Merge branch 'develop' into collected-small-fixes

doc/src/Howto_bpm.rst

@@ -17,6 +17,8 @@ producing fracture. The examples/bpm directory has sample input scripts
 for simulations of the fragmentation of an impacted plate and the
 pouring of extended, elastic bodies. See :ref:`(Clemmer) <howto-Clemmer>`
 for more general information on the approach and the LAMMPS implementation.
+Example movies illustrating some of these capabilities are found at
+https://www.lammps.org/movies.html#bpmpackage.
 
 ----------
 

doc/src/Howto_rheo.rst

@@ -15,7 +15,8 @@ details of the system, or develop new capabilities. For instance, the numerics
 associated with calculating gradients, reproducing kernels, etc. are separated
 into distinct classes to simplify the development of new integration schemes
 which can call these calculations. Additional numerical details can be found in
-:ref:`(Clemmer) <howto_rheo_clemmer>`.
+:ref:`(Clemmer) <howto_rheo_clemmer>`. Example movies illustrating some of these
+capabilities are found at https://www.lammps.org/movies.html#rheopackage.
 
 Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
 <PKG-SPH>` package is likely better suited for your application. It has fewer advanced

doc/src/Packages_details.rst

@@ -350,6 +350,7 @@ models for mesoscale simulations of solids and fracture.  See the
 * :doc:`compute nbond/atom <compute_nbond_atom>`
 * :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
 * :doc:`pair_style bpm/spring <pair_bpm_spring>`
+* https://www.lammps.org/movies.html#bpmpackage
 * ``examples/bpm``
 
 ----------
@@ -2658,6 +2659,7 @@ Thomas C. O'Connor (Carnegie Mellon University)
 * :doc:`fix rheo/viscosity <fix_rheo_viscosity>`
 * :doc:`pair_style rheo <pair_rheo>`
 * :doc:`pair_style rheo/solid <pair_rheo_solid>`
+* https://www.lammps.org/movies.html#rheopackage
 * ``examples/rheo``
 
 ----------

doc/src/Tools.rst

@@ -96,6 +96,7 @@ Miscellaneous tools
    * :ref:`LAMMPS-GUI <lammps_gui>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`Offline build tool <offline>`
+   * :ref:`Regression tester <regression>`
    * :ref:`singularity/apptainer <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`valgrind <valgrind>`
@@ -991,6 +992,30 @@ README for more info on Pizza.py and how to use these scripts.
 
 ----------
 
+.. _regression:
+
+Regression tester tool
+----------------------
+
+The regression-tests subdirectory contains a tool for performing
+regression tests with a given LAMMPS binary.  The tool launches the
+LAMMPS binary with any given input script under one of the `examples`
+subdirectories, and compares the thermo output in the generated log file
+with those in the provided log file with the same number of processors
+ub the same subdirectory. If the differences between the actual and
+reference values are within specified tolerances, the test is considered
+passed.  For each test batch, that is, a set of example input scripts,
+the mpirun command, the LAMMPS command line arguments, and the
+tolerances for individual thermo quantities can be specified in a
+configuration file in YAML format.
+
+The tool also reports if and how the run fails, and if a reference log file
+is missing.  See the README file for more information.
+
+This tool was written by Trung Nguyen at U of Chicago (ndactrung at gmail.com).
+
+----------
+
 .. _replica:
 
 replica tool

doc/src/fix_add_heat.rst

@@ -18,11 +18,11 @@ Syntax
 
        *constant* args = *rate*
          *rate* = rate of heat flow (energy/time units)
-       *linear* args = :math:`T_{target}` *k*
-         :math:`T_{target}` = target temperature (temperature units)
+       *linear* args = *Ttarget* *k*
+         *Ttarget* = target temperature (temperature units)
          *k* = prefactor (energy/(time*temperature) units)
-       *quartic* args = :math:`T_{target}` *k*
-         :math:`T_{target}` = target temperature (temperature units)
+       *quartic* args = *Ttarget* *k*
+         *Ttarget* = target temperature (temperature units)
          *k* = prefactor (energy/(time*temperature^4) units)
 
 * zero or more keyword/value pairs may be appended to args
@@ -45,9 +45,9 @@ Examples
 Description
 """""""""""
 
-This fix adds heat to particles with the temperature attribute every timestep.
-Note that this is an internal temperature of a particle intended for use with
-non-atomistic models like the discrete element method.
+This fix adds heat to particles with the temperature attribute every timestep
+at a given rate. Note that this is an internal temperature of a particle intended
+for use with non-atomistic models like the discrete element method.
 
 For the *constant* style, heat is added at the specified rate. For the *linear* style,
 heat is added at a rate of :math:`k (T_{target} - T)` where :math:`k` is the
@@ -96,7 +96,8 @@ only enabled if LAMMPS was built with that package.
 See the :doc:`Build package <Build_package>` page for more info.
 
 This fix requires that atoms store temperature and heat flow
-as defined by the :doc:`fix property/atom <fix_property_atom>` command.
+as defined by the :doc:`fix property/atom <fix_property_atom>` command or
+included in certain atom styles, such as atom_style rheo/thermal.
 
 Related commands
 """"""""""""""""

doc/utils/sphinx-config/false_positives.txt

@@ -2472,6 +2472,7 @@ ncol
 ncorr
 ncount
 nd
+ndactrung
 ndescriptors
 ndihedrals
 Ndihedraltype