihedral types
+160 impropers
+9 improper types
+
+1.7426663385337786e+00 1.8257333661465619e+01 xlo xhi
+1.7426663385337786e+00 1.8257333661465619e+01 ylo yhi
+1.7426663385337786e+00 1.8257333661465619e+01 zlo zhi
+
+Masses
+
+1 12.0112
+2 1.00797
+3 12.0112
+4 12.0112
+5 12.0112
+6 12.0112
+7 12.0112
+
+Pair Coeffs # lj/class2/coul/long
+
+1 0.064 4.01
+2 0.02 2.7
+3 0.064 4.01
+4 0.064 3.9
+5 0.054 4.01
+6 0.054 4.01
+7 0.054 4.01
+
+Bond Coeffs # class2
+
+1 1.0982 372.825 -803.453 894.317
+2 1.417 470.836 -627.618 1327.63
+3 1.501 321.902 -521.821 572.163
+4 1.0883 365.768 -725.54 781.662
+5 1.34 543.99 -1238.2 1644.03
+6 1.0883 365.768 -725.54 781.662
+7 1.501 321.902 -521.821 572.163
+8 1.101 345 -691.89 844.6
+9 1.53 299.67 -501.77 679.81
+10 1.101 345 -691.89 844.6
+11 1.501 321.902 -521.821 572.163
+12 1.101 345 -691.89 844.6
+13 1.53 299.67 -501.77 679.81
+
+Angle Coeffs # class2
+
+1 117.94 35.1558 -12.4682 0
+2 118.9 61.0226 -34.9931 0
+3 120.05 44.7148 -22.7352 0
+4 111 44.3234 -9.4454 0
+5 108.4 43.9594 -8.3924 -9.3379
+6 124.88 35.2766 -17.774 -1.6215
+7 124.88 35.2766 -17.774 -1.6215
+8 115.49 29.6363 -12.4853 -6.2218
+9 120.05 44.7148 -22.7352 0
+10 111 44.3234 -9.4454 0
+11 108.4 43.9594 -8.3924 -9.3379
+12 110.77 41.453 -10.604 5.129
+13 112.67 39.516 -7.443 -9.5583
+14 110.77 41.453 -10.604 5.129
+15 107.66 39.641 -12.921 -2.4318
+16 112.67 39.516 -7.443 -9.5583
+17 120.05 44.7148 -22.7352 0
+18 111 44.3234 -9.4454 0
+19 108.4 43.9594 -8.3924 -9.3379
+20 110.77 41.453 -10.604 5.129
+21 110.77 41.453 -10.604 5.129
+22 112.67 39.516 -7.443 -9.5583
+
+BondBond Coeffs
+
+1 1.0795 1.417 1.0982
+2 68.2856 1.417 1.417
+3 12.0676 1.417 1.501
+4 2.9168 1.501 1.0883
+5 0 1.501 1.34
+6 10.1047 1.0883 1.34
+7 10.1047 1.0883 1.34
+8 4.8506 1.0883 1.0883
+9 12.0676 1.417 1.501
+10 2.9168 1.501 1.101
+11 0 1.501 1.53
+12 3.3872 1.101 1.53
+13 0 1.53 1.53
+14 3.3872 1.101 1.53
+15 5.3316 1.101 1.101
+16 0 1.53 1.53
+17 12.0676 1.417 1.501
+18 2.9168 1.501 1.101
+19 0 1.501 1.53
+20 3.3872 1.101 1.53
+21 3.3872 1.101 1.53
+22 0 1.53 1.53
+
+BondAngle Coeffs
+
+1 20.0033 24.2183 1.417 1.0982
+2 28.8708 28.8708 1.417 1.417
+3 31.0771 47.0579 1.417 1.501
+4 26.4608 11.7717 1.501 1.0883
+5 0 0 1.501 1.34
+6 19.0592 23.3588 1.0883 1.34
+7 19.0592 23.3588 1.0883 1.34
+8 17.9795 17.9795 1.0883 1.0883
+9 31.0771 47.0579 1.417 1.501
+10 26.4608 11.7717 1.501 1.101
+11 0 0 1.501 1.53
+12 11.421 20.754 1.101 1.53
+13 8.016 8.016 1.53 1.53
+14 11.421 20.754 1.101 1.53
+15 18.103 18.103 1.101 1.101
+16 8.016 8.016 1.53 1.53
+17 31.0771 47.0579 1.417 1.501
+18 26.4608 11.7717 1.501 1.101
+19 0 0 1.501 1.53
+20 11.421 20.754 1.101 1.53
+21 11.421 20.754 1.101 1.53
+22 8.016 8.016 1.53 1.53
+
+Dihedral Coeffs # class2
+
+1 0 0 1.559 0 0 0
+2 0 0 3.9661 0 0 0
+3 0 0 4.4072 0 0 0
+4 8.3667 0 1.1932 0 0 0
+5 0 0 1.8769 0 0 0
+6 0 0 0 0 0 0
+7 0 0 0 0 0 0
+8 0 0 0 0 0 0
+9 0 0 4.8974 0 0 0
+10 0 0 1.559 0 0 0
+11 0 0 4.4072 0 0 0
+12 -0.2801 0 -0.0678 0 -0.0122 0
+13 -0.2802 0 -0.0678 0 -0.0122 0
+14 -0.0228 0 0.028 0 -0.1863 0
+15 -0.1432 0 0.0617 0 -0.1083 0
+16 0 0 0.0316 0 -0.1681 0
+17 0 0 0 0 0 0
+18 0 0 0.0316 0 -0.1681 0
+19 0 0 0.0514 0 -0.143 0
+20 0 0 1.559 0 0 0
+21 0 0 4.4072 0 0 0
+22 -0.2801 0 -0.0678 0 -0.0122 0
+23 -0.2802 0 -0.0678 0 -0.0122 0
+24 -0.0228 0 0.028 0 -0.1863 0
+25 0 0 0 0 0 0
+26 -0.1432 0 0.0617 0 -0.1083 0
+27 0 0 0.0316 0 -0.1681 0
+28 0 0 0 0 0 0
+29 0 0 0.0316 0 -0.1681 0
+30 0 0 0.0514 0 -0.143 0
+31 -0.0228 0 0.028 0 -0.1863 0
+32 -0.1432 0 0.0617 0 -0.1083 0
+33 0 0 0.0316 0 -0.1681 0
+34 0 0 0 0 0 0
+35 0 0 0.0316 0 -0.1681 0
+36 0 0 0.0514 0 -0.143 0
+
+AngleAngleTorsion Coeffs
+
+1 4.4444 117.94 120.05
+2 -4.8141 118.9 117.94
+3 -14.4097 118.9 120.05
+4 0 118.9 118.9
+5 0.3598 117.94 117.94
+6 0 120.05 111
+7 0 120.05 108.4
+8 0 108.4 124.88
+9 -7.0058 124.88 124.88
+10 4.4444 117.94 120.05
+11 -14.4097 118.9 120.05
+12 -5.8888 120.05 111
+13 0 120.05 108.4
+14 0 108.4 110.77
+15 -12.564 110.77 110.77
+16 -16.164 112.67 110.77
+17 0 108.4 112.67
+18 -16.164 110.77 112.67
+19 -22.045 112.67 112.67
+20 4.4444 117.94 120.05
+21 -14.4097 118.9 120.05
+22 -5.8888 120.05 111
+23 0 120.05 108.4
+24 0 108.4 110.77
+25 0 108.4 112.67
+26 -12.564 110.77 110.77
+27 -16.164 110.77 112.67
+28 0 112.67 108.4
+29 -16.164 112.67 110.77
+30 -22.045 112.67 112.67
+31 0 110.77 108.4
+32 -12.564 110.77 110.77
+33 -16.164 110.77 112.67
+34 0 112.67 108.4
+35 -16.164 112.67 110.77
+36 -22.045 112.67 112.67
+
+EndBondTorsion Coeffs
+
+1 0 -0.4879 0 0 -1.797 0 1.0982 1.501
+2 0 -6.8958 0 0 -0.4669 0 1.417 1.0982
+3 0 -0.6918 0 0 0.2421 0 1.417 1.501
+4 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417
+5 0 -0.689 0 0 -0.689 0 1.0982 1.0982
+6 0 0 0 0 0 0 1.417 1.0883
+7 0 0 0 0 0 0 1.417 1.34
+8 0 0 0 0 0 0 1.501 1.0883
+9 0.7129 0.5161 0 0.7129 0.5161 0 1.0883 1.0883
+10 0 -0.4879 0 0 -1.797 0 1.0982 1.501
+11 0 -0.6918 0 0 0.2421 0 1.417 1.501
+12 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101
+13 0 0 0 0 0 0 1.417 1.53
+14 0 0 0 0 0 0 1.501 1.101
+15 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+16 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+17 0 0 0 0 0 0 1.501 1.53
+18 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
+19 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+20 0 -0.4879 0 0 -1.797 0 1.0982 1.501
+21 0 -0.6918 0 0 0.2421 0 1.417 1.501
+22 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101
+23 0 0 0 0 0 0 1.417 1.53
+24 0 0 0 0 0 0 1.501 1.101
+25 0 0 0 0 0 0 1.501 1.53
+26 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+27 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
+28 0 0 0 0 0 0 1.53 1.501
+29 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+30 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+31 0 0 0 0 0 0 1.101 1.501
+32 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+33 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
+34 0 0 0 0 0 0 1.53 1.501
+35 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+36 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+
+MiddleBondTorsion Coeffs
+
+1 0 3.9421 0 1.417
+2 0 -1.1521 0 1.417
+3 0 9.1792 0 1.417
+4 27.5989 -2.312 0 1.417
+5 0 4.8228 0 1.417
+6 0 0 0 1.501
+7 0 0 0 1.501
+8 0 0 0 1.34
+9 0.8558 6.3911 0 1.34
+10 0 3.9421 0 1.417
+11 0 9.1792 0 1.417
+12 -5.5679 1.4083 0.301 1.501
+13 0 0 0 1.501
+14 0 0 0 1.53
+15 -14.261 -0.5322 -0.4864 1.53
+16 -14.879 -3.6581 -0.3138 1.53
+17 0 0 0 1.53
+18 -14.879 -3.6581 -0.3138 1.53
+19 -17.787 -7.1877 0 1.53
+20 0 3.9421 0 1.417
+21 0 9.1792 0 1.417
+22 -5.5679 1.4083 0.301 1.501
+23 0 0 0 1.501
+24 0 0 0 1.53
+25 0 0 0 1.53
+26 -14.261 -0.5322 -0.4864 1.53
+27 -14.879 -3.6581 -0.3138 1.53
+28 0 0 0 1.53
+29 -14.879 -3.6581 -0.3138 1.53
+30 -17.787 -7.1877 0 1.53
+31 0 0 0 1.53
+32 -14.261 -0.5322 -0.4864 1.53
+33 -14.879 -3.6581 -0.3138 1.53
+34 0 0 0 1.53
+35 -14.879 -3.6581 -0.3138 1.53
+36 -17.787 -7.1877 0 1.53
+
+BondBond13 Coeffs
+
+1 0.8743 1.0982 1.501
+2 -6.2741 1.417 1.0982
+3 2.5085 1.417 1.501
+4 53 1.417 1.417
+5 -1.7077 1.0982 1.0982
+6 0 1.417 1.0883
+7 0 1.417 1.34
+8 0 1.501 1.0883
+9 0 1.0883 1.0883
+10 0.8743 1.0982 1.501
+11 2.5085 1.417 1.501
+12 -3.4826 1.417 1.101
+13 0 1.417 1.53
+14 0 1.501 1.101
+15 0 1.101 1.101
+16 0 1.53 1.101
+17 0 1.501 1.53
+18 0 1.101 1.53
+19 0 1.53 1.53
+20 0.8743 1.0982 1.501
+21 2.5085 1.417 1.501
+22 -3.4826 1.417 1.101
+23 0 1.417 1.53
+24 0 1.501 1.101
+25 0 1.501 1.53
+26 0 1.101 1.101
+27 0 1.101 1.53
+28 0 1.53 1.501
+29 0 1.53 1.101
+30 0 1.53 1.53
+31 0 1.101 1.501
+32 0 1.101 1.101
+33 0 1.101 1.53
+34 0 1.53 1.501
+35 0 1.53 1.101
+36 0 1.53 1.53
+
+AngleTorsion Coeffs
+
+1 0 3.4601 0 0 -0.1242 0 117.94 120.05
+2 0 2.5014 0 0 2.7147 0 118.9 117.94
+3 0 3.8987 0 0 -4.4683 0 118.9 120.05
+4 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9
+5 0 2.4501 0 0 2.4501 0 117.94 117.94
+6 0 0 0 0 0 0 120.05 111
+7 0 0 0 0 0 0 120.05 108.4
+8 0 0 0 0 0 0 108.4 124.88
+9 -1.8911 3.254 0 -1.8911 3.254 0 124.88 124.88
+10 0 3.4601 0 0 -0.1242 0 117.94 120.05
+11 0 3.8987 0 0 -4.4683 0 118.9 120.05
+12 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111
+13 0 0 0 0 0 0 120.05 108.4
+14 0 0 0 0 0 0 108.4 110.77
+15 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+16 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+17 0 0 0 0 0 0 108.4 112.67
+18 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
+19 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+20 0 3.4601 0 0 -0.1242 0 117.94 120.05
+21 0 3.8987 0 0 -4.4683 0 118.9 120.05
+22 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111
+23 0 0 0 0 0 0 120.05 108.4
+24 0 0 0 0 0 0 108.4 110.77
+25 0 0 0 0 0 0 108.4 112.67
+26 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+27 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
+28 0 0 0 0 0 0 112.67 108.4
+29 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+30 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+31 0 0 0 0 0 0 110.77 108.4
+32 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+33 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
+34 0 0 0 0 0 0 112.67 108.4
+35 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+36 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+
+Improper Coeffs # class2
+
+1 4.8912 0
+2 7.8153 0
+3 0 0
+4 2.8561 0
+5 7.8153 0
+6 0 0
+7 0 0
+8 7.8153 0
+9 0 0
+
+AngleAngle Coeffs
+
+1 0 0 0 118.9 117.94 117.94
+2 0 0 0 118.9 120.05 120.05
+3 0 0 0 111 124.88 108.4
+4 0 0 0 115.49 124.88 124.88
+5 0 0 0 118.9 120.05 120.05
+6 0 0 0 107.66 110.77 110.77
+7 0 0 0 111 110.77 108.4
+8 0 0 0 118.9 120.05 120.05
+9 0 0 0 111 110.77 108.4
+
+Atoms # full
+
+40602 2538 2 1.2880000000000000e-01 3.3609401967585955e+00 4.4067042595247594e+00 1.7652703015153694e+01 0 1 -1
+111366 6961 2 1.2370000000000000e-01 2.5287450867535228e+00 3.4595752969959102e+00 5.5197750474116489e+00 0 0 0
+111365 6961 1 -1.2900000000000000e-01 2.2477552210789034e+00 4.1940380679220048e+00 6.2531010916436118e+00 0 0 0
+111364 6961 3 -1.8200000000000001e-02 4.6534606713809783e+00 4.0872493335204627e+00 6.6406706800933657e+00 0 0 0
+111373 6961 2 5.1600000000000000e-02 4.7065862756318362e+00 3.1388066541018711e+00 7.1483388517476536e+00 0 0 0
+107224 6702 2 1.4030000000000001e-01 4.3747823735813256e+00 6.6777036283374303e+00 1.8126826734147052e+01 1 0 -1
+107223 6702 1 -1.7340000000000000e-01 3.3819489105921479e+00 7.1051571061898393e+00 1.9476793708830493e+00 1 0 0
+40599 2538 1 -1.7340000000000000e-01 1.7897991574638404e+01 3.7109360216682128e+00 1.7502909648810935e+01 -1 1 -1
+40600 2538 2 1.4030000000000001e-01 1.7761669662555619e+01 4.2961185209612616e+00 1.6631333893439564e+01 -1 1 -1
+41356 2585 2 1.4030000000000001e-01 5.9156631480771527e+00 1.0478394367195754e+01 8.3875585503933614e+00 0 1 1
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+21 1 41347 41345 41355 41346
+22 2 41345 41347 41349 41348
+23 4 41359 41358 41360 41348
+24 3 41347 41348 41357 41358
+25 1 41347 41349 41351 41350
+26 3 107219 107220 107229 107230
+27 4 107231 107230 107232 107220
+28 1 148085 148087 148089 148088
+29 1 148087 148089 148091 148090
+30 1 40593 40603 40601 40604
+31 1 40599 40601 40603 40602
+32 1 40595 40593 40603 40594
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+34 3 41315 41316 41325 41326
+35 1 108391 108393 108395 108394
+36 1 41315 41313 41323 41314
+37 1 108385 108395 108393 108396
+38 4 148095 148094 148096 148084
+39 4 40607 40606 40608 40596
+40 3 40595 40596 40605 40606
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+46 2 111361 111363 111365 111364
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+64 2 20145 20147 20149 20148
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+75 4 65551 65550 65552 65540
+76 3 65539 65540 65549 65550
+77 3 69379 69380 69389 69390
+78 2 65537 65539 65541 65540
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+83 1 65539 65537 65547 65538
+84 1 41317 41319 41321 41320
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+86 2 41313 41315 41317 41316
+87 3 195795 195796 195805 195806
+88 2 195793 195795 195797 195796
+89 1 41319 41321 41323 41322
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+91 4 69391 69390 69392 69380
+92 1 150147 150145 150155 150146
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+94 2 150145 150147 150149 150148
+95 4 150159 150158 150160 150148
+96 1 150147 150149 150151 150150
+97 1 195795 195793 195803 195794
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+99 1 195799 195801 195803 195802
+100 1 195795 195797 195799 195798
+101 1 195797 195799 195801 195800
+102 1 107223 107225 107227 107226
+103 1 43047 43049 43051 43050
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+106 4 188735 188734 188736 188724
+107 1 43045 43047 43049 43048
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+110 1 188721 188731 188729 188732
+111 4 3055 3054 3056 3044
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+116 1 101763 101765 101767 101766
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+119 1 107217 107227 107225 107228
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+126 3 108387 108388 108397 108398
+127 4 108399 108398 108400 108388
+128 4 101775 101774 101776 101764
+129 3 101763 101764 101773 101774
+130 2 101761 101763 101765 101764
+131 1 179269 179271 179273 179272
+132 1 101763 101761 101771 101762
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+139 1 108387 108385 108395 108386
+140 4 160479 160478 160480 160468
+141 3 160467 160468 160477 160478
+142 1 160469 160471 160473 160472
+143 1 160467 160469 160471 160470
+144 1 160471 160473 160475 160474
+145 1 160465 160475 160473 160476
+146 1 160467 160465 160475 160466
+147 2 160465 160467 160469 160468
+148 4 179279 179278 179280 179268
+149 3 179267 179268 179277 179278
+150 2 179265 179267 179269 179268
+151 1 179265 179275 179273 179276
+152 1 179267 179265 179275 179266
+153 1 179267 179269 179271 179270
+154 1 179271 179273 179275 179274
+155 1 3043 3041 3051 3042
+156 1 3047 3049 3051 3050
+157 1 3041 3051 3049 3052
+158 1 41335 41337 41339 41338
+159 1 41333 41335 41337 41336
+160 1 41331 41333 41335 41334
diff --git a/lib/colvars/Makefile.deps b/lib/colvars/Makefile.deps
index 33a9dd10ed..2c0dabea6a 100644
--- a/lib/colvars/Makefile.deps
+++ b/lib/colvars/Makefile.deps
@@ -27,46 +27,58 @@ $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
 $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
  colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
  colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
- colvarproxy.h colvar_arithmeticpath.h
-$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp
+ colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
+$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \
+ colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
+ colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
+ colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
  colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
  colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h colvardeps.h \
- colvar.h colvarcomp.h colvar_arithmeticpath.h
+ colvar.h colvarcomp.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
  colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
- colvar_arithmeticpath.h
+ colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
  colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
- colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
-$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp
+ colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
+ colvar_geometricpath.h
+$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
+ colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
+ colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
+ colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
  colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
- colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
+ colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
+ colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
  colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
- colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
+ colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
+ colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
  colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
  colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
- colvar_arithmeticpath.h colvarscript.h colvarbias.h
+ colvar_arithmeticpath.h colvar_geometricpath.h colvarscript.h \
+ colvarbias.h
 $(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \
  colvarparse.h colvarparams.h
 $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
  colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
- colvarproxy.h colvar_arithmeticpath.h colvargrid.h
+ colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h \
+ colvargrid.h
 $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
  colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
  colvarparams.h colvarproxy.h colvar.h colvardeps.h colvarbias.h \
  colvarbias_abf.h colvargrid.h colvar_UIestimator.h colvarbias_alb.h \
  colvarbias_histogram.h colvarbias_meta.h colvarbias_restraint.h \
- colvarscript.h colvaratoms.h colvarcomp.h colvar_arithmeticpath.h
+ colvarscript.h colvaratoms.h colvarcomp.h colvar_arithmeticpath.h \
+ colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
 $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index b853aaa1b8..fb95bda5ec 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -33,6 +33,8 @@ colvar::colvar()
   dev_null = 0.0;
 #endif
 
+  expand_boundaries = false;
+
   description = "uninitialized colvar";
   init_dependencies();
 }
@@ -474,6 +476,8 @@ int colvar::init_custom_function(std::string const &conf)
 
 int colvar::init_grid_parameters(std::string const &conf)
 {
+  int error_code = COLVARS_OK;
+
   colvarmodule *cv = cvm::main();
 
   cvm::real default_width = width;
@@ -527,15 +531,18 @@ int colvar::init_grid_parameters(std::string const &conf)
       disable(f_cv_hard_upper_boundary);
     }
 
+    // Parse legacy wall options and set up a harmonicWalls bias if needed
+    cvm::real lower_wall_k = 0.0, upper_wall_k = 0.0;
+    cvm::real lower_wall = 0.0, upper_wall = 0.0;
     std::string lw_conf, uw_conf;
+
     if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0,
                    parse_silent)) {
       cvm::log("Reading legacy options lowerWall and lowerWallConstant: "
-               "consider using a harmonicWalls restraint\n(caution: force constant would then be scaled by width^2).\n");
-      lower_wall.type(value());
-      if (!get_keyval(conf, "lowerWall", lower_wall, lower_boundary)) {
-        cvm::log("Warning: lowerWall will need to be "
-                 "defined explicitly in the next release.\n");
+               "consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).\n");
+      if (!get_keyval(conf, "lowerWall", lower_wall)) {
+        error_code != cvm::error("Error: the value of lowerWall must be set "
+                                 "explicitly.\n", INPUT_ERROR);
       }
       lw_conf = std::string("\n\
     lowerWallConstant "+cvm::to_str(lower_wall_k*width*width)+"\n\
@@ -545,11 +552,10 @@ int colvar::init_grid_parameters(std::string const &conf)
     if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0,
                    parse_silent)) {
       cvm::log("Reading legacy options upperWall and upperWallConstant: "
-               "consider using a harmonicWalls restraint\n(caution: force constant would then be scaled by width^2).\n");
-      upper_wall.type(value());
-      if (!get_keyval(conf, "upperWall", upper_wall, upper_boundary)) {
-        cvm::log("Warning: upperWall will need to be "
-                 "defined explicitly in the next release.\n");
+               "consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).\n");
+      if (!get_keyval(conf, "upperWall", upper_wall)) {
+        error_code != cvm::error("Error: the value of upperWall must be set "
+                                 "explicitly.\n", INPUT_ERROR);
       }
       uw_conf = std::string("\n\
     upperWallConstant "+cvm::to_str(upper_wall_k*width*width)+"\n\
@@ -558,12 +564,11 @@ int colvar::init_grid_parameters(std::string const &conf)
 
     if (lw_conf.size() && uw_conf.size()) {
       if (lower_wall >= upper_wall) {
-        cvm::error("Error: the upper wall, "+
-                   cvm::to_str(upper_wall)+
-                   ", is not higher than the lower wall, "+
-                   cvm::to_str(lower_wall)+".\n",
-                   INPUT_ERROR);
-        return INPUT_ERROR;
+        error_code |= cvm::error("Error: the upper wall, "+
+                                 cvm::to_str(upper_wall)+
+                                 ", is not higher than the lower wall, "+
+                                 cvm::to_str(lower_wall)+".\n",
+                                 INPUT_ERROR);
       }
     }
 
@@ -575,7 +580,7 @@ harmonicWalls {\n\
     colvars "+this->name+"\n"+lw_conf+uw_conf+"\
     timeStepFactor "+cvm::to_str(time_step_factor)+"\n"+
                              "}\n");
-      cv->append_new_config(walls_conf);
+      error_code |= cv->append_new_config(walls_conf);
     }
   }
 
@@ -588,29 +593,27 @@ harmonicWalls {\n\
   // consistency checks for boundaries and walls
   if (is_enabled(f_cv_lower_boundary) && is_enabled(f_cv_upper_boundary)) {
     if (lower_boundary >= upper_boundary) {
-      cvm::error("Error: the upper boundary, "+
-                        cvm::to_str(upper_boundary)+
-                        ", is not higher than the lower boundary, "+
-                        cvm::to_str(lower_boundary)+".\n",
-                INPUT_ERROR);
-      return INPUT_ERROR;
+      error_code |= cvm::error("Error: the upper boundary, "+
+                               cvm::to_str(upper_boundary)+
+                               ", is not higher than the lower boundary, "+
+                               cvm::to_str(lower_boundary)+".\n",
+                               INPUT_ERROR);
     }
   }
 
-  get_keyval(conf, "expandBoundaries", expand_boundaries, false);
+  get_keyval(conf, "expandBoundaries", expand_boundaries, expand_boundaries);
   if (expand_boundaries && periodic_boundaries()) {
-    cvm::error("Error: trying to expand boundaries that already "
-               "cover a whole period of a periodic colvar.\n",
-               INPUT_ERROR);
-    return INPUT_ERROR;
+    error_code |= cvm::error("Error: trying to expand boundaries that already "
+                             "cover a whole period of a periodic colvar.\n",
+                             INPUT_ERROR);
   }
+
   if (expand_boundaries && is_enabled(f_cv_hard_lower_boundary) &&
       is_enabled(f_cv_hard_upper_boundary)) {
-    cvm::error("Error: inconsistent configuration "
-               "(trying to expand boundaries with both "
-               "hardLowerBoundary and hardUpperBoundary enabled).\n",
-               INPUT_ERROR);
-    return INPUT_ERROR;
+    error_code |= cvm::error("Error: inconsistent configuration "
+                             "(trying to expand boundaries, but both "
+                             "hardLowerBoundary and hardUpperBoundary "
+                             "are enabled).\n", INPUT_ERROR);
   }
 
   return COLVARS_OK;
@@ -2077,12 +2080,12 @@ void colvar::wrap(colvarvalue &x_unwrapped) const
 
 // ******************** INPUT FUNCTIONS ********************
 
-std::istream & colvar::read_restart(std::istream &is)
+std::istream & colvar::read_state(std::istream &is)
 {
   size_t const start_pos = is.tellg();
 
   std::string conf;
-  if ( !(is >> colvarparse::read_block("colvar", conf)) ) {
+  if ( !(is >> colvarparse::read_block("colvar", &conf)) ) {
     // this is not a colvar block
     is.clear();
     is.seekg(start_pos, std::ios::beg);
@@ -2092,15 +2095,24 @@ std::istream & colvar::read_restart(std::istream &is)
 
   {
     std::string check_name = "";
-    if ( (get_keyval(conf, "name", check_name,
-                     std::string(""), colvarparse::parse_silent)) &&
-         (check_name != name) )  {
-      cvm::error("Error: the state file does not match the "
-                 "configuration file, at colvar \""+name+"\".\n");
-    }
+    get_keyval(conf, "name", check_name,
+               std::string(""), colvarparse::parse_silent);
     if (check_name.size() == 0) {
       cvm::error("Error: Collective variable in the "
-                 "restart file without any identifier.\n");
+                 "restart file without any identifier.\n", INPUT_ERROR);
+      is.clear();
+      is.seekg(start_pos, std::ios::beg);
+      is.setstate(std::ios::failbit);
+      return is;
+    }
+
+    if (check_name != name)  {
+      if (cvm::debug()) {
+        cvm::log("Ignoring state of colvar \""+check_name+
+                 "\": this colvar is named \""+name+"\".\n");
+      }
+      is.seekg(start_pos, std::ios::beg);
+      return is;
     }
   }
 
@@ -2199,7 +2211,7 @@ std::istream & colvar::read_traj(std::istream &is)
 
 // ******************** OUTPUT FUNCTIONS ********************
 
-std::ostream & colvar::write_restart(std::ostream &os) {
+std::ostream & colvar::write_state(std::ostream &os) {
 
   os << "colvar {\n"
      << "  name " << name << "\n"
diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h
index f7d5a55627..e6fafbdec3 100644
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@@ -229,17 +229,9 @@ public:
 
   /// \brief Location of the lower boundary
   colvarvalue lower_boundary;
-  /// \brief Location of the lower wall
-  colvarvalue lower_wall;
-  /// \brief Force constant for the lower boundary potential (|x-xb|^2)
-  cvm::real   lower_wall_k;
 
   /// \brief Location of the upper boundary
   colvarvalue upper_boundary;
-  /// \brief Location of the upper wall
-  colvarvalue upper_wall;
-  /// \brief Force constant for the upper boundary potential (|x-xb|^2)
-  cvm::real   upper_wall_k;
 
   /// \brief Is the interval defined by the two boundaries periodic?
   bool periodic_boundaries() const;
@@ -453,9 +445,9 @@ public:
   std::ostream & write_traj_label(std::ostream &os);
 
   /// Read the collective variable from a restart file
-  std::istream & read_restart(std::istream &is);
+  std::istream & read_state(std::istream &is);
   /// Write the collective variable to a restart file
-  std::ostream & write_restart(std::ostream &os);
+  std::ostream & write_state(std::ostream &os);
 
   /// Write output files (if defined, e.g. in analysis mode)
   int write_output_files();
diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp
index ff7bbad19b..09bcca01b5 100644
--- a/lib/colvars/colvarbias.cpp
+++ b/lib/colvars/colvarbias.cpp
@@ -15,8 +15,10 @@
 
 
 colvarbias::colvarbias(char const *key)
-  : bias_type(to_lower_cppstr(key))
 {
+  bias_type = to_lower_cppstr(key);
+  state_keyword = bias_type;
+
   description = "uninitialized " + cvm::to_str(key) + " bias";
   init_dependencies();
   rank = 1;
@@ -25,6 +27,7 @@ colvarbias::colvarbias(char const *key)
   b_output_energy = false;
   reset();
   state_file_step = 0L;
+  matching_state = false;
 }
 
 
@@ -80,10 +83,21 @@ int colvarbias::init(std::string const &conf)
     cvm::log("Reinitializing bias \""+name+"\".\n");
   }
 
+  colvar_values.resize(num_variables());
+
+  for (i = 0; i < num_variables(); i++) {
+    colvar_values[i].type(colvars[i]->value().type());
+    colvar_forces[i].type(colvar_values[i].type());
+    previous_colvar_forces[i].type(colvar_values[i].type());
+  }
+
   output_prefix = cvm::output_prefix();
 
   get_keyval(conf, "outputEnergy", b_output_energy, b_output_energy);
 
+  // Disabled by default in base class; default value can be overridden by derived class constructor
+  get_keyval_feature(this, conf, "bypassExtendedLagrangian", f_cvb_bypass_ext_lagrangian, is_enabled(f_cvb_bypass_ext_lagrangian), parse_silent);
+
   get_keyval(conf, "timeStepFactor", time_step_factor, 1);
   if (time_step_factor < 1) {
     cvm::error("Error: timeStepFactor must be 1 or greater.\n");
@@ -114,6 +128,11 @@ int colvarbias::init_dependencies() {
     init_feature(f_cvb_apply_force, "apply force", f_type_user);
     require_feature_children(f_cvb_apply_force, f_cv_gradient);
 
+    init_feature(f_cvb_bypass_ext_lagrangian, "bypass extended-Lagrangian coordinates", f_type_user);
+    // The exclusion below prevents the inconsistency where biasing forces are applied onto
+    // the actual colvar, while total forces are measured on the extended coordinate
+    exclude_feature_self(f_cvb_bypass_ext_lagrangian, f_cvb_get_total_force);
+
     init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic);
     require_feature_children(f_cvb_get_total_force, f_cv_total_force);
 
@@ -158,6 +177,12 @@ int colvarbias::init_dependencies() {
   // only compute TI samples when deriving from colvarbias_ti
   feature_states[f_cvb_calc_ti_samples].available = false;
 
+  // The feature f_cvb_bypass_ext_lagrangian is only implemented by some derived classes
+  // (initially, harmonicWalls)
+  feature_states[f_cvb_bypass_ext_lagrangian].available = false;
+  // disabled by default; can be changed by derived classes that implement it
+  feature_states[f_cvb_bypass_ext_lagrangian].enabled = false;
+
   return COLVARS_OK;
 }
 
@@ -265,6 +290,11 @@ int colvarbias::update()
 
   has_data = true;
 
+  // Update the cached colvar values
+  for (size_t i = 0; i < num_variables(); i++) {
+    colvar_values[i] = colvars[i]->value();
+  }
+
   error_code |= calc_energy(NULL);
   error_code |= calc_forces(NULL);
 
@@ -304,9 +334,11 @@ void colvarbias::communicate_forces()
     // may send forces to the same colvar
     // which is why rescaling has to happen now: the colvar is not
     // aware of this bias' time_step_factor
-    variables(i)->add_bias_force(cvm::real(time_step_factor) * colvar_forces[i]);
-  }
-  for (i = 0; i < num_variables(); i++) {
+    if (is_enabled(f_cvb_bypass_ext_lagrangian)) {
+      variables(i)->add_bias_force_actual_value(cvm::real(time_step_factor) * colvar_forces[i]);
+    } else {
+      variables(i)->add_bias_force(cvm::real(time_step_factor) * colvar_forces[i]);
+    }
     previous_colvar_forces[i] = colvar_forces[i];
   }
 }
@@ -368,20 +400,27 @@ std::string const colvarbias::get_state_params() const
 
 int colvarbias::set_state_params(std::string const &conf)
 {
-  std::string new_name = "";
-  if (colvarparse::get_keyval(conf, "name", new_name,
-                              std::string(""), colvarparse::parse_silent) &&
-      (new_name != this->name)) {
-    cvm::error("Error: in the state file, the "
-               "\""+bias_type+"\" block has a different name, \""+new_name+
-               "\": different system?\n", INPUT_ERROR);
-  }
+  matching_state = false;
 
-  if (name.size() == 0) {
+  std::string check_name = "";
+  colvarparse::get_keyval(conf, "name", check_name,
+                          std::string(""), colvarparse::parse_silent);
+
+  if (check_name.size() == 0) {
     cvm::error("Error: \""+bias_type+"\" block within the restart file "
                "has no identifiers.\n", INPUT_ERROR);
   }
 
+  if (check_name != this->name) {
+    if (cvm::debug()) {
+      cvm::log("Ignoring state of bias \""+check_name+
+               "\": this bias is named \""+name+"\".\n");
+    }
+    return COLVARS_OK;
+  }
+
+  matching_state = true;
+
   colvarparse::get_keyval(conf, "step", state_file_step,
                           cvm::step_absolute(), colvarparse::parse_silent);
 
@@ -396,7 +435,7 @@ std::ostream & colvarbias::write_state(std::ostream &os)
   }
   os.setf(std::ios::scientific, std::ios::floatfield);
   os.precision(cvm::cv_prec);
-  os << bias_type << " {\n"
+  os << state_keyword << " {\n"
      << "  configuration {\n";
   std::istringstream is(get_state_params());
   std::string line;
@@ -415,13 +454,12 @@ std::istream & colvarbias::read_state(std::istream &is)
   size_t const start_pos = is.tellg();
 
   std::string key, brace, conf;
-  if ( !(is >> key)   || !(key == bias_type) ||
+  if ( !(is >> key)   || !(key == state_keyword || key == bias_type) ||
        !(is >> brace) || !(brace == "{") ||
-       !(is >> colvarparse::read_block("configuration", conf)) ||
+       !(is >> colvarparse::read_block("configuration", &conf)) ||
        (set_state_params(conf) != COLVARS_OK) ) {
-    if (key != bias_type)
-      cvm::log("Found key \"" + key + "\" instead of \"" + bias_type + "\"\n");
-    cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+
+    cvm::error("Error: in reading state configuration for \""+bias_type+
+               "\" bias \""+
                this->name+"\" at position "+
                cvm::to_str(static_cast<size_t>(is.tellg()))+
                " in stream.\n", INPUT_ERROR);
@@ -431,6 +469,15 @@ std::istream & colvarbias::read_state(std::istream &is)
     return is;
   }
 
+  if (matching_state == false) {
+    // This state is not for this bias
+    is.seekg(start_pos, std::ios::beg);
+    return is;
+  }
+
+  cvm::log("Restarting "+bias_type+" bias \""+name+"\" from step number "+
+           cvm::to_str(state_file_step)+".\n");
+
   if (!read_state_data(is)) {
     cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+
                this->name+"\" at position "+
diff --git a/lib/colvars/colvarbias.h b/lib/colvars/colvarbias.h
index ed72c6063d..5179c42853 100644
--- a/lib/colvars/colvarbias.h
+++ b/lib/colvars/colvarbias.h
@@ -23,9 +23,12 @@ public:
   /// Name of this bias
   std::string name;
 
-  /// Type of this bias
+  /// Keyword indicating the type of this bias
   std::string bias_type;
 
+  /// Keyword used in state files (== bias_type most of the time)
+  std::string state_keyword;
+
   /// If there is more than one bias of this type, record its rank
   int rank;
 
@@ -65,7 +68,7 @@ public:
   virtual int calc_forces(std::vector<colvarvalue> const *values);
 
   /// Send forces to the collective variables
-  virtual void communicate_forces();
+  void communicate_forces();
 
   /// Carry out operations needed before next step is run
   virtual int end_of_step();
@@ -144,10 +147,10 @@ public:
   std::istream & read_state_data_key(std::istream &is, char const *key);
 
   /// Write the bias configuration to a restart file or other stream
-  virtual std::ostream & write_state(std::ostream &os);
+  std::ostream & write_state(std::ostream &os);
 
   /// Read the bias configuration from a restart file or other stream
-  virtual std::istream & read_state(std::istream &is);
+  std::istream & read_state(std::istream &is);
 
   /// Write a label to the trajectory file (comment line)
   virtual std::ostream & write_traj_label(std::ostream &os);
@@ -207,6 +210,9 @@ protected:
   /// through each colvar object
   std::vector<colvar *>    colvars;
 
+  /// \brief Up to date value of each colvar
+  std::vector<colvarvalue> colvar_values;
+
   /// \brief Current forces from this bias to the variables
   std::vector<colvarvalue> colvar_forces;
 
@@ -226,6 +232,9 @@ protected:
   /// \brief Step number read from the last state file
   cvm::step_number         state_file_step;
 
+  /// Flag used to tell if the state string being read is for this bias
+  bool matching_state;
+
 };
 
 
diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp
index bcd532e680..5382a828f7 100644
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@@ -115,7 +115,7 @@ int colvarbias_abf::init(std::string const &conf)
     if (colvars[i]->value().type() != colvarvalue::type_scalar) {
       cvm::error("Error: ABF bias can only use scalar-type variables.\n");
     }
-    colvars[i]->enable(f_cv_grid);
+    colvars[i]->enable(f_cv_grid); // Could be a child dependency of a f_cvb_use_grids feature
     if (hide_Jacobian) {
       colvars[i]->enable(f_cv_hide_Jacobian);
     }
diff --git a/lib/colvars/colvarbias_alb.cpp b/lib/colvars/colvarbias_alb.cpp
index 1d20245fb2..3508270bf6 100644
--- a/lib/colvars/colvarbias_alb.cpp
+++ b/lib/colvars/colvarbias_alb.cpp
@@ -246,6 +246,12 @@ int colvarbias_alb::update()
 
 int colvarbias_alb::set_state_params(std::string const &conf)
 {
+  int error_code = colvarbias::set_state_params(conf);
+
+  if (error_code != COLVARS_OK) {
+    return error_code;
+  }
+
   if (!get_keyval(conf, "setCoupling", set_coupling))
     cvm::fatal_error("Error: current setCoupling  is missing from the restart.\n");
 
diff --git a/lib/colvars/colvarbias_histogram.cpp b/lib/colvars/colvarbias_histogram.cpp
index b59a63f6e3..92985b0f61 100644
--- a/lib/colvars/colvarbias_histogram.cpp
+++ b/lib/colvars/colvarbias_histogram.cpp
@@ -17,6 +17,7 @@ colvarbias_histogram::colvarbias_histogram(char const *key)
   : colvarbias(key),
     grid(NULL), out_name("")
 {
+  provide(f_cvb_bypass_ext_lagrangian); // Allow histograms of actual cv for extended-Lagrangian
 }
 
 
@@ -84,6 +85,10 @@ int colvarbias_histogram::init(std::string const &conf)
   grid = new colvar_grid_scalar();
   grid->init_from_colvars(colvars);
 
+  if (is_enabled(f_cvb_bypass_ext_lagrangian)) {
+    grid->request_actual_value();
+  }
+
   {
     std::string grid_conf;
     if (key_lookup(conf, "histogramGrid", &grid_conf)) {
diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp
index 267d556be6..05f293d872 100644
--- a/lib/colvars/colvarbias_meta.cpp
+++ b/lib/colvars/colvarbias_meta.cpp
@@ -38,7 +38,12 @@ colvarbias_meta::colvarbias_meta(char const *key)
   new_hills_begin = hills.end();
   hills_traj_os = NULL;
 
+  hill_width = 0.0;
+
+  new_hill_freq = 1000;
+
   use_grids = true;
+  grids_freq = 0;
   rebin_grids = false;
   hills_energy = NULL;
   hills_energy_gradients = NULL;
@@ -48,6 +53,8 @@ colvarbias_meta::colvarbias_meta(char const *key)
   dump_fes_save = false;
   dump_replica_fes = false;
 
+  b_hills_traj = false;
+
   ebmeta_equil_steps = 0L;
 
   replica_update_freq = 0;
@@ -58,6 +65,7 @@ colvarbias_meta::colvarbias_meta(char const *key)
 int colvarbias_meta::init(std::string const &conf)
 {
   int error_code = COLVARS_OK;
+  size_t i = 0;
 
   error_code |= colvarbias::init(conf);
   error_code |= colvarbias_ti::init(conf);
@@ -71,16 +79,38 @@ int colvarbias_meta::init(std::string const &conf)
     cvm::error("Error: hillWeight must be provided, and a positive number.\n", INPUT_ERROR);
   }
 
-  get_keyval(conf, "newHillFrequency", new_hill_freq, 1000);
+  get_keyval(conf, "newHillFrequency", new_hill_freq, new_hill_freq);
   if (new_hill_freq > 0) {
     enable(f_cvb_history_dependent);
+    if (grids_freq == 0) {
+      grids_freq = new_hill_freq;
+    }
   }
 
-  get_keyval(conf, "hillWidth", hill_width, cvm::sqrt(2.0 * PI) / 2.0);
-  cvm::log("Half-widths of the Gaussian hills (sigma's):\n");
-  for (size_t i = 0; i < num_variables(); i++) {
-    cvm::log(variables(i)->name+std::string(": ")+
-             cvm::to_str(0.5 * variables(i)->width * hill_width));
+  get_keyval(conf, "gaussianSigmas", colvar_sigmas, colvar_sigmas);
+
+  get_keyval(conf, "hillWidth", hill_width, hill_width);
+
+  if ((colvar_sigmas.size() > 0) && (hill_width > 0.0)) {
+    error_code |= cvm::error("Error: hillWidth and gaussianSigmas are "
+                             "mutually exclusive.", INPUT_ERROR);
+  }
+
+  if (hill_width > 0.0) {
+    colvar_sigmas.resize(num_variables());
+    // Print the calculated sigma parameters
+    cvm::log("Half-widths of the Gaussian hills (sigma's):\n");
+    for (i = 0; i < num_variables(); i++) {
+      colvar_sigmas[i] = variables(i)->width * hill_width / 2.0;
+      cvm::log(variables(i)->name+std::string(": ")+
+               cvm::to_str(colvar_sigmas[i]));
+    }
+  }
+
+  if (colvar_sigmas.size() == 0) {
+    error_code |= cvm::error("Error: positive values are required for "
+                             "either hillWidth or gaussianSigmas.",
+                             INPUT_ERROR);
   }
 
   {
@@ -95,11 +125,18 @@ int colvarbias_meta::init(std::string const &conf)
   get_keyval(conf, "useGrids", use_grids, use_grids);
 
   if (use_grids) {
-    get_keyval(conf, "gridsUpdateFrequency", grids_freq, new_hill_freq);
+
+    for (i = 0; i < num_variables(); i++) {
+      if (2.0*colvar_sigmas[i] < variables(i)->width) {
+        cvm::log("Warning: gaussianSigmas is too narrow for the grid "
+                 "spacing along "+variables(i)->name+".");
+      }
+    }
+
+    get_keyval(conf, "gridsUpdateFrequency", grids_freq, grids_freq);
     get_keyval(conf, "rebinGrids", rebin_grids, rebin_grids);
 
     expand_grids = false;
-    size_t i;
     for (i = 0; i < num_variables(); i++) {
       variables(i)->enable(f_cv_grid); // Could be a child dependency of a f_cvb_use_grids feature
       if (variables(i)->expand_boundaries) {
@@ -116,15 +153,17 @@ int colvarbias_meta::init(std::string const &conf)
     get_keyval(conf, "keepHills", keep_hills, keep_hills);
     get_keyval(conf, "keepFreeEnergyFiles", dump_fes_save, dump_fes_save);
 
-    hills_energy           = new colvar_grid_scalar(colvars);
-    hills_energy_gradients = new colvar_grid_gradient(colvars);
+    if (hills_energy == NULL) {
+      hills_energy           = new colvar_grid_scalar(colvars);
+      hills_energy_gradients = new colvar_grid_gradient(colvars);
+    }
 
   } else {
 
     dump_fes = false;
   }
 
-  get_keyval(conf, "writeHillsTrajectory", b_hills_traj, false);
+  get_keyval(conf, "writeHillsTrajectory", b_hills_traj, b_hills_traj);
 
   error_code |= init_replicas_params(conf);
   error_code |= init_well_tempered_params(conf);
@@ -323,7 +362,7 @@ int colvarbias_meta::clear_state_data()
 // **********************************************************************
 
 std::list<colvarbias_meta::hill>::const_iterator
-colvarbias_meta::create_hill(colvarbias_meta::hill const &h)
+colvarbias_meta::add_hill(colvarbias_meta::hill const &h)
 {
   hill_iter const hills_end = hills.end();
   hills.push_back(h);
@@ -563,12 +602,14 @@ int colvarbias_meta::update_bias()
 
     case single_replica:
 
-      create_hill(hill(hill_weight*hills_scale, colvars, hill_width));
+      add_hill(hill(cvm::step_absolute(), hill_weight*hills_scale,
+                    colvar_values, colvar_sigmas));
 
       break;
 
     case multiple_replicas:
-      create_hill(hill(hill_weight*hills_scale, colvars, hill_width, replica_id));
+      add_hill(hill(cvm::step_absolute(), hill_weight*hills_scale,
+                    colvar_values, colvar_sigmas, replica_id));
       std::ostream *replica_hills_os =
         cvm::proxy->get_output_stream(replica_hills_file);
       if (replica_hills_os) {
@@ -730,35 +771,21 @@ void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter      h_first,
                                  std::vector<colvarvalue> const *values)
 {
   size_t i = 0;
-  std::vector<colvarvalue> curr_values(num_variables());
-  for (i = 0; i < num_variables(); i++) {
-    curr_values[i].type(variables(i)->value());
-  }
-
-  if (values) {
-    for (i = 0; i < num_variables(); i++) {
-      curr_values[i] = (*values)[i];
-    }
-  } else {
-    for (i = 0; i < num_variables(); i++) {
-      curr_values[i] = variables(i)->value();
-    }
-  }
 
   for (hill_iter h = h_first; h != h_last; h++) {
 
     // compute the gaussian exponent
     cvm::real cv_sqdev = 0.0;
     for (i = 0; i < num_variables(); i++) {
-      colvarvalue const &x  = curr_values[i];
+      colvarvalue const &x  = values ? (*values)[i] : colvar_values[i];
       colvarvalue const &center = h->centers[i];
-      cvm::real const    half_width = 0.5 * h->widths[i];
-      cv_sqdev += (variables(i)->dist2(x, center)) / (half_width*half_width);
+      cvm::real const sigma = h->sigmas[i];
+      cv_sqdev += (variables(i)->dist2(x, center)) / (sigma*sigma);
     }
 
     // compute the gaussian
     if (cv_sqdev > 23.0) {
-      // set it to zero if the exponent is more negative than log(1.0E-05)
+      // set it to zero if the exponent is more negative than log(1.0E-06)
       h->value(0.0);
     } else {
       h->value(cvm::exp(-0.5*cv_sqdev));
@@ -775,22 +802,22 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
                                        std::vector<colvarvalue> const *values)
 {
   // Retrieve the value of the colvar
-  colvarvalue const x(values ? (*values)[i] : variables(i)->value());
+  colvarvalue const x(values ? (*values)[i] : colvar_values[i]);
 
   // do the type check only once (all colvarvalues in the hills series
   // were already saved with their types matching those in the
   // colvars)
 
   hill_iter h;
-  switch (variables(i)->value().type()) {
+  switch (x.type()) {
 
   case colvarvalue::type_scalar:
     for (h = h_first; h != h_last; h++) {
       if (h->value() == 0.0) continue;
       colvarvalue const &center = h->centers[i];
-      cvm::real const    half_width = 0.5 * h->widths[i];
+      cvm::real const sigma = h->sigmas[i];
       forces[i].real_value +=
-        ( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
+        ( h->weight() * h->value() * (0.5 / (sigma*sigma)) *
           (variables(i)->dist2_lgrad(x, center)).real_value );
     }
     break;
@@ -801,9 +828,9 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
     for (h = h_first; h != h_last; h++) {
       if (h->value() == 0.0) continue;
       colvarvalue const &center = h->centers[i];
-      cvm::real const    half_width = 0.5 * h->widths[i];
+      cvm::real const sigma = h->sigmas[i];
       forces[i].rvector_value +=
-        ( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
+        ( h->weight() * h->value() * (0.5 / (sigma*sigma)) *
           (variables(i)->dist2_lgrad(x, center)).rvector_value );
     }
     break;
@@ -813,9 +840,9 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
     for (h = h_first; h != h_last; h++) {
       if (h->value() == 0.0) continue;
       colvarvalue const &center = h->centers[i];
-      cvm::real const    half_width = 0.5 * h->widths[i];
+      cvm::real const sigma = h->sigmas[i];
       forces[i].quaternion_value +=
-        ( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
+        ( h->weight() * h->value() * (0.5 / (sigma*sigma)) *
           (variables(i)->dist2_lgrad(x, center)).quaternion_value );
     }
     break;
@@ -824,9 +851,9 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
     for (h = h_first; h != h_last; h++) {
       if (h->value() == 0.0) continue;
       colvarvalue const &center = h->centers[i];
-      cvm::real const    half_width = 0.5 * h->widths[i];
+      cvm::real const sigma = h->sigmas[i];
       forces[i].vector1d_value +=
-        ( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
+        ( h->weight() * h->value() * (0.5 / (sigma*sigma)) *
           (variables(i)->dist2_lgrad(x, center)).vector1d_value );
     }
     break;
@@ -1246,14 +1273,20 @@ void colvarbias_meta::read_replica_files()
 
 int colvarbias_meta::set_state_params(std::string const &state_conf)
 {
-  std::string new_replica = "";
-  if (colvarparse::get_keyval(state_conf, "replicaID", new_replica,
+  int error_code = colvarbias::set_state_params(state_conf);
+
+  if (error_code != COLVARS_OK) {
+    return error_code;
+  }
+
+  std::string check_replica = "";
+  if (colvarparse::get_keyval(state_conf, "replicaID", check_replica,
                               std::string(""), colvarparse::parse_silent) &&
-      (new_replica != this->replica_id)) {
-    cvm::error("Error: in the state file, the "
-               "\"metadynamics\" block has a different replicaID: different system?\n",
-               INPUT_ERROR);
-    return INPUT_ERROR;
+      (check_replica != this->replica_id)) {
+    return cvm::error("Error: in the state file , the "
+                      "\"metadynamics\" block has a different replicaID ("+
+                      check_replica+" instead of "+replica_id+").\n",
+                      INPUT_ERROR);
   }
 
   return COLVARS_OK;
@@ -1479,17 +1512,18 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
   if (!is) return is; // do nothing if failbit is set
 
   size_t const start_pos = is.tellg();
+  size_t i = 0;
 
   std::string data;
-  if ( !(is >> read_block("hill", data)) ) {
+  if ( !(is >> read_block("hill", &data)) ) {
     is.clear();
     is.seekg(start_pos, std::ios::beg);
     is.setstate(std::ios::failbit);
     return is;
   }
 
-  cvm::step_number h_it;
-  get_keyval(data, "step", h_it, 0L, parse_silent);
+  cvm::step_number h_it = 0L;
+  get_keyval(data, "step", h_it, h_it, parse_restart);
   if (h_it <= state_file_step) {
     if (cvm::debug())
       cvm::log("Skipping a hill older than the state file for metadynamics bias \""+
@@ -1499,31 +1533,24 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
   }
 
   cvm::real h_weight;
-  get_keyval(data, "weight", h_weight, hill_weight, parse_silent);
+  get_keyval(data, "weight", h_weight, hill_weight, parse_restart);
 
   std::vector<colvarvalue> h_centers(num_variables());
-  for (size_t i = 0; i < num_variables(); i++) {
+  for (i = 0; i < num_variables(); i++) {
     h_centers[i].type(variables(i)->value());
   }
-  {
-    // it is safer to read colvarvalue objects one at a time;
-    // TODO: change this it later
-    std::string centers_input;
-    key_lookup(data, "centers", &centers_input);
-    std::istringstream centers_is(centers_input);
-    for (size_t i = 0; i < num_variables(); i++) {
-      centers_is >> h_centers[i];
-    }
-  }
+  get_keyval(data, "centers", h_centers, h_centers, parse_restart);
 
-  std::vector<cvm::real> h_widths(num_variables());
-  get_keyval(data, "widths", h_widths,
-             std::vector<cvm::real>(num_variables(), (cvm::sqrt(2.0 * PI) / 2.0)),
-             parse_silent);
+  std::vector<cvm::real> h_sigmas(num_variables());
+  get_keyval(data, "widths", h_sigmas, h_sigmas, parse_restart);
+  for (i = 0; i < num_variables(); i++) {
+    // For backward compatibility, read the widths instead of the sigmas
+    h_sigmas[i] /= 2.0;
+  }
 
   std::string h_replica = "";
   if (comm != single_replica) {
-    get_keyval(data, "replicaID", h_replica, replica_id, parse_silent);
+    get_keyval(data, "replicaID", h_replica, replica_id, parse_restart);
     if (h_replica != replica_id)
       cvm::fatal_error("Error: trying to read a hill created by replica \""+h_replica+
                        "\" for replica \""+replica_id+
@@ -1531,7 +1558,7 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
   }
 
   hill_iter const hills_end = hills.end();
-  hills.push_back(hill(h_it, h_weight, h_centers, h_widths, h_replica));
+  hills.push_back(hill(h_it, h_weight, h_centers, h_sigmas, h_replica));
   if (new_hills_begin == hills_end) {
     // if new_hills_begin is unset, set it for the first time
     new_hills_begin = hills.end();
@@ -1753,8 +1780,8 @@ void colvarbias_meta::write_pmf()
     if (ebmeta) {
       int nt_points=pmf->number_of_points();
       for (int i = 0; i < nt_points; i++) {
-         cvm:: real pmf_val=0.0;
-         cvm:: real target_val=target_dist->value(i);
+         cvm::real pmf_val=0.0;
+         cvm::real target_val=target_dist->value(i);
          if (target_val>0) {
            pmf_val=pmf->value(i);
            pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * cvm::logn(target_val);
@@ -1794,8 +1821,8 @@ void colvarbias_meta::write_pmf()
     if (ebmeta) {
       int nt_points=pmf->number_of_points();
       for (int i = 0; i < nt_points; i++) {
-         cvm:: real pmf_val=0.0;
-         cvm:: real target_val=target_dist->value(i);
+         cvm::real pmf_val=0.0;
+         cvm::real target_val=target_dist->value(i);
          if (target_val>0) {
            pmf_val=pmf->value(i);
            pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * cvm::logn(target_val);
@@ -1889,10 +1916,10 @@ std::string colvarbias_meta::hill::output_traj()
   }
 
   os << "  ";
-  for (i = 0; i < widths.size(); i++) {
+  for (i = 0; i < sigmas.size(); i++) {
     os << " ";
     os << std::setprecision(cvm::cv_prec)
-       << std::setw(cvm::cv_width) << widths[i];
+       << std::setw(cvm::cv_width) << sigmas[i];
   }
 
   os << "  ";
@@ -1903,6 +1930,47 @@ std::string colvarbias_meta::hill::output_traj()
 }
 
 
+colvarbias_meta::hill::hill(cvm::step_number it_in,
+                            cvm::real W_in,
+                            std::vector<colvarvalue> const &cv_values,
+                            std::vector<cvm::real> const &cv_sigmas,
+                            std::string const &replica_in)
+  : it(it_in),
+    sW(1.0),
+    W(W_in),
+    centers(cv_values.size()),
+    sigmas(cv_values.size()),
+    replica(replica_in)
+{
+  for (size_t i = 0; i < cv_values.size(); i++) {
+    centers[i].type(cv_values[i]);
+    centers[i] = cv_values[i];
+    sigmas[i] = cv_sigmas[i];
+  }
+  if (cvm::debug()) {
+    cvm::log("New hill, applied to "+cvm::to_str(cv_values.size())+
+             " collective variables, with centers "+
+             cvm::to_str(centers)+", sigmas "+
+             cvm::to_str(sigmas)+" and weight "+
+             cvm::to_str(W)+".\n");
+  }
+}
+
+
+colvarbias_meta::hill::hill(colvarbias_meta::hill const &h)
+  : sW(1.0),
+    W(h.W),
+    centers(h.centers),
+    sigmas(h.sigmas),
+    it(h.it),
+    replica(h.replica)
+{}
+
+
+colvarbias_meta::hill::~hill()
+{}
+
+
 std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
 {
   os.setf(std::ios::scientific, std::ios::floatfield);
@@ -1927,12 +1995,13 @@ std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
   }
   os << "\n";
 
+  // For backward compatibility, write the widths instead of the sigmas
   os << "  widths  ";
-  for (i = 0; i < (h.widths).size(); i++) {
+  for (i = 0; i < (h.sigmas).size(); i++) {
     os << " "
        << std::setprecision(cvm::cv_prec)
        << std::setw(cvm::cv_width)
-       << h.widths[i];
+       << 2.0 * h.sigmas[i];
   }
   os << "\n";
 
diff --git a/lib/colvars/colvarbias_meta.h b/lib/colvars/colvarbias_meta.h
index abf1417c32..9f9fc63fc7 100644
--- a/lib/colvars/colvarbias_meta.h
+++ b/lib/colvars/colvarbias_meta.h
@@ -71,11 +71,14 @@ public:
 
 protected:
 
-  /// \brief width of a hill
+  /// Width of a hill in number of grid points
   ///
   /// The local width of each collective variable, multiplied by this
   /// number, provides the hill width along that direction
-  cvm::real  hill_width;
+  cvm::real hill_width;
+
+  /// The sigma parameters of the Gaussian hills
+  std::vector<cvm::real> colvar_sigmas;
 
   /// \brief Number of simulation steps between two hills
   size_t     new_hill_freq;
@@ -113,11 +116,11 @@ protected:
   /// \brief Add a new hill; if a .hills trajectory is written,
   /// write it there; if there is more than one replica, communicate
   /// it to the others
-  virtual std::list<hill>::const_iterator create_hill(hill const &h);
+  std::list<hill>::const_iterator add_hill(hill const &h);
 
   /// \brief Remove a previously saved hill (returns an iterator for
   /// the next hill in the list)
-  virtual std::list<hill>::const_iterator delete_hill(hill_iter &h);
+  std::list<hill>::const_iterator delete_hill(hill_iter &h);
 
   /// \brief Calculate the values of the hills, incrementing
   /// bias_energy
@@ -266,6 +269,9 @@ class colvarbias_meta::hill {
 
 protected:
 
+  /// Time step at which this hill was added
+  cvm::step_number it;
+
   /// Value of the hill function (ranges between 0 and 1)
   cvm::real hill_value;
 
@@ -275,83 +281,35 @@ protected:
   /// Maximum height in energy of the hill
   cvm::real W;
 
-  /// Center of the hill in the collective variable space
-  std::vector<colvarvalue>  centers;
+  /// Centers of the hill in the collective variable space
+  std::vector<colvarvalue> centers;
 
-  /// Widths of the hill in the collective variable space
-  std::vector<cvm::real>    widths;
+  /// Half-widths of the hill in the collective variable space
+  std::vector<cvm::real> sigmas;
+
+  /// Identity of the replica who added this hill
+  std::string replica;
 
 public:
 
   friend class colvarbias_meta;
 
-  /// Time step at which this hill was added
-  cvm::step_number it;
-
-  /// Identity of the replica who added this hill (only in multiple replica simulations)
-  std::string replica;
-
-  /// \brief Runtime constructor: data are read directly from
-  /// collective variables \param weight Weight of the hill \param
-  /// cv Pointer to the array of collective variables involved \param
-  /// replica (optional) Identity of the replica which creates the
-  /// hill
-  inline hill(cvm::real             const &W_in,
-              std::vector<colvar *>       &cv,
-              cvm::real             const &hill_width,
-              std::string           const &replica_in = "")
-    : sW(1.0),
-      W(W_in),
-      centers(cv.size()),
-      widths(cv.size()),
-      it(cvm::step_absolute()),
-      replica(replica_in)
-  {
-    for (size_t i = 0; i < cv.size(); i++) {
-      centers[i].type(cv[i]->value());
-      centers[i] = cv[i]->value();
-      widths[i] = cv[i]->width * hill_width;
-    }
-    if (cvm::debug())
-      cvm::log("New hill, applied to "+cvm::to_str(cv.size())+
-                " collective variables, with centers "+
-                cvm::to_str(centers)+", widths "+
-                cvm::to_str(widths)+" and weight "+
-                cvm::to_str(W)+".\n");
-  }
-
-  /// \brief General constructor: all data are explicitly passed as
-  /// arguments (used for instance when reading hills saved on a
-  /// file) \param it Time step of creation of the hill \param
-  /// weight Weight of the hill \param centers Center of the hill
-  /// \param widths Width of the hill around centers \param replica
-  /// (optional) Identity of the replica which creates the hill
-  inline hill(cvm::step_number          const &it_in,
-              cvm::real                 const &W_in,
-              std::vector<colvarvalue>  const &centers_in,
-              std::vector<cvm::real>    const &widths_in,
-              std::string               const &replica_in = "")
-    : sW(1.0),
-      W(W_in),
-      centers(centers_in),
-      widths(widths_in),
-      it(it_in),
-      replica(replica_in)
-  {}
+  /// Constructor of a hill object
+  /// \param it Step number at which the hill was added
+  /// \param W Weight of the hill (energy units)
+  /// \param cv_values Array of collective variable values
+  /// \param cv_sigmas Array of collective variable values
+  /// \param replica ID of the replica that creates the hill (optional)
+  hill(cvm::step_number it, cvm::real W,
+       std::vector<colvarvalue> const &cv_values,
+       std::vector<cvm::real> const &cv_sigmas,
+       std::string const &replica = "");
 
   /// Copy constructor
-  inline hill(colvarbias_meta::hill const &h)
-    : sW(1.0),
-      W(h.W),
-      centers(h.centers),
-      widths(h.widths),
-      it(h.it),
-      replica(h.replica)
-  {}
+  hill(colvarbias_meta::hill const &h);
 
   /// Destructor
-  inline ~hill()
-  {}
+  ~hill();
 
   /// Get the energy
   inline cvm::real energy()
@@ -440,8 +398,7 @@ public:
   std::string output_traj();
 
   /// Write the hill to an output stream
-  inline friend std::ostream & operator << (std::ostream &os,
-                                            hill const &h);
+  friend std::ostream & operator << (std::ostream &os, hill const &h);
 
 };
 
diff --git a/lib/colvars/colvarbias_restraint.cpp b/lib/colvars/colvarbias_restraint.cpp
index 1fd9c84e98..486d77688b 100644
--- a/lib/colvars/colvarbias_restraint.cpp
+++ b/lib/colvars/colvarbias_restraint.cpp
@@ -17,6 +17,7 @@
 colvarbias_restraint::colvarbias_restraint(char const *key)
   : colvarbias(key), colvarbias_ti(key)
 {
+  state_keyword = "restraint";
 }
 
 
@@ -705,67 +706,6 @@ std::ostream & colvarbias_restraint_k_moving::write_traj(std::ostream &os)
 
 
 
-// redefined due to legacy state file keyword "harmonic"
-std::istream & colvarbias_restraint::read_state(std::istream &is)
-{
-  size_t const start_pos = is.tellg();
-
-  std::string key, brace, conf;
-  if ( !(is >> key)   || !(key == "restraint" || key == "harmonic") ||
-       !(is >> brace) || !(brace == "{") ||
-       !(is >> colvarparse::read_block("configuration", conf)) ||
-       (set_state_params(conf) != COLVARS_OK) ) {
-    cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+
-               this->name+"\" at position "+
-               cvm::to_str(static_cast<size_t>(is.tellg()))+
-               " in stream.\n", INPUT_ERROR);
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
-    return is;
-  }
-
-  if (!read_state_data(is)) {
-    cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+
-               this->name+"\" at position "+
-               cvm::to_str(static_cast<size_t>(is.tellg()))+
-               " in stream.\n", INPUT_ERROR);
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
-  }
-
-  is >> brace;
-  if (brace != "}") {
-    cvm::log("brace = "+brace+"\n");
-    cvm::error("Error: corrupt restart information for \""+bias_type+"\" bias \""+
-               this->name+"\": no matching brace at position "+
-               cvm::to_str(static_cast<size_t>(is.tellg()))+" in stream.\n");
-    is.setstate(std::ios::failbit);
-  }
-
-  return is;
-}
-
-
-std::ostream & colvarbias_restraint::write_state(std::ostream &os)
-{
-  os.setf(std::ios::scientific, std::ios::floatfield);
-  os << "restraint {\n"
-     << "  configuration {\n";
-  std::istringstream is(get_state_params());
-  std::string line;
-  while (std::getline(is, line)) {
-    os << "    " << line << "\n";
-  }
-  os << "  }\n";
-  write_state_data(os);
-  os << "}\n\n";
-  return os;
-}
-
-
-
 colvarbias_restraint_harmonic::colvarbias_restraint_harmonic(char const *key)
   : colvarbias(key),
     colvarbias_ti(key),
@@ -928,6 +868,9 @@ colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls(char co
 {
   lower_wall_k = -1.0;
   upper_wall_k = -1.0;
+  // This bias implements the bias_actual_colvars feature (most others do not)
+  provide(f_cvb_bypass_ext_lagrangian);
+  set_enabled(f_cvb_bypass_ext_lagrangian); // Defaults to enabled
 }
 
 
@@ -1075,23 +1018,13 @@ int colvarbias_restraint_harmonic_walls::update()
 }
 
 
-void colvarbias_restraint_harmonic_walls::communicate_forces()
-{
-  for (size_t i = 0; i < num_variables(); i++) {
-    if (cvm::debug()) {
-      cvm::log("Communicating a force to colvar \""+
-               variables(i)->name+"\".\n");
-    }
-    // Impulse-style multiple timestep
-    variables(i)->add_bias_force_actual_value(cvm::real(time_step_factor) * colvar_forces[i]);
-  }
-}
-
-
 cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const
 {
   colvar *cv = variables(i);
-  colvarvalue const &cvv = variables(i)->actual_value();
+
+  colvarvalue const &cvv = is_enabled(f_cvb_bypass_ext_lagrangian) ?
+    variables(i)->actual_value() :
+    variables(i)->value();
 
   // For a periodic colvar, both walls may be applicable at the same time
   // in which case we pick the closer one
diff --git a/lib/colvars/colvarbias_restraint.h b/lib/colvars/colvarbias_restraint.h
index 644835f129..ac25e35646 100644
--- a/lib/colvars/colvarbias_restraint.h
+++ b/lib/colvars/colvarbias_restraint.h
@@ -35,8 +35,6 @@ public:
   virtual int set_state_params(std::string const &conf);
   // virtual std::ostream & write_state_data(std::ostream &os);
   // virtual std::istream & read_state_data(std::istream &os);
-  virtual std::ostream & write_state(std::ostream &os);
-  virtual std::istream & read_state(std::istream &is);
 
   virtual std::ostream & write_traj_label(std::ostream &os);
   virtual std::ostream & write_traj(std::ostream &os);
@@ -258,7 +256,6 @@ public:
   colvarbias_restraint_harmonic_walls(char const *key);
   virtual int init(std::string const &conf);
   virtual int update();
-  virtual void communicate_forces();
   virtual std::string const get_state_params() const;
   virtual int set_state_params(std::string const &conf);
   virtual std::ostream & write_state_data(std::ostream &os);
diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp
index 8425982be4..f83458b51c 100644
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@@ -428,11 +428,11 @@ void colvardeps::require_feature_alt(int f, int g, int h, int i, int j) {
 
 void colvardeps::print_state() {
   size_t i;
-  cvm::log("Enabled features of \"" + description + "\" (with reference count)");
+  cvm::log("Features of \"" + description + "\" ON/OFF (refcount)");
   for (i = 0; i < feature_states.size(); i++) {
-    if (is_enabled(i))
-      cvm::log("- " + features()[i]->description + " ("
-        + cvm::to_str(feature_states[i].ref_count) + ")");
+    std::string onoff = is_enabled(i) ? "ON" : "OFF";
+    cvm::log("- " + features()[i]->description + "   " + onoff + " ("
+      + cvm::to_str(feature_states[i].ref_count) + ")");
   }
   cvm::increase_depth();
   for (i=0; i<children.size(); i++) {
diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h
index 47a91ab1ac..058ac3c78c 100644
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@@ -229,6 +229,8 @@ public:
     f_cvb_awake,
     /// \brief will apply forces
     f_cvb_apply_force,
+    /// \brief force this bias to act on actual value for extended-Lagrangian coordinates
+    f_cvb_bypass_ext_lagrangian,
     /// \brief requires total forces
     f_cvb_get_total_force,
     /// \brief whether this bias should record the accumulated work
diff --git a/lib/colvars/colvargrid.h b/lib/colvars/colvargrid.h
index 9d07ba0972..6008f2068b 100644
--- a/lib/colvars/colvargrid.h
+++ b/lib/colvars/colvargrid.h
@@ -932,7 +932,7 @@ public:
     std::string key, conf;
     if ((is >> key) && (key == std::string("grid_parameters"))) {
       is.seekg(start_pos, std::ios::beg);
-      is >> colvarparse::read_block("grid_parameters", conf);
+      is >> colvarparse::read_block("grid_parameters", &conf);
       parse_params(conf, colvarparse::parse_silent);
     } else {
       cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp
index ecf0ae800d..83632d9458 100644
--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.cpp
@@ -1284,7 +1284,7 @@ std::istream & colvarmodule::read_restart(std::istream &is)
   {
     // read global restart information
     std::string restart_conf;
-    if (is >> colvarparse::read_block("configuration", restart_conf)) {
+    if (is >> colvarparse::read_block("configuration", &restart_conf)) {
 
       parse->get_keyval(restart_conf, "step",
                         it_restart, static_cast<step_number>(0),
@@ -1329,30 +1329,84 @@ std::istream & colvarmodule::read_restart(std::istream &is)
     parse->clear_keyword_registry();
   }
 
-  // colvars restart
-  cvm::increase_depth();
-  for (std::vector<colvar *>::iterator cvi = colvars.begin();
-       cvi != colvars.end();
-       cvi++) {
-    if ( !((*cvi)->read_restart(is)) ) {
-      cvm::error("Error: in reading restart configuration for collective variable \""+
-                 (*cvi)->name+"\".\n",
-                 INPUT_ERROR);
+  print_total_forces_errning(warn_total_forces);
+
+  read_objects_state(is);
+
+  return is;
+}
+
+
+
+std::istream & colvarmodule::read_objects_state(std::istream &is)
+{
+  size_t pos = 0;
+  std::string word;
+
+  while (is.good()) {
+    pos = is.tellg();
+    word.clear();
+    is >> word;
+
+    if (word.size()) {
+
+      is.seekg(pos, std::ios::beg);
+
+      if (word == "colvar") {
+
+        cvm::increase_depth();
+        for (std::vector<colvar *>::iterator cvi = colvars.begin();
+             cvi != colvars.end();
+             cvi++) {
+          if ( !((*cvi)->read_state(is)) ) {
+            // Here an error signals that the variable is a match, but the
+            // state is corrupt; otherwise, the variable rewinds is silently
+            cvm::error("Error: in reading restart configuration for "
+                       "collective variable \""+(*cvi)->name+"\".\n",
+                       INPUT_ERROR);
+          }
+          if (static_cast<size_t>(is.tellg()) > pos) break; // found it
+        }
+        cvm::decrease_depth();
+
+      } else {
+
+        cvm::increase_depth();
+        for (std::vector<colvarbias *>::iterator bi = biases.begin();
+             bi != biases.end();
+             bi++) {
+          if (((*bi)->state_keyword != word) && (*bi)->bias_type != word) {
+            // Skip biases with different type; state_keyword is used to
+            // support different versions of the state file format
+            continue;
+          }
+          if (!((*bi)->read_state(is))) {
+            // Same as above, an error means a match but the state is incorrect
+            cvm::error("Error: in reading restart configuration for bias \""+
+                       (*bi)->name+"\".\n",
+                       INPUT_ERROR);
+          }
+          if (static_cast<size_t>(is.tellg()) > pos) break; // found it
+        }
+        cvm::decrease_depth();
+      }
     }
+
+    if (static_cast<size_t>(is.tellg()) == pos) {
+      // This block has not been read by any object: discard it and move on
+      // to the next one
+      is >> colvarparse::read_block(word, NULL);
+    }
+
+    if (!is) break;
   }
 
-  // biases restart
-  for (std::vector<colvarbias *>::iterator bi = biases.begin();
-       bi != biases.end();
-       bi++) {
-    if (!((*bi)->read_state(is))) {
-      cvm::error("Error: in reading restart configuration for bias \""+
-                 (*bi)->name+"\".\n",
-                 INPUT_ERROR);
-    }
-  }
-  cvm::decrease_depth();
+  return is;
+}
 
+
+int colvarmodule::print_total_forces_errning(bool warn_total_forces)
+{
   if (warn_total_forces) {
     cvm::log(cvm::line_marker);
     cvm::log("WARNING: The definition of system forces has changed.  Please see:\n");
@@ -1367,10 +1421,11 @@ to:\n\
 and load it to continue this simulation.\n");
     output_prefix() = output_prefix()+".tmp";
     write_restart_file(output_prefix()+".colvars.state");
-    cvm::error("Exiting with error until issue is addressed.\n", INPUT_ERROR);
+    return cvm::error("Exiting with error until issue is addressed.\n",
+                      INPUT_ERROR);
   }
 
-  return is;
+  return COLVARS_OK;
 }
 
 
@@ -1499,7 +1554,7 @@ std::ostream & colvarmodule::write_restart(std::ostream &os)
   for (std::vector<colvar *>::iterator cvi = colvars.begin();
        cvi != colvars.end();
        cvi++) {
-    (*cvi)->write_restart(os);
+    (*cvi)->write_state(os);
   }
 
   for (std::vector<colvarbias *>::iterator bi = biases.begin();
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index d3bc5e1b80..9346e8e1d6 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -429,8 +429,15 @@ public:
   /// (Re)initialize the output trajectory and state file (does not write it yet)
   int setup_output();
 
-  /// Read the input restart file
+  /// Read a restart file
   std::istream & read_restart(std::istream &is);
+
+  /// Read the states of individual objects; allows for changes
+  std::istream & read_objects_state(std::istream &is);
+
+  /// If needed (old restart file), print the warning that cannot be ignored
+  int print_total_forces_errning(bool warn_total_forces);
+
   /// Write the output restart file
   std::ostream & write_restart(std::ostream &os);
 
diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp
index 77f03793a3..a09d6be9ef 100644
--- a/lib/colvars/colvarparse.cpp
+++ b/lib/colvars/colvarparse.cpp
@@ -840,6 +840,17 @@ bool colvarparse::key_lookup(std::string const &conf,
 }
 
 
+colvarparse::read_block::read_block(std::string const &key_in,
+                                    std::string *data_in)
+  : key(key_in), data(data_in)
+{
+}
+
+
+colvarparse::read_block::~read_block()
+{}
+
+
 std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
 {
   size_t start_pos = is.tellg();
@@ -856,7 +867,9 @@ std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
   }
 
   if (next != "{") {
-    (*rb.data) = next;
+    if (rb.data) {
+      *(rb.data) = next;
+    }
     return is;
   }
 
@@ -870,9 +883,15 @@ std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
       br_old = br;
       br++;
     }
-    if (brace_count) (*rb.data).append(line + "\n");
+    if (brace_count) {
+      if (rb.data) {
+        (rb.data)->append(line + "\n");
+      }
+    }
     else {
-      (*rb.data).append(line, 0, br_old);
+      if (rb.data) {
+        (rb.data)->append(line, 0, br_old);
+      }
       break;
     }
   }
diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h
index f43f6527c8..b7d42fdffa 100644
--- a/lib/colvars/colvarparse.h
+++ b/lib/colvars/colvarparse.h
@@ -272,14 +272,18 @@ public:
   /// skipping other blocks
   class read_block {
 
-    std::string const   key;
+    /// The keyword that identifies the block
+    std::string const key;
+
+    /// Where to keep the data (may be NULL)
     std::string * const data;
 
   public:
-    inline read_block(std::string const &key_in, std::string &data_in)
-      : key(key_in), data(&data_in)
-    {}
-    inline ~read_block() {}
+
+    read_block(std::string const &key_in, std::string *data_in = NULL);
+
+    ~read_block();
+
     friend std::istream & operator >> (std::istream &is, read_block const &rb);
   };
 
diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h
index aa985bedd8..cc8744d62b 100644
--- a/lib/colvars/colvars_version.h
+++ b/lib/colvars/colvars_version.h
@@ -1,3 +1,3 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2020-01-27"
+#define COLVARS_VERSION "2020-02-25"
 #endif
diff --git a/lib/gpu/cudpp_mini/cudpp_maximal_launch.cpp b/lib/gpu/cudpp_mini/cudpp_maximal_launch.cpp
index 904d101b3b..1a7542e68c 100644
--- a/lib/gpu/cudpp_mini/cudpp_maximal_launch.cpp
+++ b/lib/gpu/cudpp_mini/cudpp_maximal_launch.cpp
@@ -8,16 +8,7 @@
 // in the root directory of this source distribution.
 // ------------------------------------------------------------- 
 #include "cudpp_maximal_launch.h"
- 
-inline size_t min(size_t x, size_t y)
-{
-    return (x <= y) ? x : y;
-}
-
-inline size_t max(size_t x, size_t y)
-{
-    return (x >= y) ? x : y;
-}
+#include <algorithm>
 
 // computes next highest multiple of f from x
 inline size_t multiple(size_t x, size_t f)
@@ -65,7 +56,7 @@ size_t maxBlocks(cudaFuncAttributes &attribs,
     size_t ctaLimitSMem    = smemPerCTA > 0 ? devprop.sharedMemPerBlock / smemPerCTA : maxBlocksPerSM;
     size_t ctaLimitThreads =                  maxThreadsPerSM           / threadsPerBlock;
 
-    return devprop.multiProcessorCount * min(ctaLimitRegs, min(ctaLimitSMem, min(ctaLimitThreads, maxBlocksPerSM)));
+    return devprop.multiProcessorCount * std::min(ctaLimitRegs, std::min(ctaLimitSMem, std::min(ctaLimitThreads, (size_t)maxBlocksPerSM)));
 }
 
 extern "C"
@@ -80,15 +71,15 @@ size_t maxBlocksFromPointer(void*  kernel,
     {
         err = cudaGetDeviceProperties(&devprop, deviceID);
         if (err != cudaSuccess)
-            return -1;
+            return (size_t)-1;
 
         cudaFuncAttributes attr;
         err = cudaFuncGetAttributes(&attr, (const char*)kernel);
         if (err != cudaSuccess)
-            return -1;
+            return (size_t)-1;
 
         return maxBlocks(attr, devprop, bytesDynamicSharedMem, threadsPerBlock);
     }
 
-    return -1;    
+    return (size_t)-1;
 }
diff --git a/lib/gpu/geryon/nvd_kernel.h b/lib/gpu/geryon/nvd_kernel.h
index d03a715e1b..9293db2fe4 100644
--- a/lib/gpu/geryon/nvd_kernel.h
+++ b/lib/gpu/geryon/nvd_kernel.h
@@ -244,7 +244,7 @@ class UCL_Kernel {
   template <class dtype>
   inline void add_arg(const dtype* const arg) {
     #if CUDA_VERSION >= 4000
-    _kernel_args[_num_args]=const_cast<dtype * const>(arg);
+    _kernel_args[_num_args]=const_cast<dtype *>(arg);
     #else
     _param_size = (_param_size+__alignof(dtype)-1) & ~(__alignof(dtype)-1);
     CU_SAFE_CALL(cuParamSetv(_kernel,_param_size,(void*)arg,sizeof(dtype)));
diff --git a/lib/kokkos/cmake/kokkos_options.cmake b/lib/kokkos/cmake/kokkos_options.cmake
index e730a94664..239301925c 100644
--- a/lib/kokkos/cmake/kokkos_options.cmake
+++ b/lib/kokkos/cmake/kokkos_options.cmake
@@ -78,6 +78,7 @@ set(KOKKOS_ARCH_LIST)
 list(APPEND KOKKOS_ARCH_LIST
      None            # No architecture optimization
      AMDAVX          # (HOST) AMD chip
+     EPYC            # (HOST) AMD EPYC Zen-Core CPU
      ARMv80          # (HOST) ARMv8.0 Compatible CPU
      ARMv81          # (HOST) ARMv8.1 Compatible CPU
      ARMv8-ThunderX  # (HOST) ARMv8 Cavium ThunderX CPU
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index 64c778659c..e730466fcb 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -927,7 +927,7 @@ void PairADP::grab(FILE *fp, char *filename, int n, double *list)
   while (i < n) {
     utils::sfgets(FLERR,line,MAXLINE,fp,filename,error);
     ptr = strtok(line," \t\n\r\f");
-    list[i++] = atof(ptr);
+    if (ptr) list[i++] = atof(ptr);
     while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr);
   }
 }
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index d1b864d9e4..a1bc6e1eb4 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -797,7 +797,7 @@ void PairEAM::grab(FILE *fptr, int n, double *list)
   while (i < n) {
     utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
     ptr = strtok(line," \t\n\r\f");
-    list[i++] = atof(ptr);
+    if (ptr) list[i++] = atof(ptr);
     while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr);
   }
 }
diff --git a/src/Makefile b/src/Makefile
index 5ca583aa11..baeeda9716 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -63,7 +63,7 @@ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-c
 	   user-intel user-lb user-manifold user-meamc user-meso \
 	   user-mgpt user-misc user-mofff user-molfile \
 	   user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \
-	   user-qtb user-quip user-reaxc user-scafacos user-smd user-smtbq \
+	   user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \
 	   user-sdpd user-sph user-tally user-uef user-vtk user-yaff
 
 PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \
diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp
index 2129461c9a..dabb0bf923 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.cpp
+++ b/src/USER-COLVARS/colvarproxy_lammps.cpp
@@ -160,14 +160,20 @@ void colvarproxy_lammps::init(const char *conf_file)
   }
 }
 
-void colvarproxy_lammps::add_config_file(const char *conf_file)
+int colvarproxy_lammps::add_config_file(const char *conf_file)
 {
-  colvars->read_config_file(conf_file);
+  return colvars->read_config_file(conf_file);
 }
 
-void colvarproxy_lammps::add_config_string(const std::string &conf)
+int colvarproxy_lammps::add_config_string(const std::string &conf)
 {
-  colvars->read_config_string(conf);
+  return colvars->read_config_string(conf);
+}
+
+int colvarproxy_lammps::read_state_file(char const *state_filename)
+{
+  input_prefix() = std::string(state_filename);
+  return colvars->setup_input();
 }
 
 colvarproxy_lammps::~colvarproxy_lammps()
diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h
index 29ba5023ed..95e7d4fb32 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.h
+++ b/src/USER-COLVARS/colvarproxy_lammps.h
@@ -86,10 +86,13 @@ class colvarproxy_lammps : public colvarproxy {
   void write_output_files();
 
   // read additional config from file
-  void add_config_file(char const *config_filename);
+  int add_config_file(char const *config_filename);
 
   // read additional config from string
-  void add_config_string(const std::string &config);
+  int add_config_string(const std::string &config);
+
+  // load a state file
+  int read_state_file(char const *state_filename);
 
   // Request to set the units used internally by Colvars
   int set_unit_system(std::string const &units_in, bool check_only);
diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp
index 9863e8c20f..7ce2a93680 100644
--- a/src/USER-COLVARS/fix_colvars.cpp
+++ b/src/USER-COLVARS/fix_colvars.cpp
@@ -502,7 +502,7 @@ int FixColvars::modify_param(int narg, char **arg)
     if (me == 0) {
       if (! proxy)
         error->one(FLERR,"Cannot use fix_modify before initialization");
-      proxy->add_config_file(arg[1]);
+      return proxy->add_config_file(arg[1]) == COLVARS_OK ? 0 : 2;
     }
     return 2;
   } else if (strcmp(arg[0],"config") == 0) {
@@ -510,8 +510,16 @@ int FixColvars::modify_param(int narg, char **arg)
     if (me == 0) {
       if (! proxy)
         error->one(FLERR,"Cannot use fix_modify before initialization");
-      std::string conf(arg[1]);
-      proxy->add_config_string(conf);
+      std::string const conf(arg[1]);
+      return proxy->add_config_string(conf) == COLVARS_OK ? 0 : 2;
+    }
+    return 2;
+  } else if (strcmp(arg[0],"load") == 0) {
+    if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+    if (me == 0) {
+      if (! proxy)
+        error->one(FLERR,"Cannot use fix_modify before initialization");
+      return proxy->read_state_file(arg[1]) == COLVARS_OK ? 0 : 2;
     }
     return 2;
   }
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 9fdc18fbe5..6f16912d9c 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -48,7 +48,6 @@ dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
 dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18
 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
-fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018
 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019
 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018
 fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017
diff --git a/src/USER-REACTION/README b/src/USER-REACTION/README
new file mode 100644
index 0000000000..f099ace103
--- /dev/null
+++ b/src/USER-REACTION/README
@@ -0,0 +1,23 @@
+This package implements the DisARMMD protocol (disarmmd.org) as
+"fix bond/react." This fix allows for complex topology changes
+during a running MD simulation, when using classical force fields.
+Topology changes are defined in pre- and post-reaction molecule
+templates and can include creation and deletion of bonds, angles,
+dihedrals, impropers, atom types, bond types, angle types,
+dihedral types, improper types, and/or atomic charges.
+
+The DisARMMD protocol is a method for modeling chemical reactions in
+classical molecular dynamics simulations. It was developed to build
+physically-realistic initial configurations for amorphous or
+crosslinked materials. Any number of competing or reversible reaction
+pathways can be specified, and reacting sites can be stabilized. Other
+advanced options currently available include reaction constraints
+(e.g. angle and Arrhenius constraints), deletion of reaction
+byproducts or other small molecules, and chiral-sensitive reactions.
+
+The DisARMMD methodology is detailed in:
+    Gissinger et al., Polymer 128, 211-217 (2017)
+    https://doi.org/10.1016/j.polymer.2017.09.038
+
+This package was created by Jacob Gissinger (info@disarmmd.org),
+while at the NASA Langley Research Center.
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp
similarity index 97%
rename from src/USER-MISC/fix_bond_react.cpp
rename to src/USER-REACTION/fix_bond_react.cpp
index b14139afff..b2bb66b288 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-REACTION/fix_bond_react.cpp
@@ -60,7 +60,7 @@ static const char cite_fix_bond_react[] =
 #define BIG 1.0e20
 #define DELTA 16
 #define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm
-#define MAXCONARGS 7 // max # of arguments for any type of constraint + rxnID
+#define MAXCONARGS 10 // max # of arguments for any type of constraint + rxnID
 
 // various statuses of superimpose algorithm:
 // ACCEPT: site successfully matched to pre-reacted template
@@ -72,7 +72,7 @@ static const char cite_fix_bond_react[] =
 enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};
 
 // types of available reaction constraints
-enum{DISTANCE,ANGLE,ARRHENIUS};
+enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS};
 
 /* ---------------------------------------------------------------------- */
 
@@ -1654,10 +1654,15 @@ evaluate constraints: return 0 if any aren't satisfied
 
 int FixBondReact::check_constraints()
 {
-  tagint atom1,atom2,atom3;
+  tagint atom1,atom2,atom3,atom4;
   double delx,dely,delz,rsq;
   double delx1,dely1,delz1,delx2,dely2,delz2;
   double rsq1,rsq2,r1,r2,c,t,prrhob;
+  // for computation of dihedrals
+  double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
+  double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv;
+  double s,phi;
+  int ANDgate;
 
   double **x = atom->x;
 
@@ -1699,6 +1704,69 @@ int FixBondReact::check_constraints()
         if (c > 1.0) c = 1.0;
         if (c < -1.0) c = -1.0;
         if (acos(c) < constraints[i][5] || acos(c) > constraints[i][6]) return 0;
+      } else if (constraints[i][1] == DIHEDRAL) {
+        // phi calculation from dihedral style harmonic
+        atom1 = atom->map(glove[(int) constraints[i][2]-1][1]);
+        atom2 = atom->map(glove[(int) constraints[i][3]-1][1]);
+        atom3 = atom->map(glove[(int) constraints[i][4]-1][1]);
+        atom4 = atom->map(glove[(int) constraints[i][5]-1][1]);
+
+        vb1x = x[atom1][0] - x[atom2][0];
+        vb1y = x[atom1][1] - x[atom2][1];
+        vb1z = x[atom1][2] - x[atom2][2];
+        domain->minimum_image(vb1x,vb1y,vb1z);
+
+        vb2x = x[atom3][0] - x[atom2][0];
+        vb2y = x[atom3][1] - x[atom2][1];
+        vb2z = x[atom3][2] - x[atom2][2];
+        domain->minimum_image(vb2x,vb2y,vb2z);
+
+        vb2xm = -vb2x;
+        vb2ym = -vb2y;
+        vb2zm = -vb2z;
+        domain->minimum_image(vb2xm,vb2ym,vb2zm);
+
+        vb3x = x[atom4][0] - x[atom3][0];
+        vb3y = x[atom4][1] - x[atom3][1];
+        vb3z = x[atom4][2] - x[atom3][2];
+        domain->minimum_image(vb3x,vb3y,vb3z);
+
+        ax = vb1y*vb2zm - vb1z*vb2ym;
+        ay = vb1z*vb2xm - vb1x*vb2zm;
+        az = vb1x*vb2ym - vb1y*vb2xm;
+        bx = vb3y*vb2zm - vb3z*vb2ym;
+        by = vb3z*vb2xm - vb3x*vb2zm;
+        bz = vb3x*vb2ym - vb3y*vb2xm;
+
+        rasq = ax*ax + ay*ay + az*az;
+        rbsq = bx*bx + by*by + bz*bz;
+        rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
+        rg = sqrt(rgsq);
+
+        ra2inv = rb2inv = 0.0;
+        if (rasq > 0) ra2inv = 1.0/rasq;
+        if (rbsq > 0) rb2inv = 1.0/rbsq;
+        rabinv = sqrt(ra2inv*rb2inv);
+
+        c = (ax*bx + ay*by + az*bz)*rabinv;
+        s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
+
+        if (c > 1.0) c = 1.0;
+        if (c < -1.0) c = -1.0;
+        phi = atan2(s,c);
+
+        ANDgate = 0;
+        if (constraints[i][6] < constraints[i][7]) {
+          if (phi > constraints[i][6] && phi < constraints[i][7]) ANDgate = 1;
+        } else {
+          if (phi > constraints[i][6] || phi < constraints[i][7]) ANDgate = 1;
+        }
+        if (constraints[i][8] < constraints[i][9]) {
+          if (phi > constraints[i][8] && phi < constraints[i][9]) ANDgate = 1;
+        } else {
+          if (phi > constraints[i][8] || phi < constraints[i][9]) ANDgate = 1;
+        }
+        if (ANDgate != 1) return 0;
       } else if (constraints[i][1] == ARRHENIUS) {
         t = get_temperature();
         prrhob = constraints[i][3]*pow(t,constraints[i][4])*
@@ -3110,6 +3178,23 @@ void FixBondReact::Constraints(char *line, int myrxn)
       constraints[nconstraints][4] = tmp[2];
       constraints[nconstraints][5] = tmp[3]/180.0 * MY_PI;
       constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI;
+    } else if (strcmp(constraint_type,"dihedral") == 0) {
+      constraints[nconstraints][1] = DIHEDRAL;
+      tmp[6] = 181.0; // impossible range
+      tmp[7] = 182.0;
+      sscanf(line,"%*s %lg %lg %lg %lg %lg %lg %lg %lg",&tmp[0],&tmp[1],
+                        &tmp[2],&tmp[3],&tmp[4],&tmp[5],&tmp[6],&tmp[7]);
+      if (tmp[0] > onemol->natoms || tmp[1] > onemol->natoms ||
+          tmp[2] > onemol->natoms || tmp[3] > onemol->natoms)
+        error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
+      constraints[nconstraints][2] = tmp[0];
+      constraints[nconstraints][3] = tmp[1];
+      constraints[nconstraints][4] = tmp[2];
+      constraints[nconstraints][5] = tmp[3];
+      constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI;
+      constraints[nconstraints][7] = tmp[5]/180.0 * MY_PI;
+      constraints[nconstraints][8] = tmp[6]/180.0 * MY_PI;
+      constraints[nconstraints][9] = tmp[7]/180.0 * MY_PI;
     } else if (strcmp(constraint_type,"arrhenius") == 0) {
       constraints[nconstraints][1] = ARRHENIUS;
       constraints[nconstraints][2] = narrhenius++;
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-REACTION/fix_bond_react.h
similarity index 94%
rename from src/USER-MISC/fix_bond_react.h
rename to src/USER-REACTION/fix_bond_react.h
index 1dba13283b..84cb9401f8 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-REACTION/fix_bond_react.h
@@ -239,18 +239,17 @@ Atom IDs in molecule templates range from 1 to the number of atoms in the templa
 E or W: Bond/react: Atom affected by reaction %s too close to template edge
 
 This means an atom which changes type or connectivity during the
-reaction is too close to an 'edge' atom defined in the superimpose
-file. This could cause incorrect assignment of bonds, angle, etc.
-Generally, this means you must include more atoms in your templates,
-such that there are at least two atoms between each atom involved in
-the reaction and an edge atom.
+reaction is too close to an 'edge' atom defined in the map file. This
+could cause incorrect assignment of bonds, angle, etc. Generally, this
+means you must include more atoms in your templates, such that there
+are at least two atoms between each atom involved in the reaction and
+an edge atom.
 
 E: Bond/react: Fix bond/react needs ghost atoms from farther away
 
-This is because a processor needs to superimpose the entire unreacted
-molecule template onto simulation atoms it knows about. The
-comm_modify cutoff command can be used to extend the communication
-range.
+This is because a processor needs to map the entire unreacted molecule
+template onto simulation atoms it knows about. The comm_modify cutoff
+command can be used to extend the communication range.
 
 E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted
 
diff --git a/src/lmptype.h b/src/lmptype.h
index 65e46535fc..5c19ab7483 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -28,6 +28,12 @@
 #ifndef LMP_LMPTYPE_H
 #define LMP_LMPTYPE_H
 
+// C++11 check
+
+#if __cplusplus < 201103L
+#error LAMMPS requires a C++11 (or later) compliant compiler. Enable C++11 compatibility or upgrade the compiler.
+#endif
+
 #ifndef __STDC_LIMIT_MACROS
 #define __STDC_LIMIT_MACROS
 #endif
@@ -38,8 +44,8 @@
 
 #include <climits>
 #include <cstdlib>
-#include <stdint.h>   // <cstdint> requires C++-11
-#include <inttypes.h> // <cinttypes> requires C++-11
+#include <cstdint>
+#include <cinttypes>
 
 // grrr - IBM Power6 does not provide this def in their system header files
 
diff --git a/src/version.h b/src/version.h
index d2f1bc605c..504992bc4b 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "27 Feb 2020"
+#define LAMMPS_VERSION "3 Mar 2020"