Merge branch 'develop' into yotamfe/develop

doc/src/Build_extras.rst

@@ -126,10 +126,11 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
-   -D HIP_PATH                  # path to HIP installation. Must be set if GPU_API=HIP
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
-                                # value = sm_XX, see below
-                                # default is sm_50
+                                # value = sm_XX (see below, default is sm_50)
+   -D GPU_DEBUG=value           # enable debug code in the GPU package library, mostly useful for developers
+                                # value = yes or no (default)
+   -D HIP_PATH=value            # value = path to HIP installation. Must be set if GPU_API=HIP
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
                                 # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc

doc/src/Commands_pair.rst

@@ -39,7 +39,7 @@ OPT.
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
-   * :doc:`amoeba <pair_amoeba>`
+   * :doc:`amoeba (g) <pair_amoeba>`
    * :doc:`atm <pair_atm>`
    * :doc:`awpmd/cut <pair_awpmd>`
    * :doc:`beck (go) <pair_beck>`
@@ -126,7 +126,7 @@ OPT.
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
    * :doc:`hdnnp <pair_hdnnp>`
-   * :doc:`hippo <pair_amoeba>`
+   * :doc:`hippo (g) <pair_amoeba>`
    * :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
    * :doc:`ilp/tmd (t) <pair_ilp_tmd>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`

doc/src/fix_reaxff_species.rst

@@ -39,6 +39,9 @@ Syntax
            *masslimit* value = massmin massmax
              massmin = minimum molecular weight of species to delete
              massmax = maximum molecular weight of species to delete
+       *delete_rate_limit* value = Nlimit Nsteps
+             Nlimit = maximum number of deletions allowed to occur within interval
+             Nsteps = the interval (number of timesteps) over which to count deletions
 
 Examples
 """"""""
@@ -142,7 +145,13 @@ When using the *masslimit* keyword, each line of the *filedel* file
 contains the timestep on which deletions occurs, followed by how many
 of each species are deleted (with quantities preceding chemical
 formulae).  The *specieslist* and *masslimit* keywords cannot both be
-used in the same *reaxff/species* fix.
+used in the same *reaxff/species* fix.  The *delete_rate_limit*
+keyword can enforce an upper limit on the overall rate of molecule
+deletion.  The number of deletion occurrences is limited to Nlimit
+within an interval of Nsteps timesteps.  When using the
+*delete_rate_limit* keyword, no deletions are permitted to occur
+within the first Nsteps timesteps of the first run (after reading a
+either a data or restart file).
 
 ----------
 

doc/src/fix_rigid.rst

@@ -732,8 +732,8 @@ choices:
 
 * Use one of the 4 NPT or NPH styles for the rigid bodies.  Use the
   *dilate* all option so that it will dilate the positions of the
-  *non-rigid particles as well.  Use :doc:`fix nvt <fix_nh>` (or any
-  *other thermostat) for the non-rigid particles.
+  non-rigid particles as well.  Use :doc:`fix nvt <fix_nh>` (or any
+  other thermostat) for the non-rigid particles.
 * Use :doc:`fix npt <fix_nh>` for the group of non-rigid particles.  Use
   the *dilate* all option so that it will dilate the center-of-mass
   positions of the rigid bodies as well.  Use one of the 4 NVE or 2 NVT

doc/src/pair_amoeba.rst

@@ -1,11 +1,18 @@
 .. index:: pair_style amoeba
+.. index:: pair_style amoeba/gpu
 .. index:: pair_style hippo
+.. index:: pair_style hippo/gpu
 
 pair_style amoeba command
 =========================
 
+Accelerator Variants: *amoeba/gpu*
+
 pair_style hippo command
 ========================
+
+Accelerator Variants: *hippo/gpu*
+
 Syntax
 """"""
 
@@ -127,6 +134,10 @@ version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)
 implementation of HIPPO in LAMMPS matches the version discussed in
 :ref:`(Rackers) <amoeba-Rackers>`.
 
+.. versionadded:: TBD
+
+Accelerator support via the GPU package is available.
+
 ----------
 
 Only a single pair_coeff command is used with either the *amoeba* and
@@ -187,6 +198,19 @@ These pair styles can only be used via the *pair* keyword of the
 
 ----------
 
+.. include:: accel_styles.rst
+
+.. note::
+
+  Using the GPU accelerated pair styles 'amoeba/gpu' or 'hippo/gpu'
+  when compiling the GPU package for OpenCL has a few known issues
+  when running on integrated GPUs and the calculation may crash.
+
+  The GPU accelerated pair styles are also not (yet) compatible
+  with single precision FFTs.
+
+----------
+
 Restrictions
 """"""""""""