Merge branch 'master' into charge_regulation2

cmake/CMakeLists.txt

@@ -652,7 +652,7 @@ install(
 if(BUILD_SHARED_LIBS)
   if(CMAKE_VERSION VERSION_LESS 3.12)
     # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
-    set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
+    set(Python_ADDITIONAL_VERSIONS 3.9 3.8 3.7 3.6 3.5)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
         set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@@ -662,10 +662,10 @@ if(BUILD_SHARED_LIBS)
   endif()
   if (Python_EXECUTABLE)
     add_custom_target(
-      install-python
+      install-python ${CMAKE_COMMAND} -E remove_directory build
-      ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
       -p ${LAMMPS_PYTHON_DIR}/lammps
-      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
+      -l ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX}
       WORKING_DIRECTORY  ${LAMMPS_PYTHON_DIR}
       COMMENT "Installing LAMMPS Python module")
   else()

cmake/Modules/Packages/GPU.cmake

@@ -36,6 +36,9 @@ if(GPU_API STREQUAL "CUDA")
   option(CUDPP_OPT "Enable CUDPP_OPT" ON)
   option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
   if(CUDA_MPS_SUPPORT)
+    if(CUDPP_OPT)
+      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON")
+    endif()
     set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
   endif()
 
@@ -94,9 +97,9 @@ if(GPU_API STREQUAL "CUDA")
   if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
     string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
   endif()
-  # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+  # Ampere (GPU Arch 8.0 and 8.6) is supported by CUDA 11 and later
   if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
-    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80] -gencode arch=compute_86,code=[sm_86,compute_86]")
   endif()
   if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
     message(WARNING "Unsupported CUDA version. Use at your own risk.")

cmake/Modules/Packages/MLIAP.cmake

@@ -1,7 +1,7 @@
 # if PYTHON package is included we may also include Python support in MLIAP
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
-  find_package(Cythonize)
+  find_package(Cythonize QUIET)
   if(Cythonize_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
@@ -14,6 +14,15 @@ if(MLIAP_ENABLE_PYTHON)
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP")
   endif()
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
+      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+    endif()
+  else()
+    if(Python_VERSION VERSION_LESS 3.6)
+      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+    endif()
+  endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
   set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx)

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "24 December 2020" "2020-12-24"
+.TH LAMMPS "10 February 2021" "2021-02-10"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_extras.rst

@@ -131,7 +131,7 @@ CMake build
    -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
                                 # value = yes (default) or no
    -D CUDPP_OPT=value           # optimization setting for GPU_API=cuda
-                                # enables CUDA Performance Primitives Optimizations
+                                # enables CUDA Performance Primitives Optimizations, must be "no" for CUDA_MPS_SUPPORT=yes
                                 # value = yes (default) or no
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
@@ -219,11 +219,19 @@ Makefile if desired:
 * ``CUDA_PRECISION`` = precision (double, mixed, single)
 * ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps
 
-The file Makefile.linux_multi is set up to include support for multiple
+The file Makefile.cuda is set up to include support for multiple
 GPU architectures as supported by the CUDA toolkit in use. This is done
 through using the "--gencode " flag, which can be used multiple times and
 thus support all GPU architectures supported by your CUDA compiler.
 
+To include CUDA performance primitives set the Makefile variable
+``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.
+
+To support the CUDA multiprocessor server you can set the define
+``-DCUDA_PROXY``.  Please note that in this case you should **not** use
+the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
+to empty.
+
 If the library build is successful, 3 files should be created:
 ``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
 ``lib/gpu/Makefile.lammps``\ .  The latter has settings that enable LAMMPS

doc/src/Developer_notes.rst

@@ -1,11 +1,133 @@
-Notes for Developers and Code Maintainers
+Notes for developers and code maintainers
 -----------------------------------------
 
-This section documents how a few large sections of code with LAMMPS
+This section documents how some of the code functionality within
-work at a conceptual level.  Comments on code in source files
+LAMMPS works at a conceptual level.  Comments on code in source files
 typically document what a variable stores, what a small section of
-code does, or what a function does or its input/outputs.  The topics
+code does, or what a function does and its input/outputs.  The topics
-on this page are intended to document code at a higher level.
+on this page are intended to document code functionality at a higher level.
+
+Fix contributions to instantaneous energy, virial, and cumulative energy
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixes can calculate contributions to the instantaneous energy and/or
+virial of the system, both in a global and peratom sense.  Fixes that
+perform thermostatting or barostatting can calculate the cumulative
+energy they add to or subtract from the system, which is accessed by
+the *ecouple* and *econserve* thermodynamic keywords.  This subsection
+explains how both work and what flags to set in a new fix to enable
+this functionality.
+
+Let's start with thermostatting and barostatting fixes.  Examples are
+the :doc:`fix langevin <fix_langevin>` and :doc:`fix npt <fix_nh>`
+commands.  Here is what the fix needs to do:
+
+* Set the variable *ecouple_flag* = 1 in the constructor.  Also set
+  *scalar_flag* = 1, *extscalar* = 1, and *global_freq* to a timestep
+  increment which matches how often the fix is invoked.
+* Implement a compute_scalar() method that returns the cumulative
+  energy added or subtracted by the fix, e.g. by rescaling the
+  velocity of atoms.  The sign convention is that subtracted energy is
+  positive, added energy is negative.  This must be the total energy
+  added to the entire system, i.e. an "extensive" quantity, not a
+  per-atom energy.  Cumulative means the summed energy since the fix
+  was instantiated, even across multiple runs.  This is because the
+  energy is used by the *econserve* thermodynamic keyword to check
+  that the fix is conserving the total energy of the system,
+  i.e. potential energy + kinetic energy + coupling energy = a
+  constant.
+
+And here is how the code operates:
+
+* The Modify class makes a list of all fixes that set *ecouple_flag* = 1.
+* The :doc:`thermo_style custom <thermo_style>` command defines
+  *ecouple* and *econserve* keywords.
+* These keywords sum the energy contributions from all the
+  *ecouple_flag* = 1 fixes by invoking the energy_couple() method in
+  the Modify class, which calls the compute_scalar() method of each
+  fix in the list.
+
+------------------
+
+Next, here is how a fix contributes to the instantaneous energy and
+virial of the system.  First, it sets any or all of these flags to a
+value of 1 in their constructor:
+
+* *energy_global_flag* to contribute to global energy, example: :doc:`fix indent <fix_indent>`
+* *energy_peratom_flag* to contribute to peratom energy, :doc:`fix cmap <fix_cmap>`
+* *virial_global_flag* to contribute to global virial, example: :doc:`fix wall <fix_wall>`
+* *virial_peratom_flag* to contribute to peratom virial, example: :doc:`fix wall <fix_wall>`
+
+The fix must also do the following:
+
+* For global energy, implement a compute_scalar() method that returns
+  the energy added or subtracted on this timestep.  Here the sign
+  convention is that added energy is positive, subtracted energy is
+  negative.
+* For peratom energy, invoke the ev_init(eflag,vflag) function each
+  time the fix is invoked, which initializes per-atom energy storage.
+  The value of eflag may need to be stored from an earlier call to the
+  fix during the same timestep.  See how the :doc:`fix cmap
+  <fix_cmap>` command does this in src/MOLECULE/fix_cmap.cpp.  When an
+  energy for one or more atoms is calculated, invoke the ev_tally()
+  function to tally the contribution to each atom.  Both the ev_init()
+  and ev_tally() methods are in the parent Fix class.
+* For global and/or peratom virial, invoke the v_init(vflag) function
+  each time the fix is invoked, which initializes virial storage.
+  When forces on one or more atoms are calculated, invoke the
+  v_tally() function to tally the contribution.  Both the v_init() and
+  v_tally() methods are in the parent Fix class.  Note that there are
+  several variants of v_tally(); choose the one appropriate to your
+  fix.
+
+.. note::
+
+   The ev_init() and ev_tally() methods also account for global and
+   peratom virial contributions.  Thus you do not need to invoke the
+   v_init() and v_tally() methods, if the fix also calculates peratom
+   energies.
+
+The fix must also specify whether (by default) to include or exclude
+these contributions to the global/peratom energy/virial of the system.
+For the fix to include the contributions, set either of both of these
+variables in the constructor:
+
+* *thermo_energy* = 1, for global and peratom energy
+* *thermo_virial* = 1, for global and peratom virial
+
+Note that these variables are zeroed in fix.cpp.  Thus if you don't
+set the variables, the contributions will be excluded (by default)
+
+However, the user has ultimate control over whether to include or
+exclude the contributions of the fix via the :doc:`fix modify
+<fix_modify>` command:
+
+* fix modify *energy yes* to include global and peratom energy contributions
+* fix modify *virial yes* to include global and peratom virial contributions
+
+If the fix contributes to any of the global/peratom energy/virial
+values for the system, it should be explained on the fix doc page,
+along with the default values for the *energy yes/no* and *virial
+yes/no* settings of the :doc:`fix modify <fix_modify>` command.
+
+Finally, these 4 contributions are included in the output of 4
+computes:
+
+* global energy in :doc:`compute pe <compute_pe>`
+* peratom energy in :doc:`compute pe/atom <compute_pe_atom>`
+* global virial in :doc:`compute pressure <compute_pressure>`
+* peratom virial in :doc:`compute stress/atom <compute_stress_atom>`
+
+These computes invoke a method of the Modify class to include
+contributions from fixes that have the corresponding flags set,
+e.g. *energy_peratom_flag* and *thermo_energy* for :doc:`compute
+pe/atom <compute_pe_atom>`.
+
+Note that each compute has an optional keyword to either include or
+exclude all contributions from fixes.  Also note that :doc:`compute pe
+<compute_pe>` and :doc:`compute pressure <compute_pressure>` are what
+is used (by default) by :doc:`thermodynamic output <thermo_style>` to
+calculate values for its *pe* and *press* keywords.
 
 KSpace PPPM FFT grids
 ^^^^^^^^^^^^^^^^^^^^^

doc/src/Intro_citing.rst

@@ -38,17 +38,18 @@ In addition there are DOIs for individual stable releases. Currently there are:
 Home page
 ^^^^^^^^^
 
-The LAMMPS website at `https://lammps.sandia.gov/ <https://lammps.sandia.gov>`_ is the canonical
+The LAMMPS website at `https://lammps.sandia.gov/
-location for information about LAMMPS and more detailed lists of publications
+<https://lammps.sandia.gov>`_ is the canonical location for information
-using LAMMPS and contributing features.
+about LAMMPS and its features.
 
 Citing contributions
 ^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS has many features and uses previously published methods and
+LAMMPS has many features and that use either previously published
-algorithms or novel features. It also includes potential parameter
+methods and algorithms or novel features.  It also includes potential
-filed for specific models.  You can look up relevant publications either
+parameter filed for specific models.  Where available, a reminder about
-in the LAMMPS output to the screen, the ``log.cite`` file (which is
+references for optional features used in a specific run is printed to
-populated with references to relevant papers through embedding them into
+the screen and log file.  Style and output location can be selected with
-the source code) and in the documentation of the :doc:`corresponding commands
+the :ref:`-cite command-line switch <cite>`.  Additional references are
+given in the documentation of the :doc:`corresponding commands
 <Commands_all>` or in the :doc:`Howto tutorials <Howto>`.

doc/src/Modify_contribute.rst

@@ -206,16 +206,22 @@ packages in the src directory for examples. If you are uncertain, please ask.
   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
+  A LaTeX citation is stored in a variable at the top of the file and
-  single line of code that references the variable is added to the
+  a single line of code registering this variable is added to the
-  constructor of the class.  Whenever a user invokes your feature from
+  constructor of the class.  If there is additional functionality (which
-  their input script, this will cause LAMMPS to output the citation to a
+  may have been added later) described in a different publication,
-  log.cite file and prompt the user to examine the file.  Note that you
+  additional citation descriptions may be added for as long as they
-  should only use this for a paper you or your group authored.
+  are only registered when the corresponding keyword activating this
-  E.g. adding a cite in the code for a paper by Nose and Hoover if you
+  functionality is used.  With these options it is possible to have
-  write a fix that implements their integrator is not the intended
+  LAMMPS output a specific citation reminder whenever a user invokes
-  usage.  That kind of citation should just be in the doc page you
+  your feature from their input script.  Note that you should only use
-  provide.
+  this for the most relevant paper for a feature and a publication that
+  you or your group authored.  E.g. adding a citation 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 included in the documentation page you provide describing
+  your contribution.  If you are not sure what the best option would
+  be, please contact the LAMMPS developers for advice.
 
 Finally, as a general rule-of-thumb, the more clear and
 self-explanatory you make your documentation and README files, and the

doc/src/Packages_details.rst

@@ -668,8 +668,8 @@ A general interface for machine-learning interatomic potentials, including PyTor
 
 To use this package, also the :ref:`SNAP package <PKG-SNAP>` package needs
 to be installed.  To make the *mliappy* model available, also the
-:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version of
+:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version
-Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
+of Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
 must be installed.
 
 **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).

doc/src/Python_module.rst

@@ -26,6 +26,23 @@ There are multiple Python interface classes in the :py:mod:`lammps` module:
 
 .. _mpi4py_url: https://mpi4py.readthedocs.io
 
+.. admonition:: Version check
+   :class: note
+
+   The :py:mod:`lammps` module stores the version number of the LAMMPS
+   version it is installed from.  When initializing the
+   :py:class:`lammps <lammps.lammps>` class, this version is checked to
+   be the same as the result from :py:func:`lammps.version`, the version
+   of the LAMMPS shared library that the module interfaces to.  If the
+   they are not the same an AttributeError exception is raised since a
+   mismatch of versions (e.g.  due to incorrect use of the
+   ``LD_LIBRARY_PATH`` or ``PYTHONPATH`` environment variables can lead
+   to crashes or data corruption and otherwise incorrect behavior.
+
+.. automodule:: lammps
+   :members:
+   :noindex:
+
 ----------
 
 The ``lammps`` class API

doc/src/Run_options.rst

@@ -11,6 +11,7 @@ letter abbreviation can be used:
 * :ref:`-k or -kokkos <run-kokkos>`
 * :ref:`-l or -log <log>`
 * :ref:`-m or -mpicolor <mpicolor>`
+* :ref:`-c or -cite <cite>`
 * :ref:`-nc or -nocite <nocite>`
 * :ref:`-pk or -package <package>`
 * :ref:`-p or -partition <partition>`
@@ -220,14 +221,31 @@ links with from the lib/message directory.  See the
 
 ----------
 
+.. _cite:
+
+**-cite style or file name**
+
+Select how and where to output a reminder about citing contributions
+to the LAMMPS code that were used during the run. Available styles are
+"both", "none", "screen", or "log".  Any flag will be considered a file
+name to write the detailed citation info to.  Default is the "log" style
+where there is a short summary in the screen output and detailed citations
+in BibTeX format in the logfile.  The option "both" selects the detailed
+output for both, "none", the short output for both, and "screen" will
+write the detailed info to the screen and the short version to the log
+file.  If a dedicated citation info file is requested, the screen and
+log file output will be in the short format (same as with "none").
+
+See the :doc:`citation page <Intro_citing>` for more details on
+how to correctly reference and cite LAMMPS.
+
+----------
+
 .. _nocite:
 
 **-nocite**
 
-Disable writing the log.cite file which is normally written to list
+Disable generating a citation reminder (see above) at all.
-references for specific cite-able features used during a LAMMPS run.
-See the `citation page <https://lammps.sandia.gov/cite.html>`_ for more
-details.
 
 ----------
 

doc/src/compute_displace_atom.rst

@@ -46,11 +46,12 @@ the compute command was issued.  The value of the displacement will be
 .. note::
 
    Initial coordinates are stored in "unwrapped" form, by using the
-   image flags associated with each atom.  See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
+   image flags associated with each atom.  See the :doc:`dump custom
-   See the Atoms section of the :doc:`read_data <read_data>` command for a
+   <dump>` command for a discussion of "unwrapped" coordinates.  See
-   discussion of image flags and how they are set for each atom.  You can
+   the Atoms section of the :doc:`read_data <read_data>` command for a
-   reset the image flags (e.g. to 0) before invoking this compute by
+   discussion of image flags and how they are set for each atom.  You
-   using the :doc:`set image <set>` command.
+   can reset the image flags (e.g. to 0) before invoking this compute
+   by using the :doc:`set image <set>` command.
 
 .. note::
 

doc/src/compute_pressure.rst

@@ -122,8 +122,11 @@ Output info
 This compute calculates a global scalar (the pressure) and a global
 vector of length 6 (pressure tensor), which can be accessed by indices
 1-6.  These values can be used by any command that uses global scalar
-or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+or vector values from a compute as input.  See the :doc:`Howto output
-options.
+<Howto_output>` doc page for an overview of LAMMPS output options.
+
+The ordering of values in the symmetric pressure tensor is as follows:
+pxx, pyy, pzz, pxy, pxz, pyz.
 
 The scalar and vector values calculated by this compute are
 "intensive".  The scalar and vector values will be in pressure

doc/src/compute_reduce_chunk.rst

@@ -30,7 +30,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   compute 1 all reduce/chunk/atom mychunk min c_cluster
+   compute 1 all reduce/chunk mychunk min c_cluster
 
 Description
 """""""""""

doc/src/compute_stress_atom.rst

@@ -216,6 +216,11 @@ an identical manner to compute *stress/atom*.  See the :doc:`Howto
 output <Howto_output>` doc page for an overview of LAMMPS output
 options.
 
+The ordering of the 6 columns for *stress/atom* is as follows: xx, yy,
+zz, xy, xz, yz.  The ordering of the 9 columns for
+*centroid/stress/atom* is as follows: xx, yy, zz, xy, xz, yz, yx, zx,
+zy.
+
 The per-atom array values will be in pressure\*volume :doc:`units
 <units>` as discussed above.
 

doc/src/create_bonds.rst

@@ -125,6 +125,16 @@ cannot appear in the neighbor list, to avoid creation of duplicate
 bonds.  The neighbor list for all atom type pairs must also extend to
 a distance that encompasses the *rmax* for new bonds to create.
 
+.. note::
+
+   If you want to create bonds between pairs of 1-3 or 1-4 atoms in
+   the current bond topology, then you need to use :doc:`special_bonds
+   lj 0 1 1 <special_bonds>` to insure those pairs appear in the
+   neighbor list.  They will not appear with the default special_bonds
+   settings which are zero for 1-2, 1-3, and 1-4 atoms.  1-3 or 1-4
+   atoms are those which are 2 hops or 3 hops apart in the bond
+   topology.
+
 An additional requirement for this style is that your system must be
 ready to perform a simulation.  This means, for example, that all
 :doc:`pair_style <pair_style>` coefficients be set via the

doc/src/fix_addforce.rst

@@ -118,32 +118,38 @@ converge properly.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" inferred by the added force to the
+this fix to add the potential energy inferred by the added force to
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+the global potential energy of the system as part of
-needed so that the :doc:`minimize <minimize>` command can include the
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
-forces added by this fix in a consistent manner.  I.e. there is a
+this fix is :doc:`fix_modify energy no <fix_modify>`.  Note that this
-decrease in potential energy when atoms move in the direction of the
+energy is a fictitious quantity but is needed so that the
-added force.
+:doc:`minimize <minimize>` command can include the forces added by
+this fix in a consistent manner.  I.e. there is a decrease in
+potential energy when atoms move in the direction of the added force.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the added forces on atoms to the
+this fix to add the contribution due to the added forces on atoms to
-system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+both the global pressure and per-atom stress of the system via the
-The default is *virial no*
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost
+<run_style>` integrator the fix is adding its forces. Default is the
-level.
+outermost level.
 
 This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various :doc:`output commands <Howto_output>`.
+which can be accessed by various :doc:`output commands
-The scalar is the potential energy discussed above.  The vector is the
+<Howto_output>`.  The scalar is the potential energy discussed above.
-total force on the group of atoms before the forces on individual
+The vector is the total force on the group of atoms before the forces
-atoms are changed by the fix.  The scalar and vector values calculated
+on individual atoms are changed by the fix.  The scalar and vector
-by this fix are "extensive".
+values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_addtorque.rst

@@ -55,13 +55,15 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to :doc:`binary restart files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" inferred by the added forces to the
+this fix to add the potential "energy" inferred by the added torques
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+to the global potential energy of the system as part of
-needed so that the :doc:`minimize <minimize>` command can include the
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
-forces added by this fix in a consistent manner.  I.e. there is a
+this fix is :doc:`fix_modify energy no <fix_modify>`.  Note that this
-decrease in potential energy when atoms move in the direction of the
+is a fictitious quantity but is needed so that the :doc:`minimize
-added forces.
+<minimize>` command can include the forces added by this fix in a
+consistent manner.  I.e. there is a decrease in potential energy when
+atoms move in the direction of the added forces.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by
 this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
@@ -78,16 +80,28 @@ No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 
 The forces due to this fix are imposed during an energy minimization,
-invoked by the :doc:`minimize <minimize>` command.  You should not
+invoked by the :doc:`minimize <minimize>` command.
-specify force components with a variable that has time-dependence for
+
-use with a minimizer, since the minimizer increments the timestep as
+.. note::
-the iteration count during the minimization.
+
+   If you want the fictitious potential energy associated with the
+   added forces to be included in the total potential energy of the
+   system (the quantity being minimized), you MUST enable the
+   :doc:`fix_modify <fix_modify>` *energy* option for this fix.
+
+.. note::
+
+   You should not specify force components with a variable that has
+   time-dependence for use with a minimizer, since the minimizer
+   increments the timestep as the iteration count during the
+   minimization.
 
 Restrictions
 """"""""""""
 
 This fix is part of the USER-MISC 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.
 
 Related commands
 """"""""""""""""

doc/src/fix_atc.rst

@@ -122,10 +122,22 @@ Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 No information about this fix is written to :doc:`binary restart files
-<restart>`.  The :doc:`fix_modify <fix_modify>` options relevant to this
+<restart>`.
-fix are listed below.  No global scalar or vector or per-atom quantities
+
-are stored by this fix for access by various :doc:`output commands
+The :doc:`fix_modify <fix_modify>` *energy* option is not supported by
-<Howto_output>`.  No parameter of this fix can be used with the
+this fix, but this fix does add the kinetic energy imparted to atoms
+by the momentum coupling mode of the AtC package to the global
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.
+
+Additional :doc:`fix_modify <fix_modify>` options relevant to this
+fix are listed below.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the energy
+discussed in the previous paragraph.  The scalar value is "extensive".
+
+No parameter of this fix can be used with the
 *start/stop* keywords of the :doc:`run <run>` command.  This fix is not
 invoked during :doc:`energy minimization <minimize>`.
 
@@ -145,10 +157,10 @@ one, e.g. nve, nvt, etc. In addition, currently:
 Related commands
 """"""""""""""""
 
-After specifying this fix in your input script, several other
+After specifying this fix in your input script, several
-:doc:`fix_modify <fix_modify>` commands are used to setup the problem,
+:doc:`fix_modify AtC <fix_modify>` commands are used to setup the
-e.g. define the finite element mesh and prescribe initial and boundary
+problem, e.g. define the finite element mesh and prescribe initial and
-conditions.
+boundary conditions.  Each of these options has its own doc page.
 
 *fix_modify* commands for setup:
 
@@ -240,7 +252,8 @@ miscellaneous *fix_modify* commands:
 * :doc:`fix_modify AtC remove_species <atc_remove_species>`
 * :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
 
-Note: a set of example input files with the attendant material files are included in the ``examples/USER/atc`` folders.
+Note: a set of example input files with the attendant material files
+are included in the ``examples/USER/atc`` folders.
 
 Default
 """""""
@@ -252,30 +265,52 @@ For detailed exposition of the theory and algorithms please see:
 
 .. _Wagner:
 
-**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
+**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An
+ atomistic-to-continuum coupling method for heat transfer in solids."
+ Special Issue of Computer Methods and Applied Mechanics (2008)
+ 197:3351.
 
 .. _Zimmeman2004:
 
-**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
+**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE;
+ Klein, PA; Bammann, DJ, "Calculation of stress in atomistic
+ simulation." Special Issue of Modelling and Simulation in Materials
+ Science and Engineering (2004), 12:S319.
 
 .. _Zimmerman2010:
 
-**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
+**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A
+ material frame approach for evaluating continuum variables in
+ atomistic simulations." Journal of Computational Physics (2010),
+ 229:2364.
 
 .. _Templeton2010:
 
-**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
+**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application
+ of a field-based method to spatially varying thermal transport
+ problems in molecular dynamics." Modelling and Simulation in
+ Materials Science and Engineering (2010), 18:085007.
 
 .. _Jones:
 
-**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
+**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine,
+ JA, "Electron transport enhanced molecular dynamics for metals and
+ semi-metals." International Journal for Numerical Methods in
+ Engineering (2010), 83:940.
 
 .. _Templeton2011:
 
-**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
+**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA;
+ Wong, BM, "A long-range electric field solver for molecular dynamics
+ based on atomistic-to-continuum modeling." Journal of Chemical Theory
+ and Computation (2011), 7:1736.
 
 .. _Mandadapu:
 
-**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
+**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization
+ as a field variable from molecular dynamics simulations." Journal of
+ Chemical Physics (2013), 139:054115.
 
-Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
+Please refer to the standard finite element (FE) texts, e.g. T.J.R
+Hughes " The finite element method ", Dover 2003, for the basics of FE
+simulation.

doc/src/fix_bocs.rst

@@ -75,6 +75,39 @@ Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you
 are using *units real*\ , *V_avg* should be in cubic angstroms, and the
 coefficients should all be in atmospheres \* cubic angstroms.
 
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This fix writes the cumulative global energy change 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 fix continues in an uninterrupted
+fashion.
+
+The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+
+The cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
 Restrictions
 """"""""""""
 

doc/src/fix_bond_react.rst

@@ -41,7 +41,7 @@ Syntax
 * template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
 * map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
 * zero or more individual keyword/value pairs may be appended to each react argument
-* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges*
+* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create*
 
   .. parsed-literal::
 
@@ -59,6 +59,12 @@ Syntax
            off = allow both inter- and intramolecular reactions (default)
            inter = search for reactions between molecules with different IDs
            intra = search for reactions within the same molecule
+         *modify_create* keyword values
+           *fit* value = *all* or *fragmentID*
+             all = use all eligible atoms for create-atoms fit (default)
+             fragmentID = ID of molecule fragment used for create-atoms fit
+           *overlap* value = R
+             R = only insert atom/molecule if further than R from existing particles (distance units)
 
 Examples
 """"""""
@@ -89,7 +95,9 @@ documentation. Topology changes are defined in pre- and post-reaction
 molecule templates and can include creation and deletion of bonds,
 angles, dihedrals, impropers, bond types, angle types, dihedral types,
 atom types, or atomic charges. In addition, reaction by-products or
-other molecules can be identified and deleted.
+other molecules can be identified and deleted. Finally, atoms can be
+created and inserted at specific positions relative to the reaction
+site.
 
 Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
 pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
@@ -262,14 +270,14 @@ command page.
 
 The post-reacted molecule template contains a sample of the reaction
 site and its surrounding topology after the reaction has occurred. It
-must contain the same number of atoms as the pre-reacted template. A
+must contain the same number of atoms as the pre-reacted template
-one-to-one correspondence between the atom IDs in the pre- and
+(unless there are created atoms). A one-to-one correspondence between
-post-reacted templates is specified in the map file as described
+the atom IDs in the pre- and post-reacted templates is specified in
-below. Note that during a reaction, an atom, bond, etc. type may
+the map file as described below. Note that during a reaction, an atom,
-change to one that was previously not present in the simulation. These
+bond, etc. type may change to one that was previously not present in
-new types must also be defined during the setup of a given simulation.
+the simulation. These new types must also be defined during the setup
-A discussion of correctly handling this is also provided on the
+of a given simulation. A discussion of correctly handling this is also
-:doc:`molecule <molecule>` command page.
+provided on the :doc:`molecule <molecule>` command page.
 
 .. note::
 
@@ -283,7 +291,7 @@ A discussion of correctly handling this is also provided on the
 The map file is a text document with the following format:
 
 A map file has a header and a body. The header of map file the
-contains one mandatory keyword and four optional keywords. The
+contains one mandatory keyword and five optional keywords. The
 mandatory keyword is 'equivalences':
 
 .. parsed-literal::
@@ -296,11 +304,12 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
 .. parsed-literal::
 
    N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
-   N *deleteIDs* = # of atoms N that are specified for deletion
+   N *deleteIDs* = # of atoms N that are deleted
-   N *chiralIDs* = # of specified chiral centers N
+   N *createIDs* = # of atoms N that are created
-   N *constraints* = # of specified reaction constraints N
+   N *chiralIDs* = # of chiral centers N
+   N *constraints* = # of reaction constraints N
 
-The body of the map file contains two mandatory sections and four
+The body of the map file contains two mandatory sections and five
 optional sections. The first mandatory section begins with the keyword
 'InitiatorIDs' and lists the two atom IDs of the initiator atom pair
 in the pre-reacted molecule template. The second mandatory section
@@ -313,8 +322,10 @@ the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the
 pre-reacted molecule template. The second optional section begins with
 the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction
 template atoms to delete. The third optional section begins with the
+keyword 'CreateIDs' and lists the atom IDs of the post-reaction
+template atoms to create. The fourth optional section begins with the
 keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
-handedness should be enforced. The fourth optional section begins with
+handedness should be enforced. 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
 five types of constraints available, as discussed below: 'distance',
@@ -353,6 +364,38 @@ A sample map file is given below:
 
 ----------
 
+A user-specified set of atoms can be deleted by listing their
+pre-reaction template IDs in the DeleteIDs section. A deleted atom
+must still be included in the post-reaction molecule template, in
+which it cannot be bonded to an atom that is not deleted. In addition
+to deleting unwanted reaction by-products, this feature can be used to
+remove specific topologies, such as small rings, that may be otherwise
+indistinguishable.
+
+Atoms can be created by listing their post-reaction template IDs in
+the CreateIDs section. A created atom should not be included in the
+pre-reaction template. The inserted positions of created atoms are
+determined by the coordinates of the post-reaction template, after
+optimal translation and rotation of the post-reaction template to the
+reaction site (using a fit with atoms that are neither created nor
+deleted). The *modify_create* keyword can be used to modify the
+default behavior when creating atoms. The *modify_create* keyword has
+two sub-keywords, *fit* and *overlap*. One or more of the sub-keywords
+may be used after the *modify_create* keyword. The *fit* sub-keyword
+can be used to specify which post-reaction atoms are used for the
+optimal translation and rotation of the post-reaction template. The
+*fragmentID* value of the *fit* sub-keyword must be the name of a
+molecule fragment defined in the post-reaction :doc:`molecule
+<molecule>` template, and only atoms in this fragment are used for the
+fit. Atoms are created only if no current atom in the simulation is
+within a distance R of any created atom, including the effect of
+periodic boundary conditions if applicable. R is defined by the
+*overlap* sub-keyword. Note that the default value for R is 0.0, which
+will allow atoms to strongly overlap if you are inserting where other
+atoms are present. The velocity of each created atom is initialized in
+a random direction with a magnitude calculated from the instantaneous
+temperature of the reaction site.
+
 The handedness of atoms that are chiral centers can be enforced by
 listing their IDs in the ChiralIDs section. A chiral atom must be
 bonded to four atoms with mutually different atom types. This feature
@@ -528,15 +571,6 @@ the same molecule ID are considered for the reaction.
 
 A few other considerations:
 
-Many reactions result in one or more atoms that are considered
-unwanted by-products. Therefore, bond/react provides the option to
-delete a user-specified set of atoms. These pre-reaction atoms are
-identified in the map file. A deleted atom must still be included in
-the post-reaction molecule template, in which it cannot be bonded to
-an atom that is not deleted. In addition to deleting unwanted reaction
-by-products, this feature can be used to remove specific topologies,
-such as small rings, that may be otherwise indistinguishable.
-
 Optionally, you can enforce additional behaviors on reacting atoms.
 For example, it may be beneficial to force reacting atoms to remain at
 a certain temperature. For this, you can use the internally-created
@@ -610,14 +644,14 @@ Default
 """""""
 
 The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
-reset_mol_ids = yes, custom_charges = no, molecule = off
+reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
 
 ----------
 
 .. _Gissinger:
 
-**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
+**(Gissinger2017)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
 
 .. _Gissinger2020:
 
-**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
+**(Gissinger2020)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).

doc/src/fix_client_md.rst

@@ -47,14 +47,15 @@ for running *ab initio* MD with quantum forces.
 The group associated with this fix is ignored.
 
 The protocol and :doc:`units <units>` for message format and content
-that LAMMPS exchanges with the server code is defined on the :doc:`server md <server_md>` doc page.
+that LAMMPS exchanges with the server code is defined on the
+:doc:`server md <server_md>` doc page.
 
 Note that when using LAMMPS as an MD client, your LAMMPS input script
 should not normally contain force field commands, like a
 :doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`, or
-:doc:`kspace_style <kspace_style>` command.  However it is possible for
+:doc:`kspace_style <kspace_style>` command.  However it is possible
-a server code to only compute a portion of the full force-field, while
+for a server code to only compute a portion of the full force-field,
-LAMMPS computes the remaining part.  Your LAMMPS script can also
+while LAMMPS computes the remaining part.  Your LAMMPS script can also
 specify boundary conditions or force constraints in the usual way,
 which will be added to the per-atom forces returned by the server
 code.
@@ -69,16 +70,21 @@ LAMMPS and another code in tandem to perform a coupled simulation.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential energy computed by the server application to
+this fix to add the potential energy set by the server application to
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+the global potential energy of the system as part of
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy yes <fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the server application's contribution to the system's
+this fix to add the contribution computed by the server application to
-virial as part of :doc:`thermodynamic output <thermo_style>`.  The
+the global pressure of the system via the :doc:`compute pressure
-default is *virial yes*
+<compute_pressure>` command.  This can be accessed by
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -86,13 +92,16 @@ energy discussed above.  The scalar value calculated by this fix is
 "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
 This fix is part of the MESSAGE package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 A script that uses this command must also use the
 :doc:`message <message>` command to setup and shut down the messaging

doc/src/fix_cmap.rst

@@ -29,11 +29,12 @@ Description
 This command enables CMAP cross-terms to be added to simulations which
 use the CHARMM force field.  These are relevant for any CHARMM model
 of a peptide or protein sequences that is 3 or more amino-acid
-residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>` for details,
+residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>`
-including the analytic energy expressions for CMAP interactions.  The
+for details, including the analytic energy expressions for CMAP
-CMAP cross-terms add additional potential energy contributions to pairs
+interactions.  The CMAP cross-terms add additional potential energy
-of overlapping phi-psi dihedrals of amino-acids, which are important
+contributions to pairs of overlapping phi-psi dihedrals of
-to properly represent their conformational behavior.
+amino-acids, which are important to properly represent their
+conformational behavior.
 
 The examples/cmap directory has a sample input script and data file
 for a small peptide, that illustrates use of the fix cmap command.
@@ -93,19 +94,27 @@ the note below about how to include the CMAP energy when performing an
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the list of CMAP cross-terms to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>` command
+This fix writes the list of CMAP cross-terms 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 :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" of the CMAP interactions system's
+this fix to add the potential energy of the CMAP interactions to both
-potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+the global potential energy and peratom potential energies of the
+system as part of :doc:`thermodynamic output <thermo_style>` or
+output by the :doc:`compute pe/atom <compute_pe_atom>` command.  The
+default setting for this fix is :doc:`fix_modify energy yes
+<fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the interaction between atoms to
+this fix to add the contribution due to the CMAP interactions to both
-the system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+the global pressure and per-atom stress of the system via the
-The default is *virial yes*
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -121,8 +130,8 @@ invoked by the :doc:`minimize <minimize>` command.
 .. note::
 
    If you want the potential energy associated with the CMAP terms
-   forces to be included in the total potential energy of the system (the
+   forces to be included in the total potential energy of the system
-   quantity being minimized), you MUST enable the
+   (the quantity being minimized), you MUST not disable the
    :doc:`fix_modify <fix_modify>` *energy* option for this fix.
 
 Restrictions

doc/src/fix_colvars.rst

@@ -35,12 +35,12 @@ Examples
 Description
 """""""""""
 
-This fix interfaces LAMMPS to the collective variables "Colvars"
+This fix interfaces LAMMPS to the collective variables (Colvars)
-library, which allows to calculate potentials of mean force
+library, which allows to calculate potentials of mean force (PMFs) for
-(PMFs) for any set of colvars, using different sampling methods:
+any set of colvars, using different sampling methods: currently
-currently implemented are the Adaptive Biasing Force (ABF) method,
+implemented are the Adaptive Biasing Force (ABF) method, metadynamics,
-metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
+Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) via a
-(US) via a flexible harmonic restraint bias.
+flexible harmonic restraint bias.
 
 This documentation describes only the fix colvars command itself and
 LAMMPS specific parts of the code.  The full documentation of the
@@ -98,9 +98,11 @@ This fix writes the current status of the colvars module into
 mode status file that is written by the colvars module itself and the
 kind of information in both files is identical.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy change from the biasing force added by the fix
+this fix to add the energy change from the biasing force added by
-to the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+Colvars to the global potential energy of the system as part of
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy no <fix_modify>`.
 
 The *fix_modify configfile <config file>* option allows to add settings
 from an additional config file to the colvars module. This option can
@@ -113,15 +115,16 @@ in a pair of double quotes ("), or can span multiple lines when bracketed
 by a pair of triple double quotes (""", like python embedded documentation).
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the Colvars
-energy change due to this fix.  The scalar value calculated by this
+energy mentioned above.  The scalar value calculated by this fix is
-fix is "extensive".
+"extensive".
 
 Restrictions
 """"""""""""
 
 This fix is part of the USER-COLVARS 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.
 
 There can only be one colvars fix active at a time. Since the interface
 communicates only the minimum amount of information and colvars module

doc/src/fix_efield.rst

@@ -100,9 +100,9 @@ minimize the orientation of dipoles in an applied electric field.
 
 The *energy* keyword specifies the name of an atom-style
 :doc:`variable <variable>` which is used to compute the energy of each
-atom as function of its position.  Like variables used for *ex*\ , *ey*\ ,
+atom as function of its position.  Like variables used for *ex*\ ,
-*ez*\ , the energy variable is specified as v_name, where name is the
+*ey*\ , *ez*\ , the energy variable is specified as v_name, where name
-variable name.
+is the variable name.
 
 Note that when the *energy* keyword is used during an energy
 minimization, you must insure that the formula defined for the
@@ -117,31 +117,38 @@ minimization will not converge properly.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" inferred by the added force due to
+this fix to add the potential energy inferred by the added force due
-the electric field to the system's potential energy as part of
+to the electric field to the global potential energy of the system as
-:doc:`thermodynamic output <thermo_style>`.  This is a fictitious
+part of :doc:`thermodynamic output <thermo_style>`.  The default
-quantity but is needed so that the :doc:`minimize <minimize>` command
+setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
-can include the forces added by this fix in a consistent manner.
+Note that this energy is a fictitious quantity but is needed so that
-I.e. there is a decrease in potential energy when atoms move in the
+the :doc:`minimize <minimize>` command can include the forces added by
-direction of the added force due to the electric field.
+this fix in a consistent manner.  I.e. there is a decrease in
+potential energy when atoms move in the direction of the added force
+due to the electric field.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the added forces on atoms to the
+this fix to add the contribution due to the added forces on atoms to
-system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+both the global pressure and per-atom stress of the system via the
-The default is *virial no*
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix adding its forces. Default is the outermost level.
+<run_style>` integrator the fix adding its forces. Default is the
+outermost level.
 
 This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various :doc:`output commands <Howto_output>`.
+which can be accessed by various :doc:`output commands
-The scalar is the potential energy discussed above.  The vector is the
+<Howto_output>`.  The scalar is the potential energy discussed above.
-total force added to the group of atoms.  The scalar and vector values
+The vector is the total force added to the group of atoms.  The scalar
-calculated by this fix are "extensive".
+and vector values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_external.rst

@@ -84,7 +84,8 @@ code `Quest <quest_>`_.
 
 If mode is *pf/array* then the fix simply stores force values in an
 array.  The fix adds these forces to each atom in the group, once
-every *Napply* steps, similar to the way the :doc:`fix addforce <fix_addforce>` command works.
+every *Napply* steps, similar to the way the :doc:`fix addforce
+<fix_addforce>` command works.
 
 The name of the public force array provided by the FixExternal
 class is
@@ -150,19 +151,27 @@ of properties that the caller code may want to communicate  to LAMMPS
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" set by the external driver to the
+this fix to add the potential energy set by the external driver to
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+both the global potential energy and peratom potential energies of the
-needed so that the :doc:`minimize <minimize>` command can include the
+system as part of :doc:`thermodynamic output <thermo_style>` or output
-forces added by this fix in a consistent manner.  I.e. there is a
+by the :doc:`compute pe/atom <compute_pe_atom>` command.  The default
-decrease in potential energy when atoms move in the direction of the
+setting for this fix is :doc:`fix_modify energy yes <fix_modify>`.
-added force.
+Note that this energy may be a fictitious quantity but it is needed so
+that the :doc:`minimize <minimize>` command can include the forces
+added by this fix in a consistent manner.  I.e. there is a decrease in
+potential energy when atoms move in the direction of the added force.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the interactions computed by the
+this fix to add the contribution computed by the external program to
-external program to the system's virial as part of :doc:`thermodynamic output <thermo_style>`. The default is *virial yes*
+both the global pressure and per-atom stress of the system via the
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -178,7 +187,7 @@ invoked by the :doc:`minimize <minimize>` command.
 
    If you want the fictitious potential energy associated with the
    added forces to be included in the total potential energy of the
-   system (the quantity being minimized), you MUST enable the
+   system (the quantity being minimized), you MUST not disable the
    :doc:`fix_modify <fix_modify>` *energy* option for this fix.
 
 Restrictions

doc/src/fix_ffl.rst

@@ -76,28 +76,31 @@ Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 The instantaneous values of the extended variables are written to
-:doc:`binary restart files <restart>`.  Because the state of the random
+:doc:`binary restart files <restart>`.  Because the state of the
-number generator is not saved in restart files, this means you cannot
+random number generator is not saved in restart files, this means you
-do "exact" restarts with this fix, where the simulation continues on
+cannot do "exact" restarts with this fix, where the simulation
-the same as if no restart had taken place. However, in a statistical
+continues on the same as if no restart had taken place. However, in a
-sense, a restarted simulation should produce the same behavior.
+statistical sense, a restarted simulation should produce the same
-Note however that you should use a different seed each time you
+behavior.  Note however that you should use a different seed each time
-restart, otherwise the same sequence of random numbers will be used
+you restart, otherwise the same sequence of random numbers will be
-each time, which might lead to stochastic synchronization and
+used each time, which might lead to stochastic synchronization and
 subtle artifacts in the sampling.
 
+The cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the
 :doc:`run <run>` command for details of how to do this.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+This fix is not invoked during :doc:`energy minimization <minimize>`.
-fix to add the energy change induced by Langevin thermostatting to the
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
-
-This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
-energy change due to this fix.  The scalar value calculated by this
-fix is "extensive".
 
 Restrictions
 """"""""""""

doc/src/fix_flow_gauss.rst

@@ -55,17 +55,22 @@ momentum.
 GD applies an external fluctuating gravitational field that acts as a
 driving force to keep the system away from equilibrium. To maintain
 steady state, a profile-unbiased thermostat must be implemented to
-dissipate the heat that is added by the driving force. :doc:`Compute temp/profile <compute_temp_profile>` can be used to implement a
+dissipate the heat that is added by the driving force. :doc:`Compute
+temp/profile <compute_temp_profile>` can be used to implement a
 profile-unbiased thermostat.
 
 A common use of this fix is to compute a pressure drop across a pipe,
 pore, or membrane. The pressure profile can be computed in LAMMPS with
-:doc:`compute stress/atom <compute_stress_atom>` and :doc:`fix ave/chunk <fix_ave_chunk>`, or with the hardy method in :doc:`fix atc <fix_atc>`. Note that the simple :doc:`compute stress/atom <compute_stress_atom>` method is only accurate away
+:doc:`compute stress/atom <compute_stress_atom>` and :doc:`fix
-from inhomogeneities in the fluid, such as fixed wall atoms. Further,
+ave/chunk <fix_ave_chunk>`, or with the hardy method in :doc:`fix atc
-the computed pressure profile must be corrected for the acceleration
+<fix_atc>`. Note that the simple :doc:`compute stress/atom
+<compute_stress_atom>` method is only accurate away from
+inhomogeneities in the fluid, such as fixed wall atoms. Further, the
+computed pressure profile must be corrected for the acceleration
 applied by GD before computing a pressure drop or comparing it to
-other methods, such as the pump method :ref:`(Zhu) <Zhu>`. The pressure
+other methods, such as the pump method :ref:`(Zhu) <Zhu>`. The
-correction is discussed and described in :ref:`(Strong) <Strong>`.
+pressure correction is discussed and described in :ref:`(Strong)
+<Strong>`.
 
 For a complete example including the considerations discussed
 above, see the examples/USER/flow_gauss directory.
@@ -102,14 +107,15 @@ computed by the fix will return zero.
    of wall atoms fixed, such as :doc:`fix spring/self <fix_spring_self>`.
 
 If this fix is used in a simulation with the :doc:`rRESPA <run_style>`
-integrator, the applied acceleration must be computed and applied at the same
+integrator, the applied acceleration must be computed and applied at
-rRESPA level as the interactions between the flowing fluid and the obstacle.
+the same rRESPA level as the interactions between the flowing fluid
-The rRESPA level at which the acceleration is applied can be changed using
+and the obstacle.  The rRESPA level at which the acceleration is
-the :doc:`fix_modify <fix_modify>` *respa* option discussed below. If the
+applied can be changed using the :doc:`fix_modify <fix_modify>`
-flowing fluid and the obstacle interact through multiple interactions that are
+*respa* option discussed below. If the flowing fluid and the obstacle
-computed at different rRESPA levels, then there must be a separate flow/gauss
+interact through multiple interactions that are computed at different
-fix for each level. For example, if the flowing fluid and obstacle interact
+rRESPA levels, then there must be a separate flow/gauss fix for each
-through pairwise and long-range Coulomb interactions, which are computed at
+level. For example, if the flowing fluid and obstacle interact through
+pairwise and long-range Coulomb interactions, which are computed at
 rRESPA levels 3 and 4, respectively, then there must be two separate
 flow/gauss fixes, one that specifies *fix_modify respa 3* and one with
 *fix_modify respa 4*.
@@ -119,38 +125,49 @@ flow/gauss fixes, one that specifies *fix_modify respa 3* and one with
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix is part of the USER-MISC package.  It is only enabled if
+No information about this fix is written to :doc:`binary restart files
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+<restart>`.
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-
+this fix to add the potential energy added by the fix to the global
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+potential energy of the system as part of :doc:`thermodynamic output
-fix to subtract the work done from the
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+energy no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows the user to set at which level of the :doc:`rRESPA <run_style>`
+fix. This allows the user to set at which level of the :doc:`rRESPA
-integrator the fix computes and adds the external acceleration. Default is the
+<run_style>` integrator the fix computes and adds the external
-outermost level.
+acceleration. Default is the outermost level.
 
 This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various :doc:`output commands <Howto_output>`.
+which can be accessed by various :doc:`output commands
-The scalar is the negative of the work done on the system, see above
+<Howto_output>`.  The scalar is the negative of the work done on the
-discussion.  The vector is the total force that this fix applied to
+system, see the discussion above.  It is only calculated if the
-the group of atoms on the current timestep.  The scalar and vector
+*energy* keyword is enabled or :doc:`fix_modify energy yes
-values calculated by this fix are "extensive".
+<fix_modify>` is set.
+
+The vector is the total force that this fix applied to the group of
+atoms on the current timestep.  The scalar and vector values
+calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
 Restrictions
 """"""""""""
- none
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""
 
-:doc:`fix addforce <fix_addforce>`, :doc:`compute temp/profile <compute_temp_profile>`, :doc:`velocity <velocity>`
+:doc:`fix addforce <fix_addforce>`,
+:doc:`compute temp/profile <compute_temp_profile>`,
+:doc:`velocity <velocity>`
 
 Default
 """""""

doc/src/fix_gcmc.rst

@@ -398,12 +398,13 @@ adds all inserted atoms of the specified type to the
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the fix to :doc:`binary restart files <restart>`.  This includes information about the random
+This fix writes the state of the fix to :doc:`binary restart files
-number generator seed, the next timestep for MC exchanges,  the number
+<restart>`.  This includes information about the random number
-of MC step attempts and successes etc.  See
+generator seed, the next timestep for MC exchanges, the number of MC
-the :doc:`read_restart <read_restart>` command for info on how to
+step attempts and successes etc.  See the :doc:`read_restart
-re-specify a fix in an input script that reads a restart file, so that
+<read_restart>` command for info on how to re-specify a fix in an
-the operation of the fix continues in an uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 .. note::
 
@@ -411,8 +412,8 @@ the operation of the fix continues in an uninterrupted fashion.
    after reading the restart with :doc:`reset_timestep <reset_timestep>`.
    The fix will try to detect it and stop with an error.
 
-None of the :doc:`fix_modify <fix_modify>` options are relevant to this
+None of the :doc:`fix_modify <fix_modify>` options are relevant to
-fix.
+this fix.
 
 This fix computes a global vector of length 8, which can be accessed
 by various :doc:`output commands <Howto_output>`.  The vector values are
@@ -430,7 +431,8 @@ the following global cumulative quantities:
 The vector values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_gle.rst

@@ -103,28 +103,31 @@ Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 The instantaneous values of the extended variables are written to
-:doc:`binary restart files <restart>`.  Because the state of the random
+:doc:`binary restart files <restart>`.  Because the state of the
-number generator is not saved in restart files, this means you cannot
+random number generator is not saved in restart files, this means you
-do "exact" restarts with this fix, where the simulation continues on
+cannot do "exact" restarts with this fix, where the simulation
-the same as if no restart had taken place. However, in a statistical
+continues on the same as if no restart had taken place. However, in a
-sense, a restarted simulation should produce the same behavior.
+statistical sense, a restarted simulation should produce the same
-Note however that you should use a different seed each time you
+behavior.  Note however that you should use a different seed each time
-restart, otherwise the same sequence of random numbers will be used
+you restart, otherwise the same sequence of random numbers will be
-each time, which might lead to stochastic synchronization and
+used each time, which might lead to stochastic synchronization and
 subtle artifacts in the sampling.
 
+The cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the
 :doc:`run <run>` command for details of how to do this.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+This fix is not invoked during :doc:`energy minimization <minimize>`.
-fix to add the energy change induced by Langevin thermostatting to the
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
-
-This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
-energy change due to this fix.  The scalar value calculated by this
-fix is "extensive".
 
 Restrictions
 """"""""""""

doc/src/fix_gravity.rst

@@ -103,23 +103,27 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to :doc:`binary restart files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the gravitational potential energy of the system to the
+this fix to add the gravitational potential energy of the system to
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+the global potential energy of the system as part of
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost level.
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  This scalar is the gravitational
+:doc:`output commands <Howto_output>`.  This scalar is the
-potential energy of the particles in the defined field, namely mass \*
+gravitational potential energy of the particles in the defined field,
-(g dot x) for each particles, where x and mass are the particles
+namely mass \* (g dot x) for each particles, where x and mass are the
-position and mass, and g is the gravitational field.  The scalar value
+particles position and mass, and g is the gravitational field.  The
-calculated by this fix is "extensive".
+scalar value calculated by this fix is "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_hyper_global.rst

@@ -200,16 +200,20 @@ algorithm.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy of the bias potential to the system's
+this fix to add the energy of the bias potential to the global
-potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+energy no <fix_modify>`.
 
-This fix computes a global scalar and global vector of length 12, which
+This fix computes a global scalar and global vector of length 12,
-can be accessed by various :doc:`output commands <Howto_output>`.  The
+which can be accessed by various :doc:`output commands
-scalar is the magnitude of the bias potential (energy units) applied on
+<Howto_output>`.  The scalar is the magnitude of the bias potential
-the current timestep.  The vector stores the following quantities:
+(energy units) applied on the current timestep.  The vector stores the
+following quantities:
 
 * 1 = boost factor on this step (unitless)
 * 2 = max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless)
@@ -253,7 +257,8 @@ The scalar and vector values calculated by this fix are all
 "intensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_hyper_local.rst

@@ -370,15 +370,17 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to :doc:`binary restart files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy of the bias potential to the system's potential
+this fix to add the energy of the bias potential to the global
-energy as part of :doc:`thermodynamic output <thermo_style>`.
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+energy no <fix_modify>`.
 
 This fix computes a global scalar and global vector of length 28,
-which can be accessed by various :doc:`output commands <Howto_output>`.
+which can be accessed by various :doc:`output commands
-The scalar is the magnitude of the bias potential (energy units)
+<Howto_output>`.  The scalar is the magnitude of the bias potential
-applied on the current timestep, summed over all biased bonds.  The
+(energy units) applied on the current timestep, summed over all biased
-vector stores the following quantities:
+bonds.  The vector stores the following quantities:
 
 * 1 = average boost for all bonds on this step (unitless)
 * 2 = # of biased bonds on this step
@@ -510,8 +512,8 @@ Value 27 computes the average boost for biased bonds only on this step.
 Value 28 is the count of bonds with an absolute value of strain >= q
 on this step.
 
-The scalar and vector values calculated by this fix are all
+The scalar value is an "extensive" quantity since it grows with the
-"intensive".
+system size; the vector values are all "intensive".
 
 This fix also computes a local vector of length the number of bonds
 currently in the system.  The value for each bond is its :math:`C_{ij}`
@@ -524,7 +526,8 @@ close to 1.0, which indicates a good choice of :math:`V^{max}`.
 The local values calculated by this fix are unitless.
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_indent.rst

@@ -179,20 +179,25 @@ contains *xlat*\ , *ylat*\ , *zlat* keywords of the
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy of interaction between atoms and the indenter to
+this fix to add the energy of interaction between atoms and the
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  The energy of each particle interacting
+indenter to the global potential energy of the system as part of
-with the indenter is K/3 (r - R)\^3.
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy no <fix_modify>`. The energy of
+each particle interacting with the indenter is K/3 (r - R)\^3.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost level.
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
 
 This fix computes a global scalar energy and a global 3-vector of
-forces (on the indenter), which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar and vector values calculated
+forces (on the indenter), which can be accessed by various
-by this fix are "extensive".
+:doc:`output commands <Howto_output>`.  The scalar and vector values
+calculated by this fix are "extensive".
 
 The forces due to this fix are imposed during an energy minimization,
 invoked by the :doc:`minimize <minimize>` command.  Note that if you
@@ -204,10 +209,10 @@ check if you have done this.
 
 .. note::
 
-   If you want the atom/indenter interaction energy to be included
+   If you want the atom/indenter interaction energy to be included in
-   in the total potential energy of the system (the quantity being
+   the total potential energy of the system (the quantity being
-   minimized), you must enable the :doc:`fix_modify <fix_modify>` *energy*
+   minimized), you must enable the :doc:`fix_modify <fix_modify>`
-   option for this fix.
+   *energy* option for this fix.
 
 Restrictions
 """"""""""""

doc/src/fix_langevin.rst

@@ -230,7 +230,7 @@ conservation.
 
 .. note::
 
-   this accumulated energy does NOT include kinetic energy removed
+   This accumulated energy does NOT include kinetic energy removed
    by the *zero* flag. LAMMPS will print a warning when both options are
    active.
 
@@ -244,7 +244,8 @@ to zero by subtracting off an equal part of it from each atom in the
 group.  As a result, the center-of-mass of a system with zero initial
 momentum will not drift over time.
 
-The keyword *gjf* can be used to run the :ref:`Gronbech-Jensen/Farago <Gronbech-Jensen>` time-discretization of the Langevin model.  As
+The keyword *gjf* can be used to run the :ref:`Gronbech-Jensen/Farago
+<Gronbech-Jensen>` time-discretization of the Langevin model.  As
 described in the papers cited below, the purpose of this method is to
 enable longer timesteps to be used (up to the numerical stability
 limit of the integrator), while still producing the correct Boltzmann
@@ -252,19 +253,20 @@ distribution of atom positions.
 
 The current implementation provides the user with the option to output
 the velocity in one of two forms: *vfull* or *vhalf*\ , which replaces
-the outdated option *yes*\ . The *gjf* option *vfull* outputs the on-site
+the outdated option *yes*\ . The *gjf* option *vfull* outputs the
-velocity given in :ref:`Gronbech-Jensen/Farago <Gronbech-Jensen>`; this velocity
+on-site velocity given in :ref:`Gronbech-Jensen/Farago
-is shown to be systematically lower than the target temperature by a small
+<Gronbech-Jensen>`; this velocity is shown to be systematically lower
-amount, which grows quadratically with the timestep.
+than the target temperature by a small amount, which grows
-The *gjf* option *vhalf* outputs the 2GJ half-step velocity given in
+quadratically with the timestep.  The *gjf* option *vhalf* outputs the
-:ref:`Gronbech Jensen/Gronbech-Jensen <2Gronbech-Jensen>`; for linear systems,
+2GJ half-step velocity given in :ref:`Gronbech Jensen/Gronbech-Jensen
-this velocity is shown to not have any statistical errors for any stable time step.
+<2Gronbech-Jensen>`; for linear systems, this velocity is shown to not
-An overview of statistically correct Boltzmann and Maxwell-Boltzmann
+have any statistical errors for any stable time step.  An overview of
-sampling of true on-site and true half-step velocities is given in
+statistically correct Boltzmann and Maxwell-Boltzmann sampling of true
-:ref:`Gronbech-Jensen <1Gronbech-Jensen>`.
+on-site and true half-step velocities is given in
-Regardless of the choice of output velocity, the sampling of the configurational
+:ref:`Gronbech-Jensen <1Gronbech-Jensen>`.  Regardless of the choice
-distribution of atom positions is the same, and linearly consistent with the
+of output velocity, the sampling of the configurational distribution
-target temperature.
+of atom positions is the same, and linearly consistent with the target
+temperature.
 
 ----------
 
@@ -287,16 +289,18 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Langevin thermostatting to the
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  Note that use of this option requires
+*ecouple* and *econserve*\ , but only if the *tally* keyword to set to
-setting the *tally* keyword to *yes*\ .
+*yes*\ .  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the same
-energy change due to this fix.  The scalar value calculated by this
+cumulative energy change due to this fix described in the previous
-fix is "extensive".  Note that calculation of this quantity requires
+paragraph.  The scalar value calculated by this fix is "extensive".
-setting the *tally* keyword to *yes*\ .
+Note that calculation of this quantity also requires setting the
+*tally* keyword to *yes*\ .
 
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the

doc/src/fix_langevin_eff.rst

@@ -81,16 +81,18 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Langevin thermostatting to the
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  Note that use of this option requires
+*ecouple* and *econserve*\ , but only if the *tally* keyword to set to
-setting the *tally* keyword to *yes*\ .
+*yes*\ .  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the same
-energy change due to this fix.  The scalar value calculated by this
+cumulative energy change due to this fix described in the previous
-fix is "extensive".  Note that calculation of this quantity requires
+paragraph.  The scalar value calculated by this fix is "extensive".
-setting the *tally* keyword to *yes*\ .
+Note that calculation of this quantity also requires setting the
+*tally* keyword to *yes*\ .
 
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the

doc/src/fix_latte.rst

@@ -107,16 +107,27 @@ larger system sizes and longer time scales
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential energy computed by LATTE to the system's
+this fix to add the potential energy computed by LATTE to the global
-potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+energy yes <fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the LATTE DFTB contribution to the system's virial as part
+this fix to add the contribution compute by LATTE to the global
-of :doc:`thermodynamic output <thermo_style>`.  The default is *virial
+pressure of the system via the :doc:`compute pressure
-yes*
+<compute_pressure>` command.  This can be accessed by
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify virial yes <fix_modify>`.
+
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
+this fix to add the contribution computed by LATTE to the global
+pressure of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+virial yes <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -127,20 +138,22 @@ No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 
 The DFTB forces computed by LATTE via this fix are imposed during an
-energy minimization, invoked by the :doc:`minimize <minimize>` command.
+energy minimization, invoked by the :doc:`minimize <minimize>`
+command.
 
 .. note::
 
    If you want the potential energy associated with the DFTB
    forces to be included in the total potential energy of the system (the
-   quantity being minimized), you MUST enable the
+   quantity being minimized), you MUST not disable the
    :doc:`fix_modify <fix_modify>` *energy* option for this fix.
 
 Restrictions
 """"""""""""
 
 This fix is part of the LATTE package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 You must use metal units, as set by the :doc:`units <units>` command to
 use this fix.

doc/src/fix_lb_rigid_pc_sphere.rst

@@ -50,7 +50,8 @@ This fix is based on the :doc:`fix rigid <fix_rigid>` command, and was
 created to be used in place of that fix, to integrate the equations of
 motion of spherical rigid bodies when a lattice-Boltzmann fluid is
 present with a user-specified value of the force-coupling constant.
-The fix uses the integration algorithm described in :ref:`Mackay et al. <Mackay>` to update the positions, velocities, and orientations of
+The fix uses the integration algorithm described in :ref:`Mackay et
+al. <Mackay>` to update the positions, velocities, and orientations of
 a set of spherical rigid bodies experiencing velocity dependent
 hydrodynamic forces.  The spherical bodies are assumed to rotate as
 solid, uniform density spheres, with moments of inertia calculated
@@ -88,9 +89,18 @@ Restart, fix_modify, output, run start/stop, minimize info
 No information about the *rigid* and *rigid/nve* fixes are written to
 :doc:`binary restart files <restart>`.
 
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
+this fix to add the contribution due to the added forces on atoms to
+both the global pressure and per-atom stress of the system via the
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
+
 Similar to the :doc:`fix rigid <fix_rigid>` command: The rigid fix
-computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar value calculated by these
+computes a global scalar which can be accessed by various :doc:`output
-fixes is "intensive".  The scalar is the current temperature of the
+commands <Howto_output>`.  The scalar value calculated by these fixes
+is "intensive".  The scalar is the current temperature of the
 collection of rigid bodies.  This is averaged over all rigid bodies
 and their translational and rotational degrees of freedom.  The
 translational energy of a rigid body is 1/2 m v\^2, where m = total
@@ -130,7 +140,8 @@ Restrictions
 """"""""""""
 
 This fix is part of the USER-LB package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Can only be used if a lattice-Boltzmann fluid has been created via the
 :doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this

doc/src/fix_modify.rst

@@ -59,43 +59,58 @@ define their own compute by default, as described in their
 documentation.  Thus this option allows the user to override the
 default method for computing P.
 
-The *energy* keyword can be used with fixes that support it.
+The *energy* keyword can be used with fixes that support it, which is
-*energy yes* adds a contribution to the potential energy of the
+explained at the bottom of their doc page.  *Energy yes* will add a
-system. The fix's global and per-atom
+contribution to the potential energy of the system.  More
-energy is included in the calculation performed by the :doc:`compute pe <compute_pe>` or :doc:`compute pe/atom <compute_pe_atom>`
+specifically, the fix's global or per-atom energy is included in the
-commands.  See the :doc:`thermo_style <thermo_style>` command for info
+calculation performed by the :doc:`compute pe <compute_pe>` or
-on how potential energy is output.  For fixes that tally a global
+:doc:`compute pe/atom <compute_pe_atom>` commands.  The former is what
-energy, it can be printed by using the keyword f_ID in the
+is used the :doc:`thermo_style <thermo_style>` command for output of
-thermo_style custom command, where ID is the fix-ID of the appropriate
+any quantity that includes the global potential energy of the system.
-fix.
+Note that the :doc:`compute pe <compute_pe>` and :doc:`compute pe/atom
+<compute_pe_atom>` commands also have an option to include or exclude
+the contribution from fixes.  For fixes that tally a global energy, it
+can also be printed with thermodynamic output by using the keyword
+f_ID in the thermo_style custom command, where ID is the fix-ID of the
+appropriate fix.
 
 .. note::
 
-   You must also specify the *energy yes* setting for a fix if you
+   If you are performing an :doc:`energy minimization <minimize>` with
-   are using it when performing an :doc:`energy minimization <minimize>`
+   one of these fixes and want the energy and forces it produces to be
-   and if you want the energy and forces it produces to be part of the
+   part of the optimization criteria, you must specify the *energy
-   optimization criteria.
+   yes* setting.
-
-The *virial* keyword can be used with fixes that support it.
-*virial yes* adds a contribution to the virial of the
-system. The fix's global and per-atom
-virial is included in the calculation performed by the :doc:`compute pressure <compute_pressure>` or
-:doc:`compute stress/atom <compute_stress_atom>`
-commands.  See the :doc:`thermo_style <thermo_style>` command for info
-on how pressure is output.
 
 .. note::
 
-   You must specify the *virial yes* setting for a fix if you
+   For most fixes that support the *energy* keyword, the default
-   are doing :doc:`box relaxation <fix_box_relax>` and
+   setting is *no*.  For a few it is *yes*, when a user would expect
-   if you want virial contribution of the fix to be part of the
+   that to be the case.  The doc page of each fix gives the default.
-   relaxation criteria, although this seems unlikely.
+
+The *virial* keyword can be used with fixes that support it, which is
+explained at the bottom of their doc page.  *Virial yes* will add a
+contribution to the virial of the system.  More specifically, the
+fix's global or per-atom virial is included in the calculation
+performed by the :doc:`compute pressure <compute_pressure>` or
+:doc:`compute stress/atom <compute_stress_atom>` commands.  The former
+is what is used the :doc:`thermo_style <thermo_style>` command for
+output of any quantity that includes the global pressure of the
+system.  Note that the :doc:`compute pressure <compute_pressure>` and
+:doc:`compute stress/atom <compute_stress_atom>` commands also have an
+option to include or exclude the contribution from fixes.
 
 .. note::
 
-   This option is only supported by fixes that explicitly say
+   If you are performing an :doc:`energy minimization <minimize>` with
-   so. For some of these (e.g. the :doc:`fix shake <fix_shake>` command)
+   :doc:`box relaxation <fix_box_relax>` and one of these fixes and
-   the default setting is *virial yes*\ , for others it is *virial no*\ .
+   want the virial contribution of the fix to be part of the
+   optimization criteria, you must specify the *virial yes* setting.
+
+.. note::
+
+   For most fixes that support the *virial* keyword, the default
+   setting is *no*.  For a few it is *yes*, when a user would expect
+   that to be the case.  The doc page of each fix gives the default.
 
 For fixes that set or modify forces, it may be possible to select at
 which :doc:`r-RESPA <run_style>` level the fix operates via the *respa*
@@ -112,13 +127,15 @@ The *dynamic/dof* keyword determines whether the number of atoms N in
 the fix group and their associated degrees of freedom are re-computed
 each time a temperature is computed.  Only fix styles that calculate
 their own internal temperature use this option.  Currently this is
-only the :doc:`fix rigid/nvt/small <fix_rigid>` and :doc:`fix rigid/npt/small <fix_rigid>` commands for the purpose of
+only the :doc:`fix rigid/nvt/small <fix_rigid>` and :doc:`fix
+rigid/npt/small <fix_rigid>` commands for the purpose of
 thermostatting rigid body translation and rotation.  By default, N and
 their DOF are assumed to be constant.  If you are adding atoms or
-molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
+molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix
+deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
 expect atoms or molecules to be lost (e.g. due to exiting the
-simulation box or via :doc:`fix evaporate <fix_evaporate>`), then
+simulation box or via :doc:`fix evaporate <fix_evaporate>`), then this
-this option should be used to insure the temperature is correctly
+option should be used to insure the temperature is correctly
 normalized.
 
 .. note::

doc/src/fix_msst.rst

@@ -131,20 +131,29 @@ 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 cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
 The progress of the MSST can be monitored by printing the global
 scalar and global vector quantities computed by the fix.
 
-The scalar is the cumulative energy change due to the fix. This is
+As mentioned above, the scalar is the cumulative energy change due to
-also the energy added to the potential energy by the
+the fix.  By monitoring the thermodynamic *econserve* output, this can
-:doc:`fix_modify <fix_modify>` *energy* command.  With this command, the
+be used to test if the MD timestep is sufficiently small for accurate
-thermo keyword *etotal* prints the conserved quantity of the MSST
+integration of the dynamic equations.
-dynamic equations. This can be used to test if the MD timestep is
-sufficiently small for accurate integration of the dynamic
-equations. See also :doc:`thermo_style <thermo_style>` command.
 
-The global vector contains four values in this order:
+The global vector contains four values in the following order.  The
+vector values output by this fix are "intensive".
 
-[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, *lagrangian_position*]
+[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*,
+*lagrangian_position*]
 
 1. *dhugoniot* is the departure from the Hugoniot (temperature units).
 2. *drayleigh* is the departure from the Rayleigh line (pressure units).
@@ -157,17 +166,11 @@ headers, the following LAMMPS commands are suggested:
 .. code-block:: LAMMPS
 
    fix              msst all msst z
-   fix_modify       msst energy yes
    variable dhug    equal f_msst[1]
    variable dray    equal f_msst[2]
    variable lgr_vel equal f_msst[3]
    variable lgr_pos equal f_msst[4]
-   thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+   thermo_style     custom step temp ke pe lz pzz econserve 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".
 
 Restrictions
 """"""""""""

doc/src/fix_nh.rst

@@ -594,17 +594,20 @@ compute temperature on a subset of atoms.
    specified by the *press* keyword will be unaffected by the *temp*
    setting.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by these
+The cumulative energy change in the system imposed by these fixes, via
-fixes to add the energy change induced by Nose/Hoover thermostatting
+either thermostatting and/or barostatting, is included in the
-and barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>` keywords *ecouple* and
-:doc:`thermodynamic output <thermo_style>`.
+*econserve*.  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
-These fixes compute a global scalar and a global vector of quantities,
+These fixes compute a global scalar which can be accessed by various
-which can be accessed by various :doc:`output commands <Howto_output>`.
+:doc:`output commands <Howto_output>`.  The scalar is the same
-The scalar value calculated by these fixes is "extensive"; the vector
+cumulative energy change due to this fix described in the previous
-values are "intensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
 
-The scalar is the cumulative energy change due to the fix.
+These fixes compute also compute a global vector of quantities, which
+can be accessed by various :doc:`output commands <Howto_output>`.  The
+vector values are "intensive".
 
 The vector stores internal Nose/Hoover thermostat and barostat
 variables.  The number and meaning of the vector values depends on

doc/src/fix_nph_asphere.rst

@@ -87,7 +87,8 @@ It also means that changing attributes of *thermo_temp* or
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover barostat 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.
@@ -101,9 +102,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover barostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nph <fix_nh>` command.

doc/src/fix_nph_body.rst

@@ -84,7 +84,8 @@ It also means that changing attributes of *thermo_temp* or
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover barostat 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.
@@ -98,9 +99,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover barostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nph <fix_nh>` command.

doc/src/fix_nph_sphere.rst

@@ -100,7 +100,8 @@ It also means that changing attributes of *thermo_temp* or
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover barostat 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.
@@ -114,9 +115,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover barostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nph <fix_nh>` command.

doc/src/fix_nphug.rst

@@ -168,43 +168,47 @@ specified, then the instantaneous value in the system at the start of
 the simulation is used.
 
 The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
-supported by these fixes.  You can use them to assign a
+supported by this fix.  You can use them to assign a :doc:`compute
-:doc:`compute <compute>` you have defined to this fix which will be used
+<compute>` you have defined to this fix which will be used in its
-in its thermostatting or barostatting procedure, as described above.
+thermostatting or barostatting procedure, as described above.  If you
-If you do this, note that the kinetic energy derived from the compute
+do this, note that the kinetic energy derived from the compute
 temperature should be consistent with the virial term computed using
 all atoms for the pressure.  LAMMPS will warn you if you choose to
 compute temperature on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by these
+The cumulative energy change in the system imposed by this fix is
-fixes to add the energy change induced by Nose/Hoover thermostatting
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-and barostatting to the system's potential energy as part of
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-:doc:`thermodynamic output <thermo_style>`. Either way, this energy is \*not\*
+doc page for details.  Note that this energy is \*not\* included in
-included in the definition of internal energy E when calculating the value
+the definition of internal energy E when calculating the value of
-of Delta in the above equation.
+Delta in the above equation.
 
-These fixes compute a global scalar and a global vector of quantities,
+This fix computes a global scalar which can be accessed by various
-which can be accessed by various :doc:`output commands <Howto_output>`.
+:doc:`output commands <Howto_output>`.  The scalar is the same
-The scalar value calculated by these fixes is "extensive"; the vector
+cumulative energy change due to this fix described in the previous
-values are "intensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
 
-The scalar is the cumulative energy change due to the fix.
+This fix also computes a global vector of quantities, which can be
+accessed by various :doc:`output commands <Howto_output>`.  The scalar
+The vector values are "intensive".
 
-The vector stores three quantities unique to this fix (:math:`\Delta`, Us, and up),
+The vector stores three quantities unique to this fix (:math:`\Delta`,
-followed by all the internal Nose/Hoover thermostat and barostat
+Us, and up), followed by all the internal Nose/Hoover thermostat and
-variables defined for :doc:`fix npt <fix_nh>`. Delta is the deviation
+barostat variables defined for :doc:`fix npt <fix_nh>`. Delta is the
-of the temperature from the target temperature, given by the above equation.
+deviation of the temperature from the target temperature, given by the
-Us and up are the shock and particle velocity corresponding to a steady
+above equation.  Us and up are the shock and particle velocity
-shock calculated from the RH conditions. They have units of distance/time.
+corresponding to a steady shock calculated from the RH
+conditions. They have units of distance/time.
 
 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 the usual restrictions for :doc:`fix npt <fix_nh>` apply,
+All the usual restrictions for :doc:`fix npt <fix_nh>` apply, plus the
-plus the additional ones mentioned above.
+additional ones mentioned above.
 
 Related commands
 """"""""""""""""

doc/src/fix_npt_asphere.rst

@@ -124,10 +124,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting and
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-barostatting to the system's potential energy as part of
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-:doc:`thermodynamic output <thermo_style>`.
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix npt <fix_nh>` command.

doc/src/fix_npt_body.rst

@@ -45,7 +45,8 @@ can also have a bias velocity removed from them before thermostatting
 takes place; see the description below.
 
 Additional parameters affecting the thermostat and barostat are
-specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command.  See, for example, discussion of the *temp*\ ,
+specified by keywords and values documented with the :doc:`fix npt
+<fix_nh>` command.  See, for example, discussion of the *temp*\ ,
 *iso*\ , *aniso*\ , and *dilate* keywords.
 
 The particles in the fix group are the only ones whose velocities and
@@ -121,10 +122,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting and
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-barostatting to the system's potential energy as part of
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-:doc:`thermodynamic output <thermo_style>`.
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix npt <fix_nh>` command.

doc/src/fix_npt_cauchy.rst

@@ -487,27 +487,31 @@ compute temperature on a subset of atoms.
 .. note::
 
    If both the *temp* and *press* keywords are used in a single
-   thermo_modify command (or in two separate commands), then the order in
+   thermo_modify command (or in two separate commands), then the order
-   which the keywords are specified is important.  Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
+   in which the keywords are specified is important.  Note that a
-   an argument when it is specified.  The *temp* keyword will override
+   :doc:`pressure compute <compute_pressure>` defines its own
-   this (for the pressure compute being used by fix npt), but only if the
+   temperature compute as an argument when it is specified.  The
-   *temp* keyword comes after the *press* keyword.  If the *temp* keyword
+   *temp* keyword will override this (for the pressure compute being
-   comes before the *press* keyword, then the new pressure compute
+   used by fix npt), but only if the *temp* keyword comes after the
-   specified by the *press* keyword will be unaffected by the *temp*
+   *press* keyword.  If the *temp* keyword comes before the *press*
-   setting.
+   keyword, then the new pressure compute specified by the *press*
+   keyword will be unaffected by the *temp* setting.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix, due to
-fix to add the energy change induced by Nose/Hoover thermostatting
+thermostatting and/or barostatting, is included in the
-and barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>` keywords *ecouple* and
-:doc:`thermodynamic output <thermo_style>`.
+*econserve*.  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
-This fix computes a global scalar and a global vector of quantities,
+This fix computes a global scalar which can be accessed by various
-which can be accessed by various :doc:`output commands <Howto_output>`.
+:doc:`output commands <Howto_output>`.  The scalar is the same
-The scalar value calculated by this fix is "extensive"; the vector
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
+This fix also computes a global vector of quantities, which can be
+accessed by various :doc:`output commands <Howto_output>`.  Rhe vector
 values are "intensive".
 
-The scalar is the cumulative energy change due to the fix.
-
 The vector stores internal Nose/Hoover thermostat and barostat
 variables.  The number and meaning of the vector values depends on
 which fix is used and the settings for keywords *tchain* and *pchain*\ ,

doc/src/fix_npt_sphere.rst

@@ -93,13 +93,14 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
 since pressure is computed for the entire system.
 
 Note that these are NOT the computes used by thermodynamic output (see
-the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*
+the :doc:`thermo_style <thermo_style>` command) with ID =
-and *thermo_press*.  This means you can change the attributes of this
+*thermo_temp* and *thermo_press*.  This means you can change the
-fix's temperature or pressure via the
+attributes of this fix's temperature or pressure via the
-:doc:`compute_modify <compute_modify>` command or print this temperature
+:doc:`compute_modify <compute_modify>` command or print this
-or pressure during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
+temperature or pressure during thermodynamic output via the
-It also means that changing attributes of *thermo_temp* or
+:doc:`thermo_style custom <thermo_style>` command using the
-*thermo_press* will have no effect on this fix.
+appropriate compute-ID.  It also means that changing attributes of
+*thermo_temp* or *thermo_press* will have no effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
 with :doc:`compute commands <compute>` that calculate a temperature
@@ -129,18 +130,18 @@ a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
-supported by this fix.  You can use them to assign a
+supported by this fix.  You can use them to assign a :doc:`compute
-:doc:`compute <compute>` you have defined to this fix which will be used
+<compute>` you have defined to this fix which will be used in its
-in its thermostatting or barostatting procedure.  If you do this, note
+thermostatting or barostatting procedure.  If you do this, note that
-that the kinetic energy derived from the compute temperature should be
+the kinetic energy derived from the compute temperature should be
 consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting and
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-barostatting to the system's potential energy as part of
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-:doc:`thermodynamic output <thermo_style>`.
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix npt <fix_nh>` command.

doc/src/fix_nvt_asphere.rst

@@ -92,19 +92,21 @@ thermal degrees of freedom, and the bias is added back in.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt <fix_nh>` command.

doc/src/fix_nvt_body.rst

@@ -89,19 +89,21 @@ thermal degrees of freedom, and the bias is added back in.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt <fix_nh>` command.

doc/src/fix_nvt_sllod.rst

@@ -122,19 +122,21 @@ thermal degrees of freedom, and the bias is added back in.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt <fix_nh>` command.

doc/src/fix_nvt_sllod_eff.rst

@@ -41,19 +41,21 @@ velocity.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt/eff <fix_nh_eff>` command.

doc/src/fix_nvt_sphere.rst

@@ -106,19 +106,21 @@ thermal degrees of freedom, and the bias is added back in.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt <fix_nh>` command.

doc/src/fix_orient.rst

@@ -144,16 +144,20 @@ writing the orientation files is given in :ref:`(Wicaksono2) <Wicaksono2>`
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential energy of atom interactions with the grain
+this fix to add the potential energy of atom interactions with the
-boundary driving force to the system's potential energy as part of
+grain boundary driving force to the global potential energy of the
-:doc:`thermodynamic output <thermo_style>`.
+system as part of :doc:`thermodynamic output <thermo_style>`.  The
+default setting for this fix is :doc:`fix_modify energy no
+<fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *respa* option is supported by these
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by
-fixes. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+these fixes. This allows to set at which level of the :doc:`r-RESPA
-integrator a fix is adding its forces. Default is the outermost level.
+<run_style>` integrator a fix is adding its forces. Default is the
+outermost level.
 
 This fix calculates a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -166,13 +170,16 @@ order parameter Xi and normalized order parameter (0 to 1) for each
 atom.  The per-atom values can be accessed on any timestep.
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
 This fix is part of the MISC package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 This fix should only be used with fcc or bcc lattices.
 

doc/src/fix_orient_eco.rst

@@ -26,22 +26,24 @@ Examples
 Description
 """""""""""
 
-The fix applies a synthetic driving force to a grain boundary which can
+The fix applies a synthetic driving force to a grain boundary which
-be used for the investigation of grain boundary motion. The affiliation
+can be used for the investigation of grain boundary motion. The
-of atoms to either of the two grains forming the grain boundary is
+affiliation of atoms to either of the two grains forming the grain
-determined from an orientation-dependent order parameter as described
+boundary is determined from an orientation-dependent order parameter
-in :ref:`(Ulomek) <Ulomek>`. The potential energy of atoms is either increased by an amount
+as described in :ref:`(Ulomek) <Ulomek>`. The potential energy of
-of 0.5*\ *u0* or -0.5*\ *u0* according to the orientation of the surrounding
+atoms is either increased by an amount of 0.5*\ *u0* or -0.5*\ *u0*
-crystal. This creates a potential energy gradient which pushes atoms near
+according to the orientation of the surrounding crystal. This creates
-the grain boundary to orient according to the energetically favorable
+a potential energy gradient which pushes atoms near the grain boundary
-grain orientation. This fix is designed for applications in bicrystal system
+to orient according to the energetically favorable grain
-with one grain boundary and open ends, or two opposite grain boundaries in
+orientation. This fix is designed for applications in bicrystal system
-a periodic system. In either case, the entire system can experience a
+with one grain boundary and open ends, or two opposite grain
-displacement during the simulation which needs to be accounted for in the
+boundaries in a periodic system. In either case, the entire system can
-evaluation of the grain boundary velocity. While the basic method is
+experience a displacement during the simulation which needs to be
-described in :ref:`(Ulomek) <Ulomek>`, the implementation follows the efficient
+accounted for in the evaluation of the grain boundary velocity. While
-implementation from :ref:`(Schratt & Mohles) <Schratt>`. The synthetic potential energy added to an
+the basic method is described in :ref:`(Ulomek) <Ulomek>`, the
-atom j is given by the following formulas
+implementation follows the efficient implementation from
+:ref:`(Schratt & Mohles) <Schratt>`. The synthetic potential energy
+added to an atom j is given by the following formulas
 
 .. math::
 
@@ -60,60 +62,69 @@ atom j is given by the following formulas
 which are fully explained in :ref:`(Ulomek) <Ulomek>`
 and :ref:`(Schratt & Mohles) <Schratt>`.
 
-The force on each atom is the negative gradient of the synthetic potential energy. It
+The force on each atom is the negative gradient of the synthetic
-depends on the surrounding of this atom. An atom far from the grain boundary does not
+potential energy. It depends on the surrounding of this atom. An atom
-experience a synthetic force as its surrounding is that of an oriented single crystal
+far from the grain boundary does not experience a synthetic force as
-and thermal fluctuations are masked by the parameter *eta*\ . Near the grain boundary
+its surrounding is that of an oriented single crystal and thermal
-however, the gradient is nonzero and synthetic force terms are computed.
+fluctuations are masked by the parameter *eta*\ . Near the grain
-The orientationsFile specifies the perfect oriented crystal basis vectors for the
+boundary however, the gradient is nonzero and synthetic force terms
-two adjoining crystals. The first three lines (line=row vector) for the energetically penalized and the
+are computed.  The orientationsFile specifies the perfect oriented
-last three lines for the energetically favored grain assuming *u0* is positive. For
+crystal basis vectors for the two adjoining crystals. The first three
-negative *u0*, this is reversed. With the *cutoff* parameter, the size of the region around
+lines (line=row vector) for the energetically penalized and the last
-each atom which is used in the order parameter computation is defined. The cutoff must be
+three lines for the energetically favored grain assuming *u0* is
-smaller than the interaction range of the MD potential. It should at
+positive. For negative *u0*, this is reversed. With the *cutoff*
-least include the nearest neighbor shell. For high temperatures or low angle
+parameter, the size of the region around each atom which is used in
-grain boundaries, it might be beneficial to increase the cutoff in order to get a more
+the order parameter computation is defined. The cutoff must be smaller
-precise identification of the atoms surrounding. However, computation time will
+than the interaction range of the MD potential. It should at least
-increase as more atoms are considered in the order parameter and force computation.
+include the nearest neighbor shell. For high temperatures or low angle
-It is also worth noting that the cutoff radius must not exceed the communication
+grain boundaries, it might be beneficial to increase the cutoff in
-distance for ghost atoms in LAMMPS. With orientationsFile, the
+order to get a more precise identification of the atoms
-6 oriented crystal basis vectors is specified. Each line of the input file
+surrounding. However, computation time will increase as more atoms are
-contains the three components of a primitive lattice vector oriented according to
+considered in the order parameter and force computation.  It is also
-the grain orientation in the simulation box. The first (last) three lines correspond
+worth noting that the cutoff radius must not exceed the communication
-to the primitive lattice vectors of the first (second) grain. An example for
+distance for ghost atoms in LAMMPS. With orientationsFile, the 6
-a :math:`\Sigma\langle001\rangle` mis-orientation is given at the end.
+oriented crystal basis vectors is specified. Each line of the input
-
+file contains the three components of a primitive lattice vector
-If no synthetic energy difference between the grains is created, :math:`u0=0`, the
+oriented according to the grain orientation in the simulation box. The
-force computation is omitted. In this case, still, the order parameter of the
+first (last) three lines correspond to the primitive lattice vectors
-driving force is computed and can be used to track the grain boundary motion throughout the
+of the first (second) grain. An example for a
-simulation.
+:math:`\Sigma\langle001\rangle` mis-orientation is given at the end.
-
 
+If no synthetic energy difference between the grains is created,
+:math:`u0=0`, the force computation is omitted. In this case, still,
+the order parameter of the driving force is computed and can be used
+to track the grain boundary motion throughout the simulation.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc: `binary restart files <restart>`.
+No information about this fix is written to :doc: `binary restart
+files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-add the potential energy of atom interactions with the grain boundary
+this fix to add the potential energy of atom interactions with the
-driving force to the system's potential energy as part of thermodynamic output.
+grain boundary driving force to the global potential energy of the
-The total sum of added synthetic potential energy is computed and can be accessed
+system as part of :doc:`thermodynamic output <thermo_style>`.  The
-by various output options. The order parameter as well as the thermally masked
+default setting for this fix is :doc:`fix_modify energy no
-output parameter are stored in per-atom arrays and can also be accessed by various
+<fix_modify>`.
-:doc:`output commands <Howto_output>`.
 
-No parameter of this fix can be used with the start/stop keywords of the run command. This fix is
+This fix calculates a per-atom array with 2 columns, which can be
-not invoked during energy minimization.
+accessed by indices 1-1 by any command that uses per-atom values from
+a fix as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
 
+The first column is the order parameter for each atom; the second is
+the thermal masking value for each atom.  Both are described above.
 
+No parameter of this fix can be used with the start/stop keywords of
+the run command. This fix is not invoked during energy minimization.
 
 Restrictions
 """"""""""""
 
-This fix is part of the USER-MISC package. It is only enabled if LAMMPS was
+This fix is part of the USER-MISC package. It is only enabled if
-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.
 
 
 Related commands

doc/src/fix_plumed.rst

@@ -66,7 +66,8 @@ plumed fix in the LAMMPS input.
 
 The *plumedfile* keyword allows the user to specify the name of the
 PLUMED input file.  Instructions as to what should be included in a
-plumed input file can be found in the `documentation for PLUMED <plumeddocs_>`_
+plumed input file can be found in the `documentation for PLUMED
+<plumeddocs_>`_
 
 The *outfile* keyword allows the user to specify the name of a file in
 which to output the PLUMED log.  This log file normally just repeats the
@@ -78,31 +79,45 @@ be specified by the user in the PLUMED input file.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-When performing a restart of a calculation that involves PLUMED you must
+When performing a restart of a calculation that involves PLUMED you
-include a RESTART command in the PLUMED input file as detailed in the
+must include a RESTART command in the PLUMED input file as detailed in
-`PLUMED documentation <plumeddocs_>`_.  When the restart command is found in
+the `PLUMED documentation <plumeddocs_>`_.  When the restart command
-the PLUMED input PLUMED will append to the files that were generated in
+is found in the PLUMED input PLUMED will append to the files that were
-the run that was performed previously.  No part of the PLUMED restart
+generated in the run that was performed previously.  No part of the
-data is included in the LAMMPS restart files.  Furthermore, any history
+PLUMED restart data is included in the LAMMPS restart files.
-dependent bias potentials that were accumulated in previous calculations
+Furthermore, any history dependent bias potentials that were
-will be read in when the RESTART command is included in the PLUMED
+accumulated in previous calculations will be read in when the RESTART
-input.
+command is included in the PLUMED input.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is not supported by
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-this fix.
+this fix to add the energy change from the biasing force added by
+PLUMED to the global potential energy of the system as part of
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy yes <fix_modify>`.
 
-Nothing is computed by this fix that can be accessed by any of the
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-:doc:`output commands <Howto_output>` within LAMMPS.  All the quantities
+this fix to add the contribution from the biasing force to the global
-of interest can be output by commands that are native to PLUMED,
+pressure of the system via the :doc:`compute pressure
-however.
+<compute_pressure>` command.  This can be accessed by
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify virial yes <fix_modify>`.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the PLUMED
+energy mentioned above.  The scalar value calculated by this fix is
+"extensive".
+
+Note that other quantities of interest can be output by commands that
+are native to PLUMED.
 
 Restrictions
 """"""""""""
 
 This fix is part of the USER-PLUMED 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.
 
-There can only be one plumed fix active at a time.
+There can only be one fix plumed command active at a time.
 
 Related commands
 """"""""""""""""

doc/src/fix_poems.rst

@@ -39,14 +39,15 @@ useful for treating a large biomolecule as a collection of connected,
 coarse-grained particles.
 
 The coupling, associated motion constraints, and time integration is
-performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS)` which computes the
+performed by the software package `Parallelizable Open source
-constrained rigid-body motion of articulated (jointed) multibody
+Efficient Multibody Software (POEMS)` which computes the constrained
-systems :ref:`(Anderson) <Anderson>`.  POEMS was written and is distributed
+rigid-body motion of articulated (jointed) multibody systems
-by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
+:ref:`(Anderson) <Anderson>`.  POEMS was written and is distributed by
-and other members of his group at Rensselaer Polytechnic Institute
+Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, and
-(RPI).  Rudranarayan developed the LAMMPS/POEMS interface.  For
+other members of his group at Rensselaer Polytechnic Institute (RPI).
-copyright information on POEMS and other details, please refer to the
+Rudranarayan developed the LAMMPS/POEMS interface.  For copyright
-documents in the poems directory distributed with LAMMPS.
+information on POEMS and other details, please refer to the documents
+in the poems directory distributed with LAMMPS.
 
 This fix updates the positions and velocities of the rigid atoms with
 a constant-energy time integration, so you should not update the same
@@ -107,7 +108,16 @@ off, and there is only a single fix poems defined.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
+
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
+this fix to add the contribution due to the added forces and torques
+on atoms to both the global pressure and per-atom stress of the system
+via the :doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *bodyforces* option is supported by
 this fix style to set whether per-body forces and torques are computed
@@ -115,16 +125,18 @@ early or late in a timestep, i.e. at the post-force stage or at the
 final-integrate stage, respectively.
 
 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
+various :doc:`output commands <Howto_output>`.  No parameter of this
-can be used with the *start/stop* keywords of the :doc:`run <run>`
+fix can be used with the *start/stop* keywords of the :doc:`run <run>`
-command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+command.  This fix is not invoked during :doc:`energy minimization
+<minimize>`.
 
 Restrictions
 """"""""""""
 
-This fix is part of the :ref:`POEMS <PKG-POEMS>` package.  It is only enabled if LAMMPS
+This fix is part of the :ref:`POEMS <PKG-POEMS>` package.  It is only
-was built with that package, which also requires the POEMS library be
+enabled if LAMMPS was built with that package, which also requires the
-built and linked with LAMMPS.  See the :doc:`Build package <Build_package>` doc page for more info.
+POEMS library be built and linked with LAMMPS.  See the :doc:`Build
+package <Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""

doc/src/fix_precession_spin.rst

@@ -42,11 +42,12 @@ Examples
 Description
 """""""""""
 
-This fix applies a precession torque to each magnetic spin in the group.
+This fix applies a precession torque to each magnetic spin in the
+group.
 
-Style *zeeman* is used for the simulation of the interaction
+Style *zeeman* is used for the simulation of the interaction between
-between the magnetic spins in the defined group and an external
+the magnetic spins in the defined group and an external magnetic
-magnetic field:
+field:
 
 .. math::
 
@@ -62,17 +63,17 @@ with:
 
 The field value in Tesla is multiplied by the gyromagnetic
 ratio, :math:`g \cdot \mu_B/\hbar`, converting it into a precession frequency in
-rad.THz (in metal units and with :math:`\mu_B = 5.788\cdot 10^{-5}` eV/T).
+rad.THz (in metal units and with :math:`\mu_B = 5.788\cdot 10^{-5}`
+eV/T).
 
-As a comparison, the figure below displays the simulation of a
+As a comparison, the figure below displays the simulation of a single
-single spin (of norm :math:`\mu_i = 1.0`) submitted to an external
+spin (of norm :math:`\mu_i = 1.0`) submitted to an external magnetic
-magnetic field of :math:`\vert B_{ext}\vert = 10.0\; \mathrm{Tesla}` (and oriented along the z
+field of :math:`\vert B_{ext}\vert = 10.0\; \mathrm{Tesla}` (and
-axis).
+oriented along the z axis).  The upper plot shows the average
-The upper plot shows the average magnetization along the
+magnetization along the external magnetic field axis and the lower
-external magnetic field axis and the lower plot the Zeeman
+plot the Zeeman energy, both as a function of temperature.  The
-energy, both as a function of temperature.
+reference result is provided by the plot of the Langevin function for
-The reference result is provided by the plot of the Langevin
+the same parameters.
-function for the same parameters.
 
 .. image:: JPG/zeeman_langevin.jpg
    :align: center
@@ -88,10 +89,12 @@ for the magnetic spins in the defined group:
 
 .. math::
 
-   H_{aniso}  = -\sum_{{ i}=1}^{N} K_{an}(\mathbf{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2
+   H_{aniso} = -\sum_{{ i}=1}^{N} K_{an}(\mathbf{r}_{i})\, \left(
+   \vec{s}_{i} \cdot \vec{n}_{i} \right)^2
 
-with :math:`n` defining the direction of the anisotropy, and :math:`K` (in eV) its intensity.
+with :math:`n` defining the direction of the anisotropy, and :math:`K`
-If :math:`K > 0`, an easy axis is defined, and if :math:`K < 0`, an easy plane is defined.
+(in eV) its intensity.  If :math:`K > 0`, an easy axis is defined, and
+if :math:`K < 0`, an easy plane is defined.
 
 Style *cubic* is used to simulate a cubic anisotropy, with three
 possible easy axis for the magnetic spins in the defined group:
@@ -110,17 +113,17 @@ possible easy axis for the magnetic spins in the defined group:
    \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
    \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2
 
-with :math:`K_1` and :math:`K_{2c}` (in eV) the intensity coefficients and
+with :math:`K_1` and :math:`K_{2c}` (in eV) the intensity coefficients
-:math:`\vec{n}_1`, :math:`\vec{n}_2` and :math:`\vec{n}_3` defining the three anisotropic directions
+and :math:`\vec{n}_1`, :math:`\vec{n}_2` and :math:`\vec{n}_3`
-defined by the command (from *n1x* to *n3z*).
+defining the three anisotropic directions defined by the command (from
-For :math:`\vec{n}_1 = (1 0 0)`, :math:`\vec{n}_2 = (0 1 0)`, and :math:`\vec{n}_3 = (0 0 1)`, :math:`K_1 < 0` defines an
+*n1x* to *n3z*).  For :math:`\vec{n}_1 = (1 0 0)`, :math:`\vec{n}_2 =
+(0 1 0)`, and :math:`\vec{n}_3 = (0 0 1)`, :math:`K_1 < 0` defines an
 iron type anisotropy (easy axis along the :math:`(0 0 1)`-type cube
-edges), and :math:`K_1 > 0` defines a nickel type anisotropy (easy axis
+edges), and :math:`K_1 > 0` defines a nickel type anisotropy (easy
-along the :math:`(1 1 1)`-type cube diagonals).
+axis along the :math:`(1 1 1)`-type cube diagonals).  :math:`K_2^c >
-:math:`K_2^c > 0` also defines easy axis along the :math:`(1 1 1)`-type cube
+0` also defines easy axis along the :math:`(1 1 1)`-type cube
-diagonals.
+diagonals.  See chapter 2 of :ref:`(Skomski) <Skomski1>` for more
-See chapter 2 of :ref:`(Skomski) <Skomski1>` for more details on cubic
+details on cubic anisotropies.
-anisotropies.
 
 In all cases, the choice of :math:`(x y z)` only imposes the vector
 directions for the forces. Only the direction of the vector is
@@ -134,32 +137,35 @@ Those styles can be combined within one single command line.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-By default, the energy associated to this fix is not added to the potential
+No information about this fix is written to :doc:`binary restart files
-energy of the system.
+<restart>`.
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix
-to add this magnetic potential energy to the potential energy of the system,
 
-.. code-block:: LAMMPS
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-
+this fix to add the energy associated with the spin precession
-   fix             1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+torque to the global potential energy of the system as part of
-   fix_modify      1 energy yes
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy no <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.
+:doc:`output commands <Howto_output>`.  The scalar is the potential
+energy (in energy units) discussed in the previous paragraph.  The
+scalar value is an "extensive" quantity.
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
 Restrictions
 """"""""""""
 
 The *precession/spin* style is part of the SPIN package.  This style
 is only enabled if LAMMPS was built with this package, and if the
-atom_style "spin" was declared.  See the :doc:`Build package <Build_package>` doc page for more info.
+atom_style "spin" was declared.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
-The *precession/spin* style can only be declared once. If more
+The *precession/spin* style can only be declared once. If more than
-than one precession type (for example combining an anisotropy and a Zeeman interactions)
+one precession type (for example combining an anisotropy and a Zeeman
-has to be declared, they have to be chained in the same command
+interactions) has to be declared, they have to be chained in the same
-line (as shown in the examples above).
+command line (as shown in the examples above).
 
 Related commands
 """"""""""""""""

doc/src/fix_qbmsst.rst

@@ -152,13 +152,30 @@ Because the state of the random number generator is not written to
 "exactly" in an uninterrupted fashion. However, in a statistical
 sense, a restarted simulation should produce similar behaviors of the
 system as if it is not interrupted.  To achieve such a restart, one
-should write explicitly the same value for *q*\ , *mu*\ , *damp*\ , *f_max*,
+should write explicitly the same value for *q*\ , *mu*\ , *damp*\ ,
-*N_f*, *eta*\ , and *beta* and set *tscale* = 0 if the system is
+*f_max*, *N_f*, *eta*\ , and *beta* and set *tscale* = 0 if the system
-compressed during the first run.
+is compressed during the first run.
+
+The cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
 
 The progress of the QBMSST can be monitored by printing the global
-scalar and global vector quantities computed by the fix.  The global
+scalar and global vector quantities computed by the fix.
-vector contains five values in this order:
+
+As mentioned above, the scalar is the cumulative energy change due to
+the fix.  By monitoring the thermodynamic *econserve* output, this can
+be used to test if the MD timestep is sufficiently small for accurate
+integration of the dynamic equations.
+
+The global vector contains five values in the following order.  The
+vector values output by this fix are "intensive".
 
 [\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, *lagrangian_position*,
 *quantum_temperature*]
@@ -170,29 +187,21 @@ vector contains five values in this order:
 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
+headers, the following LAMMPS commands are suggested.
-:doc:`fix_modify <fix_modify>` energy command is also enabled to allow
-the thermo keyword *etotal* to print the quantity :math:`E^{tot}`.  See
-also the :doc:`thermo_style <thermo_style>` command.
 
 .. parsed-literal::
 
    fix             fix_id all msst z
-   fix_modify      fix_id energy yes
    variable        dhug    equal f_fix_id[1]
    variable        dray    equal f_fix_id[2]
    variable        lgr_vel equal f_fix_id[3]
    variable        lgr_pos equal f_fix_id[4]
    variable        T_qm    equal f_fix_id[5]
-   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
+   thermo_style    custom  step temp ke pe lz pzz econserve 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
+It is worth noting that the temp keyword for the :doc:`thermo_style
-energy as an extra part of :math:`E^{tot}`. This global scalar and the
+<thermo_style>` command prints the instantaneous classical temperature
-vector of 5 quantities can be accessed by various :doc:`output commands <Howto_output>`.
+:math:`T^{cl}` as described by the :doc:`fix qtb <fix_qtb>` command.
-It is worth noting that the temp keyword
-under the :doc:`thermo_style <thermo_style>` command print the
-instantaneous classical temperature :math:`T^{cl}` as described
-in the command :doc:`fix qtb <fix_qtb>`.
 
 ----------
 
@@ -200,7 +209,8 @@ 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.
 
 All cell dimensions must be periodic. This fix can not be used with a
 triclinic cell.  The QBMSST fix has been tested only for the group-ID

doc/src/fix_restrain.rst

@@ -219,15 +219,19 @@ current dihedral angle :math:`\phi` is equal to :math:`\phi_0`.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential energy associated with this fix to the
+this fix to add the potential energy associated with this fix to the
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+global potential energy of the system as part of :doc:`thermodynamic
+output <thermo_style>` The default setting for this fix is
+:doc:`fix_modify energy no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost level.
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
 
 .. note::
 

doc/src/fix_rhok.rst

@@ -45,11 +45,34 @@ temperatures :ref:`(Pedersen) <Pedersen>`.
 An example of using the interface pinning method is located in the
 *examples/USER/misc/rhok* directory.
 
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
+
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
+this fix to add the potential energy calculated by the fix to the
+global potential energy of the system as part of :doc:`thermodynamic
+output <thermo_style>`.  The default setting for this fix is
+:doc:`fix_modify energy no <fix_modify>`.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the potential
+energy discussed in the preceding paragraph.  The scalar stored by
+this fix is "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
 Restrictions
 """"""""""""
 
 This fix is part of the USER-MISC 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.
 
 Related commands
 """"""""""""""""

doc/src/fix_rigid.rst

@@ -752,25 +752,17 @@ rigid/nvt.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about the 4 NVE rigid styles is written to :doc:`binary restart files <restart>`.  The exception is if the *infile* or
+No information about the 4 NVE rigid styles is written to :doc:`binary
-*mol* keyword is used, in which case an auxiliary file is written out
+restart files <restart>`.  The exception is if the *infile* or *mol*
-with rigid body information each time a restart file is written, as
+keyword is used, in which case an auxiliary file is written out with
+rigid body information each time a restart file is written, as
 explained above for the *infile* keyword.  For the 2 NVT rigid styles,
-the state of the Nose/Hoover thermostat is written to :doc:`binary restart files <restart>`.  Ditto for the 4 NPT and NPH rigid styles, and
+the state of the Nose/Hoover thermostat is written to :doc:`binary
-the state of the Nose/Hoover barostat.  See the
+restart files <restart>`.  Ditto for the 4 NPT and NPH rigid styles,
-:doc:`read_restart <read_restart>` command for info on how to re-specify
+and the state of the Nose/Hoover barostat.  See the :doc:`read_restart
-a fix in an input script that reads a restart file, so that the
+<read_restart>` command for info on how to re-specify a fix in an
-operation of the fix continues in an uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
-
+fix continues in an uninterrupted fashion.
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by the 6
-NVT, NPT, NPH rigid styles to add the energy change induced by the
-thermostatting to the system's potential energy as part of
-:doc:`thermodynamic output <thermo_style>`.
-
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
-fix to add the contribution due to keeping the objects rigid to the
-system's virial as part of :doc:`thermodynamic output <thermo_style>`.
-The default is *virial yes*
 
 The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
 supported by the 4 NPT and NPH rigid styles to change the computes
@@ -783,6 +775,12 @@ all rigid styles to set whether per-body forces and torques are
 computed early or late in a timestep, i.e. at the post-force stage or
 at the final-integrate stage or the timestep, respectively.
 
+The cumulative energy change in the system imposed by the 6 NVT, NPT,
+NPH rigid fixes, via either thermostatting and/or barostatting, is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
 The 2 NVE rigid fixes compute a global scalar which can be accessed by
 various :doc:`output commands <Howto_output>`.  The scalar value
 calculated by these fixes is "intensive".  The scalar is the current
@@ -798,13 +796,22 @@ are removed from this calculation, but only for the *rigid* and
 
 The 6 NVT, NPT, NPH rigid fixes compute a global scalar which can be
 accessed by various :doc:`output commands <Howto_output>`.  The scalar
-value calculated by these fixes is "extensive".  The scalar is the
+is the same cumulative energy change due to these fixes described
-cumulative energy change due to the thermostatting and barostatting
+above.  The scalar value calculated by this fix is "extensive".
-the fix performs.
+
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
+these fixes to add the contribution due to the added forces on atoms
+to both the global pressure and per-atom stress of the system via the
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
 All of the *rigid* styles (not the *rigid/small* styles) compute a
-global array of values which can be accessed by various :doc:`output commands <Howto_output>`.  Similar information about the bodies
+global array of values which can be accessed by various :doc:`output
-defined by the *rigid/small* styles can be accessed via the :doc:`compute rigid/local <compute_rigid_local>` command.
+commands <Howto_output>`.  Similar information about the bodies
+defined by the *rigid/small* styles can be accessed via the
+:doc:`compute rigid/local <compute_rigid_local>` command.
 
 The number of rows in the array is equal to the number of rigid
 bodies.  The number of columns is 15.  Thus for each rigid body, 15

doc/src/fix_shake.rst

@@ -191,22 +191,29 @@ LAMMPS closely follows (:ref:`Andersen (1983) <Andersen3>`).
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+No information about these fixes is written to :doc:`binary restart
-fix to add the contribution due to keeping the constraints to the
+files <restart>`.
-system's virial as part of :doc:`thermodynamic output <thermo_style>`.
-The default is *virial yes*
 
-No information about these fixes is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-are relevant to these fixes.  No global or per-atom quantities are
+these fixes to add the contribution due to the added forces on atoms
-stored by these fixes for access by various :doc:`output commands <Howto_output>`.  No parameter of these fixes can be used
+to both the global pressure and per-atom stress of the system via the
-with the *start/stop* keywords of the :doc:`run <run>` command.  These
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
-fixes are not invoked during :doc:`energy minimization <minimize>`.
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
+
+No global or per-atom quantities are stored by these fixes for access
+by various :doc:`output commands <Howto_output>`.  No parameter of
+these fixes can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  These fixes are not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
 These fixes are part of the RIGID package.  They are 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.
 
 For computational efficiency, there can only be one shake or rattle
 fix defined in a simulation.

doc/src/fix_smd.rst

@@ -48,10 +48,12 @@ Description
 """""""""""
 
 This fix implements several options of steered MD (SMD) as reviewed in
-:ref:`(Izrailev) <Izrailev>`, which allows to induce conformational changes
+:ref:`(Izrailev) <Izrailev>`, which allows to induce conformational
-in systems and to compute the potential of mean force (PMF) along the
+changes in systems and to compute the potential of mean force (PMF)
-assumed reaction coordinate :ref:`(Park) <Park>` based on Jarzynski's
+along the assumed reaction coordinate :ref:`(Park) <Park>` based on
-equality :ref:`(Jarzynski) <Jarzynski>`.  This fix borrows a lot from :doc:`fix spring <fix_spring>` and :doc:`fix setforce <fix_setforce>`.
+Jarzynski's equality :ref:`(Jarzynski) <Jarzynski>`.  This fix borrows
+a lot from :doc:`fix spring <fix_spring>` and :doc:`fix setforce
+<fix_setforce>`.
 
 You can apply a moving spring force to a group of atoms (\ *tether*
 style) or between two groups of atoms (\ *couple* style).  The spring
@@ -108,30 +110,36 @@ 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 :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the added forces on atoms to the
+this fix to add the contribution due to the added forces on atoms to
-system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+both the global pressure and per-atom stress of the system via the
-The default is *virial no*
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *respa* option is supported by
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost level.
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
 
 This fix computes a vector list of 7 quantities, which can be accessed
-by various :doc:`output commands <Howto_output>`.  The quantities in the
+by various :doc:`output commands <Howto_output>`.  The quantities in
-vector are in this order: the x-, y-, and z-component of the pulling
+the vector are in this order: the x-, y-, and z-component of the
-force, the total force in direction of the pull, the equilibrium
+pulling force, the total force in direction of the pull, the
-distance of the spring, the distance between the two reference points,
+equilibrium distance of the spring, the distance between the two
-and finally the accumulated PMF (the sum of pulling forces times
+reference points, and finally the accumulated PMF (the sum of pulling
-displacement).
+forces times displacement).
 
 The force is the total force on the group of atoms by the spring.  In
 the case of the *couple* style, it is the force on the fix group
-(group-ID) or the negative of the force on the second group (group-ID2).
+(group-ID) or the negative of the force on the second group
-The vector values calculated by this fix are "extensive".
+(group-ID2).  The vector values calculated by this fix are
+"extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_spring.rst

@@ -100,11 +100,14 @@ last example holds the ion a distance 5 away from the pore axis
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy stored in the spring to the system's potential
+this fix to add the energy stored in the spring to the global
-energy as part of :doc:`thermodynamic output <thermo_style>`.
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`. The default setting for this fix is :doc:`fix_modify
+energy no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
 fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`

doc/src/fix_spring_chunk.rst

@@ -62,9 +62,11 @@ will define the same number of chunks. The restart data is only applied
 when the number of chunks matches. Otherwise the center of mass
 coordinates are recomputed.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy stored in all the springs to the system's potential
+this fix to add the energy stored in all the springs to the global
-energy as part of :doc:`thermodynamic output <thermo_style>`.
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+energy no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
 fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`

doc/src/fix_spring_self.rst

@@ -44,15 +44,18 @@ plane, respectively.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the original coordinates of tethered atoms to :doc:`binary restart files <restart>`, so that the spring effect will be the
+This fix writes the original coordinates of tethered atoms to
-same in a restarted simulation.  See the
+:doc:`binary restart files <restart>`, so that the spring effect will
-:doc:`read_restart <read_restart>` command for info on how to re-specify
+be the same in a restarted simulation.  See the :doc:`read_restart
-a fix in an input script that reads a restart file, so that the
+<read_restart>` command for info on how to re-specify a fix in an
-operation of the fix continues in an uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy stored in the per-atom springs to the system's
+this fix to add the energy stored in the per-atom springs to the
-potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+global potential energy of the system as part of :doc:`thermodynamic
+output <thermo_style>`.  The default setting for this fix is
+:doc:`fix_modify energy no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by
 this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`

doc/src/fix_temp_berendsen.rst

@@ -132,14 +132,15 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change implied by a velocity rescaling to the
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the same
-energy change due to this fix.  The scalar value calculated by this
+cumulative energy change due to this fix described in the previous
-fix is "extensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
 
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the

doc/src/fix_temp_csvr.rst

@@ -142,32 +142,36 @@ ensemble.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-These fixes write the cumulative global energy change and the
+These fixes write the cumulative global energy change and the random
-random number generator states to :doc:`binary restart files <restart>`.
+number generator states to :doc:`binary restart files <restart>`.  See
-See the :doc:`read_restart <read_restart>` command for info on how to
+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,
+re-specify a fix in an input script that reads a restart file, so that
-so that the selected fix continues in an uninterrupted fashion.  The
+the selected fix continues in an uninterrupted fashion.  The random
-random number generator state can only be restored when the number
+number generator state can only be restored when the number of
-of processors remains unchanged from what is recorded in the restart file.
+processors remains unchanged from what is recorded in the restart
-
+file.
-No information about these fixes are written to :doc:`binary restart files <restart>`.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by these
-fixes.  You can use it to assign a temperature :doc:`compute <compute>`
+fixes.  You can use it to assign a temperature :doc:`compute
-you have defined to these fixes which will be used in its thermostatting
+<compute>` you have defined to these fixes which will be used in its
-procedure, as described above.  For consistency, the group used by
+thermostatting procedure, as described above.  For consistency, the
-these fixes and by the compute should be the same.
+group used by these fixes and by the compute should be the same.
 
-These fixes can ramp its target temperature over multiple runs, using
+The cumulative energy change in the system imposed by these fixes is
-the *start* and *stop* keywords of the :doc:`run <run>` command.  See the
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-:doc:`run <run>` command for details of how to do this.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-
+doc page for details.
-These fixes are not invoked during :doc:`energy minimization <minimize>`.
 
 These fixes compute a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the same
-energy change due to the fix.  The scalar value calculated by this fix
+cumulative energy change due to this fix described in the previous
-is "extensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
+
+These fixes can ramp their target temperature over multiple runs,
+using the *start* and *stop* keywords of the :doc:`run <run>` command.
+See the :doc:`run <run>` command for details of how to do this.
+
+These fixes are not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_temp_rescale.rst

@@ -100,13 +100,13 @@ ID of the new compute is the fix-ID + underscore + "temp", and the
 group for the new compute is the same as the fix group.
 
 Note that this is NOT the compute used by thermodynamic output (see
-the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*.
+the :doc:`thermo_style <thermo_style>` command) with ID =
-This means you can change the attributes of this fix's temperature
+*thermo_temp*.  This means you can change the attributes of this fix's
-(e.g. its degrees-of-freedom) via the
+temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
-:doc:`compute_modify <compute_modify>` command or print this temperature
+<compute_modify>` command or print this temperature during
-during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
+thermodynamic output via the :doc:`thermo_style custom <thermo_style>`
-It also means that changing attributes of *thermo_temp* will have no
+command using the appropriate compute-ID.  It also means that changing
-effect on this fix.
+attributes of *thermo_temp* will have no effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
 with :doc:`compute commands <compute>` that calculate a temperature
@@ -114,13 +114,14 @@ after removing a "bias" from the atom velocities.  E.g. removing the
 center-of-mass velocity from a group of atoms or only calculating
 temperature on the x-component of velocity or only calculating
 temperature for atoms in a geometric region.  This is not done by
-default, but only if the :doc:`fix_modify <fix_modify>` command is used
+default, but only if the :doc:`fix_modify <fix_modify>` command is
-to assign a temperature compute to this fix that includes such a bias
+used to assign a temperature compute to this fix that includes such a
-term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+bias term.  See the doc pages for individual :doc:`compute commands
-this case, the thermostat works in the following manner: the current
+<compute>` to determine which ones include a bias.  In this case, the
-temperature is calculated taking the bias into account, bias is
+thermostat works in the following manner: the current temperature is
-removed from each atom, thermostatting is performed on the remaining
+calculated taking the bias into account, bias is removed from each
-thermal degrees of freedom, and the bias is added back in.
+atom, thermostatting is performed on the remaining thermal degrees of
+freedom, and the bias is added back in.
 
 ----------
 
@@ -139,15 +140,15 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change implied by a velocity rescaling to the
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-system's potential energy as part of :doc:`thermodynamic output
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-<thermo_style>`.
+doc page for details.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the same
-energy change due to this fix.  The scalar value calculated by this
+cumulative energy change due to this fix described in the previous
-fix is "extensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
 
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the

doc/src/fix_temp_rescale_eff.rst

@@ -38,7 +38,8 @@ particles.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a temperature :doc:`compute <compute>`
@@ -46,14 +47,15 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change implied by a velocity rescaling to the
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the same
-energy change due to this fix.  The scalar value calculated by this
+cumulative energy change due to this fix described in the previous
-fix is "extensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
 
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the

doc/src/fix_tgnh_drude.rst

@@ -218,10 +218,10 @@ a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
-supported by these fixes.  You can use them to assign a
+supported by these fixes.  You can use them to assign a :doc:`compute
-:doc:`compute <compute>` you have defined to this fix which will be used
+<compute>` you have defined to this fix which will be used in its
-in its thermostatting or barostatting procedure, as described above.
+thermostatting or barostatting procedure, as described above.  If you
-If you do this, note that the kinetic energy derived from the compute
+do this, note that the kinetic energy derived from the compute
 temperature should be consistent with the virial term computed using
 all atoms for the pressure.  LAMMPS will warn you if you choose to
 compute temperature on a subset of atoms.
@@ -229,42 +229,49 @@ compute temperature on a subset of atoms.
 .. note::
 
    If both the *temp* and *press* keywords are used in a single
-   thermo_modify command (or in two separate commands), then the order in
+   thermo_modify command (or in two separate commands), then the order
-   which the keywords are specified is important.  Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
+   in which the keywords are specified is important.  Note that a
-   an argument when it is specified.  The *temp* keyword will override
+   :doc:`pressure compute <compute_pressure>` defines its own
-   this (for the pressure compute being used by fix npt), but only if the
+   temperature compute as an argument when it is specified.  The
-   *temp* keyword comes after the *press* keyword.  If the *temp* keyword
+   *temp* keyword will override this (for the pressure compute being
-   comes before the *press* keyword, then the new pressure compute
+   used by fix npt), but only if the *temp* keyword comes after the
-   specified by the *press* keyword will be unaffected by the *temp*
+   *press* keyword.  If the *temp* keyword comes before the *press*
-   setting.
+   keyword, then the new pressure compute specified by the *press*
+   keyword will be unaffected by the *temp* setting.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by these
+The cumulative energy change in the system imposed by these fixes, due
-fixes to add the energy change induced by Nose/Hoover thermostatting
+to thermostatting and/or barostatting, are included in the
-and barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>` keywords *ecouple* and
-:doc:`thermodynamic output <thermo_style>`.
+*econserve*.  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
-These fixes compute a global scalar and a global vector of quantities,
+These fixes compute a global scalar which can be accessed by various
-which can be accessed by various :doc:`output commands <Howto_output>`.
+:doc:`output commands <Howto_output>`.  The scalar is the same
-The scalar value calculated by these fixes is "extensive"; the vector
+cumulative energy change due to this fix described in the previous
-values are "intensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
-The scalar is the cumulative energy change due to the fix.
+
-The vector stores the three temperatures :math:`T_\mathrm{M}`, :math:`T_\mathrm{R}` and :math:`T_\mathrm{D}`.
+These fixes also compute a global vector of quantities, which can be
+accessed by various :doc:`output commands <Howto_output>`.  The vector
+values are "intensive".  The vector stores the three temperatures
+:math:`T_\mathrm{M}`, :math:`T_\mathrm{R}` and :math:`T_\mathrm{D}`.
 
 These fixes can ramp their external temperature and pressure over
-multiple runs, using the *start* and *stop* keywords of the
+multiple runs, using the *start* and *stop* keywords of the :doc:`run
-:doc:`run <run>` command.  See the :doc:`run <run>` command for details of
+<run>` command.  See the :doc:`run <run>` command for details of how
-how to do this.
+to do this.
 
-These fixes are not invoked during :doc:`energy minimization <minimize>`.
+These fixes are not invoked during :doc:`energy minimization
+<minimize>`.
 
 ----------
 
 Restrictions
 """"""""""""
 
-These fixes are only available when LAMMPS was built with the USER-DRUDE package.
+These fixes are only available when LAMMPS was built with the
-These fixes cannot be used with dynamic groups as defined by the :doc:`group <group>` command.
+USER-DRUDE package.  These fixes cannot be used with dynamic groups as
-These fixes cannot be used in 2D simulations.
+defined by the :doc:`group <group>` command.  These fixes cannot be
+used in 2D simulations.
 
 *X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
 periodic.  *Xy*\ , *xz*\ , and *yz* can only be barostatted if the

doc/src/fix_ti_spring.rst

@@ -89,13 +89,14 @@ time:
 
   \lambda(\tau) = \tau
 
-where :math:`\tau` is the scaled time variable *t/t_s*. The option *2* performs
+where :math:`\tau` is the scaled time variable *t/t_s*. The option *2*
-the lambda switching at a rate defined by the following switching
+performs the lambda switching at a rate defined by the following
-function
+switching function
 
 .. math::
 
-  \lambda(\tau) = \tau^5 \left( 70 \tau^4 - 315 \tau^3 + 540 \tau^2 - 420 \tau + 126 \right)
+  \lambda(\tau) = \tau^5 \left( 70 \tau^4 - 315 \tau^3 + 540 \tau^2 -
+  420 \tau + 126 \right)
 
 This function has zero slope as lambda approaches its extreme values
 (0 and 1), according to :ref:`de Koning <deKoning96>` this results in
@@ -106,16 +107,19 @@ increase in computational resources cost.
 
 .. note::
 
-   As described in :ref:`Freitas <Freitas1>`, it is important to keep the
+   As described in :ref:`Freitas <Freitas1>`, it is important to keep
-   center-of-mass fixed during the thermodynamic integration. A nonzero
+   the center-of-mass fixed during the thermodynamic integration. A
-   total velocity will result in divergences during the integration due
+   nonzero total velocity will result in divergences during the
-   to the fact that the atoms are 'attached' to their equilibrium
+   integration due to the fact that the atoms are 'attached' to their
-   positions by the Einstein crystal. Check the option *zero* of :doc:`fix langevin <fix_langevin>` and :doc:`velocity <velocity>`. The use of
+   equilibrium positions by the Einstein crystal. Check the option
-   the Nose-Hoover thermostat (:doc:`fix nvt <fix_nh>`) is *NOT*
+   *zero* of :doc:`fix langevin <fix_langevin>` and :doc:`velocity
-   recommended due to its well documented issues with the canonical
+   <velocity>`. The use of the Nose-Hoover thermostat (:doc:`fix nvt
-   sampling of harmonic degrees of freedom (notice that the *chain*
+   <fix_nh>`) is *NOT* recommended due to its well documented issues
-   option will *NOT* solve this problem). The Langevin thermostat (:doc:`fix langevin <fix_langevin>`) correctly thermostats the system and we
+   with the canonical sampling of harmonic degrees of freedom (notice
-   advise its usage with ti/spring command.
+   that the *chain* option will *NOT* solve this problem). The
+   Langevin thermostat (:doc:`fix langevin <fix_langevin>`) correctly
+   thermostats the system and we advise its usage with ti/spring
+   command.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -127,18 +131,20 @@ be the same in a restarted simulation. See the :doc:`read restart
 input script that reads a restart file, so that the operation of the
 fix continues in an uninterrupted fashion.
 
-The :doc:`fix modify <fix_modify>` *energy* option is supported by
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
 this fix to add the energy stored in the per-atom springs to the
-system's potential energy as part of :doc:`thermodynamic output
+global potential energy of the system as part of :doc:`thermodynamic
-<thermo_style>`.
+output <thermo_style>`. The default setting for this fix is
+:doc:`fix_modify energy no <fix_modify>`.
 
 This fix computes a global scalar and a global vector quantities which
 can be accessed by various :doc:`output commands <Howto_output>`. The
 scalar is an energy which is the sum of the spring energy for each
-atom, where the per-atom energy is 0.5 \* k \* r\^2. The vector stores
+atom, where the per-atom energy is :math:`0.5 \cdot k \cdot r^2`.
-2 values.  The first value is the coupling parameter lambda.  The
+The vector stores 2 values.  The first value is the coupling parameter lambda.
-second value is the derivative of lambda with respect to the integer
+The second value is the derivative of lambda with respect to the integer
-timestep *s*, i.e. d lambda / ds.  In order to obtain d lambda / dt,
+timestep *s*, i.e. :math:`\frac{d \lambda}{d s}`.  In order to obtain
+:math:`\frac{d \lambda}{d t}`,
 where t is simulation time, this 2nd value needs to be divided by the
 timestep size (e.g. 0.5 fs).  The scalar and vector values calculated
 by this fix are "extensive".

doc/src/fix_wall.rst

@@ -331,23 +331,33 @@ perturbation on the particles:
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy of interaction between atoms and each wall to
+this fix to add the energy of interaction between atoms and all the
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+specified walls to the global potential energy of the system as part
+of :doc:`thermodynamic output <thermo_style>`.  The default setting
+for this fix is :doc:`fix_modify energy no <fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the interaction between
+this fix to add the contribution due to the interaction between atoms
-atoms and each wall to the system's virial as part of :doc:`thermodynamic output <thermo_style>`. The default is *virial no*
+and all the specified walls to both the global pressure and per-atom
+stress of the system via the :doc:`compute pressure
+<compute_pressure>` and :doc:`compute stress/atom
+<compute_stress_atom>` commands.  The former can be accessed by
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify virial no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost level.
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
 
 This fix computes a global scalar energy and a global vector of
-forces, which can be accessed by various :doc:`output commands <Howto_output>`.  Note that the scalar energy is the sum
+forces, which can be accessed by various :doc:`output commands
-of interactions with all defined walls.  If you want the energy on a
+<Howto_output>`.  Note that the scalar energy is the sum of
+interactions with all defined walls.  If you want the energy on a
 per-wall basis, you need to use multiple fix wall commands.  The
 length of the vector is equal to the number of walls defined by the
 fix.  Each vector value is the normal force on a specific wall.  Note

doc/src/fix_wall_ees.rst

@@ -56,20 +56,27 @@ Description
 """""""""""
 
 Fix *wall/ees* bounds the simulation domain on one or more of its
-faces with a flat wall that interacts with the ellipsoidal atoms in the
+faces with a flat wall that interacts with the ellipsoidal atoms in
-group by generating a force on the atom in a direction perpendicular to
+the group by generating a force on the atom in a direction
-the wall and a torque parallel with the wall.  The energy of
+perpendicular to the wall and a torque parallel with the wall.  The
-wall-particle interactions E is given by:
+energy of wall-particle interactions E is given by:
 
 .. math::
 
-   E = \epsilon \left[ \frac{2  \sigma_{LJ}^{12} \left(7 r^5+14 r^3 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n < r < r_c
+   E = \epsilon \left[ \frac{2 \sigma_{LJ}^{12} \left(7 r^5+14 r^3
+   \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945
+   \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r
+   \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{
+   \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12
+   \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n
+   < r < r_c
 
-Introduced by Babadi and Ejtehadi in :ref:`(Babadi) <BabadiEjtehadi>`. Here,
+Introduced by Babadi and Ejtehadi in :ref:`(Babadi)
-*r* is the distance from the particle to the wall at position *coord*\ ,
+<BabadiEjtehadi>`. Here, *r* is the distance from the particle to the
-and Rc is the *cutoff* distance at which the particle and wall no
+wall at position *coord*\ , and Rc is the *cutoff* distance at which
-longer interact. Also, :math:`\sigma_n` is the distance between center of
+the particle and wall no longer interact. Also, :math:`\sigma_n` is
-ellipsoid and the nearest point of its surface to the wall as shown below.
+the distance between center of ellipsoid and the nearest point of its
+surface to the wall as shown below.
 
 .. image:: JPG/fix_wall_ees_image.jpg
    :align: center
@@ -85,13 +92,15 @@ pre-factor is
 
 .. math::
 
-   8 \pi^2 \quad \rho_{wall} \quad \rho_{ellipsoid} \quad \epsilon \quad \sigma_a \quad \sigma_b \quad \sigma_c
+   8 \pi^2 \quad \rho_{wall} \quad \rho_{ellipsoid} \quad \epsilon
+   \quad \sigma_a \quad \sigma_b \quad \sigma_c
 
-where :math:`\epsilon` is the LJ energy parameter for the constituent LJ
+where :math:`\epsilon` is the LJ energy parameter for the constituent
-particles and :math:`\sigma_a`, :math:`\sigma_b`, and :math:`\sigma_c`
+LJ particles and :math:`\sigma_a`, :math:`\sigma_b`, and
-are the radii of the ellipsoidal particles. :math:`\rho_{wall}` and
+:math:`\sigma_c` are the radii of the ellipsoidal
-:math:`\rho_{ellipsoid}` are the number density of the constituent
+particles. :math:`\rho_{wall}` and :math:`\rho_{ellipsoid}` are the
-particles, in the wall and ellipsoid respectively, in units of 1/volume.
+number density of the constituent particles, in the wall and ellipsoid
+respectively, in units of 1/volume.
 
 .. note::
 
@@ -106,16 +115,56 @@ Fix *wall/region/ees* treats the surface of the geometric region defined
 by the *region-ID* as a bounding wall which interacts with nearby
 ellipsoidal particles according to the EES potential introduced above.
 
-Other details of this command are the same as for the :doc:`fix wall/region <fix_wall_region>` command.  One may also find an example
+Other details of this command are the same as for the :doc:`fix
+wall/region <fix_wall_region>` command.  One may also find an example
 of using this fix in the examples/USER/misc/ees/ directory.
 
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about these fixes are written to :doc:`binary restart
+files <restart>`.
+
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
+these fixes to add the energy of interaction between atoms and all the
+specified walls or region wall to the global potential energy of the
+system as part of :doc:`thermodynamic output <thermo_style>`.  The
+default settings for these fixes are :doc:`fix_modify energy no
+<fix_modify>`.
+
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by
+these fixes. This allows to set at which level of the :doc:`r-RESPA
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
+
+These fixes computes a global scalar and a global vector of forces,
+which can be accessed by various :doc:`output commands
+<Howto_output>`.  See the :doc:`fix wall <fix_wall>` command for a
+description of the scalar and vector.
+
+No parameter of these fixes can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to these fixes are imposed during an energy
+minimization, invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the atom/wall interaction energy to be included in
+   the total potential energy of the system (the quantity being
+   minimized), you MUST enable the :doc:`fix_modify <fix_modify>` *energy*
+   option for this fix.
+
 Restrictions
 """"""""""""
 
-This fix is part of the USER-MISC package.  It is only enabled if
+These fixes are part of the USER-MISC package.  They are only enabled
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
-This fix requires that atoms be ellipsoids as defined by the
+These fixes requires that atoms be ellipsoids as defined by the
 :doc:`atom_style ellipsoid <atom_style>` command.
 
 Related commands

doc/src/fix_wall_region.rst

@@ -194,24 +194,32 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to :doc:`binary restart files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy of interaction between atoms and the wall to the
+this fix to add the energy of interaction between atoms and the region
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+wall to the global potential energy of the system as part of
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy no <fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the interaction between
+this fix to add the contribution due to the interaction between atoms
-atoms and each wall to the system's virial as part of :doc:`thermodynamic output <thermo_style>`. The default is *virial no*
+and the region wall to both the global pressure and per-atom stress of
+the system via the :doc:`compute pressure <compute_pressure>` and
+:doc:`compute stress/atom <compute_stress_atom>` commands.  The former
+can be accessed by :doc:`thermodynamic output <thermo_style>`.  The
+default setting for this fix is :doc:`fix_modify virial no
+<fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
 fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
 integrator the fix is adding its forces. Default is the outermost level.
 
 This fix computes a global scalar energy and a global 3-length vector
-of forces, which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar energy is the sum of energy
+of forces, which can be accessed by various :doc:`output commands
-interactions for all particles interacting with the wall represented
+<Howto_output>`.  The scalar energy is the sum of energy interactions
-by the region surface.  The 3 vector quantities are the x,y,z
+for all particles interacting with the wall represented by the region
-components of the total force acting on the wall due to the particles.
+surface.  The 3 vector quantities are the x,y,z components of the
-The scalar and vector values calculated by this fix are "extensive".
+total force acting on the wall due to the particles.  The scalar and
+vector values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
@@ -221,10 +229,10 @@ invoked by the :doc:`minimize <minimize>` command.
 
 .. note::
 
-   If you want the atom/wall interaction energy to be included in
+   If you want the atom/wall interaction energy to be included in the
-   the total potential energy of the system (the quantity being
+   total potential energy of the system (the quantity being
-   minimized), you MUST enable the :doc:`fix_modify <fix_modify>` *energy*
+   minimized), you MUST enable the :doc:`fix_modify <fix_modify>`
-   option for this fix.
+   *energy* option for this fix.
 
 Restrictions
 """"""""""""

doc/src/fix_widom.rst

@@ -155,11 +155,11 @@ Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 This fix writes the state of the fix to :doc:`binary restart files
-<restart>`.  This includes information about the random number generator
+<restart>`.  This includes information about the random number
-seed, the next timestep for Widom insertions etc.  See the
+generator seed, the next timestep for Widom insertions etc.  See the
-:doc:`read_restart <read_restart>` command for info on how to re-specify
+:doc:`read_restart <read_restart>` command for info on how to
-a fix in an input script that reads a restart file, so that the
+re-specify a fix in an input script that reads a restart file, so that
-operation of the fix continues in an uninterrupted fashion.
+the operation of the fix continues in an uninterrupted fashion.
 
 .. note::
 

doc/src/kim_commands.rst

@@ -1286,7 +1286,7 @@ to cite the OpenKIM project :ref:`(Tadmor) <kim-mainpaper>`, KIM API
 in addition to the relevant scientific references for the IM.
 The citation format for an IM is displayed on its page on
 `OpenKIM <https://openkim.org>`_ along with the corresponding BibTex file,
-and is automatically added to the LAMMPS *log.cite* file.
+and is automatically added to the LAMMPS citation reminder.
 
 Citing the IM software (KIM infrastructure and specific PM or SM codes)
 used in the simulation gives credit to the researchers who developed them

doc/src/thermo_modify.rst

@@ -11,10 +11,10 @@ Syntax
    thermo_modify keyword value ...
 
 * one or more keyword/value pairs may be listed
+* keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press*
 
   .. parsed-literal::
 
-     keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press*\ :l
        *lost* value = *error* or *warn* or *ignore*
        *lost/bond* value = *error* or *warn* or *ignore*
        *norm* value = *yes* or *no*

doc/src/thermo_style.rst

@@ -20,9 +20,10 @@ Syntax
        *custom* args = list of keywords
          possible keywords = step, elapsed, elaplong, dt, time,
                              cpu, tpcpu, spcpu, cpuremain, part, timeremain,
-                             atoms, temp, press, pe, ke, etotal, enthalpy,
+                             atoms, temp, press, pe, ke, etotal,
                              evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
                              emol, elong, etail,
+                             enthalpy, ecouple, econserve,
                              vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
                              xy, xz, yz, xlat, ylat, zlat,
                              bonds, angles, dihedrals, impropers,
@@ -49,7 +50,6 @@ Syntax
            pe = total potential energy
            ke = kinetic energy
            etotal = total energy (pe + ke)
-           enthalpy = enthalpy (etotal + press\*vol)
            evdwl = van der Waals pairwise energy (includes etail)
            ecoul = Coulombic pairwise energy
            epair = pairwise energy (evdwl + ecoul + elong)
@@ -60,6 +60,9 @@ Syntax
            emol = molecular energy (ebond + eangle + edihed + eimp)
            elong = long-range kspace energy
            etail = van der Waals energy long-range tail correction
+           enthalpy = enthalpy (etotal + press\*vol)
+           ecouple = cumulative energy change due to thermo/baro statting fixes
+           econserve = pe + ke + ecouple = etotal + ecouple
            vol = volume
            density = mass density of system
            lx,ly,lz = box lengths in x,y,z
@@ -197,27 +200,33 @@ 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 :math:`\frac{1}{2} k_B T` of energy for each degree
-of freedom.  Thus, using different :doc:`compute commands <compute>` for
+of freedom.  Thus, using different :doc:`compute commands <compute>`
-calculating temperature, via the :doc:`thermo_modify temp
+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
+different computes that calculate temperature can subtract out
-non-thermal components of velocity and/or include different degrees of
+different non-thermal components of velocity and/or include different
-freedom (translational, rotational, etc).
+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
+from fixes if the :doc:`fix_modify energy yes <fix_modify>` option is
-for a fix that calculates such a contribution.  For example, the :doc:`fix wall/lj93 <fix_wall>` fix calculates the energy of atoms
+set for a fix that calculates such a contribution.  For example, the
+:doc:`fix wall/lj93 <fix_wall>` fix calculates the energy of atoms
 interacting with the wall.  See the doc pages for "individual fixes"
-to see which ones contribute.
+to see which ones contribute and whether their default
+:doc:`fix_modify energy <fix_modify>` setting is *yes* or *no*\ .
 
 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
+energy will be non-zero only if the :doc:`pair_modify tail
-is included in *evdwl*\ , *epair*\ , *pe*\ , and *etotal*\ , and the
+<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*
 and *pxx*\ , *pyy*\ , etc.
 
 ----------
 
+Here is more information on other keywords whose meaning may not be
+clear:
+
 The *step*\ , *elapsed*\ , and *elaplong* keywords refer to timestep
 count.  *Step* is the current timestep, or iteration count when a
 :doc:`minimization <minimize>` is being performed.  *Elapsed* is the
@@ -228,13 +237,14 @@ keywords for the :doc:`run <run>` for info on how to invoke a series of
 runs that keep track of an initial starting time.  If these keywords
 are not used, then *elapsed* and *elaplong* are the same value.
 
-The *dt* keyword is the current timestep size in time
+The *dt* keyword is the current timestep size in time :doc:`units
-:doc:`units <units>`.  The *time* keyword is the current elapsed
+<units>`.  The *time* keyword is the current elapsed simulation time,
-simulation time, also in time :doc:`units <units>`, which is simply
+also in time :doc:`units <units>`, which is simply (step\*dt) if the
-(step\*dt) if the timestep size has not changed and the timestep has
+timestep size has not changed and the timestep has not been reset.  If
-not been reset.  If the timestep has changed (e.g. via :doc:`fix dt/reset <fix_dt_reset>`) or the timestep has been reset (e.g. via
+the timestep has changed (e.g. via :doc:`fix dt/reset <fix_dt_reset>`)
-the "reset_timestep" command), then the simulation time is effectively
+or the timestep has been reset (e.g. via the "reset_timestep"
-a cumulative value up to the current point.
+command), then the simulation time is effectively a cumulative value
+up to the current point.
 
 The *cpu* keyword is elapsed CPU seconds since the beginning of this
 run.  The *tpcpu* and *spcpu* keywords are measures of how fast your
@@ -266,16 +276,29 @@ a filename for output specific to this partition.  See discussion of
 the :doc:`-partition command-line switch <Run_options>` for details on
 running in multi-partition mode.
 
-The *timeremain* keyword returns the remaining seconds when a
+The *timeremain* keyword is the seconds remaining when a timeout has
-timeout has been configured via the :doc:`timer timeout <timer>` command.
+been configured via the :doc:`timer timeout <timer>` command.  If the
-If the timeout timer is inactive, the value of this keyword is 0.0 and
+timeout timer is inactive, the value of this keyword is 0.0 and if the
-if the timer is expired, it is negative. This allows for example to exit
+timer is expired, it is negative. This allows for example to exit
 loops cleanly, if the timeout is expired with:
 
 .. code-block:: LAMMPS
 
    if "$(timeremain) < 0.0" then "quit 0"
 
+The *ecouple* keyword is cumulative energy change in the system due to
+any thermostatting or barostatting fixes that are being used.  A
+positive value means that energy has been subtracted from the system
+(added to the coupling reservoir).  See the *econserve* keyword for an
+explanation of why this sign choice makes sense.
+
+The *econserve* keyword is the sum of the potential and kinetic energy
+of the system as well as the energy that has been transferred by
+thermostatting or barostatting to their coupling reservoirs.  I.e. it
+is *pe* + *ke* + *econserve*\ .  Ideally, for a simulation in the NVE,
+NPH, or NPT ensembles, the *econserve* quantity should remain constant
+over time.
+
 The *fmax* and *fnorm* keywords are useful for monitoring the progress
 of an :doc:`energy minimization <minimize>`.  The *fmax* keyword
 calculates the maximum force in any dimension on any atom in the
@@ -295,12 +318,13 @@ to reduce the delay factor to insure no force interactions are missed
 by atoms moving beyond the neighbor skin distance before a rebuild
 takes place.
 
-The keywords *cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ ,
+The keywords *cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ ,
-*cellgamma*\ , correspond to the usual crystallographic quantities that
+*cellbeta*\ , *cellgamma*\ , correspond to the usual crystallographic
-define the periodic unit cell of a crystal.  See the :doc:`Howto triclinic <Howto_triclinic>` doc page for a geometric description
+quantities that define the periodic unit cell of a crystal.  See the
-of triclinic periodic cells, including a precise definition of these
+:doc:`Howto triclinic <Howto_triclinic>` doc page for a geometric
-quantities in terms of the internal LAMMPS cell dimensions *lx*\ , *ly*\ ,
+description of triclinic periodic cells, including a precise
-*lz*\ , *yz*\ , *xz*\ , *xy*\ .
+definition of these quantities in terms of the internal LAMMPS cell
+dimensions *lx*\ , *ly*\ , *lz*\ , *yz*\ , *xz*\ , *xy*\ .
 
 ----------
 
@@ -330,8 +354,8 @@ creates a global vector with 6 values.
 
 ----------
 
-The *c_ID* and *c_ID[I]* and *c_ID[I][J]* keywords allow global
+The *c_ID* and *c_ID[I]* and *c_ID[I][J]* keywords allow global values
-values calculated by a compute to be output.  As discussed on the
+calculated by a compute to be output.  As discussed on the
 :doc:`compute <compute>` doc page, computes can calculate global,
 per-atom, or local values.  Only global values can be referenced by
 this command.  However, per-atom compute values for an individual atom
@@ -353,12 +377,13 @@ kinetic energy that are summed over all atoms in the compute group.
 Intensive quantities are printed directly without normalization by
 thermo_style custom.  Extensive quantities may be normalized by the
 total number of atoms in the simulation (NOT the number of atoms in
-the compute group) when output, depending on the :doc:`thermo_modify norm <thermo_modify>` option being used.
+the compute group) when output, depending on the :doc:`thermo_modify
+norm <thermo_modify>` option being used.
 
-The *f_ID* and *f_ID[I]* and *f_ID[I][J]* keywords allow global
+The *f_ID* and *f_ID[I]* and *f_ID[I][J]* keywords allow global values
-values calculated by a fix to be output.  As discussed on the
+calculated by a fix to be output.  As discussed on the :doc:`fix
-:doc:`fix <fix>` doc page, fixes can calculate global, per-atom, or
+<fix>` doc page, fixes can calculate global, per-atom, or local
-local values.  Only global values can be referenced by this command.
+values.  Only global values can be referenced by this command.
 However, per-atom fix values can be referenced for an individual atom
 in a :doc:`variable <variable>` and the variable referenced by
 thermo_style custom, as discussed below.  See the discussion above for
@@ -377,8 +402,8 @@ energy that are summed over all atoms in the fix group.  Intensive
 quantities are printed directly without normalization by thermo_style
 custom.  Extensive quantities may be normalized by the total number of
 atoms in the simulation (NOT the number of atoms in the fix group)
-when output, depending on the :doc:`thermo_modify norm <thermo_modify>`
+when output, depending on the :doc:`thermo_modify norm
-option being used.
+<thermo_modify>` option being used.
 
 The *v_name* keyword allow the current value of a variable to be
 output.  The name in the keyword should be replaced by the variable

doc/utils/sphinx-config/false_positives.txt

@@ -508,6 +508,7 @@ cpp
 cpu
 createatoms
 createAtoms
+CreateIDs
 crespi
 Crespi
 Critchley
@@ -597,6 +598,7 @@ Dcut
 de
 dE
 De
+deallocated
 decorrelation
 debye
 Debye
@@ -787,6 +789,7 @@ ees
 eFF
 efield
 effm
+eflag
 eflux
 eg
 Eggebrecht
@@ -2537,6 +2540,8 @@ Px
 pxx
 Pxx
 Pxy
+pxy
+pxz
 py
 Py
 pydir
@@ -2548,10 +2553,13 @@ pymol
 pypar
 pythonic
 pytorch
+pyy
 Pyy
+pyz
 pz
 Pz
 Pzz
+pzz
 qbmsst
 qcore
 qdist
@@ -2680,6 +2688,7 @@ rfile
 rg
 Rg
 Rhaphson
+Rhe
 rheological
 rheology
 rhodo
@@ -3334,6 +3343,7 @@ verlet
 Verlet
 versa
 ves
+vflag
 vhi
 vibrational
 Vij

examples/SPIN/nickel/in.spin.nickel

@@ -1,6 +1,6 @@
 # fcc nickel in a 3d periodic box
 
-clear 
+clear
 units           metal
 atom_style      spin
 
@@ -8,7 +8,7 @@ dimension       3
 boundary        p p p
 
 # necessary for the serial algorithm (sametag)
-atom_modify     map array 
+atom_modify     map array
 
 lattice         fcc 3.524
 region          box block 0.0 5.0 0.0 5.0 0.0 5.0
@@ -20,7 +20,7 @@ create_atoms    1 box
 mass            1 58.69
 
 set             group all spin/random 31 0.63
-#set            group all spin 0.63 0.0 0.0 1.0 
+#set            group all spin 0.63 0.0 0.0 1.0
 velocity        all create 100 4928459 rot yes dist gaussian
 
 pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
@@ -31,7 +31,7 @@ neighbor        0.1 bin
 neigh_modify    every 10 check yes delay 20
 
 fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix_modify 	1 energy yes
+fix_modify      1 energy yes
 fix             2 all langevin/spin 0.0 0.0 21
 
 fix             3 all nve/spin lattice moving

examples/SPIN/nickel/in.spin.nickel_cubic

@@ -1,60 +1,60 @@
 # fcc nickel in a 3d periodic box
 
-clear 
+clear
-units 		metal
+units           metal
-atom_style 	spin
+atom_style      spin
 
-dimension 	3
+dimension       3
-boundary 	p p p
+boundary        p p p
 
 # necessary for the serial algorithm (sametag)
-atom_modify 	map array 
+atom_modify     map array
 
-lattice 	fcc 3.524
+lattice         fcc 3.524
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
+create_box      1 box
-create_atoms 	1 box
+create_atoms    1 box
 
 # setting mass, mag. moments, and interactions for cobalt
 
-mass		1 58.69
+mass            1 58.69
 
-set 		group all spin/random 31 0.63
+set             group all spin/random 31 0.63
-#set 		group all spin 0.63 0.0 0.0 1.0 
+#set            group all spin 0.63 0.0 0.0 1.0
-velocity 	all create 100 4928459 rot yes dist gaussian
+velocity        all create 100 4928459 rot yes dist gaussian
 
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
+pair_coeff      * * eam/alloy Ni99.eam.alloy Ni
-pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+pair_coeff      * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
 
-neighbor 	0.1 bin
+neighbor        0.1 bin
-neigh_modify 	every 10 check yes delay 20
+neigh_modify    every 10 check yes delay 20
 
-fix 		1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 &
+fix             1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 &
-				      zeeman 0.0 0.0 0.0 1.0
+                                      zeeman 0.0 0.0 0.0 1.0
-fix_modify 	1 energy yes
+fix_modify      1 energy yes
-fix 		2 all langevin/spin 0.0 0.0 21
+fix             2 all langevin/spin 0.0 0.0 21
 
-fix 		3 all nve/spin lattice moving
+fix             3 all nve/spin lattice moving
-timestep	0.0001
+timestep        0.0001
 
 # compute and output options
 
-compute 	out_mag    all spin
+compute         out_mag    all spin
-compute 	out_pe     all pe
+compute         out_pe     all pe
-compute 	out_ke     all ke
+compute         out_ke     all ke
-compute 	out_temp   all temp
+compute         out_temp   all temp
 
-variable 	magz      equal c_out_mag[3]
+variable        magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
+variable        magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
+variable        emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
+variable        tmag      equal c_out_mag[6]
 
 thermo_style    custom step time v_magnorm pe v_emag temp v_tmag etotal
 thermo          50
 
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump            1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
-run 		1000
+run             1000
 

examples/USER/dpd/dpdrx-shardlow/thermo.dpdrx.new

@@ -1,17 +0,0 @@
-# rx heats of formation for various molecules
-# multiple entries can be added to this file, LAMMPS reads the ones it needs
-# the entries are in LAMMPS "metal" units (eV)
-# Be sure the units are consistent with your input file
-
-# format of a single entry (one or more lines):
-#   species  DeltaHformation
-
-rdx     1.989907438211819
-hcn     1.400635733970104
-no2     0.343004076201018
-no      0.935781955892458
-h2o    -2.506184777415379
-n2      0.000000000000000
-h2      0.000000000000000
-co     -1.145533746031845
-co2    -4.078501848437456