Merge branch 'master' into gran_attractive

doc/src/Build_basics.rst

@@ -1,7 +1,7 @@
 Basic build options
 ===================
 
-The following topics are covered on this page, for building both with
+The following topics are covered on this page, for building with both
 CMake and make:
 
 * :ref:`Serial vs parallel build <serial>`

doc/src/Commands_all.rst

@@ -86,6 +86,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
+   * :doc:`plugin <plugin>`
    * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`

doc/src/Commands_pair.rst

@@ -187,7 +187,7 @@ OPT.
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
    * :doc:`mliap <pair_mliap>`
-   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
    * :doc:`morse/smooth/linear (o) <pair_morse>`

doc/src/Developer.rst

@@ -14,6 +14,7 @@ of time and requests from the LAMMPS user community.
    Developer_flow
    Developer_write
    Developer_notes
+   Developer_plugins
    Developer_unittest
    Classes
    Developer_utils

doc/src/Developer_plugins.rst

@@ -0,0 +1,258 @@
+Writing plugins
+---------------
+
+Plugins provide a mechanism to add functionality to a LAMMPS executable
+without recompiling LAMMPS.  The functionality for this and the
+:doc:`plugin command <plugin>` are implemented in the
+:ref:`PLUGIN package <PKG-PLUGIN>` which must be installed to use plugins.
+
+Plugins use the operating system's capability to load dynamic shared
+object (DSO) files in a way similar shared libraries and then reference
+specific functions in those DSOs.  Any DSO file with plugins has to include
+an initialization function with a specific name, "lammpsplugin_init", that
+has to follow specific rules described below.  When loading the DSO with
+the "plugin" command, this function is looked up and called and will then
+register the contained plugin(s) with LAMMPS.
+
+From the programmer perspective this can work because of the object
+oriented design of LAMMPS where all pair style commands are derived from
+the class Pair, all fix style commands from the class Fix and so on and
+usually only functions present in those base classes are called
+directly.  When a :doc:`pair_style` command or :doc:`fix` command is
+issued a new instance of such a derived class is created.  This is done
+by a so-called factory function which is mapped to the style name.  Thus
+when, for example, the LAMMPS processes the command ``pair_style lj/cut
+2.5``, LAMMPS will look up the factory function for creating the
+``PairLJCut`` class and then execute it.  The return value of that
+function is a ``Pair *`` pointer and the pointer will be assigned to the
+location for the currently active pair style.
+
+A DSO file with a plugin thus has to implement such a factory function
+and register it with LAMMPS so that it gets added to the map of available
+styles of the given category.  To register a plugin with LAMMPS an
+initialization function has to be present in the DSO file called
+``lammpsplugin_init`` which is called with three ``void *`` arguments:
+a pointer to the current LAMMPS instance, a pointer to the opened DSO
+handle, and a pointer to the registration function.  The registration
+function takes two arguments: a pointer to a ``lammpsplugin_t`` struct
+with information about the plugin and a pointer to the current LAMMPS
+instance.  Please see below for an example of how the registration is
+done.
+
+Members of ``lammpsplugin_t``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Member
+     - Description
+   * - version
+     - LAMMPS Version string the plugin was compiled for
+   * - style
+     - Style of the plugin (pair, bond, fix, command, etc.)
+   * - name
+     - Name of the plugin style
+   * - info
+     - String with information about the plugin
+   * - author
+     - String with the name and email of the author
+   * - creator.v1
+     - Pointer to factory function for pair, bond, angle, dihedral, or improper styles
+   * - creator.v2
+     - Pointer to factory function for compute, fix, or region styles
+   * - creator.v3
+     - Pointer to factory function for command styles
+   * - handle
+     - Pointer to the open DSO file handle
+
+Only one of the three alternate creator entries can be used at a time
+and which of those is determined by the style of plugin. The "creator.v1"
+element is for factory functions of supported styles computing forces (i.e.
+pair, bond, angle, dihedral, or improper styles) and the function takes
+as single argument the pointer to the LAMMPS instance. The factory function
+is cast to the ``lammpsplugin_factory1`` type before assignment.  The
+"creator.v2" element is for factory functions creating an instance of
+a fix, compute, or region style and takes three arguments: a pointer to
+the LAMMPS instance, an integer with the length of the argument list and
+a ``char **`` pointer to the list of arguments. The factory function pointer
+needs to be cast to the ``lammpsplugin_factory2`` type before assignment.
+The "creator.v3" element takes the same arguments as "creator.v3" but is
+specific to creating command styles: the factory function has to instantiate
+the command style locally passing the LAMMPS pointer as argument and then
+call its "command" member function with the number and list of arguments.
+The factory function pointer needs to be cast to the
+``lammpsplugin_factory3`` type before assignment.
+
+Pair style example
+^^^^^^^^^^^^^^^^^^
+
+As an example, a hypothetical pair style plugin "morse2" implemented in
+a class ``PairMorse2`` in the files ``pair_morse2.h`` and
+``pair_morse2.cpp`` with the factory function and initialization
+function would look like this:
+
+.. code-block:: C++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "pair_morse2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Pair *morse2creator(LAMMPS *lmp)
+  {
+    return new PairMorse2(lmp);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "pair";
+    plugin.name    = "morse2";
+    plugin.info    = "Morse2 variant pair style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
+
+The factory function in this example is called ``morse2creator()``.  It
+receives a pointer to the LAMMPS class as only argument and thus has to
+be assigned to the *creator.v1* member of the plugin struct and cast to the
+``lammpsplugin_factory1`` pointer type.  It returns a
+pointer to the allocated class instance derived from the ``Pair`` class.
+This function may be declared static to avoid clashes with other plugins.
+The name of the derived class, ``PairMorse2``, must be unique inside
+the entire LAMMPS executable.
+
+Fix style example
+^^^^^^^^^^^^^^^^^
+
+If the factory function would be for a fix or compute, which take three
+arguments (a pointer to the LAMMPS class, the number of arguments and the
+list of argument strings), then the pointer type is ``lammpsplugin_factory2``
+and it must be assigned to the *creator.v2* member of the plugin struct.
+Below is an example for that:
+
+.. code-block:: C++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "fix_nve2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
+  {
+    return new FixNVE2(lmp,argc,argv);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "fix";
+    plugin.name    = "nve2";
+    plugin.info    = "NVE2 variant fix style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
+
+Command style example
+^^^^^^^^^^^^^^^^^^^^^
+For command styles there is a third variant of factory function as
+demonstrated in the following example, which also shows that the
+implementation of the plugin class may also be within the same
+file as the plugin interface code:
+
+.. code-block:: C++
+
+   #include "lammpsplugin.h"
+
+   #include "comm.h"
+   #include "error.h"
+   #include "pointers.h"
+   #include "version.h"
+
+   #include <cstring>
+
+   namespace LAMMPS_NS {
+     class Hello : protected Pointers {
+      public:
+       Hello(class LAMMPS *lmp) : Pointers(lmp) {};
+       void command(int, char **);
+     };
+   }
+
+   using namespace LAMMPS_NS;
+
+   void Hello::command(int argc, char **argv)
+   {
+      if (argc != 1) error->all(FLERR,"Illegal hello command");
+      if (comm->me == 0)
+        utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
+   }
+
+   static void hellocreator(LAMMPS *lmp, int argc, char **argv)
+   {
+     Hello hello(lmp);
+     hello.command(argc,argv);
+   }
+
+   extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+   {
+     lammpsplugin_t plugin;
+     lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+     plugin.version = LAMMPS_VERSION;
+     plugin.style   = "command";
+     plugin.name    = "hello";
+     plugin.info    = "Hello world command v1.0";
+     plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+     plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
+     plugin.handle  = handle;
+     (*register_plugin)(&plugin,lmp);
+   }
+
+Additional Details
+^^^^^^^^^^^^^^^^^^
+
+The initialization function **must** be called ``lammpsplugin_init``, it
+**must** have C bindings and it takes three void pointers as arguments.
+The first is a pointer to the LAMMPS class that calls it and it needs to
+be passed to the registration function.  The second argument is a
+pointer to the internal handle of the DSO file, this needs to be added
+to the plugin info struct, so that the DSO can be closed and unloaded
+when all its contained plugins are unloaded.  The third argument is a
+function pointer to the registration function and needs to be stored
+in a variable of ``lammpsplugin_regfunc`` type and then called with a
+pointer to the ``lammpsplugin_t`` struct and the pointer to the LAMMPS
+instance as arguments to register a single plugin.  There may be multiple
+calls to multiple plugins in the same initialization function.
+
+To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled
+with relevant info: current LAMMPS version string, kind of style, name of
+style, info string, author string, pointer to factory function, and the
+DSO handle.  The registration function is called with a pointer to the address
+of this struct and the pointer of the LAMMPS class.  The registration function
+will then add the factory function of the plugin style to the respective
+style map under the provided name.  It will also make a copy of the struct
+in a list of all loaded plugins and update the reference counter for loaded
+plugins from this specific DSO file.
+
+The pair style itself (i.e. the PairMorse2 class in this example) can be
+written just like any other pair style that is included in LAMMPS.  For
+a plugin, the use of the ``PairStyle`` macro in the section encapsulated
+by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class
+name to the style name is done by the plugin registration function with
+the information from the ``lammpsplugin_t`` struct.  It may be included
+in case the new code is intended to be later included in LAMMPS directly.

doc/src/Developer_utils.rst

@@ -101,6 +101,9 @@ and parsing files or arguments.
 .. doxygenfunction:: split_words
    :project: progguide
 
+.. doxygenfunction:: split_lines
+   :project: progguide
+
 .. doxygenfunction:: strmatch
    :project: progguide
 

doc/src/Howto_granular.rst

@@ -18,12 +18,13 @@ This compute
 
 calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
 
-Use one of these 3 pair potentials, which compute forces and torques
+Use one of these 4 pair potentials, which compute forces and torques
 between interacting pairs of particles:
 
-* :doc:`pair_style <pair_style>` gran/history
-* :doc:`pair_style <pair_style>` gran/no_history
-* :doc:`pair_style <pair_style>` gran/hertzian
+* :doc:`pair_style gran/history <pair_gran>`
+* :doc:`pair_style gran/no_history <pair_gran>`
+* :doc:`pair_style gran/hertzian <pair_gran>`
+* :doc:`pair_style granular <pair_granular>`
 
 These commands implement fix options specific to granular systems:
 
@@ -31,6 +32,7 @@ These commands implement fix options specific to granular systems:
 * :doc:`fix pour <fix_pour>`
 * :doc:`fix viscous <fix_viscous>`
 * :doc:`fix wall/gran <fix_wall_gran>`
+* :doc:`fix wall/gran/region <fix_wall_gran_region>`
 
 The fix style *freeze* zeroes both the force and torque of frozen
 atoms, and should be used for granular system instead of the fix style

doc/src/Install_git.rst

@@ -86,33 +86,59 @@ check out any other desired branch) first.
 
 Once you have updated your local files with a ``git pull`` (or ``git
 checkout``), you still need to re-build LAMMPS if any source files have
-changed.  To do this, you should cd to the src directory and type:
+changed.  How to do this depends on the build system you are using.
 
-.. code-block:: bash
+.. tabs::
 
-   $ make purge             # remove any deprecated src files
-   $ make package-update    # sync package files with src files
-   $ make foo               # re-build for your machine (mpi, serial, etc)
+   .. tab:: CMake build
 
-just as described on the :doc:`Apply patch <Install_patch>` page,
-after a patch has been installed.
+      Change to your build folder and type:
 
-.. warning::
+      .. code-block:: bash
 
-   If you wish to edit/change a src file that is from a
-   package, you should edit the version of the file inside the package
-   sub-directory with src, then re-install the package.  The version in
-   the source directory is merely a copy and will be wiped out if you type "make
-   package-update".
+         cmake . --build
 
-.. warning::
+      CMake should auto-detect whether it needs to re-run the CMake
+      configuration step and otherwise redo the build for all files
+      that have been changed or files that depend on changed files.
+      In case some build options have been changed or renamed, you
+      may have to update those by running:
 
-   The GitHub servers support both the "git://" and
-   "https://" access protocols for anonymous read-only access.  If you
-   have a correspondingly configured GitHub account, you may also use
-   SSH access with the URL "git@github.com:lammps/lammps.git".
+      .. code-block:: bash
 
-The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
-junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
-gmail.com) and Richard Berger (Temple U, richard.berger at
-temple.edu).
+         cmake .
+
+      and then rebuild.
+
+   .. tab:: Traditional make
+
+      Switch to the src directory and type:
+
+      .. code-block:: bash
+
+         $ make purge             # remove any deprecated src files
+         $ make package-update    # sync package files with src files
+         $ make foo               # re-build for your machine (mpi, serial, etc)
+
+      Just as described on the :doc:`Apply patch <Install_patch>` page,
+      after a patch has been installed.
+
+      .. warning::
+
+         If you wish to edit/change a src file that is from a package,
+         you should edit the version of the file inside the package
+         sub-directory with src, then re-install the package.  The
+         version in the source directory is merely a copy and will be
+         wiped out if you type "make package-update".
+
+.. admonition:: Git protocols
+   :class: note
+
+   The servers at github.com support the "git://" and "https://" access
+   protocols for anonymous, read-only access.  If you have a suitably
+   configured GitHub account, you may also use SSH protocol with the
+   URL "git@github.com:lammps/lammps.git".
+
+The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
+(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
+richard.berger at temple.edu).

doc/src/Install_patch.rst

@@ -43,24 +43,54 @@ up to date.
 * A list of updated files print out to the screen.  The -b switch
   creates backup files of your originals (e.g. src/force.cpp.orig), so
   you can manually undo the patch if something goes wrong.
-* Type the following from the src directory, to enforce consistency
-  between the src and package directories.  This is OK to do even if you
-  don't use one or more packages.  If you are applying several patches
-  successively, you only need to type this once at the end. The purge
-  command removes deprecated src files if any were removed by the patch
-  from package sub-directories.
 
-  .. code-block:: bash
+* Once you have updated your local files you need to re-build LAMMPS.
+  If you are applying several patches successively, you only need to
+  do the rebuild once at the end. How to do it depends on the build
+  system you are using.
 
-     $ make purge
-     $ make package-update
+  .. tabs::
 
-* Re-build LAMMPS via the "make" command.
+     .. tab:: CMake build
 
-.. warning::
+        Change to your build folder and type:
 
-   If you wish to edit/change a source file that is part of a package,
-   you should edit the version of the file inside the package folder in
-   src, and then re-install or update the package.  The version in the
-   src directory is merely a copy and will be wiped out when you type
-   "make package-update".
+        .. code-block:: bash
+
+           cmake . --build
+
+        CMake should auto-detect whether it needs to re-run the CMake
+        configuration step and otherwise redo the build for all files
+        that have been changed or files that depend on changed files.
+        In case some build options have been changed or renamed, you
+        may have to update those by running:
+
+        .. code-block:: bash
+
+           cmake .
+
+        and then rebuild.
+
+     .. tab:: Traditional make
+
+        Switch to the src directory and type:
+
+        .. code-block:: bash
+
+           $ make purge             # remove any deprecated src files
+           $ make package-update    # sync package files with src files
+           $ make foo               # re-build for your machine (mpi, serial, etc)
+
+        to enforce consistency of the source between the src folder
+        and package directories.  This is OK to do even if you don't
+        use any packages. The "make purge" command removes any deprecated
+        src files if they were removed by the patch from a package
+        sub-directory.
+
+        .. warning::
+
+           If you wish to edit/change a src file that is from a package,
+           you should edit the version of the file inside the package
+           sub-directory with src, then re-install the package.  The
+           version in the source directory is merely a copy and will be
+           wiped out if you type "make package-update".

doc/src/Packages_details.rst

@@ -50,6 +50,7 @@ page gives those details.
    * :ref:`MSCG <PKG-MSCG>`
    * :ref:`OPT <PKG-OPT>`
    * :ref:`PERI <PKG-PERI>`
+   * :ref:`PLUGIN <PKG-PLUGIN>`
    * :ref:`POEMS <PKG-POEMS>`
    * :ref:`PYTHON <PKG-PYTHON>`
    * :ref:`QEQ <PKG-QEQ>`
@@ -843,6 +844,28 @@ Foster (UTSA).
 
 ----------
 
+.. _PKG-PLUGIN:
+
+PLUGIN package
+--------------
+
+**Contents:**
+
+A :doc:`plugin <plugin>` command that can load and unload several
+kind of styles in LAMMPS from shared object files at runtime without
+having to recompile and relink LAMMPS.
+
+**Authors:** Axel Kohlmeyer (Temple U)
+
+**Supporting info:**
+
+* src/PLUGIN: filenames -> commands
+* :doc:`plugin command <plugin>`
+* :doc:`Information on writing plugins <Developer_plugins>`
+* examples/plugin
+
+----------
+
 .. _PKG-POEMS:
 
 POEMS package
@@ -2456,6 +2479,6 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 * :doc:`bond_style mm3 <bond_mm3>`
 * :doc:`improper_style distharm <improper_distharm>`
 * :doc:`improper_style sqdistharm <improper_sqdistharm>`
-* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * examples/USER/yaff

doc/src/angle_cosine_periodic.rst

@@ -71,9 +71,3 @@ Default
 
 none
 
-----------
-
-.. _cosine-Mayo:
-
-**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
-(1990).

doc/src/commands_list.rst

@@ -77,6 +77,7 @@ Commands
    pair_style
    pair_write
    partition
+   plugin
    prd
    print
    processors

doc/src/dihedral_table.rst

@@ -15,10 +15,10 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   dihedral_style style interp Ntable
+   dihedral_style style interpolation Ntable
 
 * style = *table* or *table/cut*
-* interp = *linear* or *spline* = method of interpolation
+* interpolation = *linear* or *spline* = method of interpolation
 * Ntable = size of the internal lookup table
 
 Examples

doc/src/dump.rst

@@ -349,7 +349,7 @@ the box size stored with the snapshot.
 
 The *xtc* style writes XTC files, a compressed trajectory format used
 by the GROMACS molecular dynamics package, and described
-`here <http://manual.gromacs.org/current/online/xtc.html>`_.
+`here <https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc>`_.
 The precision used in XTC files can be adjusted via the
 :doc:`dump_modify <dump_modify>` command.  The default value of 1000
 means that coordinates are stored to 1/1000 nanometer accuracy.  XTC

doc/src/fix_ave_chunk.rst

@@ -307,7 +307,9 @@ atoms in the chunk.  The averaged output value for the chunk on the
 average over atoms across the entire *Nfreq* timescale.  For the
 *density/number* and *density/mass* values, the volume (bin volume or
 system volume) used in the final normalization will be the volume at
-the final *Nfreq* timestep.
+the final *Nfreq* timestep. For the *temp* values, degrees of freedom and
+kinetic energy are summed separately across the entire *Nfreq* timescale, and
+the output value is calculated by dividing those two sums.
 
 If the *norm* setting is *sample*\ , the chunk value is summed over
 atoms for each sample, as is the count, and an "average sample value"

doc/src/fix_cmap.rst

@@ -127,6 +127,11 @@ the :doc:`run <run>` command.
 The forces due to this fix are imposed during an energy minimization,
 invoked by the :doc:`minimize <minimize>` command.
 
+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.
+
 .. note::
 
    If you want the potential energy associated with the CMAP terms

doc/src/fix_halt.rst

@@ -115,6 +115,18 @@ The version with "bondmax" will just run somewhat faster, due to less
 overhead in computing bond lengths and not storing them in a separate
 compute.
 
+A variable can be used to implement a large variety of conditions,
+including to stop when a specific file exists.  Example:
+
+.. code-block:: LAMMPS
+
+   variable exit equal is_file(EXIT)
+   fix 10 all halt 100 v_exit != 0 error soft
+
+Will stop the current run command when a file ``EXIT`` is created
+in the current working directory.  The condition can be cleared
+by removing the file through the :doc:`shell <shell>` command.
+
 The choice of operators listed above are the usual comparison
 operators.  The XOR operation (exclusive or) is also included as "\|\^".
 In this context, XOR means that if either the attribute or avalue is

doc/src/pair_dpd.rst

@@ -150,7 +150,7 @@ shifted to be 0.0 at the cutoff distance Rc.
 The :doc:`pair_modify <pair_modify>` table option is not relevant
 for these pair styles.
 
-These pair style do not support the :doc:`pair_modify <pair_modify>`
+These pair styles do not support the :doc:`pair_modify <pair_modify>`
 tail option for adding long-range tail corrections to energy and
 pressure.
 

doc/src/pair_fep_soft.rst

@@ -363,7 +363,7 @@ Mixing, shift, table, tail correction, restart, rRESPA info
 
 The different versions of the *lj/cut/soft* pair styles support mixing.  For
 atom type pairs I,J and I != J, the :math:`\epsilon` and :math:`\sigma`
-coefficients and cutoff distance for these pair style can be mixed.  The default
+coefficients and cutoff distance for these pair styles can be mixed.  The default
 mix value is *geometric* for 12-6 styles.
 
 The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to

doc/src/pair_gayberne.rst

@@ -188,7 +188,7 @@ Restrictions
 The *gayberne* style is part of the ASPHERE package.  It is only
 enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
 
-These pair style require that atoms store torque and a quaternion to
+These pair styles require that atoms store torque and a quaternion to
 represent their orientation, as defined by the
 :doc:`atom_style <atom_style>`.  It also require they store a per-type
 :doc:`shape <set>`.  The particles cannot store a per-particle

doc/src/pair_lj_switch3_coulgauss_long.rst

@@ -1,8 +1,12 @@
 .. index:: pair_style lj/switch3/coulgauss/long
+.. index:: pair_style mm3/switch3/coulgauss/long
 
 pair_style lj/switch3/coulgauss/long command
 ============================================
 
+pair_style mm3/switch3/coulgauss/long command
+=============================================
+
 Syntax
 """"""
 
@@ -10,7 +14,7 @@ Syntax
 
    pair_style style args
 
-* style = *lj/switch3/coulgauss/long*
+* style = *lj/switch3/coulgauss/long* or *mm3/switch3/coulgauss/long*
 * args = list of arguments for a particular style
 
 .. parsed-literal::
@@ -20,6 +24,11 @@ Syntax
        cutoff2 = global cutoff for Coulombic (optional) (distance units)
        width  = width parameter of the smoothing function (distance units)
 
+     *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
+       cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Coulombic (optional) (distance units)
+       width  = width parameter of the smoothing function (distance units)
+
 Examples
 """"""""
 
@@ -31,6 +40,12 @@ Examples
    pair_style lj/switch3/coulgauss/long   12.0 10.0 3.0
    pair_coeff 1  0.2 2.5 1.2
 
+   pair_style mm3/switch3/coulgauss/long    12.0 3.0
+   pair_coeff 1  0.2 2.5 1.2
+
+   pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
+   pair_coeff 1  0.2 2.5 1.2
+
 Description
 """""""""""
 
@@ -41,8 +56,17 @@ vdW potential
 
    E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
 
-, which goes smoothly to zero at the cutoff r_c as defined
-by the switching function
+The *mm3/switch3/coulgauss/long* style evaluates the MM3
+vdW potential :ref:`(Allinger) <mm3-allinger1989>`
+
+.. math::
+
+   E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
+   r_{v,ij} & =  r_{v,i} + r_{v,j} \\
+   \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
+
+Both potentials go smoothly to zero at the cutoff r_c as defined by the
+switching function
 
 .. math::
 
@@ -85,14 +109,35 @@ commands:
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/long pair styles can be mixed.
+The default mix value is *geometric*\ .  See the "pair_modify" command
+for details.
+
 Shifting the potential energy is not necessary because the switching
 function ensures that the potential is zero at the cut-off.
 
+These pair styles support the :doc:`pair_modify <pair_modify>` table and
+options since they can tabulate the short-range portion of the
+long-range Coulombic interactions.
+
+Thes pair styles do not support the :doc:`pair_modify <pair_modify>`
+tail option for adding a long-range tail correction to the
+Lennard-Jones portion of the energy and pressure.
+
+These pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  They do not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
 Restrictions
 """"""""""""
 
-These styles are part of the USER-YAFF package.  They are only
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+These styles are part of the USER-YAFF package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""

doc/src/pair_mm3_switch3_coulgauss_long.rst

@@ -1,109 +0,0 @@
-.. index:: pair_style mm3/switch3/coulgauss/long
-
-pair_style mm3/switch3/coulgauss/long command
-=============================================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   pair_style style args
-
-* style = *mm3/switch3/coulgauss/long*
-* args = list of arguments for a particular style
-
-.. parsed-literal::
-
-     *mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
-       cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
-       cutoff2 = global cutoff for Coulombic (optional) (distance units)
-       width  = width parameter of the smoothing function (distance units)
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   pair_style mm3/switch3/coulgauss/long    12.0 3.0
-   pair_coeff 1  0.2 2.5 1.2
-
-   pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
-   pair_coeff 1  0.2 2.5 1.2
-
-Description
-"""""""""""
-
-The *mm3/switch3/coulgauss/long* style evaluates the MM3
-vdW potential :ref:`(Allinger) <mm3-allinger1989>`
-
-.. math::
-
-   E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
-   r_{v,ij} & =  r_{v,i} + r_{v,j} \\
-   \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
-
-, which goes smoothly to zero at the cutoff r_c as defined
-by the switching function
-
-.. math::
-
-   S_3(r) = \left\lbrace \begin{array}{ll}
-                       1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
-                       3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
-                       0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
-                   \end{array} \right.
-
-where w is the width defined in the arguments. This potential
-is combined with Coulomb interaction between Gaussian charge densities:
-
-.. math::
-
-   E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
-
-where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms,
-epsilon is the dielectric constant which can be set by the
-:doc:`dielectric <dielectric>` command, ::math:`\gamma_i` and
-:math:`\gamma_j` are the widths of the Gaussian charge distribution and
-erf() is the error-function.  This style has to be used in conjunction
-with the :doc:`kspace_style <kspace_style>` command
-
-If one cutoff is specified it is used for both the vdW and Coulomb
-terms.  If two cutoffs are specified, the first is used as the cutoff
-for the vdW terms, and the second is the cutoff for the Coulombic term.
-
-The following coefficients must be defined for each pair of atoms
-types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
-above, or in the data file or restart files read by the
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
-commands:
-
-* :math:`\epsilon` (energy)
-* :math:`r_v` (distance)
-* :math:`\gamma` (distance)
-
-----------
-
-Mixing, shift, table, tail correction, restart, rRESPA info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-Mixing rules are fixed for this style as defined above.
-
-Shifting the potential energy is not necessary because the switching
-function ensures that the potential is zero at the cut-off.
-
-Restrictions
-""""""""""""
-
-These styles are part of the USER-YAFF package.  They are only
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`pair_coeff <pair_coeff>`
-
-Default
-"""""""
-
-none

doc/src/pair_style.rst

@@ -250,7 +250,7 @@ accelerated styles exist.
 * :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
 * :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
 * :doc:`mie/cut <pair_mie>` - Mie potential
-* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
+* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
 * :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
 * :doc:`morse <pair_morse>` - Morse potential
 * :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential

doc/src/pair_vashishta.rst

@@ -217,7 +217,7 @@ This pair style can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-These pair style are part of the MANYBODY package.  They is only
+These pair styles are part of the MANYBODY package.  They are only
 enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
 
 These pair styles requires the :doc:`newton <newton>` setting to be "on"

doc/src/plugin.rst

@@ -0,0 +1,90 @@
+.. index:: plugin
+
+plugin command
+==============
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   plugin command args
+
+* command = *load* or *unload* or *list* or *clear*
+* args = list of arguments for a particular plugin command
+
+  .. parsed-literal::
+
+     *load* file = load plugin(s) from shared object in *file*
+     *unload* style name = unload plugin *name* of style *style*
+         *style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *compute* or *fix* or *region* or *command*
+     *list* = print a list of currently loaded plugins
+     *clear* = unload all currently loaded plugins
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   plugin load morse2plugin.so
+   plugin unload pair morse2/omp
+   plugin unload command hello
+   plugin list
+   plugin clear
+
+Description
+"""""""""""
+
+The plugin command allows to load (and unload) additional styles and
+commands into a LAMMPS binary from so-called dynamic shared object (DSO)
+files.  This enables to add new functionality to an existing LAMMPS
+binary without having to recompile and link the entire executable.
+
+The *load* command will load and initialize all plugins contained in the
+plugin DSO with the given filename.  A message with information the
+plugin style and name and more will be printed.  Individual DSO files
+may contain multiple plugins.  More details about how to write and
+compile the plugin DSO is given in programmer's guide part of the manual
+under :doc:`Developer_plugins`.
+
+The *unload* command will remove the given style or the given name from
+the list of available styles.  If the plugin style is currently in use,
+that style instance will be deleted.
+
+The *list* command will print a list of the loaded plugins and their
+styles and names.
+
+The *clear* command will unload all currently loaded plugins.
+
+
+Restrictions
+""""""""""""
+
+The *plugin* command is part of the PLUGIN package.  It is
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` doc page for
+more info. Plugins are not available on Windows.
+
+For the loading of plugins to work the LAMMPS library must be
+:ref:`compiled as a shared library <library>`.  If plugins
+access functions or classes from a package, LAMMPS must have
+been compiled with that package included.
+
+Plugins are dependent on the LAMMPS binary interface (ABI)
+and particularly the MPI library used. So they are not guaranteed
+to work when the plugin was compiled with a different MPI library
+or different compilation settings or a different LAMMPS version.
+There are no checks, so if there is a mismatch the plugin object
+will either not load or data corruption and crashes may happen.
+
+
+Related commands
+""""""""""""""""
+
+none
+
+
+Default
+"""""""
+
+none

doc/src/units.rst

@@ -87,7 +87,7 @@ energy is a derived unit (in SI units you equivalently have the relation
 * charge = reduced LJ charge, where :math:`q^* = q \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon}}`
 * dipole = reduced LJ dipole, moment where :math:`\mu^* = \mu \frac{1}{\sqrt{4 \pi \varepsilon_0 \sigma^3 \epsilon}}`
 * electric field = force/charge, where :math:`E^* = E \frac{\sqrt{4 \pi \varepsilon_0 \sigma \epsilon} \sigma}{\epsilon}`
-* density = mass/volume, where :math:`\rho^* = \rho \sigma^{dim}`
+* density = mass/volume, where :math:`\rho^* = \rho \frac{\sigma^{dim}}{m}`
 
 Note that for LJ units, the default mode of thermodynamic output via
 the :doc:`thermo_style <thermo_style>` command is to normalize all

doc/src/variable.rst

@@ -65,8 +65,8 @@ Syntax
                            bound(group,dir,region), gyration(group,region), ke(group,reigon),
                            angmom(group,dim,region), torque(group,dim,region),
                            inertia(group,dimdim,region), omega(group,dim,region)
-         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
-         feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
+         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name)
+         feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
          atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
          atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
          compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
@@ -429,7 +429,7 @@ argument.  For *equal*\ -style variables the formula computes a scalar
 quantity, which becomes the value of the variable whenever it is
 evaluated.  For *vector*\ -style variables the formula must compute a
 vector of quantities, which becomes the value of the variable whenever
-it is evaluated.  The calculated vector can be on length one, but it
+it is evaluated.  The calculated vector can be of length one, but it
 cannot be a simple scalar value like that produced by an equal-style
 compute.  I.e. the formula for a vector-style variable must have at
 least one quantity in it that refers to a global vector produced by a
@@ -821,6 +821,10 @@ Special Functions
 Special functions take specific kinds of arguments, meaning their
 arguments cannot be formulas themselves.
 
+The is_file(x) function is a test whether 'x' is a (readable) file
+and returns 1 in this case, otherwise it returns 0.  For that 'x'
+is taken as a literal string and must not have any blanks in it.
+
 The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
 each take 1 argument which is of the form "c_ID" or "c_ID[N]" or
 "f_ID" or "f_ID[N]" or "v_name".  The first two are computes and the

doc/utils/sphinx-config/false_positives.txt

@@ -1588,6 +1588,7 @@ lammps
 Lammps
 LAMMPS
 lammpsplot
+lammpsplugin
 Lampis
 Lamoureux
 Lanczos