rename some examples folders

doc/src/Examples.rst

@@ -211,6 +211,8 @@ Uppercase directories
 +------------+--------------------------------------------------------------------------------------------------+
 | UNITS      | examples that run the same simulation in lj, real, metal units                                   |
 +------------+--------------------------------------------------------------------------------------------------+
+| USER-MISC  | examples for commands in the USER-MISC packages                                                  |
++------------+--------------------------------------------------------------------------------------------------+
 | VISCOSITY  | compute viscosity via several methods                                                            |
 +------------+--------------------------------------------------------------------------------------------------+
 
@@ -224,4 +226,7 @@ of the sub-directories have their own README files which give further
 instructions.  See the :doc:`Packages_details <Packages_details>` doc
 page for more info on specific packages.
 
+Similarly the USER-MISC directory has sub-directories for examples
+corresponding to individual commands or styles in the USER-MISC package.
+
 .. _openkim: https://openkim.org

doc/src/Packages_details.rst

@@ -1461,7 +1461,7 @@ Brennan (ARL).
 * :doc:`pair_style exp6/rx <pair_exp6_rx>`
 * :doc:`pair_style multi/lucy <pair_multi_lucy>`
 * :doc:`pair_style multi/lucy/rx <pair_multi_lucy_rx>`
-* examples/PACKAGES/dpd
+* examples/PACKAGES/dpd-react
 
 ----------
 
@@ -1746,7 +1746,7 @@ src/USER-MISC/README file.
 * src/USER-MISC: filenames -> commands
 * src/USER-MISC/README
 * one page per individual command listed in src/USER-MISC/README
-* examples/PACKAGES/USER-MISC
+* examples/USER-MISC
 
 ----------
 
@@ -2442,7 +2442,7 @@ Sciences, Iran).
 * :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
 * :doc:`fix meso/move <fix_meso_move>`
 * :doc:`fix rigid/meso <fix_rigid_meso>`
-* examples/PACKAGES/sdpd
+* examples/PACKAGES/dpd-smooth
 
 ----------
 

doc/src/compute_basal_atom.rst

@@ -42,7 +42,7 @@ too frequently or to have multiple compute/dump commands, each of
 which computes this quantity.
 
 An example input script that uses this compute is provided
-in examples/PACKAGES/USER-MISC/basal.
+in examples/USER-MISC/basal.
 
 Output info
 """""""""""

doc/src/fix_dpd_energy.rst

@@ -45,7 +45,7 @@ can be specified by using fix *dpd/energy*\ , fix *nve* and pair_style
 *dpd/fdt/energy*\ .  DPD under isoenthalpic conditions can
 be specified by using fix *dpd/energy*\ , fix *nph* and pair_style
 *dpd/fdt/energy*\ .  Examples of each DPD variant are provided in the
-examples/PACKAGES/dpd directory.
+examples/PACKAGES/dpd-react directory.
 
 ----------
 

doc/src/fix_electron_stopping.rst

@@ -153,7 +153,7 @@ atoms moving above some minimum cutoff velocity (i.e., kinetic energy).
 These coefficients can be determined by fitting a quadratic polynomial to
 electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple
 'Ecut c1 c2' values can be provided for multi-species simulations in the order
-of the atom types. There is an examples/PACKAGES/USER-MISC/electron_stopping/ directory,
+of the atom types. There is an examples/USER-MISC/electron_stopping/ directory,
 which illustrates uses of this command. Details of this implementation are
 further described in :ref:`Stewart2018 <Stewart2018>` and :ref:`Lee2020 <Lee2020>`.
 

doc/src/fix_grem.rst

@@ -66,7 +66,7 @@ processors be on the order of the number of desired replicas. A
 100-replica simulation would require at least 100 processors (1 per
 world at minimum). If many replicas are needed on a small number of
 processors, multi-replica runs can be run outside of LAMMPS.  An
-example of this can be found in examples/PACKAGES/USER-MISC/grem and has no
+example of this can be found in examples/USER-MISC/grem and has no
 limit on the number of replicas per processor. However, this is very
 inefficient and error prone and should be avoided if possible.
 

doc/src/fix_pafi.rst

@@ -45,7 +45,7 @@ projection is also calculated, whose time integral can be shown to be equal to
 the true free energy gradient along the minimum free energy path local to the reference pathway.
 A detailed discussion of the projection technique can be found in :ref:`(Swinburne) <Swinburne>`.
 
-This fix can be used with LAMMPS as demonstrated in examples/PACKAGES/USER-MISC/pafi,
+This fix can be used with LAMMPS as demonstrated in examples/USER-MISC/pafi,
 though it is primarily intended to be coupled with the PAFI C++ code, developed
 at `https://github.com/tomswinburne/pafi <https://github.com/tomswinburne/pafi>`_,
 which distributes multiple LAMMPS workers in parallel to compute and collate

doc/src/fix_rhok.rst

@@ -43,7 +43,7 @@ used to study crystal-liquid interfaces and determine melting
 temperatures :ref:`(Pedersen) <Pedersen>`.
 
 An example of using the interface pinning method is located in the
-*examples/PACKAGES/USER-MISC/rhok* directory.
+*examples/USER-MISC/rhok* directory.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""

doc/src/fix_shardlow.rst

@@ -49,7 +49,7 @@ under isobaric conditions can be specified by using fix shardlow, fix
 *nph* and pair_style *dpd/fdt*\ .  DPD under isoenthalpic conditions can
 be specified by using fix shardlow, fix *nph* and pair_style
 *dpd/fdt/energy*\ .  Examples of each DPD variant are provided in the
-examples/PACKAGES/dpd directory.
+examples/PACKAGES/dpd-react directory.
 
 ----------
 

doc/src/fix_wall_ees.rst

@@ -117,7 +117,7 @@ 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
-of using this fix in the examples/PACKAGES/USER-MISC/ees/ directory.
+of using this fix in the examples/USER-MISC/ees/ directory.
 
 ----------
 

doc/src/pair_agni.rst

@@ -63,7 +63,7 @@ to specify the path for the force field file.
 An AGNI force field is fully specified by the filename which contains the
 parameters of the force field, i.e., the reference training environments
 used to construct the machine learning force field. Example force field
-and input files are provided in the examples/PACKAGES/USER-MISC/agni directory.
+and input files are provided in the examples/USER-MISC/agni directory.
 
 ----------
 

doc/src/pair_e3b.rst

@@ -111,7 +111,7 @@ If the neigh setting is too large, the pair style will use more memory than nece
 This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 4.
 The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
 
-See the examples/PACKAGES/USER-MISC/e3b directory for a complete example script.
+See the examples/USER-MISC/e3b directory for a complete example script.
 
 ----------
 

doc/src/pair_meam_sw_spline.rst

@@ -94,7 +94,7 @@ potentials.
    systems in the future.
 
 Example input scripts that use this pair style are provided
-in the examples/PACKAGES/USER-MISC/meam_sw_spline directory.
+in the examples/USER-MISC/meam_sw_spline directory.
 
 ----------
 

examples/README

@@ -5,7 +5,8 @@ problems you can run with LAMMPS.
 
 lower-case directories = simple test problems for LAMMPS and its packages
 upper-case directories = more complex problems
-PACKAGE directory with its own sub-directories = tests for specific packages
+PACKAGES directory with its own sub-directories = tests for specific packages
+USER-MISC directory with its own sub-directories = tests for commands in USER-MISC package
 
 Each is discussed below.
 
@@ -170,6 +171,12 @@ The MC directory has an example script for using LAMMPS as an
 energy-evaluation engine in a iterative Monte Carlo energy-relaxation
 loop.
 
+The PACKAGES directory contains subdirectories of example scripts for
+individual packages. Most of those are contributed by the corresponding
+package developers. See the README files in those directories
+for more info.  See the doc/html/Build_package.html file for more info
+about installing and building packages.
+
 The TIP4P directory has an example for testing forces computed on a
 GPU.
 
@@ -179,11 +186,11 @@ lj, real, and metal.  So that you can see how to scale/unscale input
 and output values read/written by LAMMPS to verify you are performing
 the same simulation in different unit systems.
 
-The PACKAGES directory contains subdirectories of example scripts for
+The USER-MISC directory contains subdirectories of example scripts for
-individual packages. Most of those are contributed by the corresponding
+individual commands in the USER-MISC package. Most of those are contributed
-package developers. See the README files in those directories
+by the corresponding developers. See the README files in those directories
 for more info.  See the doc/html/Build_package.html file for more info
-about installing and building user packages.
+about installing and building packages.
 
 The VISCOSITY directory has example scripts for computing the
 viscosity of a LJ liquid using 4 different methods.  See the