Merge branch 'develop' into dielectric-updates

cmake/CMakeLists.txt

@@ -172,6 +172,7 @@ set(STANDARD_PACKAGES
   AWPMD
   BOCS
   BODY
+  BPM
   BROWNIAN
   CG-DNA
   CG-SDK

cmake/Modules/Packages/GPU.cmake

@@ -80,14 +80,14 @@ if(GPU_API STREQUAL "CUDA")
   # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
   set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
 
-  # apply the following to build "fat" CUDA binaries only for known CUDA toolkits
+  # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
-  if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+  # only the Kepler achitecture and beyond is supported
-    message(WARNING "Untested CUDA Toolkit version. Use at your own risk")
+  if(CUDA_VERSION VERSION_LESS 8.0)
+    message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
+  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+    message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
+    set(GPU_CUDA_GENCODE "-arch=all")
   else()
-    # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
-    if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
-    endif()
     # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
     if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
       string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
@@ -120,6 +120,14 @@ if(GPU_API STREQUAL "CUDA")
     if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
       string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
     endif()
+    # Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+    endif()
+    #    # Lovelace (GPU Arch 9.x) is supported by CUDA 12.0? and later
+    #if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+    #  string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_9x,code=[sm_9x,compute_9x]")
+    #endif()
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@@ -257,13 +265,15 @@ elseif(GPU_API STREQUAL "HIP")
     find_package(CUDA REQUIRED)
     set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)")
 
+    if(CUDA_VERSION VERSION_LESS 8.0)
+      message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
+    elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+      message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
+      set(HIP_CUDA_GENCODE "-arch=all")
+    else()
       # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
       # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
       set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
-    # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
-    if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
-      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20]")
-    endif()
       # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
       if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
         string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30]")
@@ -292,8 +302,10 @@ elseif(GPU_API STREQUAL "HIP")
       if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
         string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
       endif()
+      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
       if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-      message(WARNING "Unsupported CUDA version. Use at your own risk.")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      endif()
     endif()
   endif()
 

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.0.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "8a8da217148bd9b700083b67d795af5e" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   enable_language(C)

cmake/presets/all_off.cmake

@@ -8,6 +8,7 @@ set(ALL_PACKAGES
   AWPMD
   BOCS
   BODY
+  BPM
   BROWNIAN
   CG-DNA
   CG-SDK

cmake/presets/all_on.cmake

@@ -10,6 +10,7 @@ set(ALL_PACKAGES
   AWPMD
   BOCS
   BODY
+  BPM
   BROWNIAN
   CG-DNA
   CG-SDK

cmake/presets/mingw-cross.cmake

@@ -4,6 +4,7 @@ set(WIN_PACKAGES
   AWPMD
   BOCS
   BODY
+  BPM
   BROWNIAN
   CG-DNA
   CG-SDK

cmake/presets/most.cmake

@@ -6,6 +6,7 @@ set(ALL_PACKAGES
   ASPHERE
   BOCS
   BODY
+  BPM
   BROWNIAN
   CG-DNA
   CG-SDK

cmake/presets/windows.cmake

@@ -2,6 +2,7 @@ set(WIN_PACKAGES
   ASPHERE
   BOCS
   BODY
+  BPM
   BROWNIAN
   CG-DNA
   CG-SDK

doc/src/Build_extras.rst

@@ -141,8 +141,6 @@ CMake build
 
 :code:`GPU_ARCH` settings for different GPU hardware is as follows:
 
-* sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
-* sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
 * sm_30 for Kepler (supported since CUDA 5 and until CUDA 10.x)
 * sm_35 or sm_37 for Kepler (supported since CUDA 5 and until CUDA 11.x)
 * sm_50 or sm_52 for Maxwell (supported since CUDA 6)
@@ -160,6 +158,12 @@ Thus the GPU_ARCH setting is merely an optimization, to have code for
 the preferred GPU architecture directly included rather than having to wait
 for the JIT compiler of the CUDA driver to translate it.
 
+When compiling for CUDA or HIP with CUDA, version 8.0 or later of the CUDA toolkit
+is required and a GPU architecture of Kepler or later, which must *also* be
+supported by the CUDA toolkit in use **and** the CUDA driver in use.
+When compiling for OpenCL, OpenCL version 1.2 or later is required and the
+GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
+
 When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
 using the traditional build procedure. CMake will detect files generated by that
 process and will terminate with an error and a suggestion for how to remove them.

doc/src/Commands_bond.rst

@@ -32,6 +32,8 @@ OPT.
    *
    *
    *
+   * :doc:`bpm/rotational <bond_bpm_rotational>`
+   * :doc:`bpm/spring <bond_bpm_spring>`
    * :doc:`class2 (ko) <bond_class2>`
    * :doc:`fene (iko) <bond_fene>`
    * :doc:`fene/expand (o) <bond_fene_expand>`

doc/src/Commands_compute.rst

@@ -91,6 +91,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`msd <compute_msd>`
    * :doc:`msd/chunk <compute_msd_chunk>`
    * :doc:`msd/nongauss <compute_msd_nongauss>`
+   * :doc:`nbond/atom <compute_nbond_atom>`
    * :doc:`omega/chunk <compute_omega_chunk>`
    * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
    * :doc:`pair <compute_pair>`

doc/src/Commands_fix.rst

@@ -141,6 +141,7 @@ OPT.
    * :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
    * :doc:`nve/noforce <fix_nve_noforce>`
    * :doc:`nve/sphere (ko) <fix_nve_sphere>`
+   * :doc:`nve/bpm/sphere <fix_nve_bpm_sphere>`
    * :doc:`nve/spin <fix_nve_spin>`
    * :doc:`nve/tri <fix_nve_tri>`
    * :doc:`nvk <fix_nvk>`
@@ -158,7 +159,6 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
-   * :doc:`pair/tracker <fix_pair_tracker>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`

doc/src/Commands_pair.rst

@@ -53,6 +53,7 @@ OPT.
    * :doc:`born/coul/msm (o) <pair_born>`
    * :doc:`born/coul/wolf (go) <pair_born>`
    * :doc:`born/coul/wolf/cs (g) <pair_cs>`
+   * :doc:`bpm/spring <pair_bpm_spring>`
    * :doc:`brownian (o) <pair_brownian>`
    * :doc:`brownian/poly (o) <pair_brownian>`
    * :doc:`buck (giko) <pair_buck>`

doc/src/Examples.rst

@@ -54,6 +54,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | body        | body particles, 2d system                                        |
 +-------------+------------------------------------------------------------------+
+| bpm         | BPM simulations of pouring elastic grains and plate impact       |
++-------------+------------------------------------------------------------------+
 | cmap        | CMAP 5-body contributions to CHARMM force field                  |
 +-------------+------------------------------------------------------------------+
 | colloid     | big colloid particles in a small particle solvent, 2d system     |

doc/src/Howto.rst

@@ -23,6 +23,8 @@ General howto
    Howto_library
    Howto_couple
    Howto_mdi
+   Howto_bpm
+   Howto_broken_bonds
 
 Settings howto
 ==============

doc/src/Howto_bpm.rst

@@ -0,0 +1,124 @@
+Bonded particle models
+======================
+
+The BPM package implements bonded particle models which can be used to
+simulate mesoscale solids.  Solids are constructed as a collection of
+
+particles which each represent a coarse-grained region of space much
+larger than the atomistic scale. Particles within a solid region are
+then connected by a network of bonds to provide solid elasticity.
+
+Unlike traditional bonds in molecular dynamics, the equilibrium bond
+length can vary between bonds. Bonds store the reference state.  This
+includes setting the equilibrium length equal to the initial distance
+between the two particles but can also include data on the bond
+orientation for rotational models. This produces a stress free initial
+state. Furthermore, bonds are allowed to break under large strains
+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.
+
+----------
+
+Bonds can be created using a :doc:`read data <read_data>` or
+:doc:`create bonds <create_bonds>` command. Alternatively, a
+:doc:`molecule <molecule>` template with bonds can be used with
+:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` to
+create solid grains.
+
+In this implementation, bonds store their reference state when they are
+first computed in the setup of the first simulation run. Data is then
+preserved across run commands and is written to :doc:`binary restart
+files <restart>` such that restarting the system will not reset the
+reference state of a bond. Bonds that are created midway into a run,
+such as those created by pouring grains using :doc:`fix pour
+<fix_pour>`, are initialized on that timestep.
+
+As bonds can be broken between neighbor list builds, the
+:doc:`special_bonds <special_bonds>` command works differently for BPM
+bond styles. There are two possible settings which determine how pair
+interactions work between bonded particles.  First, one can turn off
+all pair interactions between bonded particles.  Unlike :doc:`bond
+quartic <bond_quartic>`, this is not done by subtracting pair forces
+during the bond computation but rather by dynamically updating the
+special bond list. This is the default behavior of BPM bond styles and
+is done by updating the 1-2 special bond list as bonds break.  To do
+this, LAMMPS requires :doc:`newton <newton>` bond off such that all
+processors containing an atom know when a bond breaks. Additionally,
+one must do either (A) or (B).
+
+(A)
+
+Use the following special bond settings
+
+.. code-block:: LAMMPS
+
+   special_bonds lj 0 1 1 coul 1 1 1
+
+These settings accomplish two goals. First, they turn off 1-3 and 1-4
+special bond lists, which are not currently supported for BPMs. As
+BPMs often have dense bond networks, generating 1-3 and 1-4 special
+bond lists is expensive.  By setting the lj weight for 1-2 bonds to
+zero, this turns off pairwise interactions.  Even though there are no
+charges in BPM models, setting a nonzero coul weight for 1-2 bonds
+ensures all bonded neighbors are still included in the neighbor list
+in case bonds break between neighbor list builds.
+
+(B)
+
+Alternatively, one can simply overlay pair interactions such that all
+bonded particles also feel pair interactions. This can be accomplished
+by using the *overlay/pair* keyword present in all bpm bond styles and
+by using the following special bond settings
+
+.. code-block:: LAMMPS
+
+   special_bonds lj/coul 1 1 1
+
+See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
+more information.
+
+----------
+
+Currently there are two types of bonds included in the BPM
+package. The first bond style, :doc:`bond bpm/spring
+<bond_bpm_spring>`, only applies pairwise, central body forces. Point
+particles must have :doc:`bond atom style <atom_style>` and may be
+thought of as nodes in a spring network. Alternatively, the second
+bond style, :doc:`bond bpm/rotational <bond_bpm_rotational>`, resolves
+tangential forces and torques arising with the shearing, bending, and
+twisting of the bond due to rotation or displacement of particles.
+Particles are similar to those used in the :doc:`granular package
+<Howto_granular>`, :doc:`atom style sphere <atom_style>`. However,
+they must also track the current orientation of particles and store bonds
+and therefore use a :doc:`bpm/sphere atom style <atom_style>`.
+This also requires a unique integrator :doc:`fix nve/bpm/sphere
+<fix_nve_bpm_sphere>` which numerically integrates orientation similar
+to :doc:`fix nve/asphere <fix_nve_asphere>`.
+
+To monitor the fracture of bonds in the system, all BPM bond styles
+have the ability to record instances of bond breakage to output using
+the :doc:`dump local <dump>` command. Additionally, one can use
+:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
+number of bonds per atom.
+
+In addition to bond styles, a new pair style :doc:`pair bpm/spring
+<pair_bpm_spring>` was added to accompany the bpm/spring bond
+style. This pair style is simply a hookean repulsion with similar
+velocity damping as its sister bond style.
+
+----------
+
+While LAMMPS has many utilities to create and delete bonds, *only*
+the following are currently compatible with BPM bond styles:
+
+* :doc:`create_bonds <create_bonds>`
+* :doc:`delete_bonds <delete_bonds>`
+* :doc:`fix bond/create <fix_bond_create>`
+* :doc:`fix bond/break <fix_bond_break>`
+* :doc:`fix bond/swap <fix_bond_swap>`
+
+Note :doc:`create_bonds <create_bonds>` requires certain special_bonds settings.
+To subtract pair interactions, one will need to switch between different
+special_bonds settings in the input script. An example is found in
+examples/bpm/impact.

doc/src/Howto_broken_bonds.rst

@@ -0,0 +1,48 @@
+Broken Bonds
+============
+
+Typically, bond interactions persist for the duration of a simulation
+in LAMMPS. However, there are some exceptions that allow for bonds to
+break including the :doc:`quartic bond style <bond_quartic>` and the
+bond styles in the :doc:`BPM package <Howto_bpm>` which contains the
+:doc:`bpm/spring <bond_bpm_spring>` and
+:doc:`bpm/rotational <bond_bpm_rotational>` bond styles. In these cases,
+a bond can be broken if it is stretched beyond a user-defined threshold.
+LAMMPS accomplishes this by setting the bond type to zero such that the
+bond force is no longer computed.
+
+Users are normally able to weight the contribution of pair forces to atoms
+that are bonded using the :doc:`special_bonds command <special_bonds>`.
+When bonds break, this is not always the case. For the quartic bond style,
+pair forces are always turned off between bonded particles. LAMMPS does
+this via a computational sleight-of-hand. It subtracts the pairwise
+interaction as part of the bond computation. When the bond breaks, the
+subtraction stops.  For this to work, the pairwise interaction must always
+be computed by the :doc:`pair_style <pair_style>` command, whether the bond
+is broken or not.  This means that :doc:`special_bonds <special_bonds>` must
+be set to 1,1,1. After the bond breaks, the pairwise interaction between the
+two atoms is turned on, since they are no longer bonded.
+
+In the BPM package, one can either turn off all pair interactions between
+bonded particles or leave them on, overlaying pair forces on top of bond
+forces. To remove pair forces, the special bond list is dynamically
+updated. More details can be found on the :doc:`Howto BPM <Howto_bpm>`
+page.
+
+Bonds can also be broken by fixes which change bond topology, including
+:doc:`fix bond/break <fix_bond_break>` and
+:doc:`fix bond/react <fix_bond_react>`. These fixes will automatically
+trigger a rebuild of the neighbor list and update special bond data structures
+when bonds are broken.
+
+Note that when bonds are dumped to a file via the :doc:`dump local <dump>` command, bonds with type 0 are not included.  The
+:doc:`delete_bonds <delete_bonds>` command can also be used to query the
+status of broken bonds or permanently delete them, e.g.:
+
+.. code-block:: LAMMPS
+
+   delete_bonds all stats
+   delete_bonds all bond 0 remove
+
+The compute :doc:`nbond/atom <compute_nbond_atom>` can also be used
+to tally the current number of bonds per atom, excluding broken bonds.

doc/src/Packages_details.rst

@@ -32,6 +32,7 @@ page gives those details.
    * :ref:`AWPMD <PKG-AWPMD>`
    * :ref:`BOCS <PKG-BOCS>`
    * :ref:`BODY <PKG-BODY>`
+   * :ref:`BPM <PKG-BPM>`
    * :ref:`BROWNIAN <PKG-BROWNIAN>`
    * :ref:`CG-DNA <PKG-CG-DNA>`
    * :ref:`CG-SDK <PKG-CG-SDK>`
@@ -283,6 +284,33 @@ overview.
 
 ----------
 
+.. _PKG-BPM:
+
+BPM package
+------------
+
+**Contents:**
+
+Pair styles, bond styles, fixes, and computes for bonded particle
+models for mesoscale simulations of solids and fracture.  See the
+:doc:`Howto bpm <Howto_bpm>` page for an overview.
+
+**Authors:** Joel T. Clemmer (Sandia National Labs)
+
+**Supporting info:**
+
+* src/BPM filenames -> commands
+* :doc:`Howto_bpm <Howto_bpm>`
+* :doc:`atom_style bpm/sphere <atom_style>`
+* :doc:`bond_style bpm/rotational <bond_bpm_rotational>`
+* :doc:`bond_style bpm/spring <bond_bpm_spring>`
+* :doc:`compute nbond/atom <compute_nbond_atom>`
+* :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
+* :doc:`pair_style bpm/spring <pair_bpm_spring>`
+* examples/bpm
+
+----------
+
 .. _PKG-BROWNIAN:
 
 BROWNIAN package
@@ -1557,7 +1585,6 @@ listing, "ls src/MISC", to see the list of commands.
 * :doc:`pair_style list <pair_list>`
 * :doc:`pair_style srp <pair_srp>`
 * :doc:`pair_style tracker <pair_tracker>`
-* :doc:`fix pair/tracker <fix_pair_tracker>`
 
 ----------
 

doc/src/Packages_list.rst

@@ -58,6 +58,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`Howto body <Howto_body>`
      - body
      - no
+   * - :ref:`BPM <PKG-BPM>`
+     - bonded particle models
+     - :doc:`Howto bpm <Howto_bpm>`
+     - bpm
+     - no
    * - :ref:`BROWNIAN <PKG-BROWNIAN>`
      - Brownian dynamics, self-propelled particles
      - :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>`

doc/src/atom_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    atom_style style args
 
-* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
+* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
 
   .. parsed-literal::
 
@@ -21,6 +21,7 @@ Syntax
                          see the :doc:`Howto body <Howto_body>` doc
                          page for details
          *sphere* arg = 0/1 (optional) for static/dynamic particle radii
+         *bpm/sphere* arg = 0/1 (optional) for static/dynamic particle radii
          *tdpd* arg = Nspecies
            Nspecies = # of chemical species
          *template* arg = template-ID
@@ -120,6 +121,8 @@ quantities.
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *sphere*     | diameter, mass, angular velocity                    | granular models                      |
 +--------------+-----------------------------------------------------+--------------------------------------+
+| *bpm/sphere* | diameter, mass, angular velocity, quaternion        | granular bonded particle models (BPM)|
++--------------+-----------------------------------------------------+--------------------------------------+
 | *spin*       | magnetic moment                                     | system with magnetic particles       |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *tdpd*       | chemical concentration                              | tDPD particles                       |
@@ -141,8 +144,9 @@ quantities.
    output the custom values.
 
 All of the above styles define point particles, except the *sphere*,
-*ellipsoid*, *electron*, *peri*, *wavepacket*, *line*, *tri*, and
+*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
-*body* styles, which define finite-size particles.  See the :doc:`Howto spherical <Howto_spherical>` page for an overview of using
+*tri*, and *body* styles, which define finite-size particles.  See the
+:doc:`Howto spherical <Howto_spherical>` page for an overview of using
 finite-size particle models with LAMMPS.
 
 All of the point-particle styles assign mass to particles on a
@@ -150,15 +154,15 @@ per-type basis, using the :doc:`mass <mass>` command, The finite-size
 particle styles assign mass to individual particles on a per-particle
 basis.
 
-For the *sphere* style, the particles are spheres and each stores a
+For the *sphere* and *bpm/sphere* styles, the particles are spheres and each stores a
 per-particle diameter and mass.  If the diameter > 0.0, the particle
 is a finite-size sphere.  If the diameter = 0.0, it is a point
 particle.  Note that by use of the *disc* keyword with the :doc:`fix
 nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
 :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
-<fix_npt_sphere>` commands, spheres can be effectively treated as 2d
+<fix_npt_sphere>` commands for the *sphere* style, spheres can be effectively treated as 2d
 discs for a 2d simulation if desired.  See also the :doc:`set
-density/disc <set>` command.  The *sphere* style takes an optional 0
+density/disc <set>` command.  The *sphere* and *bpm/sphere* styles take an optional 0
 or 1 argument.  A value of 0 means the radius of each sphere is
 constant for the duration of the simulation.  A value of 1 means the
 radii may vary dynamically during the simulation, e.g. due to use of
@@ -195,6 +199,8 @@ position, which is represented by the eradius = electron size.
 For the *peri* style, the particles are spherical and each stores a
 per-particle mass and volume.
 
+The *bpm/sphere* style is part of the BPM package.
+
 The *oxdna* style is for coarse-grained nucleotides and stores the
 3'-to-5' polarity of the nucleotide strand, which is set through
 the bond topology in the data file. The first (second) atom in a

doc/src/bond_bpm_rotational.rst

@@ -0,0 +1,258 @@
+.. index:: bond_style bpm/rotational
+
+bond_style bpm/rotational command
+=================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style bpm/rotational keyword value attribute1 attribute2 ...
+
+* optional keyword = *overlay/pair* or *store/local* or *smooth*
+
+  .. parsed-literal::
+
+       *store/local* values = fix_ID N attributes ...
+          * fix_ID = ID of associated internal fix to store data
+          * N = prepare data for output every this many timesteps
+          * attributes = zero or more of the below attributes may be appended
+
+            *id1, id2* = IDs of 2 atoms in the bond
+            *time* = the timestep the bond broke
+            *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
+            *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
+
+       *overlay/pair* value = none
+          bonded particles will still interact with pair forces
+
+       *smooth* value = *yes* or *no*
+          smooths bond forces near the breaking point
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style bpm/rotational
+   bond_coeff 1 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
+
+   bond_style bpm/rotational myfix 1000 time id1 id2
+   fix myfix all store/local 1000 3
+   dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
+   dump_modify 1 write_header no
+
+Description
+"""""""""""
+
+The *bpm/rotational* bond style computes forces and torques based on
+deviations from the initial reference state of the two atoms.  The
+reference state is stored by each bond when it is first computed in
+the setup of a run. Data is then preserved across run commands and is
+written to :doc:`binary restart files <restart>` such that restarting
+the system will not reset the reference state of a bond.
+
+Forces include a normal and tangential component. The base normal force
+has a magnitude of
+
+.. math::
+
+   f_r = k_r (r - r_0)
+
+where :math:`k_r` is a stiffness and :math:`r` is the current distance and
+:math:`r_0` is the initial distance between the two particles.
+
+A tangential force is applied perpendicular to the normal direction
+which is proportional to the tangential shear displacement with a
+stiffness of :math:`k_s`. This tangential force also induces a torque.
+In addition, bending and twisting torques are also applied to
+particles which are proportional to angular bending and twisting
+displacements with stiffnesses of :math`k_b` and :math:`k_t',
+respectively.  Details on the calculations of shear displacements and
+angular displacements can be found in :ref:`(Wang) <Wang2009>` and
+:ref:`(Wang and Mora) <Wang2009b>`.
+
+Bonds will break under sufficient stress. A breaking criteria is calculated
+
+.. math::
+
+   B = \mathrm{max}\{0, \frac{f_r}{f_{r,c}} + \frac{|f_s|}{f_{s,c}} +
+       \frac{|\tau_b|}{\tau_{b,c}} + \frac{|\tau_t|}{\tau_{t,c}} \}
+
+where :math:`|f_s|` is the magnitude of the shear force and
+:math:`|\tau_b|` and :math:`|\tau_t|` are the magnitudes of the
+bending and twisting forces, respectively. The corresponding variables
+:math:`f_{r,c}` :math:`f_{s,c}`, :math:`\tau_{b,c}`, and
+:math:`\tau_{t,c}` are critical limits to each force or torque.  If
+:math:`B` is ever equal to or exceeds one, the bond will break.  This
+is done by setting by setting its type to 0 such that forces and
+torques are no longer computed.
+
+After computing the base magnitudes of the forces and torques, they
+can be optionally multiplied by an extra factor :math:`w` to smoothly
+interpolate forces and torques to zero as the bond breaks. This term
+is calculated as :math:`w = (1.0 - B^4)`. This smoothing factor can be
+added or removed using the *smooth* keyword.
+
+Finally, additional damping forces and torques are applied to the two
+particles. A force is applied proportional to the difference in the
+normal velocity of particles using a similar construction as
+dissipative particle dynamics (:ref:`(Groot) <Groot3>`):
+
+.. math::
+
+   F_D = - \gamma_n w (\hat{r} \bullet \vec{v})
+
+where :math:`\gamma_n` is the damping strength, :math:`\hat{r}` is the
+radial normal vector, and :math:`\vec{v}` is the velocity difference
+between the two particles. Similarly, tangential forces are applied to
+each atom proportional to the relative differences in sliding
+velocities with a constant prefactor :math:`\gamma_s` (:ref:`(Wang et
+al.) <Wang20152>`) along with their associated torques. The rolling and
+twisting components of the relative angular velocities of the two
+atoms are also damped by applying torques with prefactors of
+:math:`\gamma_r` and :math:`\gamma_t`, respectively.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example 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:`k_r`           (force/distance units)
+* :math:`k_s`           (force/distance units)
+* :math:`k_t`           (force*distance/radians units)
+* :math:`k_b`           (force*distance/radians units)
+* :math:`f_{r,c}`       (force units)
+* :math:`f_{s,c}`       (force units)
+* :math:`\tau_{b,c}`    (force*distance units)
+* :math:`\tau_{t,c}`    (force*distance units)
+* :math:`\gamma_n`      (force/velocity units)
+* :math:`\gamma_s`      (force/velocity units)
+* :math:`\gamma_r`      (force*distance/velocity units)
+* :math:`\gamma_t`      (force*distance/velocity units)
+
+By default, pair forces are not calculated between bonded particles.
+Pair forces can alternatively be overlaid on top of bond forces using
+the *overlay/pair* keyword. These settings require specific
+:doc:`special_bonds <special_bonds>` settings described in the
+restrictions.  Further details can be found in the `:doc: how to
+<Howto_BPM>` page on BPMs.
+
+If the *store/local* keyword is used, this fix will track bonds that
+break during the simulation. Whenever a bond breaks, data is processed
+and transferred to an internal fix labeled *fix_ID*. This allows the
+local data to be accessed by other LAMMPS commands.
+Following any optional keyword/value arguments, a list of one or more
+attributes is specified.  These include the IDs of the two atoms in
+the bond. The other attributes for the two atoms include the timestep
+during which the bond broke and the current/initial center of mass
+position of the two atoms.
+
+Data is continuously accumulated over intervals of *N*
+timesteps. At the end of each interval, all of the saved accumulated
+data is deleted to make room for new data. Individual datum may
+therefore persist anywhere between *1* to *N* timesteps depending on
+when they are saved. This data can be accessed using the *fix_ID* and a
+:doc:`dump local <dump>` command. To ensure all data is output,
+the dump frequency should correspond to the same interval of *N*
+timesteps. A dump frequency of an integer multiple of *N* can be used
+to regularly output a sample of the accumulated data.
+
+Note that when unbroken bonds are dumped to a file via the
+:doc:`dump local <dump>` command, bonds with type 0 (broken bonds)
+are not included.
+The :doc:`delete_bonds <delete_bonds>` command can also be used to
+query the status of broken bonds or permanently delete them, e.g.:
+
+.. code-block:: LAMMPS
+
+   delete_bonds all stats
+   delete_bonds all bond 0 remove
+
+
+----------
+
+Restart and other info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This bond style writes the reference state of each bond to
+:doc:`binary restart files <restart>`. Loading a restart file will
+properly resume bonds.
+
+The single() function of these pair styles returns 0.0 for the energy
+of a pairwise interaction, since energy is not conserved in these
+dissipative potentials.  It also returns only the normal component of
+the pairwise interaction force.
+
+The accumulated data is not written to restart files and should be
+output before a restart file is written to avoid missing data.
+
+The internal fix calculates a local vector or local array depending on the
+number of input values.  The length of the vector or number of rows in
+the array is the number of recorded, lost interactions.  If a single
+input is specified, a local vector is produced.  If two or more inputs
+are specified, a local array is produced where the number of columns =
+the number of inputs.  The vector or array can be accessed by any
+command that uses local values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
+output options.
+
+The vector or array will be floating point values that correspond to
+the specified attribute.
+
+Restrictions
+""""""""""""
+
+This bond style can only be used if LAMMPS was built with the BPM
+package. See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+By default if pair interactions are to be disabled, this bond style
+requires setting
+
+.. code-block:: LAMMPS
+
+   special_bonds lj 0 1 1 coul 1 1 1
+
+and :doc:`newton <newton>` must be set to bond off.  If the
+*overlay/pair* option is used, this bond style alternatively requires
+setting
+
+.. code-block:: LAMMPS
+
+   special_bonds lj/coul 1 1 1
+
+The *bpm/rotational* style requires :doc:`atom style bpm/sphere <atom_style>`.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`, :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
+
+Default
+"""""""
+
+The option defaults are *smooth* = *yes*
+
+----------
+
+.. _Wang2009:
+
+**(Wang)** Wang, Acta Geotechnica, 4,
+p 117-127 (2009).
+
+.. _Wang2009b:
+
+**(Wang and Mora)** Wang, Mora, Advances in Geocomputing,
+119, p 183-228 (2009).
+
+.. _Groot3:
+
+**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
+
+.. _Wang20152:
+
+**(Wang et al, 2015)** Wang, Y., Alonso-Marroquin, F., & Guo,
+W. W. (2015).  Rolling and sliding in 3-D discrete element
+models. Particuology, 23, 49-55.

doc/src/bond_bpm_spring.rst

@@ -0,0 +1,202 @@
+.. index:: bond_style bpm/spring
+
+bond_style bpm/spring command
+=============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style bpm/spring keyword value attribute1 attribute2 ...
+
+* optional keyword = *overlay/pair* or *store/local* or *smooth*
+
+  .. parsed-literal::
+
+       *store/local* values = fix_ID N attributes ...
+          * fix_ID = ID of associated internal fix to store data
+          * N = prepare data for output every this many timesteps
+          * attributes = zero or more of the below attributes may be appended
+
+            *id1, id2* = IDs of 2 atoms in the bond
+            *time* = the timestep the bond broke
+            *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
+            *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
+
+       *overlay/pair* value = none
+          bonded particles will still interact with pair forces
+
+       *smooth* value = *yes* or *no*
+          smooths bond forces near the breaking point
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style bpm/spring
+   bond_coeff 1 1.0 0.05 0.1
+
+   bond_style bpm/spring myfix 1000 time id1 id2
+   dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
+   dump_modify 1 write_header no
+
+Description
+"""""""""""
+
+The *bpm/spring* bond style computes forces and torques based on
+deviations from the initial reference state of the two atoms.  The
+reference state is stored by each bond when it is first computed in
+the setup of a run. Data is then preserved across run commands and is
+written to :doc:`binary restart files <restart>` such that restarting
+the system will not reset the reference state of a bond.
+
+This bond style only applies central-body forces which conserve the
+translational and rotational degrees of freedom of a bonded set of
+particles. The force has a magnitude of
+
+.. math::
+
+   F = k (r - r_0) w
+
+where :math:`k_r` is a stiffness, :math:`r` is the current distance
+and :math:`r_0` is the initial distance between the two particles, and
+:math:`w` is an optional smoothing factor discussed below. Bonds will
+break at a strain of :math:`\epsilon_c`.  This is done by setting by
+setting its type to 0 such that forces are no longer computed.
+
+An additional damping force is applied to the bonded
+particles.  This forces is proportional to the difference in the
+normal velocity of particles using a similar construction as
+dissipative particle dynamics (:ref:`(Groot) <Groot4>`):
+
+.. math::
+
+   F_D = - \gamma w (\hat{r} \bullet \vec{v})
+
+where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
+radial normal vector, and :math:`\vec{v}` is the velocity difference
+between the two particles.
+
+The smoothing factor :math:`w` can be added or removed using the
+*smooth* keyword. It is constructed such that forces smoothly go
+to zero, avoiding discontinuities, as bonds approach the critical strain
+
+.. math::
+
+   w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 .
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example 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:`k`             (force/distance units)
+* :math:`\epsilon_c`    (unit less)
+* :math:`\gamma`        (force/velocity units)
+
+By default, pair forces are not calculated between bonded particles.
+Pair forces can alternatively be overlaid on top of bond forces using
+the *overlay/pair* keyword. These settings require specific
+:doc:`special_bonds <special_bonds>` settings described in the
+restrictions.  Further details can be found in the `:doc: how to
+<Howto_BPM>` page on BPMs.
+
+If the *store/local* keyword is used, this fix will track bonds that
+break during the simulation. Whenever a bond breaks, data is processed
+and transferred to an internal fix labeled *fix_ID*. This allows the
+local data to be accessed by other LAMMPS commands.
+Following any optional keyword/value arguments, a list of one or more
+attributes is specified.  These include the IDs of the two atoms in
+the bond. The other attributes for the two atoms include the timestep
+during which the bond broke and the current/initial center of mass
+position of the two atoms.
+
+Data is continuously accumulated over intervals of *N*
+timesteps. At the end of each interval, all of the saved accumulated
+data is deleted to make room for new data. Individual datum may
+therefore persist anywhere between *1* to *N* timesteps depending on
+when they are saved. This data can be accessed using the *fix_ID* and a
+:doc:`dump local <dump>` command. To ensure all data is output,
+the dump frequency should correspond to the same interval of *N*
+timesteps. A dump frequency of an integer multiple of *N* can be used
+to regularly output a sample of the accumulated data.
+
+Note that when unbroken bonds are dumped to a file via the
+:doc:`dump local <dump>` command, bonds with type 0 (broken bonds)
+are not included.
+The :doc:`delete_bonds <delete_bonds>` command can also be used to
+query the status of broken bonds or permanently delete them, e.g.:
+
+.. code-block:: LAMMPS
+
+   delete_bonds all stats
+   delete_bonds all bond 0 remove
+
+----------
+
+Restart and other info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This bond style writes the reference state of each bond to
+:doc:`binary restart files <restart>`. Loading a restart
+file will properly resume bonds.
+
+The single() function of these pair styles returns 0.0 for the energy
+of a pairwise interaction, since energy is not conserved in these
+dissipative potentials.
+
+The accumulated data is not written to restart files and should be
+output before a restart file is written to avoid missing data.
+
+The internal fix calculates a local vector or local array depending on the
+number of input values.  The length of the vector or number of rows in
+the array is the number of recorded, lost interactions.  If a single
+input is specified, a local vector is produced.  If two or more inputs
+are specified, a local array is produced where the number of columns =
+the number of inputs.  The vector or array can be accessed by any
+command that uses local values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
+output options.
+
+The vector or array will be floating point values that correspond to
+the specified attribute.
+
+Restrictions
+""""""""""""
+
+This bond style can only be used if LAMMPS was built with the BPM
+package. See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+By default if pair interactions are to be disabled, this bond style
+requires setting
+
+.. code-block:: LAMMPS
+
+   special_bonds lj 0 1 1 coul 1 1 1
+
+and :doc:`newton <newton>` must be set to bond off.  If the
+*overlay/pair* option is used, this bond style alternatively requires
+setting
+
+.. code-block:: LAMMPS
+
+   special_bonds lj/coul 1 1 1
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`, :doc:`pair bpm/spring <pair_bpm_spring>`
+
+Default
+"""""""
+
+The option defaults are *smooth* = *yes*
+
+----------
+
+.. _Groot4:
+
+**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).

doc/src/bond_quartic.rst

@@ -67,7 +67,8 @@ local maximum.  If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks"
 the bond, which means two things.  First, the bond potential is turned
 off by setting its type to 0, and is no longer computed.  Second, a
 pairwise interaction between the two atoms is turned on, since they
-are no longer bonded.
+are no longer bonded. See the :doc:`Howto <Howto_broken_bonds>` page
+on broken bonds for more information.
 
 LAMMPS does the second task via a computational sleight-of-hand.  It
 subtracts the pairwise interaction as part of the bond computation.

doc/src/bond_style.rst

@@ -84,6 +84,8 @@ accelerated styles exist.
 * :doc:`zero <bond_zero>` - topology but no interactions
 * :doc:`hybrid <bond_hybrid>` - define multiple styles of bond interactions
 
+* :doc:`bpm/rotational <bond_bpm_rotational>` - breakable bond with forces and torques based on deviation from reference state
+* :doc:`bpm/spring <bond_bpm_spring>` - breakable bond with forces based on deviation from reference length
 * :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
 * :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
 * :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles

doc/src/compute.rst

@@ -236,6 +236,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms
 * :doc:`msd/chunk <compute_msd_chunk>` - mean-squared displacement for each chunk
 * :doc:`msd/nongauss <compute_msd_nongauss>` - MSD and non-Gaussian parameter of group of atoms
+* :doc:`nbond/atom <compute_nbond_atom>` - calculates number of bonds per atom
 * :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
 * :doc:`orientorder/atom <compute_orientorder_atom>` - Steinhardt bond orientational order parameters Ql
 * :doc:`pair <compute_pair>` - values computed by a pair style

doc/src/compute_nbond_atom.rst

@@ -0,0 +1,52 @@
+.. index:: compute nbond/atom
+
+compute nbond/atom command
+==========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID nbond/atom
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* nbond/atom = style name of this compute command
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all nbond/atom
+
+Description
+"""""""""""
+
+Define a computation that computes the number of bonds each atom is
+part of.  Bonds which are broken are not counted in the tally.  See
+the :doc:`Howto broken bonds <Howto_bpm>` page for more information.
+The number of bonds will be zero for atoms not in the specified
+compute group. This compute does not depend on Newton bond settings.
+
+Output info
+"""""""""""
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the :doc:`Howto output <Howto_output>` doc page for an overview of
+LAMMPS output options.
+
+Restrictions
+""""""""""""
+
+This fix can only be used if LAMMPS was built with the BPM package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+Default
+"""""""
+
+none

doc/src/dump_modify.rst

@@ -474,8 +474,9 @@ The *fileper* keyword is documented below with the *nfile* keyword.
 
 The *header* keyword toggles whether the dump file will include a
 header.  Excluding a header will reduce the size of the dump file for
-fixes such as :doc:`fix pair/tracker <fix_pair_tracker>` which do not
+data produced by :doc:`pair tracker <pair_tracker>` or
-require the information typically written to the header.
+:doc:`bpm bond styles <Howto_bpm>` which may not require the
+information typically written to the header.
 
 ----------
 

doc/src/fix.rst

@@ -284,6 +284,7 @@ accelerated styles exist.
 * :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` -
 * :doc:`nve/noforce <fix_nve_noforce>` - NVE without forces (v only)
 * :doc:`nve/sphere <fix_nve_sphere>` - NVE for spherical particles
+* :doc:`nve/bpm/sphere <fix_nve_bpm_sphere>` - NVE for spherical particles used in the BPM package
 * :doc:`nve/spin <fix_nve_spin>` - NVE for a spin or spin-lattice system
 * :doc:`nve/tri <fix_nve_tri>` - NVE for triangles
 * :doc:`nvk <fix_nvk>` - constant kinetic energy time integration
@@ -301,7 +302,6 @@ accelerated styles exist.
 * :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
 * :doc:`orient/eco <fix_orient_eco>` - add generalized grain boundary migration force
 * :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
-* :doc:`pair/tracker <fix_pair_tracker>` - track properties of pairwise interactions
 * :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
 * :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
 * :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane

doc/src/fix_bond_break.rst

@@ -113,6 +113,9 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local
    may need to thermostat your system to compensate for energy changes
    resulting from broken bonds (and angles, dihedrals, impropers).
 
+See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for more
+information on related features in LAMMPS.
+
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info

doc/src/fix_nve_bpm_sphere.rst

@@ -0,0 +1,87 @@
+.. index:: fix nve/bpm/sphere
+
+fix nve/bpm/sphere command
+==========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID nve/bpm/sphere
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* nve/bpm/sphere = style name of this fix command
+* zero or more keyword/value pairs may be appended
+* keyword = *disc*
+
+  .. parsed-literal::
+
+       *disc* value = none = treat particles as 2d discs, not spheres
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all nve/bpm/sphere
+   fix 1 all nve/bpm/sphere disc
+
+Description
+"""""""""""
+
+Perform constant NVE integration to update position, velocity, angular
+velocity, and quaternion orientation for finite-size spherical
+particles in the group each timestep.  V is volume; E is energy.  This
+creates a system trajectory consistent with the microcanonical
+ensemble.
+
+This fix differs from the :doc:`fix nve <fix_nve>` command, which
+assumes point particles and only updates their position and velocity.
+It also differs from the :doc:`fix nve/sphere <fix_nve_sphere>`
+command which assumes finite-size spheroid particles which do not
+store a quaternion.  It thus does not update a particle's orientation
+or quaternion.
+
+If the *disc* keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the :doc:`dimension <dimension>` keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.  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 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 requires that atoms store torque, angular velocity (omega), a
+radius, and a quaternion as defined by the :doc:`atom_style bpm/sphere
+<atom_style>` command.
+
+All particles in the group must be finite-size spheres with
+quaternions.  They cannot be point particles.
+
+Use of the *disc* keyword is only allowed for 2d simulations, as
+defined by the :doc:`dimension <dimension>` keyword.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nve <fix_nve>`, :doc:`fix nve/sphere <fix_nve_sphere>`
+
+Default
+"""""""
+
+none
+

doc/src/fix_pair_tracker.rst

@@ -1,124 +0,0 @@
-.. index:: fix pair/tracker
-
-fix pair/tracker command
-========================
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   fix ID group-ID pair/tracker N attribute1 attribute2 ... keyword values ...
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* pair/tracker = style name of this fix command
-* N = prepare data for output every this many timesteps
-* one or more attributes may be appended
-
-  .. parsed-literal::
-
-       possible attributes = id1 id2 time/created time/broken time/total
-                             rmin rave x y z
-
-  .. parsed-literal::
-
-          id1, id2 = IDs of the 2 atoms in each pair interaction
-          time/created = the time that the 2 atoms began interacting
-          time/broken = the time that the 2 atoms stopped interacting
-          time/total = the total time the 2 atoms interacted
-          r/min = the minimum radial distance between the 2 atoms during the interaction
-          r/ave = the average radial distance between the 2 atoms during the interaction
-          x, y, z = the center of mass position of the 2 atoms when they stopped interacting
-
-* zero or more keyword/value pairs may be appended
-* keyword = *time/min* or *type/include*
-
-  .. parsed-literal::
-
-       *time/min* value = T
-         T = minimum interaction time
-       *type/include* value = arg1 arg2
-         arg = separate lists of types (see below)
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 1 all pair/tracker 1000 id1 id2 time/min 100
-   fix 1 all pair/tracker 1000 time/created time/broken type/include 1 * type/include 2 3,4
-
-Description
-"""""""""""
-
-Tracks properties of pairwise interactions between two atoms and records data
-whenever the atoms move beyond the interaction cutoff.
-Must be used in conjunction with :doc:`pair tracker <pair_tracker>`.
-Data is accumulated over a span of *N* timesteps before being deleted.
-The number of datums generated, aggregated across all processors, equals
-the number of broken interactions. Interactions are only included if both
-atoms are included in the specified fix group. Additional filters can be
-applied using the *time/min* or *type/include* keywords described below.
-
-.. note::
-
-   For extremely long-lived interactions, the calculation of *r/ave* may not be
-   correct due to double overflow.
-
-The *time/min* keyword sets a minimum amount of time that an interaction must
-persist to be included. This setting can be used to censor short-lived interactions.
-The *type/include* keyword filters interactions based on the types of the two atoms.
-Data is only saved for interactions between atoms with types in the two lists.
-Each list consists of a series of type
-ranges separated by commas. The range can be specified as a
-single numeric value, or a wildcard asterisk can be used to specify a range
-of values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  For
-example, if M = the number of atom types, then an asterisk with no numeric
-values means all types from 1 to M.  A leading asterisk means all types
-from 1 to n (inclusive).  A trailing asterisk means all types from n to M
-(inclusive).  A middle asterisk means all types from m to n (inclusive).
-Multiple *type/include* keywords may be added.
-
-----------
-
-Restart, fix_modify, run start/stop, minimize info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-No information about this fix is written to :doc:`binary restart files <restart>`.
-None of the :doc:`fix_modify <fix_modify>` options are
-relevant to this fix.
-No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.
-
-Output info
-"""""""""""
-
-This compute calculates a local vector or local array depending on the
-number of input values.  The length of the vector or number of rows in
-the array is the number of recorded, lost interactions.  If a single input is
-specified, a local vector is produced.  If two or more inputs are
-specified, a local array is produced where the number of columns = the
-number of inputs.  The vector or array can be accessed by any command
-that uses local values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
-options.
-
-The vector or array values will be doubles that correspond to the
-specified attribute.
-
-Restrictions
-""""""""""""
-
-Must be used in conjunction with :doc:`pair style tracker <pair_tracker>`.
-
-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>` page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`pair tracker <pair_tracker>`
-
-Default
-"""""""
-
-none

doc/src/pair_bpm_spring.rst

@@ -0,0 +1,114 @@
+.. index:: pair_style bpm/spring
+
+pair_style bpm/spring command
+=============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style bpm/spring
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style bpm/spring
+   pair_coeff * * 1.0 1.0 1.0
+   pair_coeff 1 1 1.0 1.0 1.0
+
+Description
+"""""""""""
+
+Style *bpm/spring* computes pairwise forces with the formula
+
+.. math::
+
+   F = k (r - r_c)
+
+where :math:`k` is a stiffness and :math:`r_c` is the cutoff length.
+An additional damping force is also applied to interacting
+particles. The force is proportional to the difference in the
+normal velocity of particles
+
+.. math::
+
+   F_D = - \gamma w (\hat{r} \bullet \vec{v})
+
+where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
+radial normal vector, :math:`\vec{v}` is the velocity difference
+between the two particles, and :math:`w` is a smoothing factor.
+This smoothing factor is constructed such that damping forces go to zero
+as particles come out of contact to avoid discontinuities. It is
+given by
+
+.. math::
+
+   w = 1.0 - \left( \frac{r}{r_c} \right)^8 .
+
+This pair style is designed for use in a spring-based bonded particle
+model.  It mirrors the construction of the :doc:`bpm/spring
+<bond_bpm_spring>` bond style.
+
+This pair interaction is always applied to pairs of non-bonded particles
+that are within the interaction distance. For pairs of bonded particles
+that are within the interaction distance, there is the option to either
+include this pair interaction and overlay the pair force over the bond
+force or to exclude this pair interaction such that the two particles
+only interact via the bond force. See discussion of the *overlay/pair*
+option for BPM bond styles and the :doc:`special_bonds <special_bonds>`
+command in the `:doc: how to <Howto_BPM>` page on BPMs for more details.
+
+The following coefficients must be defined for each pair of atom 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, or by mixing as described below:
+
+* :math:`k`             (force/distance units)
+* :math:`r_c`           (distance units)
+* :math:`\gamma`        (force/velocity units)
+
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed.  A is always mixed via a
+*geometric* rule.  The cutoff is mixed according to the pair_modify
+mix value.  The default mix value is *geometric*\ .  See the
+"pair_modify" command for details.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift option, since the pair interaction goes to 0.0 at the cutoff.
+
+The :doc:`pair_modify <pair_modify>` table and tail options are not
+relevant for this pair style.
+
+This pair style writes its 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.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*, *middle*, *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`, :doc:`bond bpm/spring <bond_bpm_spring>`
+
+Default
+"""""""
+
+none

doc/src/pair_lj_long.rst

@@ -238,7 +238,7 @@ none
 
 .. _Veld2:
 
-**(In 't Veld)** In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
+**(In 't Veld)** In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
 
 .. _Jorgensen4:
 

doc/src/pair_style.rst

@@ -131,6 +131,7 @@ accelerated styles exist.
 * :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulomb
 * :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulomb
 * :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulomb and core/shell model
+* :doc:`bpm/spring <pair_bpm_spring>` - repulsive harmonic force with damping
 * :doc:`brownian <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics
 * :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity
 * :doc:`buck <pair_buck>` - Buckingham potential

doc/src/pair_tracker.rst

@@ -8,89 +8,182 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   pair_style tracker keyword
+   pair_style tracker fix_ID N keyword values attribute1 attribute2 ...
 
-* zero or more keyword/arg pairs may be appended
+* fix_ID = ID of associated internal fix to store data
-* keyword = *finite*
+* N = prepare data for output every this many timesteps
+* zero or more keywords may be appended
+* keyword = *finite* or *time/min* or *type/include*
 
   .. parsed-literal::
 
       *finite* value = none
          pair style uses atomic diameters to identify contacts
+      *time/min* value = T
+         T = minimum number of timesteps of interaction
+      *type/include* value = list1 list2
+         list1,list2 = separate lists of types (see below)
+
+* one or more attributes may be appended
+
+  .. parsed-literal::
+
+       possible attributes = id1 id2 time/created time/broken time/total
+                             r/min r/ave x y z
+
+  .. parsed-literal::
+
+          id1, id2 = IDs of the 2 atoms in each pair interaction
+          time/created = the timestep that the 2 atoms began interacting
+          time/broken = the timestep that the 2 atoms stopped interacting
+          time/total = the total number of timesteps the 2 atoms interacted
+          r/min = the minimum radial distance between the 2 atoms during the interaction (distance units)
+          r/ave = the average radial distance between the 2 atoms during the interaction (distance units)
+          x, y, z = the center of mass position of the 2 atoms when they stopped interacting (distance units)
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   pair_style hybrid/overlay tracker ...
+   pair_style hybrid/overlay tracker myfix 1000 id1 id2 type/include 1 * type/include 2 3,4  lj/cut 2.5
    pair_coeff 1 1 tracker 2.0
 
-   pair_style hybrid/overlay tracker finite ...
+   pair_style hybrid/overlay tracker myfix 1000 finite x y z time/min 100 granular
    pair_coeff * * tracker
 
-   fix 1 all pair/tracker 1000 time/created time/broken
+   dump 1 all local 1000 dump.local f_myfix[1] f_myfix[2] f_myfix[3]
-   dump 1 all local 1000 dump.local f_1[1] f_1[2]
    dump_modify 1 write_header no
 
 Description
 """""""""""
 
-Style *tracker* monitors information about pairwise interactions.
+Style *tracker* monitors information about pairwise interactions.  It
-It does not calculate any forces on atoms.
+does not calculate any forces on atoms. :doc:`Pair hybrid/overlay
-:doc:`Pair hybrid/overlay <pair_hybrid>` can be used to combine this pair
+<pair_hybrid>` can be used to combine this pair style with any other
-style with another pair style. Style *tracker*  must be used in conjunction
+pair style, as shown in the examples above.
-with about :doc:`fix pair_tracker <fix_pair_tracker>` which contains
-information on what data can be output.
 
-If the *finite* keyword is not defined, the following coefficients must be
+At each timestep, if two neighboring atoms move beyond the interaction
-defined for each pair of atom types via the :doc:`pair_coeff <pair_coeff>`
+cutoff, pairwise data is processed and transferred to an internal fix
-command as in the examples above, or in the data file or restart files
+labeled *fix_ID*. This allows the local data to be accessed by other
-read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+LAMMPS commands. Additional
-commands, or by mixing as described below:
+filters can be applied using the *time/min* or *type/include* keywords
+described below.  Note that this is the interaction cutoff defined by
+this pair style, not the short-range cutoff defined by the pair style
+that is calculating forces on atoms.
+
+Following any optional keyword/value arguments, a list of one or more
+attributes is specified.  These include the IDs of the two atoms in
+the pair.  The other attributes for the pair of atoms are the
+duration of time they were "interacting" or at the point in time they
+started or stopped interacting.  In this context, "interacting" means
+the time window during which the two atoms were closer than the
+interaction cutoff distance.  The attributes for time/* refer to
+timesteps.
+
+Data is continuously accumulated by the internal fix over intervals of *N*
+timesteps. At the end of each interval, all of the saved accumulated
+data is deleted to make room for new data. Individual datum may
+therefore persist anywhere between *1* to *N* timesteps depending on
+when they are saved. This data can be accessed using the *fix_ID* and a
+:doc:`dump local <dump>` command. To ensure all data is output,
+the dump frequency should correspond to the same interval of *N*
+timesteps. A dump frequency of an integer multiple of *N* can be used
+to regularly output a sample of the accumulated data.
+
+----------
+
+The following optional keywords may be used.
+
+If the *finite* keyword is not used, the following coefficients must
+be defined for each pair of atom 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, or by mixing as described
+below:
 
 * cutoff (distance units)
 
-If the *finite* keyword is defined, no coefficients may be defined.
+If the *finite* keyword is used, there are no additional coefficients
-Interaction cutoffs are alternatively calculated based on the
+to set for each pair of atom types via the
-diameter of finite particles.
+:doc:`pair_coeff <pair_coeff>` command. Interaction cutoffs are
+instead calculated based on the diameter of finite particles. However
+you must still use the :doc:`pair_coeff <pair_coeff>` for all atom
+types. For example the command
 
+.. code-block:: LAMMPS
+
+   pair_coeff * *
+
+should be used.
+
+The *time/min* keyword sets a minimum amount of time that an
+interaction must persist to be included.  This setting can be used to
+censor short-lived interactions.
+
+The *type/include* keyword filters interactions based on the types of
+the two atoms.  Data is only saved for interactions between atoms
+whose two atom types appear in *list1* and *list2*.  Atom type 1 must
+be in list1 and atom type 2 in list2.  Or vice versa.
+
+Each type list consists of a series of type ranges separated by
+commas.  Each range can be specified as a single numeric value, or a
+wildcard asterisk can be used to specify a range of values.  This
+takes the form "\*" or "\*n" or "n\*" or "m\*n".  For example, if M =
+the number of atom types, then an asterisk with no numeric values
+means all types from 1 to M.  A leading asterisk means all types from
+1 to n (inclusive).  A trailing asterisk means all types from n to M
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).  Note that the *type/include* keyword can be specified
+multiple times.
 
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 For atom type pairs I,J and I != J, the cutoff coefficient and cutoff
-distance for this pair style can be mixed.  The cutoff is always mixed via a
+distance for this pair style can be mixed.  The cutoff is always mixed
-*geometric* rule.  The cutoff is mixed according to the pair_modify
+via a *geometric* rule.  The cutoff is mixed according to the
-mix value.  The default mix value is *geometric*\ .  See the
+pair_modify mix value.  The default mix value is *geometric*\ .  See
-"pair_modify" command for details.
+the "pair_modify" command for details.
 
-This pair style writes its information to :doc:`binary restart files <restart>`, so
+This pair style writes its information to :doc:`binary restart files
-pair_style and pair_coeff commands do not need
+<restart>`, so pair_style and pair_coeff commands do not need to be
-to be specified in an input script that reads a restart file.
+specified in an input script that reads a restart file.
 
 The :doc:`pair_modify <pair_modify>` shift, table, and tail options
 are not relevant for this pair style.
 
+The accumulated data is not written to restart files and should be
+output before a restart file is written to avoid missing data.
+
+The internal fix calculates a local vector or local array depending on the
+number of input values.  The length of the vector or number of rows in
+the array is the number of recorded, lost interactions.  If a single
+input is specified, a local vector is produced.  If two or more inputs
+are specified, a local array is produced where the number of columns =
+the number of inputs.  The vector or array can be accessed by any
+command that uses local values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
+output options.
+
+The vector or array will be floating point values that correspond to
+the specified attribute.
+
 ----------
 
 Restrictions
 """"""""""""
 
-A corresponding :doc:`fix pair_tracker <fix_pair_tracker>` must be defined
-to use this pair style.
-
-This pair style is currently incompatible with granular pair styles that extend
-beyond the contact (e.g. JKR and DMT).
-
 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>` page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style is currently incompatible with granular pair styles
+that extend beyond the contact (e.g. JKR and DMT).
 
 Related commands
 """"""""""""""""
 
-:doc:`fix pair_tracker <fix_pair_tracker>`
-
 Default
 """""""
 

doc/src/read_data.rst

@@ -650,6 +650,8 @@ of analysis.
      - atom-ID atom-type rho esph cv x y z
    * - sphere
      - atom-ID atom-type diameter density x y z
+   * - bpm/sphere
+     - atom-ID molecule-ID atom-type diameter density x y z
    * - spin
      - atom-ID atom-type x y z spx spy spz sp
    * - tdpd

doc/utils/sphinx-config/false_positives.txt

@@ -328,6 +328,8 @@ boxzlo
 bp
 bpclermont
 bpls
+bpm
+BPM
 br
 Branduardi
 Branicio
@@ -1149,8 +1151,10 @@ gdot
 GeC
 Geier
 gencode
+Geocomputing
 georg
 Georg
+Geotechnica
 germain
 Germann
 Germano
@@ -1320,6 +1324,7 @@ Holm
 holonomic
 Homebrew
 hooke
+hookean
 Hookean
 hostname
 hotpink
@@ -2074,6 +2079,7 @@ monopole
 monovalent
 Montalenti
 Montero
+Mora
 Morefoo
 Morfill
 Mori
@@ -2203,6 +2209,7 @@ Nbin
 Nbins
 nbody
 Nbody
+nbond
 nbonds
 nbondtype
 Nbondtype
@@ -3174,6 +3181,7 @@ Steinhauser
 Stepaniants
 stepwise
 Stesmans
+stiffnesses
 Stillinger
 stk
 stochastically

examples/bpm/impact/in.bpm.impact.rotational

@@ -0,0 +1,51 @@
+units           lj
+dimension       3
+boundary        f f f
+atom_style      bpm/sphere
+special_bonds   lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+newton          on off
+comm_modify     vel yes cutoff 2.6
+lattice         fcc 1.0
+region          box block -25 15 -22 22 -22 22
+create_box      1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
+
+region          disk cylinder x 0.0 0.0 20.0 -0.5 0.5
+create_atoms    1 region disk
+group           plate region disk
+
+region          ball sphere 8.0 0.0 0.0 6.0
+create_atoms    1 region ball
+group           projectile region ball
+
+displace_atoms  all random 0.1 0.1 0.1 134598738
+
+neighbor        1.0 bin
+pair_style      gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
+pair_coeff      1 1
+
+fix             1 all nve/bpm/sphere
+
+create_bonds    many plate plate 1 0.0 1.5
+create_bonds    many projectile projectile 2 0.0 1.5
+
+neighbor        0.3 bin
+special_bonds   lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+bond_style      bpm/rotational store/local brkbond 100 time id1 id2
+bond_coeff      1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.2 0.002 0.002
+bond_coeff      2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.2 0.002 0.002
+
+velocity        projectile set -0.05 0.0 0.0
+compute         nbond all nbond/atom
+compute         tbond all reduce sum c_nbond
+
+timestep        0.05
+thermo_style    custom step ke pe pxx pyy pzz c_tbond
+thermo          100
+thermo_modify   lost ignore lost/bond ignore
+#dump            1 all custom 100 atomDump id radius x y z c_nbond
+
+dump            2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
+dump_modify     2 header no
+
+run             7500

examples/bpm/impact/in.bpm.impact.spring

@@ -0,0 +1,53 @@
+units           lj
+dimension       3
+boundary        f f f
+atom_style      bond
+special_bonds   lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+newton          on off
+comm_modify     vel yes cutoff 2.6
+lattice         fcc 1.0
+region          box block -25 15 -22 22 -22 22
+create_box      1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
+
+region          disk cylinder x 0.0 0.0 20.0 -0.5 0.5
+create_atoms    1 region disk
+group           plate region disk
+
+region          ball sphere 8.0 0.0 0.0 6.0
+create_atoms    1 region ball
+group           projectile region ball
+
+displace_atoms  all random 0.1 0.1 0.1 134598738
+
+mass            1 1.0
+
+neighbor        1.0 bin
+pair_style      bpm/spring
+pair_coeff      1 1 1.0 1.0 1.0
+
+fix             1 all nve
+
+create_bonds    many plate plate 1 0.0 1.5
+create_bonds    many projectile projectile 2 0.0 1.5
+
+neighbor        0.3 bin
+special_bonds   lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+bond_style      bpm/spring store/local brkbond 100 time id1 id2
+bond_coeff      1 1.0 0.04 1.0
+bond_coeff      2 1.0 0.20 1.0
+
+velocity        projectile set -0.05 0.0 0.0
+compute         nbond all nbond/atom
+compute         tbond all reduce sum c_nbond
+
+timestep        0.1
+thermo_style    custom step ke pe pxx pyy pzz c_tbond
+thermo          100
+thermo_modify   lost ignore lost/bond ignore
+#dump            1 all custom 100 atomDump id x y z c_nbond
+
+dump            2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
+dump_modify     2 header no
+
+run             7500

examples/bpm/impact/log.17Feb2022.impact.rotational.g++.4

@@ -0,0 +1,219 @@
+LAMMPS (17 Feb 2022)
+units           lj
+dimension       3
+boundary        f f f
+atom_style      bpm/sphere
+special_bonds   lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+newton          on off
+comm_modify     vel yes cutoff 2.6
+lattice         fcc 1.0
+Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
+region          box block -25 15 -22 22 -22 22
+create_box      1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
+Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
+  1 by 2 by 2 MPI processor grid
+
+region          disk cylinder x 0.0 0.0 20.0 -0.5 0.5
+create_atoms    1 region disk
+Created 7529 atoms
+  using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
+  create_atoms CPU = 0.002 seconds
+group           plate region disk
+7529 atoms in group plate
+
+region          ball sphere 8.0 0.0 0.0 6.0
+create_atoms    1 region ball
+Created 3589 atoms
+  using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
+  create_atoms CPU = 0.001 seconds
+group           projectile region ball
+3589 atoms in group projectile
+
+displace_atoms  all random 0.1 0.1 0.1 134598738
+Displacing atoms ...
+
+neighbor        1.0 bin
+pair_style      gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
+pair_coeff      1 1
+
+fix             1 all nve/bpm/sphere
+
+create_bonds    many plate plate 1 0.0 1.5
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2
+  ghost atom cutoff = 2.6
+  binsize = 1, bins = 64 70 70
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command create_bonds, occasional
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair gran/hooke/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Added 38559 bonds, new total = 38559
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        1        1       
+    15 = max # of 1-2 neighbors
+   101 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+create_bonds    many projectile projectile 2 0.0 1.5
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+WARNING: Bonds are defined but no bond style is set (../force.cpp:192)
+WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:194)
+Added 21869 bonds, new total = 60428
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        1        1       
+    16 = max # of 1-2 neighbors
+   101 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+
+neighbor        0.3 bin
+special_bonds   lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+bond_style      bpm/rotational store/local brkbond 100 time id1 id2
+bond_coeff      1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.2 0.002 0.002
+bond_coeff      2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.2 0.002 0.002
+
+velocity        projectile set -0.05 0.0 0.0
+compute         nbond all nbond/atom
+compute         tbond all reduce sum c_nbond
+
+timestep        0.05
+thermo_style    custom step ke pe pxx pyy pzz c_tbond
+thermo          100
+thermo_modify   lost ignore lost/bond ignore
+#dump            1 all custom 100 atomDump id radius x y z c_nbond
+
+dump            2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
+dump_modify     2 header no
+
+run             7500
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.3
+  ghost atom cutoff = 2.6
+  binsize = 0.65, bins = 98 108 108
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair gran/hooke/history, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.35 Mbytes
+Step KinEng PotEng Pxx Pyy Pzz c_tbond 
+       0 0.00053238861            0 3.8217307e-05            0            0      10.8703 
+     100 0.00053238861            0 3.8217307e-05 1.2166373e-20 1.2308212e-20      10.8703 
+     200 0.00053238861            0 3.8217307e-05 1.2454467e-20 1.2479589e-20      10.8703 
+     300 0.00053238861            0 3.8217307e-05 1.2256702e-20 1.2621091e-20      10.8703 
+     400 0.00053238861            0 3.8217307e-05 1.2170534e-20 1.2751666e-20      10.8703 
+     500 0.00053093549            0 3.8484194e-05 7.645531e-08 1.4861825e-07      10.8703 
+     600 0.00051485902            0 4.0340751e-05 3.8615876e-07 4.8663463e-07    10.869221 
+     700 0.00049942978            0 3.8684008e-05 4.5363318e-07 4.4560229e-07     10.85501 
+     800 0.00049465262            0 3.6604612e-05 1.4755468e-07 2.0062093e-07    10.820651 
+     900 0.00048784775            0 3.5333139e-05 3.5118328e-07 6.6697625e-07    10.769563 
+    1000 0.00048345699            0 3.4702137e-05 7.0312998e-07 4.0218318e-07    10.730347 
+    1100 0.00047945073            0 3.5065961e-05 6.2813891e-07 7.4640359e-07    10.703184 
+    1200 0.00047512604            0 3.4833144e-05 8.5208604e-07 8.7277583e-07    10.686634 
+    1300 0.00047401428            0 3.4236869e-05 1.0321827e-06 7.4545242e-07       10.678 
+    1400 0.00047619121            0 3.4416549e-05 8.7518021e-07 7.3979503e-07    10.671704 
+    1500 0.0004668728            0 3.4495751e-05 1.4077823e-06 1.517373e-06    10.666127 
+    1600 0.00045088371            0 3.3264301e-05 1.8499661e-06 1.9842415e-06     10.66073 
+    1700 0.00044275099            0 3.2471064e-05 1.9028747e-06 2.2248947e-06      10.6458 
+    1800 0.0004424362            0 3.1846336e-05 1.6208492e-06 1.9291602e-06    10.620615 
+    1900 0.00043678957            0 3.1260936e-05 1.4673956e-06 1.6120523e-06    10.603166 
+    2000 0.00042747562            0 3.0652107e-05 1.6455486e-06  1.53127e-06    10.576003 
+    2100 0.0004214344            0 3.0240727e-05 1.8873967e-06 1.5258622e-06    10.539845 
+    2200 0.00041712779            0 3.0329566e-05 1.8846152e-06 1.4971471e-06     10.49937 
+    2300 0.00041095769            0 3.0000572e-05 2.3585924e-06 1.6773177e-06    10.471668 
+    2400 0.00040883568            0 2.9625158e-05 1.9105554e-06 1.8720763e-06     10.45116 
+    2500 0.00040762685            0 2.9441541e-05 1.6848938e-06 1.8877532e-06    10.437309 
+    2600 0.00040579873            0 2.9255988e-05 1.7523874e-06 1.636423e-06    10.422378 
+    2700 0.00040340975            0 2.9035693e-05 1.673158e-06 1.9038932e-06    10.410505 
+    2800 0.00040170914            0 2.8829361e-05 1.6711978e-06 1.9776001e-06    10.400792 
+    2900 0.00040015113            0 2.8614186e-05 1.5982427e-06 1.7994733e-06    10.393416 
+    3000 0.00040029253            0 2.8470718e-05 1.5589166e-06 1.6682302e-06    10.385321 
+    3100 0.00040037329            0 2.8483376e-05 1.2831526e-06 1.4788005e-06    10.378485 
+    3200 0.00040142612            0 2.8481287e-05 1.1577988e-06 1.3495778e-06    10.373988 
+    3300 0.00040105092            0 2.8547009e-05 1.2155138e-06 1.2633439e-06    10.370031 
+    3400 0.00039950673            0 2.8340939e-05 1.1182251e-06 1.1624668e-06    10.364274 
+    3500 0.00039715236            0 2.824813e-05 1.3086462e-06 1.2029185e-06    10.360496 
+    3600 0.00039446552            0 2.8112283e-05 1.1232321e-06 1.0077217e-06    10.353121 
+    3700 0.00039263296            0 2.7927975e-05 1.1083636e-06 1.2091857e-06    10.346645 
+    3800 0.00039061341            0 2.7819957e-05 1.1836841e-06 1.3566272e-06    10.341069 
+    3900 0.00038985051            0 2.7681947e-05 1.3588359e-06 1.4099727e-06    10.329196 
+    4000 0.00038815347            0 2.7492102e-05 1.1111719e-06 1.1700718e-06    10.318043 
+    4100 0.00038651302            0 2.7444105e-05 9.9563429e-07 1.4085969e-06    10.311027 
+    4200 0.00038565809            0 2.7177341e-05 9.5736307e-07 1.0404482e-06    10.299155 
+    4300 0.0003847255            0 2.7029216e-05 9.6204756e-07 1.140804e-06    10.292319 
+    4400 0.0003844421            0 2.6841047e-05 9.6570404e-07 1.2319818e-06    10.286203 
+    4500 0.0003842788            0 2.6633558e-05 9.6452478e-07 1.1954945e-06    10.278287 
+    4600 0.00038365139            0 2.6514403e-05 9.6185846e-07 1.2002452e-06    10.270732 
+    4700 0.00038271503            0 2.6374349e-05 9.4061833e-07 1.1774211e-06    10.264796 
+    4800 0.00038233688            0 2.638398e-05 1.1644119e-06 1.3746239e-06     10.25742 
+    4900 0.00038223496            0 2.6279821e-05 1.1345508e-06 1.4709213e-06    10.246987 
+    5000 0.00038219402            0 2.6188871e-05 1.0115151e-06 1.2024203e-06    10.240511 
+    5100 0.00038195153            0 2.6137945e-05 1.009856e-06 1.1961088e-06    10.236014 
+    5200 0.00038170903            0 2.6103563e-05 1.0046761e-06 1.1881008e-06    10.232236 
+    5300 0.00038194303            0 2.6111938e-05 1.0533375e-06 1.2621634e-06    10.230617 
+    5400 0.00038147407            0 2.6078641e-05 1.082228e-06 1.2915223e-06    10.230098 
+    5500 0.00038156894            0 2.6084488e-05 1.1395485e-06 1.3592644e-06    10.227759 
+    5600 0.00038169434            0 2.6085704e-05 1.1173618e-06 1.3003599e-06      10.2256 
+    5700 0.00038219734            0 2.6095279e-05 1.1026614e-06 1.280455e-06    10.223621 
+    5800 0.00038268758            0 2.6113437e-05 1.1096198e-06 1.2565503e-06    10.222902 
+    5900 0.00038300658            0 2.6131709e-05 1.1123595e-06 1.235992e-06    10.222182 
+    6000 0.00038250316            0 2.606995e-05 1.1590744e-06 1.2888416e-06    10.221123 
+    6100 0.0003821526            0 2.6025605e-05 1.1434025e-06 1.3141861e-06    10.219503 
+    6200 0.00038185711            0 2.5991255e-05 1.1471391e-06 1.3427373e-06    10.219503 
+    6300 0.00038197679            0 2.5996965e-05 1.1338082e-06 1.3315258e-06    10.218604 
+    6400 0.00038232311            0 2.6035805e-05 1.1353407e-06 1.3306683e-06    10.217884 
+    6500 0.00038255543            0 2.6091572e-05 1.1768703e-06 1.3629611e-06    10.217704 
+    6600 0.00038251887            0 2.6068968e-05 1.1808094e-06 1.3969697e-06    10.217344 
+    6700 0.00038177389            0 2.6004288e-05 1.1659866e-06 1.423638e-06    10.218084 
+    6800 0.00038096291            0 2.5969494e-05 1.1377343e-06 1.4348787e-06    10.218103 
+    6900 0.00038090601            0 2.5951546e-05 1.1327767e-06 1.4311663e-06    10.217024 
+    7000 0.00038088094            0 2.5946255e-05 1.1652568e-06 1.4567559e-06    10.215944 
+    7100 0.00038094624            0 2.5972593e-05 1.1558871e-06 1.4692935e-06    10.214684 
+    7200 0.00038168738            0   2.6002e-05 1.1562707e-06 1.4881081e-06    10.212705 
+    7300 0.00038200854            0 2.6038768e-05 1.1339903e-06 1.4808455e-06    10.212345 
+    7400 0.00038187543            0 2.6044759e-05 1.101743e-06 1.4758679e-06    10.213084 
+    7500 0.00038165297            0 2.6004536e-05 1.0892731e-06 1.4872621e-06    10.214742 
+Loop time of 28.804 on 4 procs for 7500 steps with 11111 atoms
+
+Performance: 1124843.305 tau/day, 260.380 timesteps/s
+97.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.26977    | 0.28058    | 0.2866     |   1.3 |  0.97
+Bond    | 22.742     | 23.598     | 24.671     |  16.6 | 81.92
+Neigh   | 0.54555    | 0.5728     | 0.60272    |   3.2 |  1.99
+Comm    | 1.4024     | 2.5619     | 3.5079     |  54.8 |  8.89
+Output  | 0.025307   | 0.025833   | 0.027022   |   0.4 |  0.09
+Modify  | 1.592      | 1.6506     | 1.7059     |   4.0 |  5.73
+Other   |            | 0.1147     |            |       |  0.40
+
+Nlocal:        2777.75 ave        2887 max        2682 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Nghost:         1152.5 ave        1189 max        1125 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+Neighs:        11515.5 ave       12520 max       10831 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 46062
+Ave neighs/atom = 4.1456215
+Ave special neighs/atom = 10.214742
+Neighbor list builds = 408
+Dangerous builds = 0
+Total wall time: 0:00:28

examples/bpm/impact/log.17Feb2022.impact.spring.g++.4

@@ -0,0 +1,221 @@
+LAMMPS (17 Feb 2022)
+units           lj
+dimension       3
+boundary        f f f
+atom_style      bond
+special_bonds   lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+newton          on off
+comm_modify     vel yes cutoff 2.6
+lattice         fcc 1.0
+Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
+region          box block -25 15 -22 22 -22 22
+create_box      1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
+Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
+  1 by 2 by 2 MPI processor grid
+
+region          disk cylinder x 0.0 0.0 20.0 -0.5 0.5
+create_atoms    1 region disk
+Created 7529 atoms
+  using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
+  create_atoms CPU = 0.001 seconds
+group           plate region disk
+7529 atoms in group plate
+
+region          ball sphere 8.0 0.0 0.0 6.0
+create_atoms    1 region ball
+Created 3589 atoms
+  using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
+  create_atoms CPU = 0.000 seconds
+group           projectile region ball
+3589 atoms in group projectile
+
+displace_atoms  all random 0.1 0.1 0.1 134598738
+Displacing atoms ...
+
+mass            1 1.0
+
+neighbor        1.0 bin
+pair_style      bpm/spring
+pair_coeff      1 1 1.0 1.0 1.0
+
+fix             1 all nve
+
+create_bonds    many plate plate 1 0.0 1.5
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2
+  ghost atom cutoff = 2.6
+  binsize = 1, bins = 64 70 70
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command create_bonds, occasional
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair bpm/spring, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Added 38559 bonds, new total = 38559
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        1        1       
+    15 = max # of 1-2 neighbors
+   101 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+create_bonds    many projectile projectile 2 0.0 1.5
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+WARNING: Bonds are defined but no bond style is set (../force.cpp:192)
+WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:194)
+Added 21869 bonds, new total = 60428
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        1        1       
+    16 = max # of 1-2 neighbors
+   101 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+
+neighbor        0.3 bin
+special_bonds   lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+bond_style      bpm/spring store/local brkbond 100 time id1 id2
+bond_coeff      1 1.0 0.04 1.0
+bond_coeff      2 1.0 0.20 1.0
+
+velocity        projectile set -0.05 0.0 0.0
+compute         nbond all nbond/atom
+compute         tbond all reduce sum c_nbond
+
+timestep        0.1
+thermo_style    custom step ke pe pxx pyy pzz c_tbond
+thermo          100
+thermo_modify   lost ignore lost/bond ignore
+#dump            1 all custom 100 atomDump id x y z c_nbond
+
+dump            2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
+dump_modify     2 header no
+
+run             7500
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.3
+  ghost atom cutoff = 2.6
+  binsize = 0.65, bins = 98 108 108
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair bpm/spring, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 17.74 | 17.74 | 17.74 Mbytes
+Step KinEng PotEng Pxx Pyy Pzz c_tbond 
+       0 0.0010167873            0 7.298968e-05            0            0      10.8703 
+     100 0.0010167873            0 7.298968e-05 -8.7429897e-20 -8.8470837e-20      10.8703 
+     200 0.0010167873            0 7.298968e-05 -7.2809565e-20 -8.0915788e-20      10.8703 
+     300 0.0009951439            0 9.9273671e-05 8.1569216e-06 8.0922512e-06    10.868142 
+     400 0.00095142792            0 0.00012669557 -1.3413721e-05 -1.4800745e-05    10.849793 
+     500 0.00092272662            0 8.1708784e-05 -9.7488701e-06 -1.3603634e-05    10.819752 
+     600 0.00088967612            0 6.2587266e-05 -5.1954127e-06 -6.781587e-06    10.797985 
+     700 0.00086070919            0 8.8529902e-05 -9.9431205e-06 -7.9905211e-06    10.776579 
+     800 0.00083543943            0 7.5920357e-05 3.6381024e-07 3.7747551e-06    10.759309 
+     900 0.00081190799            0 6.3678219e-05 5.4158243e-06 1.2751247e-05    10.744199 
+    1000 0.00078828988            0 7.3079869e-05 -6.6410613e-06 -1.198683e-06    10.728368 
+    1100 0.00075664718            0 6.2976995e-05 -4.7863299e-06 -3.9814556e-06    10.711819 
+    1200 0.00072472205            0 4.9680233e-05 9.3093553e-06 4.4426393e-06     10.69401 
+    1300 0.00070176532            0 5.4048176e-05 1.3051954e-05 7.5448558e-06    10.671164 
+    1400 0.00068599319            0 5.4062404e-05 9.9930199e-06 1.0353154e-05    10.650117 
+    1500 0.0006786164            0 4.5038593e-05 8.067571e-06 9.8825461e-06    10.636266 
+    1600 0.00067466823            0 4.6733251e-05 9.8595584e-06 1.1551081e-05    10.621335 
+    1700 0.00066847126            0 5.1472453e-05 2.1569974e-07 6.0070599e-06      10.6127 
+    1800 0.00065711827            0 5.0355189e-05 -8.030203e-06 -3.1395588e-06    10.599568 
+    1900 0.00063882539            0 4.7146888e-05 -2.0596242e-05 -1.6494542e-05    10.581939 
+    2000 0.00061717894            0 4.6698781e-05 -2.5473048e-05 -2.7703615e-05    10.567188 
+    2100 0.00059261327            0 3.7701055e-05 -2.4637803e-05 -3.3919162e-05    10.552617 
+    2200 0.00056527158            0 3.2239421e-05 -1.8786685e-05 -2.4202734e-05    10.538406 
+    2300 0.00054054919            0 2.7410334e-05 -6.701111e-06 -7.4354974e-06    10.520777 
+    2400 0.00051820065            0 2.2997206e-05 1.5623767e-05 1.8687824e-05    10.501889 
+    2500 0.00049647925            0 1.746693e-05 2.8814144e-05 3.5569425e-05    10.487498 
+    2600 0.00047837258            0 1.4127067e-05 3.4245611e-05 4.0208577e-05    10.472387 
+    2700 0.00046626924            0 1.3714876e-05 3.7922196e-05 4.1550346e-05    10.456377 
+    2800 0.0004560167            0 1.5260976e-05 3.5632577e-05 3.7885738e-05    10.440007 
+    2900 0.00045331059            0 1.5194832e-05 3.1036124e-05 2.8633755e-05    10.427955 
+    3000 0.00045227799            0 1.4877378e-05 1.9327028e-05 2.1189487e-05    10.414283 
+    3100 0.00044866178            0 2.0424612e-05 -2.7242288e-06 7.7121438e-06     10.40349 
+    3200 0.00044336453            0 2.3276121e-05 -1.979069e-05 -4.2311089e-06    10.395575 
+    3300 0.00043526526            0 2.3338132e-05 -2.834945e-05 -1.7302033e-05    10.389998 
+    3400 0.00042817758            0 2.4374527e-05 -2.9870076e-05 -3.0623264e-05    10.382803 
+    3500 0.00042182658            0 2.6120627e-05 -2.9449521e-05 -3.787776e-05    10.378126 
+    3600 0.00041794291            0 2.4736957e-05 -2.4098172e-05 -3.0529166e-05    10.373628 
+    3700 0.0004156005            0 2.7543305e-05 -1.2431749e-05 -1.8626096e-05     10.37075 
+    3800 0.0004141461            0 2.4630482e-05 -6.345489e-06 -1.7375803e-05    10.368771 
+    3900 0.00041328832            0 2.2220142e-05 4.1471034e-07 -1.3339476e-05    10.366972 
+    4000 0.00041121725            0 2.3491321e-05 1.1284551e-05 -5.8651834e-06    10.364634 
+    4100 0.00040761876            0 2.6688248e-05 1.9721625e-05 3.7536871e-06    10.362655 
+    4200 0.00040301362            0 2.7601916e-05 1.9212118e-05 9.7175996e-06    10.359417 
+    4300 0.00040001545            0 2.7243769e-05 1.6889359e-05 1.1857147e-05      10.3551 
+    4400 0.00039654521            0 2.561083e-05 1.3863551e-05 1.0593597e-05    10.351142 
+    4500 0.00039435924            0 2.4366458e-05 1.2545563e-05 1.1323962e-05    10.348804 
+    4600 0.00039250006            0 2.3719127e-05 1.1015167e-05 8.5964046e-06    10.348444 
+    4700 0.00039145496            0 2.2943915e-05 8.7824224e-06 5.0397129e-06    10.346825 
+    4800 0.00039105331            0 2.4005757e-05 7.5899773e-06 9.033741e-07    10.344846 
+    4900 0.0003898798            0 2.3819433e-05 4.9673894e-06 -2.3466459e-06    10.343587 
+    5000 0.00038747508            0 2.3605028e-05 -1.1717437e-06 -6.1096657e-06    10.343047 
+    5100 0.00038549022            0 2.3453798e-05 -9.9256693e-06 -9.3584148e-06    10.341788 
+    5200 0.00038283936            0 2.5243567e-05 -1.5877598e-05 -9.9474447e-06    10.340169 
+    5300 0.00038140888            0 2.5522223e-05 -1.9331435e-05 -1.1067039e-05     10.33873 
+    5400 0.00037916674            0 2.5181488e-05 -2.1581255e-05 -1.1252641e-05    10.336931 
+    5500 0.00037782932            0 2.691805e-05 -1.5768241e-05 -5.6704695e-06    10.334952 
+    5600 0.00037628832            0 2.5851445e-05 -1.4239811e-05 -1.9122536e-06    10.333153 
+    5700 0.00037451913            0 2.4758416e-05 -1.3252284e-05 -1.9222041e-06    10.331714 
+    5800 0.00037328662            0 2.2507032e-05 -9.6704092e-06 -7.5470215e-06    10.330095 
+    5900 0.00037253111            0 2.3303086e-05 -4.2828034e-06 -7.888056e-06    10.328476 
+    6000 0.00037171133            0 2.4042456e-05 -4.7684985e-06 -6.5164336e-06    10.327397 
+    6100 0.00036986726            0 2.4938695e-05 -4.8738316e-06 -4.5380007e-06    10.327037 
+    6200 0.0003675822            0 2.3322229e-05 -4.6333093e-06 -5.7086464e-06    10.327037 
+    6300 0.00036552389            0 2.1435354e-05 -4.8971566e-06 -3.5935426e-06    10.327037 
+    6400 0.00036488091            0 2.0813994e-05 -3.8333319e-06 -3.6595059e-06    10.327037 
+    6500 0.00036447973            0 2.2241876e-05 8.7797361e-08 -4.141203e-06    10.327037 
+    6600 0.00036383343            0 2.269485e-05 4.9364593e-06 1.3062133e-06    10.326677 
+    6700 0.00036305076            0 2.1838759e-05 6.4587048e-06 4.7758772e-06    10.326318 
+    6800 0.00036226601            0 2.2916622e-05 6.044926e-06 5.0291597e-06    10.325598 
+    6900 0.00036175279            0 2.2691667e-05 6.9998847e-06 5.8988637e-06    10.324699 
+    7000 0.00036143633            0 2.1725813e-05 8.1268152e-06 5.0390503e-06    10.324519 
+    7100 0.0003610248            0 2.1799675e-05  8.65795e-06 3.1360368e-06    10.323439 
+    7200 0.00036086259            0 2.2198029e-05 5.1764734e-06 5.4798783e-07     10.32308 
+    7300 0.00036099757            0 2.4160496e-05 1.0310325e-06 -5.115075e-07     10.32254 
+    7400 0.00036129334            0 2.5325018e-05 -9.4918158e-07 -1.7064957e-06     10.32218 
+    7500 0.00036136655            0 2.3513198e-05 -3.8618451e-06 -4.4344772e-06    10.321281 
+Loop time of 4.51074 on 4 procs for 7500 steps with 11118 atoms
+
+Performance: 14365719.597 tau/day, 1662.699 timesteps/s
+93.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.25733    | 0.26952    | 0.28068    |   1.6 |  5.98
+Bond    | 1.9391     | 2.0128     | 2.0851     |   3.7 | 44.62
+Neigh   | 0.56308    | 0.5941     | 0.62077    |   2.8 | 13.17
+Comm    | 0.68282    | 0.80856    | 0.94406    |  10.7 | 17.93
+Output  | 0.19287    | 0.1933     | 0.19426    |   0.1 |  4.29
+Modify  | 0.53239    | 0.55343    | 0.57349    |   2.0 | 12.27
+Other   |            | 0.07902    |            |       |  1.75
+
+Nlocal:         2779.5 ave        2862 max        2686 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost:        1183.25 ave        1220 max        1134 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:        11828.8 ave       12387 max       11053 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 47315
+Ave neighs/atom = 4.2557115
+Ave special neighs/atom = 10.321461
+Neighbor list builds = 421
+Dangerous builds = 11
+Total wall time: 0:00:04

examples/bpm/pour/in.bpm.pour

@@ -0,0 +1,35 @@
+units           lj
+dimension       3
+boundary        m m m
+atom_style      bpm/sphere
+special_bonds   lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+newton          on off
+comm_modify     vel yes cutoff 3.3
+region          box block -15 15 -15 15 0 60.0
+create_box      1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
+
+molecule        my_mol "rect.mol"
+region          wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in
+region          dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in
+
+pair_style      gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1
+bond_style      bpm/rotational
+pair_coeff      1 1
+bond_coeff      1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002
+
+compute         nbond all nbond/atom
+compute         tbond all reduce sum c_nbond
+compute_modify  thermo_temp dynamic/dof yes
+
+fix             1 all wall/gran hertz/history 1.0 NULL 0.5 NULL 0.1 1 zplane 0.0 NULL
+fix             2 all wall/gran/region hertz/history 1.0 NULL 0.5 NULL 0.1 1 region wall_cyl
+fix             3 all gravity 1e-4 vector 0 0 -1
+fix             4 all deposit 40 0 1500 712511343 mol my_mol region dropzone near 2.0 vz -0.05 -0.05
+fix             5 all nve/bpm/sphere
+
+timestep        0.05
+thermo_style    custom step ke pe pxx pyy pzz c_tbond
+thermo          100
+#dump            1 all custom 500 atomDump id radius x y z c_nbond mol
+
+run             100000

examples/bpm/pour/rect.mol

@@ -0,0 +1,568 @@
+#Made with create_mol.py
+
+63 atoms 
+297 bonds 
+
+Coords
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+246 1 48 57
+247 1 48 59
+248 1 49 51
+249 1 49 52
+250 1 49 53
+251 1 49 55
+252 1 49 56
+253 1 49 58
+254 1 49 61
+255 1 50 51
+256 1 50 54
+257 1 50 59
+258 1 51 53
+259 1 51 54
+260 1 51 56
+261 1 51 59
+262 1 51 63
+263 1 52 53
+264 1 52 54
+265 1 52 61
+266 1 53 54
+267 1 53 56
+268 1 53 61
+269 1 53 62
+270 1 53 63
+271 1 54 63
+272 1 55 56
+273 1 55 57
+274 1 55 58
+275 1 55 59
+276 1 55 61
+277 1 56 57
+278 1 56 58
+279 1 56 59
+280 1 56 60
+281 1 56 61
+282 1 56 62
+283 1 56 63
+284 1 57 58
+285 1 57 59
+286 1 57 60
+287 1 57 62
+288 1 58 60
+289 1 58 61
+290 1 58 62
+291 1 59 60
+292 1 59 63
+293 1 60 62
+294 1 60 63
+295 1 61 62
+296 1 61 63
+297 1 62 63

examples/mdi/in.aimd.driver.plugin

@@ -23,7 +23,7 @@ fix		1 all nve
 # NPT
 #fix             1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
 
-fix             2 all mdi/aimd plugin
+fix             2 all mdi/aimd
 fix_modify      2 energy yes virial yes
 
 thermo_style    custom step temp pe etotal press vol

examples/mdi/sequence_driver.py

@@ -286,18 +286,15 @@ while iarg < narg:
 
 if not mdiarg: error()
 
+mdi.MDI_Init(mdiarg)
+
 # LAMMPS engine is a stand-alone code
 # world = MPI communicator for just this driver
 # invoke perform_tasks() directly
 
 if not plugin:
-  mdi.MDI_Init(mdiarg)
   world = mdi.MDI_MPI_get_world_comm()
-
-  # connect to engine
-
   mdicomm = mdi.MDI_Accept_Communicator()
-
   perform_tasks(world,mdicomm,None)
 
 # LAMMPS engine is a plugin library
@@ -305,7 +302,6 @@ if not plugin:
 # MDI will call back to perform_tasks()
 
 if plugin:
-  mdi.MDI_Init(mdiarg)
   world = MPI.COMM_WORLD
   plugin_args += " -mdi \"-role ENGINE -name lammps -method LINK\""
   mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None)

lib/gpu/Makefile.linux_multi

@@ -13,14 +13,6 @@ endif
 
 NVCC = nvcc
 
-# obsolete hardware. not supported by current drivers anymore.
-#CUDA_ARCH = -arch=sm_13
-#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
-
-# Fermi hardware
-#CUDA_ARCH = -arch=sm_20
-#CUDA_ARCH = -arch=sm_21
-
 # Kepler hardware
 #CUDA_ARCH = -arch=sm_30
 #CUDA_ARCH = -arch=sm_32
@@ -45,6 +37,9 @@ CUDA_ARCH = -arch=sm_50
 #CUDA_ARCH = -arch=sm_80
 #CUDA_ARCH = -arch=sm_86
 
+# Hopper hardware
+#CUDA_ARCH = -arch=sm_90
+
 CUDA_CODE = -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] \
 	    -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] \
 	    -gencode arch=compute_70,code=[sm_70,compute_70] -gencode arch=compute_75,code=[sm_75,compute_75] \

lib/gpu/README

@@ -171,7 +171,13 @@ NOTE: when compiling with CMake, all of the considerations listed below
 are considered within the CMake configuration process, so no separate
 compilation of the gpu library is required. Also this will build in support
 for all compute architecture that are supported by the CUDA toolkit version
-used to build the gpu library.
+used to build the gpu library.  A similar setup is possible using
+Makefile.linux_multi after adjusting the settings for the CUDA toolkit in use.
+
+Only CUDA toolkit version 8.0 and later and only GPU architecture 3.0
+(aka Kepler) and later are supported by this version of LAMMPS. If you want
+to use older hard- or software you have to compile for OpenCL or use an older
+version of LAMMPS.
 
 If you do not want to use a fat binary, that supports multiple CUDA
 architectures, the CUDA_ARCH must be set to match the GPU architecture. This
@@ -225,7 +231,8 @@ If GERYON_NUMA_FISSION is defined at build time, LAMMPS will consider separate
 NUMA nodes on GPUs or accelerators as separate devices. For example, a 2-socket
 CPU would appear as two separate devices for OpenCL (and LAMMPS would require
 two MPI processes to use both sockets with the GPU library - each with its
-own device ID as output by ocl_get_devices).
+own device ID as output by ocl_get_devices). OpenCL version 1.2 or later is
+required.
 
 For a debug build, use "-DUCL_DEBUG -DGERYON_KERNEL_DUMP" and remove
 "-DUCL_NO_EXIT" and "-DMPI_GERYON" from the build options.

lib/gpu/geryon/hip_device.h

@@ -379,18 +379,9 @@ UCL_Device::UCL_Device() {
     prop.regsPerBlock = hip_prop.regsPerBlock;
     prop.clockRate = hip_prop.clockRate;
     prop.computeMode = hip_prop.computeMode;
-    //CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.memPitch, CU_DEVICE_ATTRIBUTE_MAX_PITCH, dev));
-    //CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.textureAlign, CU_DEVICE_ATTRIBUTE_TEXTURE_ALIGNMENT, dev));
 
-    //#if CUDA_VERSION >= 2020
-    //CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.kernelExecTimeoutEnabled, CU_DEVICE_ATTRIBUTE_KERNEL_EXEC_TIMEOUT,dev));
     CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.integrated, hipDeviceAttributeIntegrated, dev));
-    //CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.canMapHostMemory, CU_DEVICE_ATTRIBUTE_CAN_MAP_HOST_MEMORY, dev));
-    //#endif
-    //#if CUDA_VERSION >= 3010
     prop.concurrentKernels = hip_prop.concurrentKernels;
-    //CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.ECCEnabled, CU_DEVICE_ATTRIBUTE_ECC_ENABLED, dev));
-    //#endif
 
     _properties.push_back(prop);
   }
@@ -447,13 +438,11 @@ void UCL_Device::clear() {
 
 // List all devices along with all properties
 void UCL_Device::print_all(std::ostream &out) {
-  //#if CUDA_VERSION >= 2020
   int driver_version;
   hipDriverGetVersion(&driver_version);
   out << "Driver Version:                           "
       << driver_version/1000 << "." << driver_version%100
                   << std::endl;
-  //#endif
 
   if (num_devices() == 0)
     out << "There is no device supporting HIP\n";
@@ -470,12 +459,10 @@ void UCL_Device::print_all(std::ostream &out) {
       out << "No\n";
     out << "  Total amount of global memory:                 "
         << gigabytes(i) << " GB\n";
-    //#if CUDA_VERSION >= 2000
     out << "  Number of compute units/multiprocessors:       "
         << _properties[i].multiProcessorCount << std::endl;
     out << "  Number of cores:                               "
         << cores(i) << std::endl;
-    //#endif
     out << "  Total amount of constant memory:               "
         << _properties[i].totalConstantMemory << " bytes\n";
     out << "  Total amount of local/shared memory per block: "
@@ -494,58 +481,29 @@ void UCL_Device::print_all(std::ostream &out) {
         << _properties[i].maxGridSize[0] << " x "
         << _properties[i].maxGridSize[1] << " x "
         << _properties[i].maxGridSize[2] << std::endl;
-    //out << "  Maximum memory pitch:                          "
-    //    << max_pitch(i) << " bytes\n";
-    //out << "  Texture alignment:                             "
-    //    << _properties[i].textureAlign << " bytes\n";
     out << "  Clock rate:                                    "
         << clock_rate(i) << " GHz\n";
-    //#if CUDA_VERSION >= 2020
-    //out << "  Run time limit on kernels:                     ";
-    //if (_properties[i].kernelExecTimeoutEnabled)
-    //  out << "Yes\n";
-    //else
-    //  out << "No\n";
     out << "  Integrated:                                    ";
     if (_properties[i].integrated)
       out << "Yes\n";
     else
       out << "No\n";
-    //out << "  Support host page-locked memory mapping:       ";
-    //if (_properties[i].canMapHostMemory)
-    //  out << "Yes\n";
-    //else
-    //  out << "No\n";
     out << "  Compute mode:                                  ";
     if (_properties[i].computeMode == hipComputeModeDefault)
       out << "Default\n"; // multiple threads can use device
-//#if CUDA_VERSION >= 8000
-//    else if (_properties[i].computeMode == hipComputeModeExclusiveProcess)
-//#else
     else if (_properties[i].computeMode == hipComputeModeExclusive)
-//#endif
       out << "Exclusive\n"; // only thread can use device
     else if (_properties[i].computeMode == hipComputeModeProhibited)
       out << "Prohibited\n"; // no thread can use device
-    //#if CUDART_VERSION >= 4000
     else if (_properties[i].computeMode == hipComputeModeExclusiveProcess)
       out << "Exclusive Process\n"; // multiple threads 1 process
-    //#endif
     else
       out << "Unknown\n";
-    //#endif
-    //#if CUDA_VERSION >= 3010
     out << "  Concurrent kernel execution:                   ";
     if (_properties[i].concurrentKernels)
       out << "Yes\n";
     else
       out << "No\n";
-    //out << "  Device has ECC support enabled:                ";
-    //if (_properties[i].ECCEnabled)
-    //  out << "Yes\n";
-    //else
-    //  out << "No\n";
-    //#endif
   }
 }
 

lib/gpu/geryon/hip_macros.h

@@ -5,11 +5,7 @@
 #include <cassert>
 #include <hip/hip_runtime.h>
 
-//#if CUDA_VERSION >= 3020
 #define CUDA_INT_TYPE size_t
-//#else
-//#define CUDA_INT_TYPE unsigned
-//#endif
 
 #ifdef MPI_GERYON
 #include "mpi.h"

lib/gpu/geryon/hip_texture.h

@@ -71,9 +71,6 @@ class UCL_Texture {
 
   /// Make a texture reference available to kernel
   inline void allow(UCL_Kernel &) {
-    //#if CUDA_VERSION < 4000
-    //CU_SAFE_CALL(cuParamSetTexRef(kernel._kernel, CU_PARAM_TR_DEFAULT, _tex));
-    //#endif
   }
 
  private:

lib/gpu/geryon/nvd_device.h

@@ -320,6 +320,9 @@ class UCL_Device {
 
 // Grabs the properties for all devices
 UCL_Device::UCL_Device() {
+#if CUDA_VERSION < 8000
+#error CUDA Toolkit version 8 or later required
+#endif
   CU_SAFE_CALL_NS(cuInit(0));
   CU_SAFE_CALL_NS(cuDeviceGetCount(&_num_devices));
   for (int i=0; i<_num_devices; ++i) {
@@ -358,16 +361,12 @@ UCL_Device::UCL_Device() {
     CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.clockRate, CU_DEVICE_ATTRIBUTE_CLOCK_RATE, dev));
     CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.textureAlign, CU_DEVICE_ATTRIBUTE_TEXTURE_ALIGNMENT, dev));
 
-    #if CUDA_VERSION >= 2020
     CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.kernelExecTimeoutEnabled, CU_DEVICE_ATTRIBUTE_KERNEL_EXEC_TIMEOUT,dev));
     CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.integrated, CU_DEVICE_ATTRIBUTE_INTEGRATED, dev));
     CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.canMapHostMemory, CU_DEVICE_ATTRIBUTE_CAN_MAP_HOST_MEMORY, dev));
     CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.computeMode, CU_DEVICE_ATTRIBUTE_COMPUTE_MODE,dev));
-    #endif
-    #if CUDA_VERSION >= 3010
     CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.concurrentKernels, CU_DEVICE_ATTRIBUTE_CONCURRENT_KERNELS, dev));
     CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.ECCEnabled, CU_DEVICE_ATTRIBUTE_ECC_ENABLED, dev));
-    #endif
 
     _properties.push_back(prop);
   }
@@ -415,13 +414,10 @@ void UCL_Device::clear() {
 
 // List all devices along with all properties
 void UCL_Device::print_all(std::ostream &out) {
-  #if CUDA_VERSION >= 2020
   int driver_version;
   cuDriverGetVersion(&driver_version);
   out << "CUDA Driver Version:                           "
-      << driver_version/1000 << "." << driver_version%100
+      << driver_version/1000 << "." << driver_version%100 << std::endl;
-                  << std::endl;
-  #endif
 
   if (num_devices() == 0)
     out << "There is no device supporting CUDA\n";
@@ -438,12 +434,10 @@ void UCL_Device::print_all(std::ostream &out) {
       out << "No\n";
     out << "  Total amount of global memory:                 "
         << gigabytes(i) << " GB\n";
-    #if CUDA_VERSION >= 2000
     out << "  Number of compute units/multiprocessors:       "
         << _properties[i].multiProcessorCount << std::endl;
     out << "  Number of cores:                               "
         << cores(i) << std::endl;
-    #endif
     out << "  Total amount of constant memory:               "
         << _properties[i].totalConstantMemory << " bytes\n";
     out << "  Total amount of local/shared memory per block: "
@@ -468,7 +462,6 @@ void UCL_Device::print_all(std::ostream &out) {
         << _properties[i].textureAlign << " bytes\n";
     out << "  Clock rate:                                    "
         << clock_rate(i) << " GHz\n";
-    #if CUDA_VERSION >= 2020
     out << "  Run time limit on kernels:                     ";
     if (_properties[i].kernelExecTimeoutEnabled)
       out << "Yes\n";
@@ -487,22 +480,14 @@ void UCL_Device::print_all(std::ostream &out) {
     out << "  Compute mode:                                  ";
     if (_properties[i].computeMode == CU_COMPUTEMODE_DEFAULT)
       out << "Default\n"; // multiple threads can use device
-#if CUDA_VERSION >= 8000
     else if (_properties[i].computeMode == CU_COMPUTEMODE_EXCLUSIVE_PROCESS)
-#else
-    else if (_properties[i].computeMode == CU_COMPUTEMODE_EXCLUSIVE)
-#endif
       out << "Exclusive\n"; // only thread can use device
     else if (_properties[i].computeMode == CU_COMPUTEMODE_PROHIBITED)
       out << "Prohibited\n"; // no thread can use device
-    #if CUDART_VERSION >= 4000
     else if (_properties[i].computeMode == CU_COMPUTEMODE_EXCLUSIVE_PROCESS)
       out << "Exclusive Process\n"; // multiple threads 1 process
-    #endif
     else
       out << "Unknown\n";
-    #endif
-    #if CUDA_VERSION >= 3010
     out << "  Concurrent kernel execution:                   ";
     if (_properties[i].concurrentKernels)
       out << "Yes\n";
@@ -513,7 +498,6 @@ void UCL_Device::print_all(std::ostream &out) {
       out << "Yes\n";
     else
       out << "No\n";
-    #endif
   }
 }
 

lib/gpu/geryon/nvd_kernel.h

@@ -165,17 +165,11 @@ class UCL_Program {
 class UCL_Kernel {
  public:
   UCL_Kernel() : _dimensions(1), _num_args(0) {
-    #if CUDA_VERSION < 4000
-    _param_size=0;
-    #endif
     _num_blocks[0]=0;
   }
 
   UCL_Kernel(UCL_Program &program, const char *function) :
     _dimensions(1), _num_args(0) {
-    #if CUDA_VERSION < 4000
-    _param_size=0;
-    #endif
     _num_blocks[0]=0;
     set_function(program,function);
     _cq=program._cq;
@@ -211,11 +205,7 @@ class UCL_Kernel {
     if (index==_num_args)
       add_arg(arg);
     else if (index<_num_args)
-      #if CUDA_VERSION >= 4000
       _kernel_args[index]=arg;
-      #else
-      CU_SAFE_CALL(cuParamSetv(_kernel, _offsets[index], arg, sizeof(dtype)));
-      #endif
     else
       assert(0==1); // Must add kernel parameters in sequential order
   }
@@ -242,15 +232,7 @@ class UCL_Kernel {
 
   /// Add a kernel argument.
   inline void add_arg(const CUdeviceptr* const arg) {
-    #if CUDA_VERSION >= 4000
     _kernel_args[_num_args]=(void *)arg;
-    #else
-    void* ptr = (void*)(size_t)(*arg);
-    _param_size = (_param_size + __alignof(ptr) - 1) & ~(__alignof(ptr) - 1);
-    CU_SAFE_CALL(cuParamSetv(_kernel, _param_size, &ptr, sizeof(ptr)));
-    _offsets.push_back(_param_size);
-    _param_size+=sizeof(ptr);
-    #endif
     _num_args++;
     if (_num_args>UCL_MAX_KERNEL_ARGS) assert(0==1);
   }
@@ -258,14 +240,7 @@ class UCL_Kernel {
   /// Add a kernel argument.
   template <class dtype>
   inline void add_arg(const dtype* const arg) {
-    #if CUDA_VERSION >= 4000
     _kernel_args[_num_args]=const_cast<dtype *>(arg);
-    #else
-    _param_size = (_param_size+__alignof(dtype)-1) & ~(__alignof(dtype)-1);
-    CU_SAFE_CALL(cuParamSetv(_kernel,_param_size,(void*)arg,sizeof(dtype)));
-    _offsets.push_back(_param_size);
-    _param_size+=sizeof(dtype);
-    #endif
     _num_args++;
     if (_num_args>UCL_MAX_KERNEL_ARGS) assert(0==1);
   }
@@ -298,13 +273,9 @@ class UCL_Kernel {
     _num_blocks[0]=num_blocks;
     _num_blocks[1]=1;
     _num_blocks[2]=1;
-    #if CUDA_VERSION >= 4000
     _block_size[0]=block_size;
     _block_size[1]=1;
     _block_size[2]=1;
-    #else
-    CU_SAFE_CALL(cuFuncSetBlockShape(_kernel,block_size,1,1));
-    #endif
   }
 
   /// Set the number of thread blocks and the number of threads in each block
@@ -323,13 +294,9 @@ class UCL_Kernel {
     _num_blocks[0]=num_blocks_x;
     _num_blocks[1]=num_blocks_y;
     _num_blocks[2]=1;
-    #if CUDA_VERSION >= 4000
     _block_size[0]=block_size_x;
     _block_size[1]=block_size_y;
     _block_size[2]=1;
-    #else
-    CU_SAFE_CALL(cuFuncSetBlockShape(_kernel,block_size_x,block_size_y,1));
-    #endif
   }
 
   /// Set the number of thread blocks and the number of threads in each block
@@ -350,14 +317,9 @@ class UCL_Kernel {
     _num_blocks[0]=num_blocks_x;
     _num_blocks[1]=num_blocks_y;
     _num_blocks[2]=1;
-    #if CUDA_VERSION >= 4000
     _block_size[0]=block_size_x;
     _block_size[1]=block_size_y;
     _block_size[2]=block_size_z;
-    #else
-    CU_SAFE_CALL(cuFuncSetBlockShape(_kernel,block_size_x,block_size_y,
-                                     block_size_z));
-    #endif
   }
 
   /// Set the number of thread blocks and the number of threads in each block
@@ -373,23 +335,14 @@ class UCL_Kernel {
 
   /// Run the kernel in the default command queue
   inline void run() {
-    #if CUDA_VERSION >= 4000
     CU_SAFE_CALL(cuLaunchKernel(_kernel,_num_blocks[0],_num_blocks[1],
                                 _num_blocks[2],_block_size[0],_block_size[1],
                                 _block_size[2],0,_cq,_kernel_args,nullptr));
-    #else
-    CU_SAFE_CALL(cuParamSetSize(_kernel,_param_size));
-    CU_SAFE_CALL(cuLaunchGridAsync(_kernel,_num_blocks[0],_num_blocks[1],_cq));
-    #endif
   }
 
   /// Clear any arguments associated with the kernel
   inline void clear_args() {
     _num_args=0;
-    #if CUDA_VERSION < 4000
-    _offsets.clear();
-    _param_size=0;
-    #endif
   }
 
   /// Return the default command queue/stream associated with this data
@@ -406,13 +359,8 @@ class UCL_Kernel {
   unsigned _num_args;
   friend class UCL_Texture;
 
-  #if CUDA_VERSION >= 4000
   unsigned _block_size[3];
   void * _kernel_args[UCL_MAX_KERNEL_ARGS];
-  #else
-  std::vector<unsigned> _offsets;
-  unsigned _param_size;
-  #endif
 };
 
 } // namespace

lib/gpu/geryon/nvd_macros.h

@@ -5,11 +5,7 @@
 #include <cassert>
 #include <cuda.h>
 
-#if CUDA_VERSION >= 3020
 #define CUDA_INT_TYPE size_t
-#else
-#define CUDA_INT_TYPE unsigned
-#endif
 
 #ifdef MPI_GERYON
 #include "mpi.h"

lib/gpu/geryon/nvd_texture.h

@@ -69,9 +69,6 @@ class UCL_Texture {
 
   /// Make a texture reference available to kernel
   inline void allow(UCL_Kernel &kernel) {
-    #if CUDA_VERSION < 4000
-    CU_SAFE_CALL(cuParamSetTexRef(kernel._kernel, CU_PARAM_TR_DEFAULT, _tex));
-    #endif
   }
 
  private:

lib/gpu/geryon/ucl_nv_kernel.h

@@ -25,21 +25,8 @@
 #ifndef UCL_NV_KERNEL_H
 #define UCL_NV_KERNEL_H
 
-#if (__CUDA_ARCH__ < 200)
-#define mul24 __mul24
-#define MEM_THREADS 16
-#else
 #define mul24(X,Y) (X)*(Y)
 #define MEM_THREADS 32
-#endif
-
-#ifdef CUDA_PRE_THREE
-struct __builtin_align__(16) _double4
-{
-  double x, y, z, w;
-};
-typedef struct _double4 double4;
-#endif
 
 #define GLOBAL_ID_X threadIdx.x+mul24(blockIdx.x,blockDim.x)
 #define GLOBAL_ID_Y threadIdx.y+mul24(blockIdx.y,blockDim.y)

lib/gpu/lal_pre_cuda_hip.h

@@ -58,49 +58,6 @@
 #define MAX_BIO_SHARED_TYPES 128
 #define PPPM_MAX_SPLINE 8
 
-// -------------------------------------------------------------------------
-//                          LEGACY DEVICE CONFIGURATION
-// -------------------------------------------------------------------------
-
-#ifdef __CUDA_ARCH__
-
-#if (__CUDA_ARCH__ < 200)
-
-#undef CONFIG_ID
-#define CONFIG_ID 101
-#define MEM_THREADS 16
-#undef THREADS_PER_ATOM
-#define THREADS_PER_ATOM 1
-#undef THREADS_PER_CHARGE
-#define THREADS_PER_CHARGE 16
-#undef BLOCK_PAIR
-#define BLOCK_PAIR 64
-#undef BLOCK_BIO_PAIR
-#define BLOCK_BIO_PAIR 64
-#undef BLOCK_NBOR_BUILD
-#define BLOCK_NBOR_BUILD 64
-#undef MAX_SHARED_TYPES
-#define MAX_SHARED_TYPES 8
-#undef SHUFFLE_AVAIL
-#define SHUFFLE_AVAIL 0
-
-#elseif (__CUDA_ARCH__ < 300)
-
-#undef CONFIG_ID
-#define CONFIG_ID 102
-#undef BLOCK_PAIR
-#define BLOCK_PAIR 128
-#undef BLOCK_BIO_PAIR
-#define BLOCK_BIO_PAIR 128
-#undef MAX_SHARED_TYPES
-#define MAX_SHARED_TYPES 8
-#undef SHUFFLE_AVAIL
-#define SHUFFLE_AVAIL 0
-
-#endif
-
-#endif
-
 // -------------------------------------------------------------------------
 //                              KERNEL MACROS
 // -------------------------------------------------------------------------
@@ -111,12 +68,6 @@
 
 #define fast_mul(X,Y) (X)*(Y)
 
-#ifdef __CUDA_ARCH__
-#if (__CUDA_ARCH__ < 200)
-#define fast_mul __mul24
-#endif
-#endif
-
 #define EVFLAG 1
 #define NOUNROLL
 #define GLOBAL_ID_X threadIdx.x+fast_mul(blockIdx.x,blockDim.x)
@@ -220,14 +171,6 @@
 //                           KERNEL MACROS - MATH
 // -------------------------------------------------------------------------
 
-#ifdef CUDA_PRE_THREE
-struct __builtin_align__(16) _double4
-{
-  double x, y, z, w;
-};
-typedef struct _double4 double4;
-#endif
-
 #ifdef _DOUBLE_DOUBLE
 
 #define ucl_exp exp

lib/mdi/Install.py

@@ -34,12 +34,12 @@ make lib-meam args="-m ifort"   # build MEAM lib with custom Makefile.ifort (usi
 
 # settings
 
-version = "1.3.0"
+version = "1.3.2"
 url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
 
 # known checksums for different MDI versions. used to validate the download.
 checksums = { \
-              '1.3.0' : '8a8da217148bd9b700083b67d795af5e', \
+              '1.3.2' : '836f5da400d8cff0f0e4435640f9454f', \
               }
 
 # print error message or help

src/.gitignore

@@ -254,6 +254,21 @@
 /pair_mesont_tpm.cpp
 /pair_mesont_tpm.h
 
+/atom_vec_bpm_sphere.cpp
+/atom_vec_bpm_sphere.h
+/bond_bpm.cpp
+/bond_bpm.h
+/bond_bpm_rotational.cpp
+/bond_bpm_rotational.h
+/bond_bpm_spring.cpp
+/bond_bpm_spring.h
+/compute_nbond_atom.cpp
+/compute_nbond_atom.h
+/fix_nve_bpm_sphere.cpp
+/fix_nve_bpm_sphere.h
+/pair_bpm_spring.cpp
+/pair_bpm_spring.h
+
 /compute_adf.cpp
 /compute_adf.h
 /compute_contact_atom.cpp
@@ -792,8 +807,6 @@
 /fix_orient_eco.h
 /fix_orient_fcc.cpp
 /fix_orient_fcc.h
-/fix_pair_tracker.cpp
-/fix_pair_tracker.h
 /fix_peri_neigh.cpp
 /fix_peri_neigh.h
 /fix_phonon.cpp
@@ -1524,3 +1537,4 @@
 /pair_smtbq.h
 /pair_vashishta*.cpp
 /pair_vashishta*.h
+

src/BPM/atom_vec_bpm_sphere.cpp

@@ -0,0 +1,245 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "atom_vec_bpm_sphere.h"
+
+#include "atom.h"
+#include "error.h"
+#include "fix.h"
+#include "fix_adapt.h"
+#include "math_const.h"
+#include "modify.h"
+#include "utils.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using MathConst::MY_PI;
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecBPMSphere::AtomVecBPMSphere(LAMMPS *_lmp) : AtomVec(_lmp)
+{
+  mass_type = PER_ATOM;
+  molecular = Atom::MOLECULAR;
+  bonds_allow = 1;
+
+  atom->molecule_flag = 1;
+  atom->sphere_flag = 1;
+  atom->radius_flag = atom->rmass_flag = atom->omega_flag = atom->torque_flag = atom->quat_flag = 1;
+
+  // strings with peratom variables to include in each AtomVec method
+  // strings cannot contain fields in corresponding AtomVec default strings
+  // order of fields in a string does not matter
+  // except: fields_data_atom & fields_data_vel must match data file
+
+  // clang-format off
+  fields_grow       = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
+                               "omega torque quat";
+  fields_copy       = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
+                               "omega quat";
+  fields_comm       = (char *) "";
+  fields_comm_vel   = (char *) "omega quat";
+  fields_reverse    = (char *) "torque";
+  fields_border     = (char *) "molecule radius rmass";
+  fields_border_vel = (char *) "molecule radius rmass omega quat";
+  fields_exchange   = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
+                               "omega quat";
+  fields_restart    = (char *) "molecule num_bond bond_type bond_atom radius rmass omega quat";
+  fields_create     = (char *) "molecule num_bond nspecial radius rmass omega quat";
+  fields_data_atom  = (char *) "id molecule type radius rmass x";
+  fields_data_vel   = (char *) "id v omega";
+  // clang-format on
+
+  bond_per_atom = 0;
+  bond_negative = NULL;
+}
+
+/* ----------------------------------------------------------------------
+   process sub-style args
+   optional arg = 0/1 for static/dynamic particle radii
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::process_args(int narg, char **arg)
+{
+  if (narg != 0 && narg != 1) error->all(FLERR, "Illegal atom_style bpm/sphere command");
+
+  radvary = 0;
+  if (narg == 1) {
+    radvary = utils::numeric(FLERR, arg[0], true, lmp);
+    if (radvary < 0 || radvary > 1) error->all(FLERR, "Illegal atom_style bpm/sphere command");
+  }
+
+  // dynamic particle radius and mass must be communicated every step
+
+  if (radvary) {
+    fields_comm = (char *) "radius rmass";
+    fields_comm_vel = (char *) "radius rmass omega";
+  }
+
+  // delay setting up of fields until now
+
+  setup_fields();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::init()
+{
+  AtomVec::init();
+
+  // check if optional radvary setting should have been set to 1
+
+  for (int i = 0; i < modify->nfix; i++)
+    if (strcmp(modify->fix[i]->style, "adapt") == 0) {
+      FixAdapt *fix = (FixAdapt *) modify->fix[i];
+      if (fix->diamflag && radvary == 0)
+        error->all(FLERR, "Fix adapt changes atom radii but atom_style bpm/sphere is not dynamic");
+    }
+}
+
+/* ----------------------------------------------------------------------
+   set local copies of all grow ptrs used by this class, except defaults
+   needed in replicate when 2 atom classes exist and it calls pack_restart()
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::grow_pointers()
+{
+  radius = atom->radius;
+  rmass = atom->rmass;
+  omega = atom->omega;
+  quat = atom->quat;
+
+  num_bond = atom->num_bond;
+  bond_type = atom->bond_type;
+  nspecial = atom->nspecial;
+}
+
+/* ----------------------------------------------------------------------
+   initialize non-zero atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::create_atom_post(int ilocal)
+{
+  radius[ilocal] = 0.5;
+  rmass[ilocal] = 4.0 * MY_PI / 3.0 * 0.5 * 0.5 * 0.5;
+
+  quat[ilocal][0] = 1.0;
+  quat[ilocal][1] = 0.0;
+  quat[ilocal][2] = 0.0;
+  quat[ilocal][3] = 0.0;
+}
+
+/* ----------------------------------------------------------------------
+   modify values for AtomVec::pack_restart() to pack
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::pack_restart_pre(int ilocal)
+{
+  // insure bond_negative vector is needed length
+
+  if (bond_per_atom < atom->bond_per_atom) {
+    delete[] bond_negative;
+    bond_per_atom = atom->bond_per_atom;
+    bond_negative = new int[bond_per_atom];
+  }
+
+  // flip any negative types to positive and flag which ones
+
+  any_bond_negative = 0;
+  for (int m = 0; m < num_bond[ilocal]; m++) {
+    if (bond_type[ilocal][m] < 0) {
+      bond_negative[m] = 1;
+      bond_type[ilocal][m] = -bond_type[ilocal][m];
+      any_bond_negative = 1;
+    } else
+      bond_negative[m] = 0;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   unmodify values packed by AtomVec::pack_restart()
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::pack_restart_post(int ilocal)
+{
+  // restore the flagged types to their negative values
+
+  if (any_bond_negative) {
+    for (int m = 0; m < num_bond[ilocal]; m++)
+      if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];
+  }
+}
+
+/* ----------------------------------------------------------------------
+   initialize other atom quantities after AtomVec::unpack_restart()
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::unpack_restart_init(int ilocal)
+{
+  nspecial[ilocal][0] = 0;
+  nspecial[ilocal][1] = 0;
+  nspecial[ilocal][2] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   modify what AtomVec::data_atom() just unpacked
+   or initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::data_atom_post(int ilocal)
+{
+  radius_one = 0.5 * atom->radius[ilocal];
+  radius[ilocal] = radius_one;
+  if (radius_one > 0.0) rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
+
+  if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
+
+  omega[ilocal][0] = 0.0;
+  omega[ilocal][1] = 0.0;
+  omega[ilocal][2] = 0.0;
+
+  quat[ilocal][0] = 1.0;
+  quat[ilocal][1] = 0.0;
+  quat[ilocal][2] = 0.0;
+  quat[ilocal][3] = 0.0;
+
+  num_bond[ilocal] = 0;
+  nspecial[ilocal][0] = 0;
+  nspecial[ilocal][1] = 0;
+  nspecial[ilocal][2] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   modify values for AtomVec::pack_data() to pack
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::pack_data_pre(int ilocal)
+{
+  radius_one = radius[ilocal];
+  rmass_one = rmass[ilocal];
+
+  radius[ilocal] *= 2.0;
+  if (radius_one != 0.0)
+    rmass[ilocal] = rmass_one / (4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one);
+}
+
+/* ----------------------------------------------------------------------
+   unmodify values packed by AtomVec::pack_data()
+------------------------------------------------------------------------- */
+
+void AtomVecBPMSphere::pack_data_post(int ilocal)
+{
+  radius[ilocal] = radius_one;
+  rmass[ilocal] = rmass_one;
+}

src/BPM/atom_vec_bpm_sphere.h

@@ -0,0 +1,82 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef ATOM_CLASS
+// clang-format off
+AtomStyle(bpm/sphere,AtomVecBPMSphere);
+// clang-format on
+#else
+
+#ifndef LMP_ATOM_VEC_BPM_SPHERE_H
+#define LMP_ATOM_VEC_BPM_SPHERE_H
+
+#include "atom_vec.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecBPMSphere : public AtomVec {
+ public:
+  AtomVecBPMSphere(class LAMMPS *);
+  void process_args(int, char **) override;
+  void init() override;
+
+  void grow_pointers() override;
+  void create_atom_post(int) override;
+  void pack_restart_pre(int) override;
+  void pack_restart_post(int) override;
+  void unpack_restart_init(int) override;
+  void data_atom_post(int) override;
+  void pack_data_pre(int) override;
+  void pack_data_post(int) override;
+
+ private:
+  int *num_bond;
+  int **bond_type;
+  int **nspecial;
+
+  double *radius, *rmass;
+  double **omega, **torque, **quat;
+
+  int any_bond_negative;
+  int bond_per_atom;
+  int *bond_negative;
+
+  int radvary;
+  double radius_one, rmass_one;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Per-processor system is too big
+
+The number of owned atoms plus ghost atoms on a single
+processor must fit in 32-bit integer.
+
+E: Invalid atom type in Atoms section of data file
+
+Atom types must range from 1 to specified # of types.
+
+E: Invalid radius in Atoms section of data file
+
+Radius must be >= 0.0.
+
+E: Invalid density in Atoms section of data file
+
+Density value cannot be <= 0.0.
+
+*/

src/BPM/bond_bpm.cpp

@@ -0,0 +1,415 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "bond_bpm.h"
+
+#include "atom.h"
+#include "domain.h"
+#include "error.h"
+#include "fix_bond_history.h"
+#include "fix_store_local.h"
+#include "fix_update_special_bonds.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+
+#include <vector>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+BondBPM::BondBPM(LAMMPS *_lmp) :
+    Bond(_lmp), id_fix_dummy(nullptr), id_fix_dummy2(nullptr), id_fix_update(nullptr),
+    id_fix_bond_history(nullptr), id_fix_store_local(nullptr), id_fix_prop_atom(nullptr),
+    fix_store_local(nullptr), fix_bond_history(nullptr), fix_update_special_bonds(nullptr),
+    pack_choice(nullptr), output_data(nullptr)
+
+{
+  overlay_flag = 0;
+  prop_atom_flag = 0;
+  nvalues = 0;
+
+  r0_max_estimate = 0.0;
+  max_stretch = 1.0;
+
+  // create dummy fix as placeholder for FixUpdateSpecialBonds & BondHistory
+  // this is so final order of Modify:fix will conform to input script
+  // BondHistory technically only needs this if updateflag = 1
+
+  id_fix_dummy = utils::strdup("BPM_DUMMY");
+  modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy));
+
+  id_fix_dummy2 = utils::strdup("BPM_DUMMY2");
+  modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy2));
+}
+
+/* ---------------------------------------------------------------------- */
+
+BondBPM::~BondBPM()
+{
+  delete[] pack_choice;
+
+  if (id_fix_dummy) modify->delete_fix(id_fix_dummy);
+  if (id_fix_dummy2) modify->delete_fix(id_fix_dummy2);
+  if (id_fix_update) modify->delete_fix(id_fix_update);
+  if (id_fix_bond_history) modify->delete_fix(id_fix_bond_history);
+  if (id_fix_store_local) modify->delete_fix(id_fix_store_local);
+  if (id_fix_prop_atom) modify->delete_fix(id_fix_prop_atom);
+
+  delete[] id_fix_dummy;
+  delete[] id_fix_dummy2;
+  delete[] id_fix_update;
+  delete[] id_fix_bond_history;
+  delete[] id_fix_store_local;
+  delete[] id_fix_prop_atom;
+
+  memory->destroy(output_data);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::init_style()
+{
+  if (id_fix_store_local) {
+    auto ifix = modify->get_fix_by_id(id_fix_store_local);
+    if (!ifix) error->all(FLERR, "Cannot find fix store/local");
+    if (strcmp(ifix->style, "STORE_LOCAL") != 0)
+      error->all(FLERR, "Incorrect fix style matched, not store/local");
+    fix_store_local = dynamic_cast<FixStoreLocal *>(ifix);
+    fix_store_local->nvalues = nvalues;
+  }
+
+  if (overlay_flag) {
+    if (force->special_lj[1] != 1.0)
+      error->all(FLERR,
+                 "With overlay/pair, BPM bond styles require special_bonds weight of 1.0 for "
+                 "first neighbors");
+    if (id_fix_update) {
+      modify->delete_fix(id_fix_update);
+      delete[] id_fix_update;
+      id_fix_update = nullptr;
+    }
+  } else {
+    // Require atoms know about all of their bonds and if they break
+    if (force->newton_bond)
+      error->all(FLERR, "Without overlay/pair, BPM bond styles require Newton bond off");
+
+    // special lj must be 0 1 1 to censor pair forces between bonded particles
+    // special coulomb must be 1 1 1 to ensure all pairs are included in the
+    //   neighbor list and 1-3 and 1-4 special bond lists are skipped
+    if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
+      error->all(FLERR,
+                 "Without overlay/pair, BPM bond sytles requires special LJ weights = 0,1,1");
+    if (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
+        force->special_coul[3] != 1.0)
+      error->all(FLERR,
+                 "Without overlay/pair, BPM bond sytles requires special Coulomb weights = 1,1,1");
+
+    if (id_fix_dummy) {
+      id_fix_update = utils::strdup("BPM_UPDATE_SPECIAL_BONDS");
+      fix_update_special_bonds = dynamic_cast<FixUpdateSpecialBonds *>(modify->replace_fix(
+          id_fix_dummy, fmt::format("{} all UPDATE_SPECIAL_BONDS", id_fix_update), 1));
+      delete[] id_fix_dummy;
+      id_fix_dummy = nullptr;
+    }
+  }
+
+  if (force->angle || force->dihedral || force->improper)
+    error->all(FLERR, "Bond style bpm cannot be used with 3,4-body interactions");
+  if (atom->molecular == 2)
+    error->all(FLERR, "Bond style bpm cannot be used with atom style template");
+
+  // special 1-3 and 1-4 weights must be 1 to prevent building 1-3 and 1-4 special bond lists
+  if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 || force->special_coul[2] != 1.0 ||
+      force->special_coul[3] != 1.0)
+    error->all(FLERR, "Bond style bpm requires 1-3 and 1-4 special weights of 1.0");
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+   All args before store/local command are saved for potential args
+     for specific bond BPM substyles
+   All args after optional store/local command are variables stored
+     in the compute store/local
+------------------------------------------------------------------------- */
+
+void BondBPM::settings(int narg, char **arg)
+{
+  leftover_iarg.clear();
+
+  int iarg = 0;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "store/local") == 0) {
+      nvalues = 0;
+      id_fix_store_local = utils::strdup(arg[iarg + 1]);
+      store_local_freq = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
+      pack_choice = new FnPtrPack[narg - iarg - 1];
+      iarg += 3;
+      while (iarg < narg) {
+        if (strcmp(arg[iarg], "id1") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_id1;
+        } else if (strcmp(arg[iarg], "id2") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_id2;
+        } else if (strcmp(arg[iarg], "time") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_time;
+        } else if (strcmp(arg[iarg], "x") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_x;
+        } else if (strcmp(arg[iarg], "y") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_y;
+        } else if (strcmp(arg[iarg], "z") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_z;
+        } else if (strcmp(arg[iarg], "x/ref") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_x_ref;
+          prop_atom_flag = 1;
+        } else if (strcmp(arg[iarg], "y/ref") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_y_ref;
+          prop_atom_flag = 1;
+        } else if (strcmp(arg[iarg], "z/ref") == 0) {
+          pack_choice[nvalues++] = &BondBPM::pack_z_ref;
+          prop_atom_flag = 1;
+        } else {
+          break;
+        }
+        iarg++;
+      }
+    } else if (strcmp(arg[iarg], "overlay/pair") == 0) {
+      overlay_flag = 1;
+      iarg++;
+    } else {
+      leftover_iarg.push_back(iarg);
+      iarg++;
+    }
+  }
+
+  if (id_fix_store_local) {
+
+    if (nvalues == 0)
+      error->all(FLERR, "Storing local data must include at least one value to output");
+    memory->create(output_data, nvalues, "bond/bpm:output_data");
+
+    auto ifix = modify->get_fix_by_id(id_fix_store_local);
+    if (!ifix)
+      ifix = modify->add_fix(
+          fmt::format("{} all STORE_LOCAL {} {}", id_fix_store_local, store_local_freq, nvalues));
+    fix_store_local = dynamic_cast<FixStoreLocal *>(ifix);
+
+    // Use property/atom to save reference positions as it can transfer to ghost atoms
+    // This won't work for instances where bonds are added (e.g. fix pour) but in those cases
+    // a reference state isn't well defined
+    if (prop_atom_flag == 1) {
+
+      id_fix_prop_atom = utils::strdup("BPM_property_atom");
+      char *x_ref_id = utils::strdup("BPM_X_REF");
+      char *y_ref_id = utils::strdup("BPM_Y_REF");
+      char *z_ref_id = utils::strdup("BPM_Z_REF");
+
+      ifix = modify->get_fix_by_id(id_fix_prop_atom);
+      if (!ifix)
+        ifix = modify->add_fix(fmt::format("{} all property/atom {} {} {} ghost yes",
+                                           id_fix_prop_atom, x_ref_id, y_ref_id, z_ref_id));
+
+      int type_flag;
+      int col_flag;
+      index_x_ref = atom->find_custom(x_ref_id, type_flag, col_flag);
+      index_y_ref = atom->find_custom(y_ref_id, type_flag, col_flag);
+      index_z_ref = atom->find_custom(z_ref_id, type_flag, col_flag);
+
+      delete[] x_ref_id;
+      delete[] y_ref_id;
+      delete[] z_ref_id;
+
+      if (ifix->restart_reset) {
+        ifix->restart_reset = 0;
+      } else {
+        double *x_ref = atom->dvector[index_x_ref];
+        double *y_ref = atom->dvector[index_y_ref];
+        double *z_ref = atom->dvector[index_z_ref];
+
+        double **x = atom->x;
+        for (int i = 0; i < atom->nlocal; i++) {
+          x_ref[i] = x[i][0];
+          y_ref[i] = x[i][1];
+          z_ref[i] = x[i][2];
+        }
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   used to check bond communiction cutoff - not perfect, estimates based on local-local only
+------------------------------------------------------------------------- */
+
+double BondBPM::equilibrium_distance(int /*i*/)
+{
+  // Ghost atoms may not yet be communicated, this may only be an estimate
+  if (r0_max_estimate == 0) {
+    int type, j;
+    double delx, dely, delz, r;
+    double **x = atom->x;
+    for (int i = 0; i < atom->nlocal; i++) {
+      for (int m = 0; m < atom->num_bond[i]; m++) {
+        type = atom->bond_type[i][m];
+        if (type == 0) continue;
+
+        j = atom->map(atom->bond_atom[i][m]);
+        if (j == -1) continue;
+
+        delx = x[i][0] - x[j][0];
+        dely = x[i][1] - x[j][1];
+        delz = x[i][2] - x[j][2];
+        domain->minimum_image(delx, dely, delz);
+
+        r = sqrt(delx * delx + dely * dely + delz * delz);
+        if (r > r0_max_estimate) r0_max_estimate = r;
+      }
+    }
+
+    double temp;
+    MPI_Allreduce(&r0_max_estimate, &temp, 1, MPI_DOUBLE, MPI_MAX, world);
+    r0_max_estimate = temp;
+  }
+
+  // Divide out heuristic prefactor added in comm class
+  return max_stretch * r0_max_estimate / 1.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::process_broken(int i, int j)
+{
+  if (fix_store_local) {
+    for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
+
+    fix_store_local->add_data(output_data, i, j);
+  }
+
+  if (fix_update_special_bonds) fix_update_special_bonds->add_broken_bond(i, j);
+
+  // Manually search and remove from atom arrays
+  // need to remove in case special bonds arrays rebuilt
+  int m, n;
+  int nlocal = atom->nlocal;
+
+  tagint *tag = atom->tag;
+  tagint **bond_atom = atom->bond_atom;
+  int **bond_type = atom->bond_type;
+  int *num_bond = atom->num_bond;
+
+  if (i < nlocal) {
+    for (m = 0; m < num_bond[i]; m++) {
+      if (bond_atom[i][m] == tag[j]) {
+        bond_type[i][m] = 0;
+        n = num_bond[i];
+        bond_type[i][m] = bond_type[i][n - 1];
+        bond_atom[i][m] = bond_atom[i][n - 1];
+        fix_bond_history->shift_history(i, m, n - 1);
+        fix_bond_history->delete_history(i, n - 1);
+        num_bond[i]--;
+        break;
+      }
+    }
+  }
+
+  if (j < nlocal) {
+    for (m = 0; m < num_bond[j]; m++) {
+      if (bond_atom[j][m] == tag[i]) {
+        bond_type[j][m] = 0;
+        n = num_bond[j];
+        bond_type[j][m] = bond_type[j][n - 1];
+        bond_atom[j][m] = bond_atom[j][n - 1];
+        fix_bond_history->shift_history(j, m, n - 1);
+        fix_bond_history->delete_history(j, n - 1);
+        num_bond[j]--;
+        break;
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   one method for every keyword bond bpm can output
+   the atom property is packed into array or vector
+------------------------------------------------------------------------- */
+
+void BondBPM::pack_id1(int n, int i, int /*j*/)
+{
+  tagint *tag = atom->tag;
+  output_data[n] = tag[i];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::pack_id2(int n, int /*i*/, int j)
+{
+  tagint *tag = atom->tag;
+  output_data[n] = tag[j];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::pack_time(int n, int /*i*/, int /*j*/)
+{
+  bigint time = update->ntimestep;
+  output_data[n] = time;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::pack_x(int n, int i, int j)
+{
+  double **x = atom->x;
+  output_data[n] = (x[i][0] + x[j][0]) * 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::pack_y(int n, int i, int j)
+{
+  double **x = atom->x;
+  output_data[n] = (x[i][1] + x[j][1]) * 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::pack_z(int n, int i, int j)
+{
+  double **x = atom->x;
+  output_data[n] = (x[i][2] + x[j][2]) * 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::pack_x_ref(int n, int i, int j)
+{
+  double *x = atom->dvector[index_x_ref];
+  output_data[n] = (x[i] + x[j]) * 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::pack_y_ref(int n, int i, int j)
+{
+  double *y = atom->dvector[index_y_ref];
+  output_data[n] = (y[i] + y[j]) * 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPM::pack_z_ref(int n, int i, int j)
+{
+  double *z = atom->dvector[index_z_ref];
+  output_data[n] = (z[i] + z[j]) * 0.5;
+}

src/BPM/bond_bpm.h

@@ -0,0 +1,98 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_BOND_BPM_H
+#define LMP_BOND_BPM_H
+
+#include "bond.h"
+
+#include <vector>
+
+namespace LAMMPS_NS {
+
+class BondBPM : public Bond {
+ public:
+  BondBPM(class LAMMPS *);
+  ~BondBPM() override;
+  void compute(int, int) override = 0;
+  void coeff(int, char **) override = 0;
+  void init_style() override;
+  void settings(int, char **) override;
+  double equilibrium_distance(int) override;
+  void write_restart(FILE *) override{};
+  void read_restart(FILE *) override{};
+  void write_data(FILE *) override{};
+  double single(int, double, int, int, double &) override = 0;
+
+ protected:
+  double r0_max_estimate;
+  double max_stretch;
+  int store_local_freq;
+
+  std::vector<int> leftover_iarg;
+
+  char *id_fix_dummy, *id_fix_dummy2;
+  char *id_fix_update, *id_fix_bond_history;
+  char *id_fix_store_local, *id_fix_prop_atom;
+  class FixStoreLocal *fix_store_local;
+  class FixBondHistory *fix_bond_history;
+  class FixUpdateSpecialBonds *fix_update_special_bonds;
+
+  void process_broken(int, int);
+  typedef void (BondBPM::*FnPtrPack)(int, int, int);
+  FnPtrPack *pack_choice;    // ptrs to pack functions
+  double *output_data;
+
+  int prop_atom_flag, nvalues, overlay_flag;
+  int index_x_ref, index_y_ref, index_z_ref;
+
+  void pack_id1(int, int, int);
+  void pack_id2(int, int, int);
+  void pack_time(int, int, int);
+  void pack_x(int, int, int);
+  void pack_y(int, int, int);
+  void pack_z(int, int, int);
+  void pack_x_ref(int, int, int);
+  void pack_y_ref(int, int, int);
+  void pack_z_ref(int, int, int);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Cannot find fix store/local
+
+Fix id cannot be found.
+
+E: Illegal bond_style command
+
+Self-explanatory.
+
+E: Bond style bpm must include at least one value to output
+
+Must include at least one bond property to store in fix store/local
+
+E: Bond style bpm cannot be used with 3,4-body interactions
+
+No angle, dihedral, or improper styles can be defined when using
+bond style bpm.
+
+E: Bond style bpm cannot be used with atom style template
+
+This bond style can change the bond topology which is not
+allowed with this atom style.
+
+*/

src/BPM/bond_bpm_rotational.cpp

@@ -0,0 +1,796 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "bond_bpm_rotational.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "fix_bond_history.h"
+#include "force.h"
+#include "math_const.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "modify.h"
+#include "neighbor.h"
+
+#include <cmath>
+
+#define EPSILON 1e-10
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+BondBPMRotational::BondBPMRotational(LAMMPS *_lmp) : BondBPM(_lmp)
+{
+  Kr = nullptr;
+  Ks = nullptr;
+  Kt = nullptr;
+  Kb = nullptr;
+  Fcr = nullptr;
+  Fcs = nullptr;
+  Tct = nullptr;
+  Tcb = nullptr;
+  gnorm = nullptr;
+  gslide = nullptr;
+  groll = nullptr;
+  gtwist = nullptr;
+  partial_flag = 1;
+  smooth_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+BondBPMRotational::~BondBPMRotational()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(Kr);
+    memory->destroy(Ks);
+    memory->destroy(Kt);
+    memory->destroy(Kb);
+    memory->destroy(Fcr);
+    memory->destroy(Fcs);
+    memory->destroy(Tct);
+    memory->destroy(Tcb);
+    memory->destroy(gnorm);
+    memory->destroy(gslide);
+    memory->destroy(groll);
+    memory->destroy(gtwist);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+double BondBPMRotational::acos_limit(double c)
+{
+  if (c > 1.0) c = 1.0;
+  if (c < -1.0) c = -1.0;
+  return acos(c);
+}
+
+/* ----------------------------------------------------------------------
+  Store data for a single bond - if bond added after LAMMPS init (e.g. pour)
+------------------------------------------------------------------------- */
+
+double BondBPMRotational::store_bond(int n, int i, int j)
+{
+  double delx, dely, delz, r, rinv;
+  double **x = atom->x;
+  tagint *tag = atom->tag;
+  double **bondstore = fix_bond_history->bondstore;
+
+  if (tag[i] < tag[j]) {
+    delx = x[i][0] - x[j][0];
+    dely = x[i][1] - x[j][1];
+    delz = x[i][2] - x[j][2];
+  } else {
+    delx = x[j][0] - x[i][0];
+    dely = x[j][1] - x[i][1];
+    delz = x[j][2] - x[i][2];
+  }
+
+  r = sqrt(delx * delx + dely * dely + delz * delz);
+  rinv = 1.0 / r;
+
+  bondstore[n][0] = r;
+  bondstore[n][1] = delx * rinv;
+  bondstore[n][2] = dely * rinv;
+  bondstore[n][3] = delz * rinv;
+
+  if (i < atom->nlocal) {
+    for (int m = 0; m < atom->num_bond[i]; m++) {
+      if (atom->bond_atom[i][m] == tag[j]) {
+        fix_bond_history->update_atom_value(i, m, 0, r);
+        fix_bond_history->update_atom_value(i, m, 1, delx * rinv);
+        fix_bond_history->update_atom_value(i, m, 2, dely * rinv);
+        fix_bond_history->update_atom_value(i, m, 3, delz * rinv);
+      }
+    }
+  }
+
+  if (j < atom->nlocal) {
+    for (int m = 0; m < atom->num_bond[j]; m++) {
+      if (atom->bond_atom[j][m] == tag[i]) {
+        fix_bond_history->update_atom_value(j, m, 0, r);
+        fix_bond_history->update_atom_value(j, m, 1, delx * rinv);
+        fix_bond_history->update_atom_value(j, m, 2, dely * rinv);
+        fix_bond_history->update_atom_value(j, m, 3, delz * rinv);
+      }
+    }
+  }
+
+  return r;
+}
+
+/* ----------------------------------------------------------------------
+  Store data for all bonds called once
+------------------------------------------------------------------------- */
+
+void BondBPMRotational::store_data()
+{
+  int i, j, m, type;
+  double delx, dely, delz, r, rinv;
+  double **x = atom->x;
+  int **bond_type = atom->bond_type;
+  tagint *tag = atom->tag;
+
+  for (i = 0; i < atom->nlocal; i++) {
+    for (m = 0; m < atom->num_bond[i]; m++) {
+      type = bond_type[i][m];
+
+      //Skip if bond was turned off
+      if (type < 0) continue;
+
+      // map to find index n for tag
+      j = atom->map(atom->bond_atom[i][m]);
+      if (j == -1) error->one(FLERR, "Atom missing in BPM bond");
+
+      // Save orientation as pointing towards small tag
+      if (tag[i] < tag[j]) {
+        delx = x[i][0] - x[j][0];
+        dely = x[i][1] - x[j][1];
+        delz = x[i][2] - x[j][2];
+      } else {
+        delx = x[j][0] - x[i][0];
+        dely = x[j][1] - x[i][1];
+        delz = x[j][2] - x[i][2];
+      }
+
+      // Get closest image in case bonded with ghost
+      domain->minimum_image(delx, dely, delz);
+      r = sqrt(delx * delx + dely * dely + delz * delz);
+      rinv = 1.0 / r;
+
+      fix_bond_history->update_atom_value(i, m, 0, r);
+      fix_bond_history->update_atom_value(i, m, 1, delx * rinv);
+      fix_bond_history->update_atom_value(i, m, 2, dely * rinv);
+      fix_bond_history->update_atom_value(i, m, 3, delz * rinv);
+    }
+  }
+
+  fix_bond_history->post_neighbor();
+}
+
+/* ----------------------------------------------------------------------
+  Calculate forces using formulation in:
+    1) Y. Wang Acta Geotechnica 2009
+    2) P. Mora & Y. Wang Advances in Geomcomputing 2009
+---------------------------------------------------------------------- */
+
+double BondBPMRotational::elastic_forces(int i1, int i2, int type, double &Fr, double r_mag,
+                                         double r0_mag, double r_mag_inv, double * /*rhat*/,
+                                         double *r, double *r0, double *force1on2,
+                                         double *torque1on2, double *torque2on1)
+{
+  double breaking, temp, r0_dot_rb, c, gamma;
+  double psi, theta, cos_phi, sin_phi;
+  double mag_in_plane, mag_out_plane;
+  double Fs_mag, Tt_mag, Tb_mag;
+
+  double q1[4], q2[4];
+  double q2inv[4], mq[4], mqinv[4], qp21[4], q21[4], qtmp[4];
+  double rb[3], rb_x_r0[3], s[3], t[3];
+  double Fs[3], Fsp[3], F_rot[3], Ftmp[3];
+  double Ts[3], Tb[3], Tt[3], Tbp[3], Ttp[3], Tsp[3], T_rot[3], Ttmp[3];
+
+  double **quat = atom->quat;
+
+  q1[0] = quat[i1][0];
+  q1[1] = quat[i1][1];
+  q1[2] = quat[i1][2];
+  q1[3] = quat[i1][3];
+
+  q2[0] = quat[i2][0];
+  q2[1] = quat[i2][1];
+  q2[2] = quat[i2][2];
+  q2[3] = quat[i2][3];
+
+  // Calculate normal forces, rb = bond vector in particle 1's frame
+  MathExtra::qconjugate(q2, q2inv);
+  MathExtra::quatrotvec(q2inv, r, rb);
+  Fr = Kr[type] * (r_mag - r0_mag);
+
+  MathExtra::scale3(Fr * r_mag_inv, rb, F_rot);
+
+  // Calculate forces due to tangential displacements (no rotation)
+  r0_dot_rb = MathExtra::dot3(r0, rb);
+  c = r0_dot_rb * r_mag_inv / r0_mag;
+  gamma = acos_limit(c);
+
+  MathExtra::cross3(rb, r0, rb_x_r0);
+  MathExtra::cross3(rb, rb_x_r0, s);
+  MathExtra::norm3(s);
+
+  MathExtra::scale3(Ks[type] * r_mag * gamma, s, Fs);
+
+  // Calculate torque due to tangential displacements
+  MathExtra::cross3(r0, rb, t);
+  MathExtra::norm3(t);
+
+  MathExtra::scale3(0.5 * r_mag * Ks[type] * r_mag * gamma, t, Ts);
+
+  // Relative rotation force/torque
+  // Use representation of X'Y'Z' rotations from Wang, Mora 2009
+  temp = r_mag + rb[2];
+  if (temp < 0.0) temp = 0.0;
+  mq[0] = sqrt(2) * 0.5 * sqrt(temp * r_mag_inv);
+
+  temp = sqrt(rb[0] * rb[0] + rb[1] * rb[1]);
+  if (temp != 0.0) {
+    mq[1] = -sqrt(2) * 0.5 / temp;
+    temp = r_mag - rb[2];
+    if (temp < 0.0) temp = 0.0;
+    mq[1] *= sqrt(temp * r_mag_inv);
+    mq[2] = -mq[1];
+    mq[1] *= rb[1];
+    mq[2] *= rb[0];
+  } else {
+    // If aligned along z axis, x,y terms zero (r_mag-rb[2] = 0)
+    mq[1] = 0.0;
+    mq[2] = 0.0;
+  }
+  mq[3] = 0.0;
+
+  // qp21 = opposite of r^\circ_21 in Wang
+  // q21 = opposite of r_21 in Wang
+  MathExtra::quatquat(q2inv, q1, qp21);
+  MathExtra::qconjugate(mq, mqinv);
+  MathExtra::quatquat(mqinv, qp21, qtmp);
+  MathExtra::quatquat(qtmp, mq, q21);
+
+  temp = sqrt(q21[0] * q21[0] + q21[3] * q21[3]);
+  if (temp != 0.0) {
+    c = q21[0] / temp;
+    psi = 2.0 * acos_limit(c);
+  } else {
+    c = 0.0;
+    psi = 0.0;
+  }
+
+  // Map negative rotations
+  if (q21[3] < 0.0)    // sin = q21[3]/temp
+    psi = -psi;
+
+  if (q21[3] == 0.0) psi = 0.0;
+
+  c = q21[0] * q21[0] - q21[1] * q21[1] - q21[2] * q21[2] + q21[3] * q21[3];
+  theta = acos_limit(c);
+
+  // Separately calculte magnitude of quaternion in x-y and out of x-y planes
+  // to avoid dividing by zero
+  mag_out_plane = (q21[0] * q21[0] + q21[3] * q21[3]);
+  mag_in_plane = (q21[1] * q21[1] + q21[2] * q21[2]);
+
+  if (mag_in_plane == 0.0) {
+    // No rotation => no bending/shear torque or extra shear force
+    // achieve by setting cos/sin = 0
+    cos_phi = 0.0;
+    sin_phi = 0.0;
+  } else if (mag_out_plane == 0.0) {
+    // Calculate angle in plane
+    cos_phi = q21[2] / sqrt(mag_in_plane);
+    sin_phi = -q21[1] / sqrt(mag_in_plane);
+  } else {
+    // Default equations in Mora, Wang 2009
+    cos_phi = q21[1] * q21[3] + q21[0] * q21[2];
+    sin_phi = q21[2] * q21[3] - q21[0] * q21[1];
+
+    cos_phi /= sqrt(mag_out_plane * mag_in_plane);
+    sin_phi /= sqrt(mag_out_plane * mag_in_plane);
+  }
+
+  Tbp[0] = -Kb[type] * theta * sin_phi;
+  Tbp[1] = Kb[type] * theta * cos_phi;
+  Tbp[2] = 0.0;
+
+  Ttp[0] = 0.0;
+  Ttp[1] = 0.0;
+  Ttp[2] = Kt[type] * psi;
+
+  Fsp[0] = -0.5 * Ks[type] * r_mag * theta * cos_phi;
+  Fsp[1] = -0.5 * Ks[type] * r_mag * theta * sin_phi;
+  Fsp[2] = 0.0;
+
+  Tsp[0] = 0.25 * Ks[type] * r_mag * r_mag * theta * sin_phi;
+  Tsp[1] = -0.25 * Ks[type] * r_mag * r_mag * theta * cos_phi;
+  Tsp[2] = 0.0;
+
+  // Rotate forces/torques back to 1st particle's frame
+
+  MathExtra::quatrotvec(mq, Fsp, Ftmp);
+  MathExtra::quatrotvec(mq, Tsp, Ttmp);
+  for (int m = 0; m < 3; m++) {
+    Fs[m] += Ftmp[m];
+    Ts[m] += Ttmp[m];
+  }
+
+  MathExtra::quatrotvec(mq, Tbp, Tb);
+  MathExtra::quatrotvec(mq, Ttp, Tt);
+
+  // Sum forces and calculate magnitudes
+  F_rot[0] += Fs[0];
+  F_rot[1] += Fs[1];
+  F_rot[2] += Fs[2];
+  MathExtra::quatrotvec(q2, F_rot, force1on2);
+
+  T_rot[0] = Ts[0] + Tt[0] + Tb[0];
+  T_rot[1] = Ts[1] + Tt[1] + Tb[1];
+  T_rot[2] = Ts[2] + Tt[2] + Tb[2];
+  MathExtra::quatrotvec(q2, T_rot, torque1on2);
+
+  T_rot[0] = Ts[0] - Tt[0] - Tb[0];
+  T_rot[1] = Ts[1] - Tt[1] - Tb[1];
+  T_rot[2] = Ts[2] - Tt[2] - Tb[2];
+  MathExtra::quatrotvec(q2, T_rot, torque2on1);
+
+  Fs_mag = MathExtra::len3(Fs);
+  Tt_mag = MathExtra::len3(Tt);
+  Tb_mag = MathExtra::len3(Tb);
+
+  breaking = Fr / Fcr[type] + Fs_mag / Fcs[type] + Tb_mag / Tcb[type] + Tt_mag / Tct[type];
+  if (breaking < 0.0) breaking = 0.0;
+
+  return breaking;
+}
+
+/* ----------------------------------------------------------------------
+  Calculate damping using formulation in
+        Y. Wang, F. Alonso-Marroquin, W. Guo 2015
+  Note: n points towards 1 vs pointing towards 2
+---------------------------------------------------------------------- */
+
+void BondBPMRotational::damping_forces(int i1, int i2, int type, double &Fr, double *rhat,
+                                       double *r, double *force1on2, double *torque1on2,
+                                       double *torque2on1)
+{
+  double v1dotr, v2dotr, w1dotr, w2dotr;
+  double s1[3], s2[3], tdamp[3], tmp[3];
+  double vn1[3], vn2[3], vt1[3], vt2[3], vroll[3];
+  double wxn1[3], wxn2[3], wn1[3], wn2[3];
+
+  double **v = atom->v;
+  double **omega = atom->omega;
+
+  // Damp normal velocity difference
+  v1dotr = MathExtra::dot3(v[i1], rhat);
+  v2dotr = MathExtra::dot3(v[i2], rhat);
+
+  MathExtra::scale3(v1dotr, rhat, vn1);
+  MathExtra::scale3(v2dotr, rhat, vn2);
+
+  MathExtra::sub3(vn1, vn2, tmp);
+  MathExtra::scale3(gnorm[type], tmp);
+  Fr = MathExtra::lensq3(tmp);
+  MathExtra::add3(force1on2, tmp, force1on2);
+
+  // Damp tangential objective velocities
+  MathExtra::sub3(v[i1], vn1, vt1);
+  MathExtra::sub3(v[i2], vn2, vt2);
+
+  MathExtra::sub3(vt2, vt1, tmp);
+  MathExtra::scale3(0.5, tmp);
+
+  MathExtra::cross3(omega[i1], r, s1);
+  MathExtra::scale3(-0.5, s1);
+  MathExtra::sub3(s1, tmp, s1);    // Eq 12
+
+  MathExtra::cross3(omega[i2], r, s2);
+  MathExtra::scale3(0.5, s2);
+  MathExtra::add3(s2, tmp, s2);    // Eq 13
+
+  MathExtra::sub3(s1, s2, tmp);
+  MathExtra::scale3(gslide[type], tmp);
+  MathExtra::add3(force1on2, tmp, force1on2);
+
+  // Apply corresponding torque
+  MathExtra::cross3(r, tmp, tdamp);
+  MathExtra::scale3(0.5, tdamp);
+  MathExtra::add3(torque1on2, tdamp, torque1on2);
+  MathExtra::add3(torque2on1, tdamp, torque2on1);
+
+  // Damp rolling
+  MathExtra::cross3(omega[i1], rhat, wxn1);
+  MathExtra::cross3(omega[i2], rhat, wxn2);
+  MathExtra::sub3(wxn1, wxn2, vroll);    // Eq. 31
+  MathExtra::cross3(r, vroll, tdamp);
+
+  MathExtra::scale3(0.5 * groll[type], tdamp);
+  MathExtra::add3(torque1on2, tdamp, torque1on2);
+  MathExtra::scale3(-1.0, tdamp);
+  MathExtra::add3(torque2on1, tdamp, torque2on1);
+
+  // Damp twist
+  w1dotr = MathExtra::dot3(omega[i1], rhat);
+  w2dotr = MathExtra::dot3(omega[i2], rhat);
+
+  MathExtra::scale3(w1dotr, rhat, wn1);
+  MathExtra::scale3(w2dotr, rhat, wn2);
+
+  MathExtra::sub3(wn1, wn2, tdamp);    // Eq. 38
+  MathExtra::scale3(0.5 * gtwist[type], tdamp);
+  MathExtra::add3(torque1on2, tdamp, torque1on2);
+  MathExtra::scale3(-1.0, tdamp);
+  MathExtra::add3(torque2on1, tdamp, torque2on1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPMRotational::compute(int eflag, int vflag)
+{
+
+  if (!fix_bond_history->stored_flag) {
+    fix_bond_history->stored_flag = true;
+    store_data();
+  }
+
+  int i1, i2, itmp, n, type;
+  double r[3], r0[3], rhat[3];
+  double rsq, r0_mag, r_mag, r_mag_inv;
+  double Fr, breaking, smooth;
+  double force1on2[3], torque1on2[3], torque2on1[3];
+
+  ev_init(eflag, vflag);
+
+  double **x = atom->x;
+  double **f = atom->f;
+  double **torque = atom->torque;
+  tagint *tag = atom->tag;
+  int **bondlist = neighbor->bondlist;
+  int nbondlist = neighbor->nbondlist;
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+
+  double **bondstore = fix_bond_history->bondstore;
+
+  for (n = 0; n < nbondlist; n++) {
+
+    // skip bond if already broken
+    if (bondlist[n][2] <= 0) continue;
+
+    i1 = bondlist[n][0];
+    i2 = bondlist[n][1];
+    type = bondlist[n][2];
+    r0_mag = bondstore[n][0];
+
+    // Ensure pair is always ordered such that r0 points in
+    // a consistent direction and to ensure numerical operations
+    // are identical to minimize the possibility that a bond straddling
+    // an mpi grid (newton off) doesn't break on one proc but not the other
+    if (tag[i2] < tag[i1]) {
+      itmp = i1;
+      i1 = i2;
+      i2 = itmp;
+    }
+
+    // If bond hasn't been set - should be initialized to zero
+    if (r0_mag < EPSILON || std::isnan(r0_mag)) r0_mag = store_bond(n, i1, i2);
+
+    r0[0] = bondstore[n][1];
+    r0[1] = bondstore[n][2];
+    r0[2] = bondstore[n][3];
+    MathExtra::scale3(r0_mag, r0);
+
+    // Note this is the reverse of Mora & Wang
+    MathExtra::sub3(x[i1], x[i2], r);
+
+    rsq = MathExtra::lensq3(r);
+    r_mag = sqrt(rsq);
+    r_mag_inv = 1.0 / r_mag;
+    MathExtra::scale3(r_mag_inv, r, rhat);
+
+    // ------------------------------------------------------//
+    //  Calculate forces, check if bond breaks
+    // ------------------------------------------------------//
+
+    breaking = elastic_forces(i1, i2, type, Fr, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2,
+                              torque1on2, torque2on1);
+
+    if (breaking >= 1.0) {
+      bondlist[n][2] = 0;
+      process_broken(i1, i2);
+      continue;
+    }
+
+    damping_forces(i1, i2, type, Fr, rhat, r, force1on2, torque1on2, torque2on1);
+
+    if (smooth_flag) {
+      smooth = breaking * breaking;
+      smooth = 1.0 - smooth * smooth;
+    } else {
+      smooth = 1.0;
+    }
+
+    // ------------------------------------------------------//
+    //  Apply forces and torques to particles
+    // ------------------------------------------------------//
+
+    if (newton_bond || i1 < nlocal) {
+      f[i1][0] -= force1on2[0] * smooth;
+      f[i1][1] -= force1on2[1] * smooth;
+      f[i1][2] -= force1on2[2] * smooth;
+
+      torque[i1][0] += torque2on1[0] * smooth;
+      torque[i1][1] += torque2on1[1] * smooth;
+      torque[i1][2] += torque2on1[2] * smooth;
+    }
+
+    if (newton_bond || i2 < nlocal) {
+      f[i2][0] += force1on2[0] * smooth;
+      f[i2][1] += force1on2[1] * smooth;
+      f[i2][2] += force1on2[2] * smooth;
+
+      torque[i2][0] += torque1on2[0] * smooth;
+      torque[i2][1] += torque1on2[1] * smooth;
+      torque[i2][2] += torque1on2[2] * smooth;
+    }
+
+    if (evflag) ev_tally(i1, i2, nlocal, newton_bond, 0.0, Fr * smooth, r[0], r[1], r[2]);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPMRotational::allocate()
+{
+  allocated = 1;
+  const int np1 = atom->nbondtypes + 1;
+
+  memory->create(Kr, np1, "bond:Kr");
+  memory->create(Ks, np1, "bond:Ks");
+  memory->create(Kt, np1, "bond:Kt");
+  memory->create(Kb, np1, "bond:Kb");
+  memory->create(Fcr, np1, "bond:Fcr");
+  memory->create(Fcs, np1, "bond:Fcs");
+  memory->create(Tct, np1, "bond:Tct");
+  memory->create(Tcb, np1, "bond:Tcb");
+  memory->create(gnorm, np1, "bond:gnorm");
+  memory->create(gslide, np1, "bond:gslide");
+  memory->create(groll, np1, "bond:groll");
+  memory->create(gtwist, np1, "bond:gtwist");
+
+  memory->create(setflag, np1, "bond:setflag");
+  for (int i = 1; i < np1; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more types
+------------------------------------------------------------------------- */
+
+void BondBPMRotational::coeff(int narg, char **arg)
+{
+  if (narg != 13) error->all(FLERR, "Incorrect args for bond coefficients");
+  if (!allocated) allocate();
+
+  int ilo, ihi;
+  utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
+
+  double Kr_one = utils::numeric(FLERR, arg[1], false, lmp);
+  double Ks_one = utils::numeric(FLERR, arg[2], false, lmp);
+  double Kt_one = utils::numeric(FLERR, arg[3], false, lmp);
+  double Kb_one = utils::numeric(FLERR, arg[4], false, lmp);
+  double Fcr_one = utils::numeric(FLERR, arg[5], false, lmp);
+  double Fcs_one = utils::numeric(FLERR, arg[6], false, lmp);
+  double Tct_one = utils::numeric(FLERR, arg[7], false, lmp);
+  double Tcb_one = utils::numeric(FLERR, arg[8], false, lmp);
+  double gnorm_one = utils::numeric(FLERR, arg[9], false, lmp);
+  double gslide_one = utils::numeric(FLERR, arg[10], false, lmp);
+  double groll_one = utils::numeric(FLERR, arg[11], false, lmp);
+  double gtwist_one = utils::numeric(FLERR, arg[12], false, lmp);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    Kr[i] = Kr_one;
+    Ks[i] = Ks_one;
+    Kt[i] = Kt_one;
+    Kb[i] = Kb_one;
+    Fcr[i] = Fcr_one;
+    Fcs[i] = Fcs_one;
+    Tct[i] = Tct_one;
+    Tcb[i] = Tcb_one;
+    gnorm[i] = gnorm_one;
+    gslide[i] = gslide_one;
+    groll[i] = groll_one;
+    gtwist[i] = gtwist_one;
+    setflag[i] = 1;
+    count++;
+
+    if (Fcr[i] / Kr[i] > max_stretch) max_stretch = Fcr[i] / Kr[i];
+  }
+
+  if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   check for correct settings and create fix
+------------------------------------------------------------------------- */
+
+void BondBPMRotational::init_style()
+{
+  BondBPM::init_style();
+
+  if (!atom->quat_flag || !atom->sphere_flag)
+    error->all(FLERR, "Bond bpm/rotational requires atom style bpm/sphere");
+  if (comm->ghost_velocity == 0)
+    error->all(FLERR, "Bond bpm/rotational requires ghost atoms store velocity");
+
+  if (domain->dimension == 2)
+    error->warning(FLERR, "Bond style bpm/rotational not intended for 2d use");
+
+  if (!id_fix_bond_history) {
+    id_fix_bond_history = utils::strdup("HISTORY_BPM_ROTATIONAL");
+    fix_bond_history = dynamic_cast<FixBondHistory *>(modify->replace_fix(
+        id_fix_dummy2, fmt::format("{} all BOND_HISTORY 0 4", id_fix_bond_history), 1));
+    delete[] id_fix_dummy2;
+    id_fix_dummy2 = nullptr;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPMRotational::settings(int narg, char **arg)
+{
+  BondBPM::settings(narg, arg);
+
+  int iarg;
+  for (std::size_t i = 0; i < leftover_iarg.size(); i++) {
+    iarg = leftover_iarg[i];
+    if (strcmp(arg[iarg], "smooth") == 0) {
+      if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command");
+      smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
+      i += 1;
+    } else {
+      error->all(FLERR, "Illegal bond_style command");
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void BondBPMRotational::write_restart(FILE *fp)
+{
+  fwrite(&Kr[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&Ks[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&Kt[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&Kb[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&Fcr[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&Fcs[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&Tct[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&Tcb[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&gnorm[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&gslide[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&groll[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&gtwist[1], sizeof(double), atom->nbondtypes, fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void BondBPMRotational::read_restart(FILE *fp)
+{
+  allocate();
+
+  if (comm->me == 0) {
+    utils::sfread(FLERR, &Kr[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &Ks[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &Kt[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &Kb[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &Fcr[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &Fcs[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &Tct[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &Tcb[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &gnorm[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &gslide[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &groll[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &gtwist[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+  }
+  MPI_Bcast(&Kr[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&Ks[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&Kt[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&Kb[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&Fcr[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&Fcs[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&Tct[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&Tcb[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&gnorm[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&gslide[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&groll[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&gtwist[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+
+  for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void BondBPMRotational::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->nbondtypes; i++)
+    fprintf(fp, "%d %g %g %g %g %g %g %g %g %g %g %g %g\n", i, Kr[i], Ks[i], Kt[i], Kb[i], Fcr[i],
+            Fcs[i], Tct[i], Tcb[i], gnorm[i], gslide[i], groll[i], gtwist[i]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double BondBPMRotational::single(int type, double rsq, int i, int j, double &fforce)
+{
+  // Not yet enabled
+  if (type <= 0) return 0.0;
+
+  int itmp;
+  if (atom->tag[j] < atom->tag[i]) {
+    itmp = i;
+    i = j;
+    j = itmp;
+  }
+
+  double r0_mag, r_mag, r_mag_inv;
+  double r0[3], r[3], rhat[3];
+  for (int n = 0; n < atom->num_bond[i]; n++) {
+    if (atom->bond_atom[i][n] == atom->tag[j]) {
+      r0_mag = fix_bond_history->get_atom_value(i, n, 0);
+      r0[0] = fix_bond_history->get_atom_value(i, n, 1);
+      r0[1] = fix_bond_history->get_atom_value(i, n, 2);
+      r0[2] = fix_bond_history->get_atom_value(i, n, 3);
+    }
+  }
+
+  double **x = atom->x;
+  MathExtra::scale3(r0_mag, r0);
+  MathExtra::sub3(x[i], x[j], r);
+
+  r_mag = sqrt(rsq);
+  r_mag_inv = 1.0 / r_mag;
+  MathExtra::scale3(r_mag_inv, r, rhat);
+
+  double breaking, smooth, Fr;
+  double force1on2[3], torque1on2[3], torque2on1[3];
+  breaking = elastic_forces(i, j, type, Fr, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2,
+                            torque1on2, torque2on1);
+  fforce = Fr;
+  damping_forces(i, j, type, Fr, rhat, r, force1on2, torque1on2, torque2on1);
+  fforce += Fr;
+
+  if (smooth_flag) {
+    smooth = breaking * breaking;
+    smooth = 1.0 - smooth * smooth;
+    fforce *= smooth;
+  }
+  return 0.0;
+}

src/BPM/bond_bpm_rotational.h

@@ -0,0 +1,83 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef BOND_CLASS
+// clang-format off
+BondStyle(bpm/rotational,BondBPMRotational);
+// clang-format on
+#else
+
+#ifndef LMP_BOND_BPM_ROTATIONAL_H
+#define LMP_BOND_BPM_ROTATIONAL_H
+
+#include "bond_bpm.h"
+
+namespace LAMMPS_NS {
+
+class BondBPMRotational : public BondBPM {
+ public:
+  BondBPMRotational(class LAMMPS *);
+  ~BondBPMRotational() override;
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  void settings(int, char **) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, double, int, int, double &) override;
+
+ protected:
+  double *Kr, *Ks, *Kt, *Kb, *gnorm, *gslide, *groll, *gtwist;
+  double *Fcr, *Fcs, *Tct, *Tcb;
+  int smooth_flag;
+
+  double acos_limit(double);
+
+  double elastic_forces(int, int, int, double &, double, double, double, double *, double *,
+                        double *, double *, double *, double *);
+  void damping_forces(int, int, int, double &, double *, double *, double *, double *, double *);
+
+  void allocate();
+  void store_data();
+  double store_bond(int, int, int);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Atom missing in BPM bond
+
+Bonded atom cannot be found
+
+E: Incorrect args for bond coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: Bond bpm/rotational requires atom style bpm/sphere
+
+Self-explanatory.
+
+E: Bond style bpm requires 1-3 and 1-4 special weights of 1.0
+
+Self-explanatory.
+
+W: Bond style bpm/rotational not intended for 2d use, may be inefficient
+
+This bond style will perform a lot of unnecessary calculations in 2d
+
+*/

src/BPM/bond_bpm_spring.cpp

@@ -0,0 +1,380 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "bond_bpm_spring.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "fix_bond_history.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "neighbor.h"
+
+#define EPSILON 1e-10
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+BondBPMSpring::BondBPMSpring(LAMMPS *_lmp) : BondBPM(_lmp), k(nullptr), ecrit(nullptr), gamma(nullptr)
+{
+  partial_flag = 1;
+  smooth_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+BondBPMSpring::~BondBPMSpring()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(k);
+    memory->destroy(ecrit);
+    memory->destroy(gamma);
+  }
+}
+
+/* ----------------------------------------------------------------------
+  Store data for a single bond - if bond added after LAMMPS init (e.g. pour)
+------------------------------------------------------------------------- */
+
+double BondBPMSpring::store_bond(int n, int i, int j)
+{
+  double delx, dely, delz, r;
+  double **x = atom->x;
+  double **bondstore = fix_bond_history->bondstore;
+  tagint *tag = atom->tag;
+
+  delx = x[i][0] - x[j][0];
+  dely = x[i][1] - x[j][1];
+  delz = x[i][2] - x[j][2];
+
+  r = sqrt(delx * delx + dely * dely + delz * delz);
+  bondstore[n][0] = r;
+
+  if (i < atom->nlocal) {
+    for (int m = 0; m < atom->num_bond[i]; m++) {
+      if (atom->bond_atom[i][m] == tag[j]) { fix_bond_history->update_atom_value(i, m, 0, r); }
+    }
+  }
+
+  if (j < atom->nlocal) {
+    for (int m = 0; m < atom->num_bond[j]; m++) {
+      if (atom->bond_atom[j][m] == tag[i]) { fix_bond_history->update_atom_value(j, m, 0, r); }
+    }
+  }
+
+  return r;
+}
+
+/* ----------------------------------------------------------------------
+  Store data for all bonds called once
+------------------------------------------------------------------------- */
+
+void BondBPMSpring::store_data()
+{
+  int i, j, m, type;
+  double delx, dely, delz, r;
+  double **x = atom->x;
+  int **bond_type = atom->bond_type;
+
+  for (i = 0; i < atom->nlocal; i++) {
+    for (m = 0; m < atom->num_bond[i]; m++) {
+      type = bond_type[i][m];
+
+      //Skip if bond was turned off
+      if (type < 0) continue;
+
+      // map to find index n
+      j = atom->map(atom->bond_atom[i][m]);
+      if (j == -1) error->one(FLERR, "Atom missing in BPM bond");
+
+      delx = x[i][0] - x[j][0];
+      dely = x[i][1] - x[j][1];
+      delz = x[i][2] - x[j][2];
+
+      // Get closest image in case bonded with ghost
+      domain->minimum_image(delx, dely, delz);
+      r = sqrt(delx * delx + dely * dely + delz * delz);
+
+      fix_bond_history->update_atom_value(i, m, 0, r);
+    }
+  }
+
+  fix_bond_history->post_neighbor();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPMSpring::compute(int eflag, int vflag)
+{
+
+  if (!fix_bond_history->stored_flag) {
+    fix_bond_history->stored_flag = true;
+    store_data();
+  }
+
+  int i1, i2, itmp, n, type;
+  double delx, dely, delz, delvx, delvy, delvz;
+  double e, rsq, r, r0, rinv, smooth, fbond, dot;
+
+  ev_init(eflag, vflag);
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  tagint *tag = atom->tag;
+  int **bondlist = neighbor->bondlist;
+  int nbondlist = neighbor->nbondlist;
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+
+  double **bondstore = fix_bond_history->bondstore;
+
+  for (n = 0; n < nbondlist; n++) {
+
+    // skip bond if already broken
+    if (bondlist[n][2] <= 0) continue;
+
+    i1 = bondlist[n][0];
+    i2 = bondlist[n][1];
+    type = bondlist[n][2];
+    r0 = bondstore[n][0];
+
+    // Ensure pair is always ordered to ensure numerical operations
+    // are identical to minimize the possibility that a bond straddling
+    // an mpi grid (newton off) doesn't break on one proc but not the other
+    if (tag[i2] < tag[i1]) {
+      itmp = i1;
+      i1 = i2;
+      i2 = itmp;
+    }
+
+    // If bond hasn't been set - should be initialized to zero
+    if (r0 < EPSILON || std::isnan(r0)) r0 = store_bond(n, i1, i2);
+
+    delx = x[i1][0] - x[i2][0];
+    dely = x[i1][1] - x[i2][1];
+    delz = x[i1][2] - x[i2][2];
+
+    rsq = delx * delx + dely * dely + delz * delz;
+    r = sqrt(rsq);
+    e = (r - r0) / r0;
+
+    if (fabs(e) > ecrit[type]) {
+      bondlist[n][2] = 0;
+      process_broken(i1, i2);
+      continue;
+    }
+
+    rinv = 1.0 / r;
+    fbond = k[type] * (r0 - r);
+
+    delvx = v[i1][0] - v[i2][0];
+    delvy = v[i1][1] - v[i2][1];
+    delvz = v[i1][2] - v[i2][2];
+    dot = delx * delvx + dely * delvy + delz * delvz;
+    fbond -= gamma[type] * dot * rinv;
+    fbond *= rinv;
+
+    if (smooth_flag) {
+      smooth = (r - r0) / (r0 * ecrit[type]);
+      smooth *= smooth;
+      smooth *= smooth;
+      smooth *= smooth;
+      smooth = 1 - smooth;
+      fbond *= smooth;
+    }
+
+    if (newton_bond || i1 < nlocal) {
+      f[i1][0] += delx * fbond;
+      f[i1][1] += dely * fbond;
+      f[i1][2] += delz * fbond;
+    }
+
+    if (newton_bond || i2 < nlocal) {
+      f[i2][0] -= delx * fbond;
+      f[i2][1] -= dely * fbond;
+      f[i2][2] -= delz * fbond;
+    }
+
+    if (evflag) ev_tally(i1, i2, nlocal, newton_bond, 0.0, fbond, delx, dely, delz);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPMSpring::allocate()
+{
+  allocated = 1;
+  const int np1 = atom->nbondtypes + 1;
+
+  memory->create(k, np1, "bond:k");
+  memory->create(ecrit, np1, "bond:ecrit");
+  memory->create(gamma, np1, "bond:gamma");
+
+  memory->create(setflag, np1, "bond:setflag");
+  for (int i = 1; i < np1; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more types
+------------------------------------------------------------------------- */
+
+void BondBPMSpring::coeff(int narg, char **arg)
+{
+  if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients");
+  if (!allocated) allocate();
+
+  int ilo, ihi;
+  utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
+
+  double k_one = utils::numeric(FLERR, arg[1], false, lmp);
+  double ecrit_one = utils::numeric(FLERR, arg[2], false, lmp);
+  double gamma_one = utils::numeric(FLERR, arg[3], false, lmp);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    k[i] = k_one;
+    ecrit[i] = ecrit_one;
+    gamma[i] = gamma_one;
+    setflag[i] = 1;
+    count++;
+
+    if (1.0 + ecrit[i] > max_stretch) max_stretch = 1.0 + ecrit[i];
+  }
+
+  if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   check for correct settings and create fix
+------------------------------------------------------------------------- */
+
+void BondBPMSpring::init_style()
+{
+  BondBPM::init_style();
+
+  if (comm->ghost_velocity == 0)
+    error->all(FLERR, "Bond bpm/spring requires ghost atoms store velocity");
+
+  if (!id_fix_bond_history) {
+    id_fix_bond_history = utils::strdup("HISTORY_BPM_SPRING");
+    fix_bond_history = dynamic_cast<FixBondHistory *>(modify->replace_fix(
+        id_fix_dummy2, fmt::format("{} all BOND_HISTORY 0 1", id_fix_bond_history), 1));
+    delete[] id_fix_dummy2;
+    id_fix_dummy2 = nullptr;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondBPMSpring::settings(int narg, char **arg)
+{
+  BondBPM::settings(narg, arg);
+
+  int iarg;
+  for (std::size_t i = 0; i < leftover_iarg.size(); i++) {
+    iarg = leftover_iarg[i];
+    if (strcmp(arg[iarg], "smooth") == 0) {
+      if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command");
+      smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
+      i += 1;
+    } else {
+      error->all(FLERR, "Illegal bond_style command");
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void BondBPMSpring::write_restart(FILE *fp)
+{
+  fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&ecrit[1], sizeof(double), atom->nbondtypes, fp);
+  fwrite(&gamma[1], sizeof(double), atom->nbondtypes, fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void BondBPMSpring::read_restart(FILE *fp)
+{
+  allocate();
+
+  if (comm->me == 0) {
+    utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &ecrit[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+    utils::sfread(FLERR, &gamma[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
+  }
+  MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&ecrit[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&gamma[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
+
+  for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void BondBPMSpring::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->nbondtypes; i++)
+    fprintf(fp, "%d %g %g %g\n", i, k[i], ecrit[i], gamma[i]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double BondBPMSpring::single(int type, double rsq, int i, int j, double &fforce)
+{
+  if (type <= 0) return 0.0;
+
+  double r0;
+  for (int n = 0; n < atom->num_bond[i]; n++) {
+    if (atom->bond_atom[i][n] == atom->tag[j]) r0 = fix_bond_history->get_atom_value(i, n, 0);
+  }
+
+  double r = sqrt(rsq);
+  double rinv = 1.0 / r;
+  fforce = k[type] * (r0 - r);
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double delx = x[i][0] - x[j][0];
+  double dely = x[i][1] - x[j][1];
+  double delz = x[i][2] - x[j][2];
+  double delvx = v[i][0] - v[j][0];
+  double delvy = v[i][1] - v[j][1];
+  double delvz = v[i][2] - v[j][2];
+  double dot = delx * delvx + dely * delvy + delz * delvz;
+  fforce -= gamma[type] * dot * rinv;
+  fforce *= rinv;
+
+  if (smooth_flag) {
+    double smooth = (r - r0) / (r0 * ecrit[type]);
+    smooth *= smooth;
+    smooth *= smooth;
+    smooth *= smooth;
+    smooth = 1 - smooth;
+    fforce *= smooth;
+  }
+
+  return 0.0;
+}

src/BPM/bond_bpm_spring.h

@@ -0,0 +1,68 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef BOND_CLASS
+// clang-format off
+BondStyle(bpm/spring,BondBPMSpring);
+// clang-format on
+#else
+
+#ifndef LMP_BOND_BPM_SPRING_H
+#define LMP_BOND_BPM_SPRING_H
+
+#include "bond_bpm.h"
+
+namespace LAMMPS_NS {
+
+class BondBPMSpring : public BondBPM {
+ public:
+  BondBPMSpring(class LAMMPS *);
+  ~BondBPMSpring() override;
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  void settings(int, char **) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, double, int, int, double &) override;
+
+ protected:
+  double *k, *ecrit, *gamma;
+  int smooth_flag;
+
+  void allocate();
+  void store_data();
+  double store_bond(int, int, int);
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Atom missing in BPM bond
+
+Bonded atom cannot be found
+
+E: Incorrect args for bond coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: Bond style bpm requires 1-3 and 1-4 special weights of 1.0
+
+Self-explanatory.
+
+*/

src/BPM/compute_nbond_atom.cpp

@@ -0,0 +1,145 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "compute_nbond_atom.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "update.h"
+
+#include <string.h>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) :
+    Compute(_lmp, narg, arg), nbond(nullptr)
+{
+  if (narg < 3) error->all(FLERR, "Illegal compute nbond/atom command");
+
+  peratom_flag = 1;
+  size_peratom_cols = 0;
+  peatomflag = 1;
+  timeflag = 1;
+  comm_reverse = 1;
+
+  nmax = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeNBondAtom::~ComputeNBondAtom()
+{
+  memory->destroy(nbond);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeNBondAtom::compute_peratom()
+{
+
+  invoked_peratom = update->ntimestep;
+  if (update->eflag_atom != invoked_peratom)
+    error->all(FLERR, "Per-atom nbond was not tallied on needed timestep");
+
+  // grow local nbond array if necessary
+  // needs to be atom->nmax in length
+
+  if (atom->nmax > nmax) {
+    memory->destroy(nbond);
+    nmax = atom->nmax;
+    memory->create(nbond, nmax, "nbond/atom:nbond");
+    vector_atom = nbond;
+  }
+
+  // npair includes ghosts if either newton flag is set
+  //   b/c some bonds/dihedrals call pair::ev_tally with pairwise info
+  // nbond includes ghosts if newton_bond is set
+  // ntotal includes ghosts if either newton flag is set
+  // KSpace includes ghosts if tip4pflag is set
+
+  int nlocal = atom->nlocal;
+  tagint **bond_atom = atom->bond_atom;
+  int **bond_type = atom->bond_type;
+
+  int ntotal = nlocal;
+  if (force->newton) ntotal += atom->nghost;
+
+  // set local nbond array
+  int i, j, k;
+  int *num_bond = atom->num_bond;
+  int newton_bond = force->newton_bond;
+
+  for (i = 0; i < ntotal; i++) nbond[i] = 0;
+
+  for (i = 0; i < nlocal; i++) {
+    for (j = 0; j < num_bond[i]; j++) {
+      if (bond_type[i][j] <= 0) continue;
+
+      k = atom->map(bond_atom[i][j]);
+      if (k < 0) continue;
+
+      nbond[i] += 1;
+      if (newton_bond) nbond[k] += 1;
+    }
+  }
+
+  // communicate ghost nbond between neighbor procs
+  if (force->newton) comm->reverse_comm(this);
+
+  // zero nbond of atoms not in group
+  // only do this after comm since ghost contributions must be included
+  int *mask = atom->mask;
+
+  for (i = 0; i < nlocal; i++)
+    if (!(mask[i] & groupbit)) nbond[i] = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int ComputeNBondAtom::pack_reverse_comm(int n, int first, double *buf)
+{
+  int i, m, last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) buf[m++] = nbond[i];
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeNBondAtom::unpack_reverse_comm(int n, int *list, double *buf)
+{
+  int i, j, m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    nbond[j] += buf[m++];
+  }
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputeNBondAtom::memory_usage()
+{
+  double bytes = nmax * sizeof(double);
+  return bytes;
+}

src/BPM/compute_nbond_atom.h

@@ -0,0 +1,61 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+// clang-format off
+ComputeStyle(nbond/atom,ComputeNBondAtom);
+// clang-format on
+#else
+
+#ifndef LMP_COMPUTE_NBOND_ATOM_H
+#define LMP_COMPUTE_NBOND_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeNBondAtom : public Compute {
+ public:
+  ComputeNBondAtom(class LAMMPS *, int, char **);
+  ~ComputeNBondAtom() override;
+  void init() override {}
+  void compute_peratom() override;
+  int pack_reverse_comm(int, int, double *) override;
+  void unpack_reverse_comm(int, int *, double *) override;
+  double memory_usage() override;
+
+ private:
+  int nmax;
+  double *nbond;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Per-atom energy was not tallied on needed timestep
+
+You are using a thermo keyword that requires potentials to
+have tallied energy, but they didn't on this timestep.  See the
+variable doc page for ideas on how to make this work.
+
+*/

src/BPM/fix_nve_bpm_sphere.cpp

@@ -0,0 +1,157 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_nve_bpm_sphere.h"
+
+#include "atom.h"
+#include "atom_vec.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "math_extra.h"
+
+#include <cmath>
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+using namespace MathExtra;
+
+/* ---------------------------------------------------------------------- */
+
+FixNVEBPMSphere::FixNVEBPMSphere(LAMMPS *_lmp, int narg, char **arg) : FixNVE(_lmp, narg, arg)
+{
+  if (narg < 3) error->all(FLERR, "Illegal fix nve/bpm/sphere command");
+
+  time_integrate = 1;
+
+  // process extra keywords
+  // inertia = moment of inertia prefactor for sphere or disc
+
+  inertia = 0.4;
+
+  int iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "disc") == 0) {
+      inertia = 0.5;
+      if (domain->dimension != 2)
+        error->all(FLERR, "Fix nve/bpm/sphere disc requires 2d simulation");
+      iarg++;
+    } else
+      error->all(FLERR, "Illegal fix nve/bpm/sphere command");
+  }
+
+  inv_inertia = 1.0 / inertia;
+
+  // error checks
+
+  if (!atom->quat_flag || !atom->sphere_flag)
+    error->all(FLERR, "Fix nve/bpm/sphere requires atom style bpm/sphere");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVEBPMSphere::init()
+{
+  FixNVE::init();
+
+  // check that all particles are finite-size spheres
+  // no point particles allowed
+
+  double *radius = atom->radius;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit)
+      if (radius[i] == 0.0) error->one(FLERR, "Fix nve/bpm/sphere requires extended particles");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVEBPMSphere::initial_integrate(int /*vflag*/)
+{
+  double dtq, dtfm, dtirotate, particle_inertia;
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  double **omega = atom->omega;
+  double **torque = atom->torque;
+  double **quat = atom->quat;
+  double *radius = atom->radius;
+  double *rmass = atom->rmass;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  // set timestep here since dt may have changed or come via rRESPA
+  dtq = 0.5 * dtv;
+
+  // update v,x,omega,quat for all particles
+  // d_omega/dt = torque / inertia
+
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      dtfm = dtf / rmass[i];
+      v[i][0] += dtfm * f[i][0];
+      v[i][1] += dtfm * f[i][1];
+      v[i][2] += dtfm * f[i][2];
+      x[i][0] += dtv * v[i][0];
+      x[i][1] += dtv * v[i][1];
+      x[i][2] += dtv * v[i][2];
+
+      particle_inertia = inertia * (radius[i] * radius[i] * rmass[i]);
+      dtirotate = dtf / particle_inertia;
+      omega[i][0] += dtirotate * torque[i][0];
+      omega[i][1] += dtirotate * torque[i][1];
+      omega[i][2] += dtirotate * torque[i][2];
+
+      MathExtra::richardson_sphere(quat[i], omega[i], dtq);
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVEBPMSphere::final_integrate()
+{
+  double dtfm, dtirotate, particle_inertia;
+
+  double **v = atom->v;
+  double **f = atom->f;
+  double **omega = atom->omega;
+  double **torque = atom->torque;
+  double *rmass = atom->rmass;
+  double *radius = atom->radius;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  // update v,omega for all particles
+  // d_omega/dt = torque / inertia
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      dtfm = dtf / rmass[i];
+      v[i][0] += dtfm * f[i][0];
+      v[i][1] += dtfm * f[i][1];
+      v[i][2] += dtfm * f[i][2];
+
+      particle_inertia = inertia * (radius[i] * radius[i] * rmass[i]);
+      dtirotate = dtf / particle_inertia;
+      omega[i][0] += dtirotate * torque[i][0];
+      omega[i][1] += dtirotate * torque[i][1];
+      omega[i][2] += dtirotate * torque[i][2];
+    }
+}

src/BPM/fix_nve_bpm_sphere.h

@@ -0,0 +1,71 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(nve/bpm/sphere,FixNVEBPMSphere);
+// clang-format on
+#else
+
+#ifndef LMP_FIX_NVE_BPM_SPHERE_H
+#define LMP_FIX_NVE_BPM_SPHERE_H
+
+#include "fix_nve.h"
+
+namespace LAMMPS_NS {
+
+class FixNVEBPMSphere : public FixNVE {
+ public:
+  FixNVEBPMSphere(class LAMMPS *, int, char **);
+
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
+
+ protected:
+  double inertia, inv_inertia;
+  int extra;
+  int dlm;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Fix nve/bpm/sphere disc requires 2d simulation
+
+UNDOCUMENTED
+
+E: Fix nve/bpm/sphere requires atom style bpm/sphere
+
+Self-explanatory.
+
+E: Fix nve/bpm/sphere update dipole requires atom attribute mu
+
+An atom style with this attribute is needed.
+
+E: Fix nve/bpm/sphere requires extended particles
+
+This fix can only be used for particles of a finite size.
+
+
+*/

src/BPM/pair_bpm_spring.cpp

@@ -0,0 +1,326 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "pair_bpm_spring.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairBPMSpring::PairBPMSpring(LAMMPS *_lmp) : Pair(_lmp)
+{
+  writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairBPMSpring::~PairBPMSpring()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(k);
+    memory->destroy(cut);
+    memory->destroy(gamma);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairBPMSpring::compute(int eflag, int vflag)
+{
+  int i, j, ii, jj, inum, jnum, itype, jtype;
+  double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
+  double r, rsq, rinv, factor_lj;
+  int *ilist, *jlist, *numneigh, **firstneigh;
+  double vxtmp, vytmp, vztmp, delvx, delvy, delvz, dot, smooth;
+
+  evdwl = 0.0;
+  if (eflag || vflag)
+    ev_setup(eflag, vflag);
+  else
+    evflag = vflag_fdotr = 0;
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+  double *special_lj = force->special_lj;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    vxtmp = v[i][0];
+    vytmp = v[i][1];
+    vztmp = v[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
+
+      if (factor_lj == 0) continue;
+
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx * delx + dely * dely + delz * delz;
+      jtype = type[j];
+
+      if (rsq < cutsq[itype][jtype]) {
+        r = sqrt(rsq);
+
+        rinv = 1.0 / r;
+        fpair = k[itype][jtype] * (cut[itype][jtype] - r);
+
+        smooth = rsq / cutsq[itype][jtype];
+        smooth *= smooth;
+        smooth *= smooth;
+        smooth = 1.0 - smooth;
+        delvx = vxtmp - v[j][0];
+        delvy = vytmp - v[j][1];
+        delvz = vztmp - v[j][2];
+        dot = delx * delvx + dely * delvy + delz * delvz;
+        fpair -= gamma[itype][jtype] * dot * smooth * rinv;
+
+        fpair *= factor_lj * rinv;
+        if (eflag) evdwl = 0.0;
+
+        f[i][0] += delx * fpair;
+        f[i][1] += dely * fpair;
+        f[i][2] += delz * fpair;
+
+        if (newton_pair || j < nlocal) {
+          f[j][0] -= delx * fpair;
+          f[j][1] -= dely * fpair;
+          f[j][2] -= delz * fpair;
+        }
+
+        if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
+      }
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairBPMSpring::allocate()
+{
+  allocated = 1;
+  const int np1 = atom->ntypes + 1;
+
+  memory->create(setflag, np1, np1, "pair:setflag");
+  for (int i = 1; i < np1; i++)
+    for (int j = i; j < np1; j++) setflag[i][j] = 0;
+
+  memory->create(cutsq, np1, np1, "pair:cutsq");
+
+  memory->create(k, np1, np1, "pair:k");
+  memory->create(cut, np1, np1, "pair:cut");
+  memory->create(gamma, np1, np1, "pair:gamma");
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairBPMSpring::settings(int narg, char ** /*arg*/)
+{
+  if (narg != 0) error->all(FLERR, "Illegal pair_style command");
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairBPMSpring::coeff(int narg, char **arg)
+{
+  if (narg != 5) error->all(FLERR, "Incorrect args for pair coefficients");
+  if (!allocated) allocate();
+
+  int ilo, ihi, jlo, jhi;
+  utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
+  utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
+
+  double k_one = utils::numeric(FLERR, arg[2], false, lmp);
+  double cut_one = utils::numeric(FLERR, arg[3], false, lmp);
+  double gamma_one = utils::numeric(FLERR, arg[4], false, lmp);
+
+  if (cut_one <= 0.0) error->all(FLERR, "Incorrect args for pair coefficients");
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo, i); j <= jhi; j++) {
+      k[i][j] = k_one;
+      cut[i][j] = cut_one;
+      gamma[i][j] = gamma_one;
+
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairBPMSpring::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0) {
+    cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
+    k[i][j] = mix_energy(k[i][i], k[j][j], cut[i][i], cut[j][j]);
+    gamma[i][j] = mix_energy(gamma[i][i], gamma[j][j], cut[i][i], cut[j][j]);
+  }
+
+  cut[j][i] = cut[i][j];
+  k[j][i] = k[i][j];
+  gamma[j][i] = gamma[i][j];
+
+  return cut[i][j];
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairBPMSpring::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i, j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j], sizeof(int), 1, fp);
+      if (setflag[i][j]) {
+        fwrite(&k[i][j], sizeof(double), 1, fp);
+        fwrite(&cut[i][j], sizeof(double), 1, fp);
+        fwrite(&gamma[i][j], sizeof(double), 1, fp);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairBPMSpring::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i, j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) fread(&setflag[i][j], sizeof(int), 1, fp);
+      MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+          fread(&k[i][j], sizeof(double), 1, fp);
+          fread(&cut[i][j], sizeof(double), 1, fp);
+          fread(&gamma[i][j], sizeof(double), 1, fp);
+        }
+        MPI_Bcast(&k[i][j], 1, MPI_DOUBLE, 0, world);
+        MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
+        MPI_Bcast(&gamma[i][j], 1, MPI_DOUBLE, 0, world);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairBPMSpring::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp, "%d %g %g %g\n", i, k[i][i], cut[i][i], gamma[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairBPMSpring::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp, "%d %d %g %g %g\n", i, j, k[i][j], cut[i][j], gamma[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairBPMSpring::single(int i, int j, int itype, int jtype, double rsq, double /*factor_coul*/,
+                             double factor_lj, double &fforce)
+{
+  double fpair, r, rinv;
+  double delx, dely, delz, delvx, delvy, delvz, dot, smooth;
+
+  if (rsq > cutsq[itype][jtype]) return 0.0;
+
+  double **x = atom->x;
+  double **v = atom->v;
+
+  r = sqrt(rsq);
+  rinv = 1.0 / r;
+
+  fpair = k[itype][jtype] * (cut[itype][jtype] - r);
+
+  smooth = rsq / cutsq[itype][jtype];
+  smooth *= smooth;
+  smooth = 1.0 - smooth;
+  delx = x[i][0] - x[j][0];
+  dely = x[i][1] - x[j][1];
+  delz = x[i][2] - x[j][2];
+  delvx = v[i][0] - v[j][0];
+  delvy = v[i][1] - v[j][1];
+  delvz = v[i][2] - v[j][2];
+  dot = delx * delvx + dely * delvy + delz * delvz;
+  fpair -= gamma[itype][jtype] * dot * rinv * smooth;
+
+  fpair *= factor_lj;
+  fforce = fpair;
+
+  return 0.0;
+}

src/BPM/pair_bpm_spring.h

@@ -0,0 +1,64 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+// clang-format off
+PairStyle(bpm/spring,PairBPMSpring);
+// clang-format on
+#else
+
+#ifndef LMP_PAIR_BPM_SPRING_H
+#define LMP_PAIR_BPM_SPRING_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairBPMSpring : public Pair {
+ public:
+  PairBPMSpring(class LAMMPS *);
+  ~PairBPMSpring() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
+
+ protected:
+  double **k, **cut, **gamma;
+
+  void allocate();
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+*/

src/GRANULAR/fix_pour.cpp

@@ -136,8 +136,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR,"Invalid atom type in fix pour mol command");
 
       if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols)
-        error->all(FLERR,"Fix pour molecule template ID must be same "
+        error->all(FLERR,"Fix pour molecule template ID must be same as atom style template ID");
-                   "as atom style template ID");
       onemols[i]->check_attributes(0);
 
       // fix pour uses geoemetric center of molecule for insertion

src/GRANULAR/pair_gran_hertz_history.cpp

@@ -45,7 +45,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
 {
   int i,j,ii,jj,inum,jnum;
   double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
-  double radi,radj,radsum,rsq,r,rinv,rsqinv;
+  double radi,radj,radsum,rsq,r,rinv,rsqinv,factor_lj;
   double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
   double wr1,wr2,wr3;
   double vtr1,vtr2,vtr3,vrel;
@@ -91,6 +91,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
+  double *special_lj = force->special_lj;
 
   inum = list->inum;
   ilist = list->ilist;
@@ -114,8 +115,11 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
 
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
       j &= NEIGHMASK;
 
+      if (factor_lj == 0) continue;
+
       delx = xtmp - x[j][0];
       dely = ytmp - x[j][1];
       delz = ztmp - x[j][2];
@@ -247,6 +251,9 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
         fx = delx*ccel + fs1;
         fy = dely*ccel + fs2;
         fz = delz*ccel + fs3;
+        fx *= factor_lj;
+        fy *= factor_lj;
+        fz *= factor_lj;
         f[i][0] += fx;
         f[i][1] += fy;
         f[i][2] += fz;
@@ -254,6 +261,9 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
         tor1 = rinv * (dely*fs3 - delz*fs2);
         tor2 = rinv * (delz*fs1 - delx*fs3);
         tor3 = rinv * (delx*fs2 - dely*fs1);
+        tor1 *= factor_lj;
+        tor2 *= factor_lj;
+        tor3 *= factor_lj;
         torque[i][0] -= radi*tor1;
         torque[i][1] -= radi*tor2;
         torque[i][2] -= radi*tor3;

src/GRANULAR/pair_gran_hooke.cpp

@@ -42,7 +42,7 @@ void PairGranHooke::compute(int eflag, int vflag)
 {
   int i,j,ii,jj,inum,jnum;
   double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
-  double radi,radj,radsum,rsq,r,rinv,rsqinv;
+  double radi,radj,radsum,rsq,r,rinv,rsqinv,factor_lj;
   double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
   double wr1,wr2,wr3;
   double vtr1,vtr2,vtr3,vrel;
@@ -82,6 +82,7 @@ void PairGranHooke::compute(int eflag, int vflag)
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
+  double *special_lj = force->special_lj;
 
   inum = list->inum;
   ilist = list->ilist;
@@ -101,8 +102,11 @@ void PairGranHooke::compute(int eflag, int vflag)
 
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
       j &= NEIGHMASK;
 
+      if (factor_lj == 0) continue;
+
       delx = xtmp - x[j][0];
       dely = ytmp - x[j][1];
       delz = ztmp - x[j][2];
@@ -187,6 +191,9 @@ void PairGranHooke::compute(int eflag, int vflag)
         fx = delx*ccel + fs1;
         fy = dely*ccel + fs2;
         fz = delz*ccel + fs3;
+        fx *= factor_lj;
+        fy *= factor_lj;
+        fz *= factor_lj;
         f[i][0] += fx;
         f[i][1] += fy;
         f[i][2] += fz;
@@ -194,6 +201,9 @@ void PairGranHooke::compute(int eflag, int vflag)
         tor1 = rinv * (dely*fs3 - delz*fs2);
         tor2 = rinv * (delz*fs1 - delx*fs3);
         tor3 = rinv * (delx*fs2 - dely*fs1);
+        tor1 *= factor_lj;
+        tor2 *= factor_lj;
+        tor3 *= factor_lj;
         torque[i][0] -= radi*tor1;
         torque[i][1] -= radi*tor2;
         torque[i][2] -= radi*tor3;

src/GRANULAR/pair_gran_hooke_history.cpp

@@ -103,7 +103,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
 {
   int i, j, ii, jj, inum, jnum;
   double xtmp, ytmp, ztmp, delx, dely, delz, fx, fy, fz;
-  double radi, radj, radsum, rsq, r, rinv, rsqinv;
+  double radi, radj, radsum, rsq, r, rinv, rsqinv, factor_lj;
   double vr1, vr2, vr3, vnnr, vn1, vn2, vn3, vt1, vt2, vt3;
   double wr1, wr2, wr3;
   double vtr1, vtr2, vtr3, vrel;
@@ -151,6 +151,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
+  double *special_lj = force->special_lj;
 
   inum = list->inum;
   ilist = list->ilist;
@@ -174,8 +175,11 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
 
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
       j &= NEIGHMASK;
 
+      if (factor_lj == 0) continue;
+
       delx = xtmp - x[j][0];
       dely = ytmp - x[j][1];
       delz = ztmp - x[j][2];
@@ -306,6 +310,9 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
         fx = delx * ccel + fs1;
         fy = dely * ccel + fs2;
         fz = delz * ccel + fs3;
+        fx *= factor_lj;
+        fy *= factor_lj;
+        fz *= factor_lj;
         f[i][0] += fx;
         f[i][1] += fy;
         f[i][2] += fz;
@@ -313,6 +320,9 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
         tor1 = rinv * (dely * fs3 - delz * fs2);
         tor2 = rinv * (delz * fs1 - delx * fs3);
         tor3 = rinv * (delx * fs2 - dely * fs1);
+        tor1 *= factor_lj;
+        tor2 *= factor_lj;
+        tor3 *= factor_lj;
         torque[i][0] -= radi * tor1;
         torque[i][1] -= radi * tor2;
         torque[i][2] -= radi * tor3;

src/GRANULAR/pair_granular.cpp

@@ -150,7 +150,7 @@ void PairGranular::compute(int eflag, int vflag)
 {
   int i,j,ii,jj,inum,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,nx,ny,nz;
-  double radi,radj,radsum,rsq,r,rinv;
+  double radi,radj,radsum,rsq,r,rinv,factor_lj;
   double Reff, delta, dR, dR2, dist_to_contact;
 
   double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
@@ -222,6 +222,7 @@ void PairGranular::compute(int eflag, int vflag)
   double *rmass = atom->rmass;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
+  double *special_lj = force->special_lj;
 
   inum = list->inum;
   ilist = list->ilist;
@@ -249,8 +250,11 @@ void PairGranular::compute(int eflag, int vflag)
 
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
       j &= NEIGHMASK;
 
+      if (factor_lj == 0) continue;
+
       delx = xtmp - x[j][0];
       dely = ytmp - x[j][1];
       delz = ztmp - x[j][2];
@@ -651,6 +655,9 @@ void PairGranular::compute(int eflag, int vflag)
         fx = nx*Fntot + fs1;
         fy = ny*Fntot + fs2;
         fz = nz*Fntot + fs3;
+        fx *= factor_lj;
+        fy *= factor_lj;
+        fz *= factor_lj;
 
         f[i][0] += fx;
         f[i][1] += fy;
@@ -659,6 +666,9 @@ void PairGranular::compute(int eflag, int vflag)
         tor1 = ny*fs3 - nz*fs2;
         tor2 = nz*fs1 - nx*fs3;
         tor3 = nx*fs2 - ny*fs1;
+        tor1 *= factor_lj;
+        tor2 *= factor_lj;
+        tor3 *= factor_lj;
 
         dist_to_contact = radi-0.5*delta;
         torque[i][0] -= dist_to_contact*tor1;
@@ -666,9 +676,9 @@ void PairGranular::compute(int eflag, int vflag)
         torque[i][2] -= dist_to_contact*tor3;
 
         if (twist_model[itype][jtype] != TWIST_NONE) {
-          tortwist1 = magtortwist * nx;
+          tortwist1 = magtortwist * nx * factor_lj;
-          tortwist2 = magtortwist * ny;
+          tortwist2 = magtortwist * ny * factor_lj;
-          tortwist3 = magtortwist * nz;
+          tortwist3 = magtortwist * nz * factor_lj;
 
           torque[i][0] += tortwist1;
           torque[i][1] += tortwist2;
@@ -676,9 +686,9 @@ void PairGranular::compute(int eflag, int vflag)
         }
 
         if (roll_model[itype][jtype] != ROLL_NONE) {
-          torroll1 = Reff*(ny*fr3 - nz*fr2); // n cross fr
+          torroll1 = Reff*(ny*fr3 - nz*fr2) * factor_lj; // n cross fr
-          torroll2 = Reff*(nz*fr1 - nx*fr3);
+          torroll2 = Reff*(nz*fr1 - nx*fr3) * factor_lj;
-          torroll3 = Reff*(nx*fr2 - ny*fr1);
+          torroll3 = Reff*(nx*fr2 - ny*fr1) * factor_lj;
 
           torque[i][0] += torroll1;
           torque[i][1] += torroll2;

src/KOKKOS/pair_sw_kokkos.cpp

@@ -78,8 +78,6 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   eflag = eflag_in;
   vflag = vflag_in;
 
-  if (neighflag == FULL) no_virial_fdotr_compute = 1;
-
   ev_init(eflag,vflag,0);
 
   // reallocate per-atom arrays if necessary
@@ -134,39 +132,27 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
   int max_neighs = d_neighbors.extent(1);
 
-  if (((int) d_neighbors_short.extent(1) != max_neighs) ||
+  if (((int) d_neighbors_short.extent(1) < max_neighs) ||
-      ((int) d_neighbors_short.extent(0) != ignum)) {
+      ((int) d_neighbors_short.extent(0) < ignum)) {
-    d_neighbors_short = Kokkos::View<int**,DeviceType>("SW::neighbors_short",ignum,max_neighs);
+    d_neighbors_short = Kokkos::View<int**,DeviceType>("SW::neighbors_short",ignum*1.2,max_neighs);
   }
-  if ((int)d_numneigh_short.extent(0)!=ignum)
+  if ((int)d_numneigh_short.extent(0) < ignum)
-    d_numneigh_short = Kokkos::View<int*,DeviceType>("SW::numneighs_short",ignum);
+    d_numneigh_short = Kokkos::View<int*,DeviceType>("SW::numneighs_short",ignum*1.2);
-  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairSWComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);
+  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairSWComputeShortNeigh>(0,inum), *this);
 
   // loop over neighbor list of my atoms
 
   if (neighflag == HALF) {
     if (evflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairSWComputeHalf<HALF,1> >(0,inum),*this,ev);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairSWCompute<HALF,1> >(0,inum),*this,ev);
     else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairSWComputeHalf<HALF,0> >(0,inum),*this);
+      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairSWCompute<HALF,0> >(0,inum),*this);
     ev_all += ev;
   } else if (neighflag == HALFTHREAD) {
     if (evflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairSWComputeHalf<HALFTHREAD,1> >(0,inum),*this,ev);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairSWCompute<HALFTHREAD,1> >(0,inum),*this,ev);
     else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairSWComputeHalf<HALFTHREAD,0> >(0,inum),*this);
+      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairSWCompute<HALFTHREAD,0> >(0,inum),*this);
-    ev_all += ev;
-  } else if (neighflag == FULL) {
-    if (evflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairSWComputeFullA<FULL,1> >(0,inum),*this,ev);
-    else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairSWComputeFullA<FULL,0> >(0,inum),*this);
-    ev_all += ev;
-
-    if (evflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairSWComputeFullB<FULL,1> >(0,ignum),*this,ev);
-    else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairSWComputeFullB<FULL,0> >(0,ignum),*this);
     ev_all += ev;
   }
 
@@ -216,6 +202,7 @@ template<class DeviceType>
 KOKKOS_INLINE_FUNCTION
 void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeShortNeigh, const int& ii) const {
     const int i = d_ilist[ii];
+    const int itype = d_map[type[i]];
     const X_FLOAT xtmp = x(i,0);
     const X_FLOAT ytmp = x(i,1);
     const X_FLOAT ztmp = x(i,2);
@@ -225,18 +212,20 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeShortNeigh, const int&
     for (int jj = 0; jj < jnum; jj++) {
       int j = d_neighbors(i,jj);
       j &= NEIGHMASK;
+      const int jtype = d_map[type[j]];
 
       const X_FLOAT delx = xtmp - x(j,0);
       const X_FLOAT dely = ytmp - x(j,1);
       const X_FLOAT delz = ztmp - x(j,2);
       const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
 
-      if (rsq < cutmax*cutmax) {
+      const int ijparam = d_elem3param(itype,jtype,jtype);
-        d_neighbors_short(i,inside) = j;
+      if (rsq < d_params[ijparam].cutsq) {
+        d_neighbors_short(ii,inside) = j;
         inside++;
       }
     }
-    d_numneigh_short(i) = inside;
+    d_numneigh_short(ii) = inside;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -244,7 +233,7 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeShortNeigh, const int&
 template<class DeviceType>
 template<int NEIGHFLAG, int EVFLAG>
 KOKKOS_INLINE_FUNCTION
-void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
+void PairSWKokkos<DeviceType>::operator()(TagPairSWCompute<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
 
   // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
 
@@ -264,15 +253,14 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>
 
   // two-body interactions, skip half of them
 
-  const int jnum = d_numneigh_short[i];
+  const int jnum = d_numneigh_short[ii];
 
   F_FLOAT fxtmpi = 0.0;
   F_FLOAT fytmpi = 0.0;
   F_FLOAT fztmpi = 0.0;
 
   for (int jj = 0; jj < jnum; jj++) {
-    int j = d_neighbors_short(i,jj);
+    int j = d_neighbors_short(ii,jj);
-    j &= NEIGHMASK;
     const tagint jtag = tag[j];
 
     if (itag > jtag) {
@@ -293,7 +281,6 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>
     const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
 
     const int ijparam = d_elem3param(itype,jtype,jtype);
-    if (rsq >= d_params[ijparam].cutsq) continue;
 
     twobody(d_params[ijparam],rsq,fpair,eflag,evdwl);
 
@@ -313,23 +300,20 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>
   const int jnumm1 = jnum - 1;
 
   for (int jj = 0; jj < jnumm1; jj++) {
-    int j = d_neighbors_short(i,jj);
+    int j = d_neighbors_short(ii,jj);
-    j &= NEIGHMASK;
     const int jtype = d_map[type[j]];
     const int ijparam = d_elem3param(itype,jtype,jtype);
     delr1[0] = x(j,0) - xtmp;
     delr1[1] = x(j,1) - ytmp;
     delr1[2] = x(j,2) - ztmp;
     const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
-    if (rsq1 >= d_params[ijparam].cutsq) continue;
 
     F_FLOAT fxtmpj = 0.0;
     F_FLOAT fytmpj = 0.0;
     F_FLOAT fztmpj = 0.0;
 
     for (int kk = jj+1; kk < jnum; kk++) {
-      int k = d_neighbors_short(i,kk);
+      int k = d_neighbors_short(ii,kk);
-      k &= NEIGHMASK;
       const int ktype = d_map[type[k]];
       const int ikparam = d_elem3param(itype,ktype,ktype);
       const int ijkparam = d_elem3param(itype,jtype,ktype);
@@ -339,8 +323,6 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>
       delr2[2] = x(k,2) - ztmp;
       const F_FLOAT rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
 
-      if (rsq2 >= d_params[ikparam].cutsq) continue;
-
       threebody_kk(d_params[ijparam],d_params[ikparam],d_params[ijkparam],
                 rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
 
@@ -373,203 +355,9 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>
 template<class DeviceType>
 template<int NEIGHFLAG, int EVFLAG>
 KOKKOS_INLINE_FUNCTION
-void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>, const int &ii) const {
+void PairSWKokkos<DeviceType>::operator()(TagPairSWCompute<NEIGHFLAG,EVFLAG>, const int &ii) const {
   EV_FLOAT ev;
-  this->template operator()<NEIGHFLAG,EVFLAG>(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>(), ii, ev);
+  this->template operator()<NEIGHFLAG,EVFLAG>(TagPairSWCompute<NEIGHFLAG,EVFLAG>(), ii, ev);
-}
-
-/* ---------------------------------------------------------------------- */
-
-template<class DeviceType>
-template<int NEIGHFLAG, int EVFLAG>
-KOKKOS_INLINE_FUNCTION
-void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullA<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
-
-  F_FLOAT delr1[3],delr2[3],fj[3],fk[3];
-  F_FLOAT evdwl = 0.0;
-  F_FLOAT fpair = 0.0;
-
-  const int i = d_ilist[ii];
-
-  const int itype = d_map[type[i]];
-  const X_FLOAT xtmp = x(i,0);
-  const X_FLOAT ytmp = x(i,1);
-  const X_FLOAT ztmp = x(i,2);
-
-  // two-body interactions
-
-  const int jnum = d_numneigh_short[i];
-
-  F_FLOAT fxtmpi = 0.0;
-  F_FLOAT fytmpi = 0.0;
-  F_FLOAT fztmpi = 0.0;
-
-  for (int jj = 0; jj < jnum; jj++) {
-    int j = d_neighbors_short(i,jj);
-    j &= NEIGHMASK;
-
-    const int jtype = d_map[type[j]];
-
-    const X_FLOAT delx = xtmp - x(j,0);
-    const X_FLOAT dely = ytmp - x(j,1);
-    const X_FLOAT delz = ztmp - x(j,2);
-    const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
-
-    const int ijparam = d_elem3param(itype,jtype,jtype);
-
-    if (rsq >= d_params[ijparam].cutsq) continue;
-
-    twobody(d_params[ijparam],rsq,fpair,eflag,evdwl);
-
-    fxtmpi += delx*fpair;
-    fytmpi += dely*fpair;
-    fztmpi += delz*fpair;
-
-    if (EVFLAG) {
-      if (eflag) ev.evdwl += 0.5*evdwl;
-      if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG>(ev,i,j,evdwl,fpair,delx,dely,delz);
-    }
-  }
-
-  const int jnumm1 = jnum - 1;
-
-  for (int jj = 0; jj < jnumm1; jj++) {
-    int j = d_neighbors_short(i,jj);
-    j &= NEIGHMASK;
-    const int jtype = d_map[type[j]];
-    const int ijparam = d_elem3param(itype,jtype,jtype);
-    delr1[0] = x(j,0) - xtmp;
-    delr1[1] = x(j,1) - ytmp;
-    delr1[2] = x(j,2) - ztmp;
-    const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
-
-    if (rsq1 >= d_params[ijparam].cutsq) continue;
-
-    for (int kk = jj+1; kk < jnum; kk++) {
-      int k = d_neighbors_short(i,kk);
-      k &= NEIGHMASK;
-      const int ktype = d_map[type[k]];
-      const int ikparam = d_elem3param(itype,ktype,ktype);
-      const int ijkparam = d_elem3param(itype,jtype,ktype);
-
-      delr2[0] = x(k,0) - xtmp;
-      delr2[1] = x(k,1) - ytmp;
-      delr2[2] = x(k,2) - ztmp;
-      const F_FLOAT rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
-
-      if (rsq2 >= d_params[ikparam].cutsq) continue;
-
-      threebody_kk(d_params[ijparam],d_params[ikparam],d_params[ijkparam],
-                rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
-
-      fxtmpi -= fj[0] + fk[0];
-      fytmpi -= fj[1] + fk[1];
-      fztmpi -= fj[2] + fk[2];
-
-      if (EVFLAG) {
-        if (eflag) ev.evdwl += evdwl;
-        if (vflag_either || eflag_atom) this->template ev_tally3<NEIGHFLAG>(ev,i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
-      }
-    }
-  }
-
-  f(i,0) += fxtmpi;
-  f(i,1) += fytmpi;
-  f(i,2) += fztmpi;
-}
-
-template<class DeviceType>
-template<int NEIGHFLAG, int EVFLAG>
-KOKKOS_INLINE_FUNCTION
-void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullA<NEIGHFLAG,EVFLAG>, const int &ii) const {
-  EV_FLOAT ev;
-  this->template operator()<NEIGHFLAG,EVFLAG>(TagPairSWComputeFullA<NEIGHFLAG,EVFLAG>(), ii, ev);
-}
-
-/* ---------------------------------------------------------------------- */
-
-template<class DeviceType>
-template<int NEIGHFLAG, int EVFLAG>
-KOKKOS_INLINE_FUNCTION
-void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullB<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
-
-  F_FLOAT delr1[3],delr2[3],fj[3],fk[3];
-  F_FLOAT evdwl = 0.0;
-
-  const int i = d_ilist[ii];
-
-  const int itype = d_map[type[i]];
-  const X_FLOAT xtmpi = x(i,0);
-  const X_FLOAT ytmpi = x(i,1);
-  const X_FLOAT ztmpi = x(i,2);
-
-  const int jnum = d_numneigh_short[i];
-
-  F_FLOAT fxtmpi = 0.0;
-  F_FLOAT fytmpi = 0.0;
-  F_FLOAT fztmpi = 0.0;
-
-  for (int jj = 0; jj < jnum; jj++) {
-    int j = d_neighbors_short(i,jj);
-    j &= NEIGHMASK;
-    if (j >= nlocal) continue;
-    const int jtype = d_map[type[j]];
-    const int jiparam = d_elem3param(jtype,itype,itype);
-    const X_FLOAT xtmpj = x(j,0);
-    const X_FLOAT ytmpj = x(j,1);
-    const X_FLOAT ztmpj = x(j,2);
-
-    delr1[0] = xtmpi - xtmpj;
-    delr1[1] = ytmpi - ytmpj;
-    delr1[2] = ztmpi - ztmpj;
-    const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
-
-    if (rsq1 >= d_params[jiparam].cutsq) continue;
-
-    const int j_jnum = d_numneigh_short[j];
-
-    for (int kk = 0; kk < j_jnum; kk++) {
-      int k = d_neighbors_short(j,kk);
-      k &= NEIGHMASK;
-      if (k == i) continue;
-      const int ktype = d_map[type[k]];
-      const int jkparam = d_elem3param(jtype,ktype,ktype);
-      const int jikparam = d_elem3param(jtype,itype,ktype);
-
-      delr2[0] = x(k,0) - xtmpj;
-      delr2[1] = x(k,1) - ytmpj;
-      delr2[2] = x(k,2) - ztmpj;
-      const F_FLOAT rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
-
-      if (rsq2 >= d_params[jkparam].cutsq) continue;
-
-      if (vflag_atom)
-        threebody_kk(d_params[jiparam],d_params[jkparam],d_params[jikparam],
-                  rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
-      else
-        threebodyj(d_params[jiparam],d_params[jkparam],d_params[jikparam],
-                  rsq1,rsq2,delr1,delr2,fj);
-
-      fxtmpi += fj[0];
-      fytmpi += fj[1];
-      fztmpi += fj[2];
-
-      if (EVFLAG)
-        if (vflag_atom || eflag_atom) ev_tally3_atom(ev,i,evdwl,0.0,fj,fk,delr1,delr2);
-    }
-  }
-
-  f(i,0) += fxtmpi;
-  f(i,1) += fytmpi;
-  f(i,2) += fztmpi;
-}
-
-template<class DeviceType>
-template<int NEIGHFLAG, int EVFLAG>
-KOKKOS_INLINE_FUNCTION
-void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullB<NEIGHFLAG,EVFLAG>, const int &ii) const {
-  EV_FLOAT ev;
-  this->template operator()<NEIGHFLAG,EVFLAG>(TagPairSWComputeFullB<NEIGHFLAG,EVFLAG>(), ii, ev);
 }
 
 /* ----------------------------------------------------------------------
@@ -613,9 +401,9 @@ void PairSWKokkos<DeviceType>::init_style()
   request->set_kokkos_host(std::is_same<DeviceType,LMPHostType>::value &&
                            !std::is_same<DeviceType,LMPDeviceType>::value);
   request->set_kokkos_device(std::is_same<DeviceType,LMPDeviceType>::value);
-  // always request a full neighbor list
+
-  request->enable_full();
+  if (neighflag == FULL)
-  if (neighflag == FULL) request->enable_ghost();
+    error->all(FLERR,"Must use half neighbor list style with pair sw/kk");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -732,52 +520,6 @@ void PairSWKokkos<DeviceType>::threebody_kk(const Param& paramij, const Param& p
 
 /* ---------------------------------------------------------------------- */
 
-template<class DeviceType>
-KOKKOS_INLINE_FUNCTION
-void PairSWKokkos<DeviceType>::threebodyj(const Param& paramij, const Param& paramik, const Param& paramijk,
-                       const F_FLOAT& rsq1, const F_FLOAT& rsq2, F_FLOAT *delr1, F_FLOAT *delr2, F_FLOAT *fj) const
-{
-  F_FLOAT r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1;
-  F_FLOAT r2, rainv2, gsrainv2, expgsrainv2;
-  F_FLOAT rinv12,cs,delcs,delcssq,facexp,facrad,frad1;
-  F_FLOAT facang,facang12,csfacang,csfac1;
-
-  r1 = sqrt(rsq1);
-  rinvsq1 = 1.0/rsq1;
-  rainv1 = 1.0/(r1 - paramij.cut);
-  gsrainv1 = paramij.sigma_gamma * rainv1;
-  gsrainvsq1 = gsrainv1*rainv1/r1;
-  expgsrainv1 = exp(gsrainv1);
-
-  r2 = sqrt(rsq2);
-  rainv2 = 1.0/(r2 - paramik.cut);
-  gsrainv2 = paramik.sigma_gamma * rainv2;
-  expgsrainv2 = exp(gsrainv2);
-
-  rinv12 = 1.0/(r1*r2);
-  cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12;
-  delcs = cs - paramijk.costheta;
-  delcssq = delcs*delcs;
-
-  facexp = expgsrainv1*expgsrainv2;
-
-  // facrad = sqrt(paramij.lambda_epsilon*paramik.lambda_epsilon) *
-  //          facexp*delcssq;
-
-  facrad = paramijk.lambda_epsilon * facexp*delcssq;
-  frad1 = facrad*gsrainvsq1;
-  facang = paramijk.lambda_epsilon2 * facexp*delcs;
-  facang12 = rinv12*facang;
-  csfacang = cs*facang;
-  csfac1 = rinvsq1*csfacang;
-
-  fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12;
-  fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12;
-  fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 template<int NEIGHFLAG>
 KOKKOS_INLINE_FUNCTION
@@ -785,7 +527,6 @@ void PairSWKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j
       const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
                 const F_FLOAT &dely, const F_FLOAT &delz) const
 {
-  const int VFLAG = vflag_either;
 
   // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
 
@@ -798,11 +539,10 @@ void PairSWKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j
   if (eflag_atom) {
     const E_FLOAT epairhalf = 0.5 * epair;
     a_eatom[i] += epairhalf;
-    if (NEIGHFLAG != FULL)
     a_eatom[j] += epairhalf;
   }
 
-  if (VFLAG) {
+  if (vflag_either) {
     const E_FLOAT v0 = delx*delx*fpair;
     const E_FLOAT v1 = dely*dely*fpair;
     const E_FLOAT v2 = delz*delz*fpair;
@@ -811,21 +551,12 @@ void PairSWKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j
     const E_FLOAT v5 = dely*delz*fpair;
 
     if (vflag_global) {
-      if (NEIGHFLAG != FULL) {
       ev.v[0] += v0;
       ev.v[1] += v1;
       ev.v[2] += v2;
       ev.v[3] += v3;
       ev.v[4] += v4;
       ev.v[5] += v5;
-      } else {
-        ev.v[0] += 0.5*v0;
-        ev.v[1] += 0.5*v1;
-        ev.v[2] += 0.5*v2;
-        ev.v[3] += 0.5*v3;
-        ev.v[4] += 0.5*v4;
-        ev.v[5] += 0.5*v5;
-      }
     }
 
     if (vflag_atom) {
@@ -836,7 +567,6 @@ void PairSWKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j
       a_vatom(i,4) += 0.5*v4;
       a_vatom(i,5) += 0.5*v5;
 
-      if (NEIGHFLAG != FULL) {
       a_vatom(j,0) += 0.5*v0;
       a_vatom(j,1) += 0.5*v1;
       a_vatom(j,2) += 0.5*v2;
@@ -845,7 +575,6 @@ void PairSWKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j
       a_vatom(j,5) += 0.5*v5;
     }
   }
-  }
 }
 
 /* ----------------------------------------------------------------------
@@ -863,8 +592,6 @@ void PairSWKokkos<DeviceType>::ev_tally3(EV_FLOAT &ev, const int &i, const int &
 {
   F_FLOAT epairthird,v[6];
 
-  const int VFLAG = vflag_either;
-
   // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
 
   auto v_eatom = ScatterViewHelper<NeedDup_v<NEIGHFLAG,DeviceType>,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
@@ -876,13 +603,11 @@ void PairSWKokkos<DeviceType>::ev_tally3(EV_FLOAT &ev, const int &i, const int &
   if (eflag_atom) {
     epairthird = THIRD * (evdwl + ecoul);
     a_eatom[i] += epairthird;
-    if (NEIGHFLAG != FULL) {
     a_eatom[j] += epairthird;
     a_eatom[k] += epairthird;
   }
-  }
 
-  if (VFLAG) {
+  if (vflag_either) {
     v[0] = drji[0]*fj[0] + drki[0]*fk[0];
     v[1] = drji[1]*fj[1] + drki[1]*fk[1];
     v[2] = drji[2]*fj[2] + drki[2]*fk[2];
@@ -904,7 +629,6 @@ void PairSWKokkos<DeviceType>::ev_tally3(EV_FLOAT &ev, const int &i, const int &
       a_vatom(i,2) += THIRD*v[2]; a_vatom(i,3) += THIRD*v[3];
       a_vatom(i,4) += THIRD*v[4]; a_vatom(i,5) += THIRD*v[5];
 
-      if (NEIGHFLAG != FULL) {
       a_vatom(j,0) += THIRD*v[0]; a_vatom(j,1) += THIRD*v[1];
       a_vatom(j,2) += THIRD*v[2]; a_vatom(j,3) += THIRD*v[3];
       a_vatom(j,4) += THIRD*v[4]; a_vatom(j,5) += THIRD*v[5];
@@ -914,7 +638,6 @@ void PairSWKokkos<DeviceType>::ev_tally3(EV_FLOAT &ev, const int &i, const int &
       a_vatom(k,4) += THIRD*v[4]; a_vatom(k,5) += THIRD*v[5];
     }
   }
-  }
 }
 
 /* ----------------------------------------------------------------------
@@ -931,14 +654,12 @@ void PairSWKokkos<DeviceType>::ev_tally3_atom(EV_FLOAT & /*ev*/, const int &i,
 {
   F_FLOAT epairthird,v[6];
 
-  const int VFLAG = vflag_either;
-
   if (eflag_atom) {
     epairthird = THIRD * (evdwl + ecoul);
     d_eatom[i] += epairthird;
   }
 
-  if (VFLAG) {
+  if (vflag_either) {
     v[0] = drji[0]*fj[0] + drki[0]*fk[0];
     v[1] = drji[1]*fj[1] + drki[1]*fk[1];
     v[2] = drji[2]*fj[2] + drki[2]*fk[2];

src/KOKKOS/pair_sw_kokkos.h

@@ -27,13 +27,7 @@ PairStyle(sw/kk/host,PairSWKokkos<LMPHostType>);
 #include "pair_kokkos.h"
 
 template<int NEIGHFLAG, int EVFLAG>
-struct TagPairSWComputeHalf{};
+struct TagPairSWCompute{};
-
-template<int NEIGHFLAG, int EVFLAG>
-struct TagPairSWComputeFullA{};
-
-template<int NEIGHFLAG, int EVFLAG>
-struct TagPairSWComputeFullB{};
 
 struct TagPairSWComputeShortNeigh{};
 
@@ -42,7 +36,7 @@ namespace LAMMPS_NS {
 template<class DeviceType>
 class PairSWKokkos : public PairSW {
  public:
-  enum {EnabledNeighFlags=FULL};
+  enum {EnabledNeighFlags=HALF|HALFTHREAD};
   enum {COUL_FLAG=0};
   typedef DeviceType device_type;
   typedef ArrayTypes<DeviceType> AT;
@@ -56,27 +50,11 @@ class PairSWKokkos : public PairSW {
 
   template<int NEIGHFLAG, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
+  void operator()(TagPairSWCompute<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
 
   template<int NEIGHFLAG, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>, const int&) const;
+  void operator()(TagPairSWCompute<NEIGHFLAG,EVFLAG>, const int&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairSWComputeFullA<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairSWComputeFullA<NEIGHFLAG,EVFLAG>, const int&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairSWComputeFullB<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairSWComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
 
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairSWComputeShortNeigh, const int&) const;
@@ -121,10 +99,6 @@ class PairSWKokkos : public PairSW {
   void threebody_kk(const Param&, const Param&, const Param&, const F_FLOAT&, const F_FLOAT&, F_FLOAT *, F_FLOAT *,
                     F_FLOAT *, F_FLOAT *, const int&, F_FLOAT&) const;
 
-  KOKKOS_INLINE_FUNCTION
-  void threebodyj(const Param&, const Param&, const Param&, const F_FLOAT&, const F_FLOAT&, F_FLOAT *, F_FLOAT *,
-                 F_FLOAT *) const;
-
   typename AT::t_x_array_randomread x;
   typename AT::t_f_array f;
   typename AT::t_tagint_1d tag;
@@ -180,7 +154,7 @@ class PairSWKokkos : public PairSW {
 
 /* ERROR/WARNING messages:
 
-E: Cannot use chosen neighbor list style with pair sw/kk
+E: Must use half neighbor list style with pair sw/kk
 
 Self-explanatory.
 

src/KOKKOS/pair_tersoff_kokkos.h

@@ -30,20 +30,14 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos<LMPHostType>);
 namespace LAMMPS_NS {
 
 template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffComputeHalf{};
+struct TagPairTersoffCompute{};
-
-template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffComputeFullA{};
-
-template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffComputeFullB{};
 
 struct TagPairTersoffComputeShortNeigh{};
 
 template<class DeviceType>
 class PairTersoffKokkos : public PairTersoff {
  public:
-  enum {EnabledNeighFlags=FULL};
+  enum {EnabledNeighFlags=HALF|HALFTHREAD};
   enum {COUL_FLAG=0};
   typedef DeviceType device_type;
   typedef ArrayTypes<DeviceType> AT;
@@ -52,90 +46,75 @@ class PairTersoffKokkos : public PairTersoff {
   PairTersoffKokkos(class LAMMPS *);
   ~PairTersoffKokkos() override;
   void compute(int, int) override;
+  void coeff(int, char **) override;
   void init_style() override;
 
   template<int NEIGHFLAG, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffComputeHalf<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
+  void operator()(TagPairTersoffCompute<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
 
   template<int NEIGHFLAG, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffComputeHalf<NEIGHFLAG,EVFLAG>, const int&) const;
+  void operator()(TagPairTersoffCompute<NEIGHFLAG,EVFLAG>, const int&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffComputeFullA<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffComputeFullA<NEIGHFLAG,EVFLAG>, const int&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffComputeFullB<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
 
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairTersoffComputeShortNeigh, const int&) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_fc_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_fc_k(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dfc(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_dfc(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_fc_k_and_ters_dfc(const int &i, const int &j, const int &k, const F_FLOAT &r, double &fc, double &dfc) const;
+  void ters_fc_k_and_ters_dfc(const Param& param, const F_FLOAT &r, double &fc, double &dfc) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_fa_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_fa_k(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dfa(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_dfa(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_fa_k_and_ters_dfa(const int &i, const int &j, const int &k, const F_FLOAT &r, double &fa, double &dfa) const;
+  void ters_fa_k_and_ters_dfa(const Param& param, const F_FLOAT &r, double &fa, double &dfa) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_bij_k(const int &i, const int &j, const int &k, const F_FLOAT &bo) const;
+  double ters_bij_k(const Param& param, const F_FLOAT &bo) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dbij(const int &i, const int &j, const int &k, const F_FLOAT &bo) const;
+  double ters_dbij(const Param& param, const F_FLOAT &bo) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_bij_k_and_ters_dbij(const int &i, const int &j, const int &k, const F_FLOAT &bo, double &bij, double &prefactor) const;
+  void ters_bij_k_and_ters_dbij(const Param& param, const F_FLOAT &bo, double &bij, double &prefactor) const;
 
   KOKKOS_INLINE_FUNCTION
-  double bondorder(const int &i, const int &j, const int &k,
+  double bondorder(const Param& param,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const;
+  double ters_gijk(const Param& param, const F_FLOAT &cos) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const;
+  double ters_dgijk(const Param& param, const F_FLOAT &cos) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_gijk_and_ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos, double& gijk, double& dgijk) const;
+  void ters_gijk_and_ters_dgijk(const Param& param, const F_FLOAT &cos, double& gijk, double& dgijk) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthb(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthb(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthbj(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthbj(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fj, F_FLOAT *fk) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthbk(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthbk(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fk) const;
@@ -163,17 +142,6 @@ class PairTersoffKokkos : public PairTersoff {
   KOKKOS_INLINE_FUNCTION
   int sbmask(const int& j) const;
 
-  struct params_ters{
-    KOKKOS_INLINE_FUNCTION
-    params_ters() {powerm=0;gamma=0;lam3=0;c=0;d=0;h=0;powern=0;beta=0;lam2=0;bigb=0;
-                  bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;};
-    KOKKOS_INLINE_FUNCTION
-    params_ters(int /*i*/) {powerm=0;gamma=0;lam3=0;c=0;d=0;h=0;powern=0;beta=0;lam2=0;bigb=0;
-                  bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;};
-    F_FLOAT powerm, gamma, lam3, c, d, h, powern, beta, lam2, bigb, bigr,
-            bigd, lam1, biga, cutsq, c1, c2, c3, c4;
-  };
-
   template<int NEIGHFLAG>
   KOKKOS_INLINE_FUNCTION
   void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
@@ -189,16 +157,21 @@ class PairTersoffKokkos : public PairTersoff {
   void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
                 F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const;
 
-  void allocate() override;
   void setup_params() override;
 
  protected:
   typedef Kokkos::DualView<int***,DeviceType> tdual_int_3d;
-  Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType> k_params;
+  typedef typename tdual_int_3d::t_dev_const_randomread t_int_3d_randomread;
-  typename Kokkos::DualView<params_ters***,
+  typedef typename tdual_int_3d::t_host t_host_int_3d;
-    Kokkos::LayoutRight,DeviceType>::t_dev_const_um paramskk;
+
-  // hardwired to space for 12 atom types
+  t_int_3d_randomread d_elem3param;
-  //params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+  typename AT::t_int_1d_randomread d_map;
+
+  typedef Kokkos::DualView<Param*,DeviceType> tdual_param_1d;
+  typedef typename tdual_param_1d::t_dev t_param_1d;
+  typedef typename tdual_param_1d::t_host t_host_param_1d;
+
+  t_param_1d d_params;
 
   int inum;
   typename AT::t_x_array_randomread x;
@@ -254,11 +227,7 @@ class PairTersoffKokkos : public PairTersoff {
 
 /* ERROR/WARNING messages:
 
-E: Cannot (yet) use full neighbor list style with tersoff/kk
+E: Must use half neighbor list style with pair tersoff/kk
-
-Self-explanatory.
-
-E: Cannot use chosen neighbor list style with tersoff/kk
 
 Self-explanatory.
 

src/KOKKOS/pair_tersoff_mod_kokkos.h

@@ -30,20 +30,14 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos<LMPHostType>);
 namespace LAMMPS_NS {
 
 template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffMODComputeHalf{};
+struct TagPairTersoffMODCompute{};
-
-template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffMODComputeFullA{};
-
-template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffMODComputeFullB{};
 
 struct TagPairTersoffMODComputeShortNeigh{};
 
 template<class DeviceType>
 class PairTersoffMODKokkos : public PairTersoffMOD {
  public:
-  enum {EnabledNeighFlags=FULL};
+  enum {EnabledNeighFlags=HALF|HALFTHREAD};
   enum {COUL_FLAG=0};
   typedef DeviceType device_type;
   typedef ArrayTypes<DeviceType> AT;
@@ -52,78 +46,63 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
   PairTersoffMODKokkos(class LAMMPS *);
   ~PairTersoffMODKokkos() override;
   void compute(int, int) override;
+  void coeff(int, char **) override;
   void init_style() override;
 
   template<int NEIGHFLAG, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffMODComputeHalf<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
+  void operator()(TagPairTersoffMODCompute<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
 
   template<int NEIGHFLAG, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffMODComputeHalf<NEIGHFLAG,EVFLAG>, const int&) const;
+  void operator()(TagPairTersoffMODCompute<NEIGHFLAG,EVFLAG>, const int&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffMODComputeFullA<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffMODComputeFullA<NEIGHFLAG,EVFLAG>, const int&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffMODComputeFullB<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffMODComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
 
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairTersoffMODComputeShortNeigh, const int&) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_fc_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_fc_k(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dfc(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_dfc(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_fa_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_fa_k(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dfa(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_dfa(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_bij_k(const int &i, const int &j, const int &k, const F_FLOAT &bo) const;
+  double ters_bij_k(const Param& param, const F_FLOAT &bo) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dbij(const int &i, const int &j, const int &k, const F_FLOAT &bo) const;
+  double ters_dbij(const Param& param, const F_FLOAT &bo) const;
 
   KOKKOS_INLINE_FUNCTION
-  double bondorder(const int &i, const int &j, const int &k,
+  double bondorder(const Param& param,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const;
+  double ters_gijk(const Param& param, const F_FLOAT &cos) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const;
+  double ters_dgijk(const Param& param, const F_FLOAT &cos) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthb(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthb(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthbj(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthbj(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fj, F_FLOAT *fk) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthbk(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthbk(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fk) const;
@@ -151,17 +130,6 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
   KOKKOS_INLINE_FUNCTION
   int sbmask(const int& j) const;
 
-  struct params_ters {
-    KOKKOS_INLINE_FUNCTION
-    params_ters() {powerm=0;lam3=0;h=0;powern=0;beta=0;lam2=0;bigb=0;bigr=0;bigd=0;
-      lam1=0;biga=0;powern_del=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;c5=0;ca1=0;ca4=0;};
-    KOKKOS_INLINE_FUNCTION
-    params_ters(int /*i*/) {powerm=0;lam3=0;h=0;powern=0;beta=0;lam2=0;bigb=0;bigr=0;bigd=0;
-      lam1=0;biga=0;powern_del=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;c5=0;ca1=0;ca4=0;};
-    F_FLOAT powerm, lam3, h, powern, beta, lam2, bigb, bigr, bigd,
-      lam1, biga, powern_del, cutsq, c1, c2, c3, c4, c5, ca1, ca4;
-  };
-
   template<int NEIGHFLAG>
   KOKKOS_INLINE_FUNCTION
   void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
@@ -177,18 +145,21 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
   void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
                 F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const;
 
-  void allocate() override;
   void setup_params() override;
 
  protected:
-  using KKDeviceType = typename KKDevice<DeviceType>::value;
-
   typedef Kokkos::DualView<int***,DeviceType> tdual_int_3d;
-  Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType> k_params;
+  typedef typename tdual_int_3d::t_dev_const_randomread t_int_3d_randomread;
-  typename Kokkos::DualView<params_ters***,
+  typedef typename tdual_int_3d::t_host t_host_int_3d;
-    Kokkos::LayoutRight,DeviceType>::t_dev_const_um paramskk;
+
-  // hardwired to space for 12 atom types
+  t_int_3d_randomread d_elem3param;
-  //params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+  typename AT::t_int_1d_randomread d_map;
+
+  typedef Kokkos::DualView<Param*,DeviceType> tdual_param_1d;
+  typedef typename tdual_param_1d::t_dev t_param_1d;
+  typedef typename tdual_param_1d::t_host t_host_param_1d;
+
+  t_param_1d d_params;
 
   int inum;
   typename AT::t_x_array_randomread x;
@@ -203,6 +174,7 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
 
   int need_dup;
 
+  using KKDeviceType = typename KKDevice<DeviceType>::value;
 
   template<typename DataType, typename Layout>
   using DupScatterView = KKScatterView<DataType, Layout, KKDeviceType, KKScatterSum, KKScatterDuplicated>;
@@ -213,6 +185,7 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
   DupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> dup_f;
   DupScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout> dup_eatom;
   DupScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout> dup_vatom;
+
   NonDupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> ndup_f;
   NonDupScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout> ndup_eatom;
   NonDupScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout> ndup_vatom;
@@ -242,11 +215,7 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
 
 /* ERROR/WARNING messages:
 
-E: Cannot (yet) use full neighbor list style with tersoff/mod/kk
+E: Must use half neighbor list style with pair tersoff/mod/kk
-
-Self-explanatory.
-
-E: Cannot use chosen neighbor list style with tersoff/mod/kk
 
 Self-explanatory.
 

src/KOKKOS/pair_tersoff_zbl_kokkos.h

@@ -30,20 +30,14 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos<LMPHostType>);
 namespace LAMMPS_NS {
 
 template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffZBLComputeHalf{};
+struct TagPairTersoffZBLCompute{};
-
-template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffZBLComputeFullA{};
-
-template<int NEIGHFLAG, int EVFLAG>
-struct TagPairTersoffZBLComputeFullB{};
 
 struct TagPairTersoffZBLComputeShortNeigh{};
 
 template<class DeviceType>
 class PairTersoffZBLKokkos : public PairTersoffZBL {
  public:
-  enum {EnabledNeighFlags=FULL};
+  enum {EnabledNeighFlags=HALF|HALFTHREAD};
   enum {COUL_FLAG=0};
   typedef DeviceType device_type;
   typedef ArrayTypes<DeviceType> AT;
@@ -52,77 +46,63 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
   PairTersoffZBLKokkos(class LAMMPS *);
   ~PairTersoffZBLKokkos() override;
   void compute(int, int) override;
+  void coeff(int, char **) override;
   void init_style() override;
 
   template<int NEIGHFLAG, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffZBLComputeHalf<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
+  void operator()(TagPairTersoffZBLCompute<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
 
   template<int NEIGHFLAG, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffZBLComputeHalf<NEIGHFLAG,EVFLAG>, const int&) const;
+  void operator()(TagPairTersoffZBLCompute<NEIGHFLAG,EVFLAG>, const int&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffZBLComputeFullA<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffZBLComputeFullA<NEIGHFLAG,EVFLAG>, const int&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffZBLComputeFullB<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
-
-  template<int NEIGHFLAG, int EVFLAG>
-  KOKKOS_INLINE_FUNCTION
-  void operator()(TagPairTersoffZBLComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
 
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairTersoffZBLComputeShortNeigh, const int&) const;
-  KOKKOS_INLINE_FUNCTION
-  double ters_fc_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dfc(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_fc_k(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_fa_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_dfc(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dfa(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double ters_fa_k(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_bij_k(const int &i, const int &j, const int &k, const F_FLOAT &bo) const;
+  double ters_dfa(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dbij(const int &i, const int &j, const int &k, const F_FLOAT &bo) const;
+  double ters_bij_k(const Param& param, const F_FLOAT &bo) const;
 
   KOKKOS_INLINE_FUNCTION
-  double bondorder(const int &i, const int &j, const int &k,
+  double ters_dbij(const Param& param, const F_FLOAT &bo) const;
+
+  KOKKOS_INLINE_FUNCTION
+  double bondorder(const Param& param,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const;
+  double ters_gijk(const Param& param, const F_FLOAT &cos) const;
 
   KOKKOS_INLINE_FUNCTION
-  double ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const;
+  double ters_dgijk(const Param& param, const F_FLOAT &cos) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthb(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthb(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthbj(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthbj(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fj, F_FLOAT *fk) const;
 
   KOKKOS_INLINE_FUNCTION
-  void ters_dthbk(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+  void ters_dthbk(const Param& param, const F_FLOAT &prefactor,
               const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
               const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2,
               F_FLOAT *fk) const;
@@ -150,17 +130,6 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
   KOKKOS_INLINE_FUNCTION
   int sbmask(const int& j) const;
 
-  struct params_ters {
-    KOKKOS_INLINE_FUNCTION
-    params_ters() {powerm=0;gamma=0;lam3=0;c=0;d=0;h=0;powern=0;beta=0;lam2=0;bigb=0;
-          bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;Z_i=0;Z_j=0;ZBLcut=0;ZBLexpscale=0;};
-    KOKKOS_INLINE_FUNCTION
-    params_ters(int /*i*/) {powerm=0;gamma=0;lam3=0;c=0;d=0;h=0;powern=0;beta=0;lam2=0;bigb=0;
-          bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;Z_i=0;Z_j=0;ZBLcut=0;ZBLexpscale=0;};
-    F_FLOAT powerm, gamma, lam3, c, d, h, powern, beta, lam2, bigb, bigr,
-      bigd, lam1, biga, cutsq, c1, c2, c3, c4, Z_i, Z_j, ZBLcut, ZBLexpscale;
-  };
-
   template<int NEIGHFLAG>
   KOKKOS_INLINE_FUNCTION
   void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
@@ -176,22 +145,27 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
   void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
                 F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const;
 
-  void allocate() override;
   void setup_params() override;
 
   KOKKOS_INLINE_FUNCTION
-  double fermi_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double fermi_k(const Param& param, const F_FLOAT &r) const;
 
   KOKKOS_INLINE_FUNCTION
-  double fermi_d_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
+  double fermi_d_k(const Param& param, const F_FLOAT &r) const;
 
  protected:
   typedef Kokkos::DualView<int***,DeviceType> tdual_int_3d;
-  Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType> k_params;
+  typedef typename tdual_int_3d::t_dev_const_randomread t_int_3d_randomread;
-  typename Kokkos::DualView<params_ters***,
+  typedef typename tdual_int_3d::t_host t_host_int_3d;
-    Kokkos::LayoutRight,DeviceType>::t_dev_const_um paramskk;
+
-  // hardwired to space for 12 atom types
+  t_int_3d_randomread d_elem3param;
-  //params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+  typename AT::t_int_1d_randomread d_map;
+
+  typedef Kokkos::DualView<Param*,DeviceType> tdual_param_1d;
+  typedef typename tdual_param_1d::t_dev t_param_1d;
+  typedef typename tdual_param_1d::t_host t_host_param_1d;
+
+  t_param_1d d_params;
 
   int inum;
   typename AT::t_x_array_randomread x;
@@ -256,11 +230,7 @@ E: Pair tersoff/zbl/kk requires metal or real units
 
 This is a current restriction of this pair potential.
 
-E: Cannot (yet) use full neighbor list style with tersoff/zbl/kk
+E: Must use half neighbor list style with pair tersoff/zlb/kk
-
-Self-explanatory.
-
-E: Cannot use chosen neighbor list style with tersoff/zbl/kk
 
 Self-explanatory.
 

src/MANYBODY/pair_tersoff.h

@@ -38,7 +38,6 @@ class PairTersoff : public Pair {
 
   static constexpr int NPARAMS_PER_LINE = 17;
 
- protected:
   struct Param {
     double lam1, lam2, lam3;
     double c, d, h;
@@ -56,6 +55,7 @@ class PairTersoff : public Pair {
     double c0;    // added for TersoffMODC
   };
 
+ protected:
   Param *params;      // parameter set for an I-J-K interaction
   double cutmax;      // max cutoff for all elements
   int maxshort;       // size of short neighbor list array

src/MC/fix_bond_break.cpp

@@ -19,11 +19,14 @@
 #include "error.h"
 #include "force.h"
 #include "memory.h"
+#include "modify.h"
 #include "neighbor.h"
 #include "random_mars.h"
 #include "respa.h"
 #include "update.h"
 
+#include "fix_bond_history.h"
+
 #include <cstring>
 
 using namespace LAMMPS_NS;
@@ -258,6 +261,10 @@ void FixBondBreak::post_integrate()
   commflag = 1;
   comm->forward_comm(this,2);
 
+  // find instances of bond history to delete data
+  auto histories = modify->get_fix_by_style("BOND_HISTORY");
+  int n_histories = histories.size();
+
   // break bonds
   // if both atoms list each other as winning bond partner
   // and probability constraint is satisfied
@@ -292,7 +299,13 @@ void FixBondBreak::post_integrate()
         for (k = m; k < num_bond[i]-1; k++) {
           bond_atom[i][k] = bond_atom[i][k+1];
           bond_type[i][k] = bond_type[i][k+1];
+          if (n_histories > 0)
+            for (auto &ihistory: histories)
+              dynamic_cast<FixBondHistory *>(ihistory)->shift_history(i,k,k+1);
         }
+        if (n_histories > 0)
+          for (auto &ihistory: histories)
+            dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i,num_bond[i]-1);
         num_bond[i]--;
         break;
       }

src/MC/fix_bond_create_angle.cpp

@@ -17,21 +17,15 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_bond_create_angle.h"
+
 #include "atom.h"
+
 #include <cmath>
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-FixBondCreateAngle::FixBondCreateAngle(LAMMPS *lmp, int narg, char **arg) :
-  FixBondCreate(lmp, narg, arg)
-{
-
-}
-
-/* ---------------------------------------------------------------------- */
-
 int FixBondCreateAngle::constrain(int i, int j, double amin, double amax)
 {
   double **x = atom->x;

src/MC/fix_bond_create_angle.h

@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
 
 class FixBondCreateAngle : public FixBondCreate {
  public:
-  FixBondCreateAngle(class LAMMPS *, int, char **);
+  FixBondCreateAngle(LAMMPS *_lmp, int narg, char **arg) : FixBondCreate(_lmp, narg, arg) {}
 
  private:
   int constrain(int, int, double, double) override;

src/MC/fix_bond_swap.cpp

@@ -22,6 +22,7 @@
 #include "compute.h"
 #include "domain.h"
 #include "error.h"
+#include "fix_bond_history.h"
 #include "force.h"
 #include "memory.h"
 #include "modify.h"
@@ -446,6 +447,10 @@ void FixBondSwap::post_integrate()
   if (!accept) return;
   naccept++;
 
+  // find instances of bond/history to reset history
+  auto histories = modify->get_fix_by_style("BOND_HISTORY");
+  int n_histories = histories.size();
+
   // change bond partners of affected atoms
   // on atom i: bond i-inext changes to i-jnext
   // on atom j: bond j-jnext changes to j-inext
@@ -453,13 +458,33 @@ void FixBondSwap::post_integrate()
   // on atom jnext: bond jnext-j changes to jnext-i
 
   for (ibond = 0; ibond < num_bond[i]; ibond++)
-    if (bond_atom[i][ibond] == tag[inext]) bond_atom[i][ibond] = tag[jnext];
+    if (bond_atom[i][ibond] == tag[inext]) {
+      if (n_histories > 0)
+        for (auto &ihistory: histories)
+          dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i,ibond);
+      bond_atom[i][ibond] = tag[jnext];
+    }
   for (jbond = 0; jbond < num_bond[j]; jbond++)
-    if (bond_atom[j][jbond] == tag[jnext]) bond_atom[j][jbond] = tag[inext];
+    if (bond_atom[j][jbond] == tag[jnext]) {
+      if (n_histories > 0)
+        for (auto &ihistory: histories)
+          dynamic_cast<FixBondHistory *>(ihistory)->delete_history(j,jbond);
+      bond_atom[j][jbond] = tag[inext];
+    }
   for (ibond = 0; ibond < num_bond[inext]; ibond++)
-    if (bond_atom[inext][ibond] == tag[i]) bond_atom[inext][ibond] = tag[j];
+    if (bond_atom[inext][ibond] == tag[i]) {
+      if (n_histories > 0)
+        for (auto &ihistory: histories)
+          dynamic_cast<FixBondHistory *>(ihistory)->delete_history(inext,ibond);
+      bond_atom[inext][ibond] = tag[j];
+    }
   for (jbond = 0; jbond < num_bond[jnext]; jbond++)
-    if (bond_atom[jnext][jbond] == tag[j]) bond_atom[jnext][jbond] = tag[i];
+    if (bond_atom[jnext][jbond] == tag[j]) {
+      if (n_histories > 0)
+        for (auto &ihistory: histories)
+          dynamic_cast<FixBondHistory *>(ihistory)->delete_history(jnext,jbond);
+      bond_atom[jnext][jbond] = tag[i];
+    }
 
   // set global tags of 4 atoms in bonds
 

src/MDI/fix_mdi_aimd.cpp

@@ -29,7 +29,7 @@ enum { NATIVE, REAL, METAL };    // LAMMPS units which MDI supports
 
 FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 {
-  if (narg > 4) error->all(FLERR, "Illegal fix mdi/aimd command");
+  if (narg != 3) error->all(FLERR, "Illegal fix mdi/aimd command");
 
   scalar_flag = 1;
   global_freq = 1;
@@ -38,16 +38,6 @@ FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
   virial_global_flag = 1;
   thermo_energy = thermo_virial = 1;
 
-  // check for plugin arg
-
-  plugin = 0;
-  if (narg == 4) {
-    if (strcmp(arg[3], "plugin") == 0)
-      plugin = 1;
-    else
-      error->all(FLERR, "Illegal fix mdi/aimd command");
-  }
-
   // check requirements for LAMMPS to work with MDI as an engine
 
   if (atom->tag_enable == 0) error->all(FLERR, "Cannot use MDI engine without atom IDs");
@@ -62,6 +52,11 @@ FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
   if (role != MDI_DRIVER)
     error->all(FLERR, "Must invoke LAMMPS as an MDI driver to use fix mdi/aimd");
 
+  // mdicomm will be one-time initialized in init()
+  // cannot be done here for a plugin library, b/c mdi plugin command is later
+
+  mdicomm = MDI_COMM_NULL;
+
   // storage for all atoms
 
   buf3 = buf3all = nullptr;
@@ -78,13 +73,6 @@ FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 
   unit_conversions();
 
-  // connect to MDI engine, only if engine is stand-alone code
-
-  if (!plugin) {
-    MDI_Accept_communicator(&mdicomm);
-    if (mdicomm <= 0) error->all(FLERR, "Unable to connect to MDI engine");
-  }
-
   nprocs = comm->nprocs;
 }
 
@@ -92,7 +80,8 @@ FixMDIAimd::FixMDIAimd(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 
 FixMDIAimd::~FixMDIAimd()
 {
-  // send exit command to engine, only if engine is stand-alone code
+  // send exit command to engine if it is a stand-alone code
+  // for plugin, this happens in MDIPlugin::plugin_wrapper()
 
   if (!plugin) {
     int ierr = MDI_Send_command("EXIT", mdicomm);
@@ -118,6 +107,30 @@ int FixMDIAimd::setmask()
 
 /* ---------------------------------------------------------------------- */
 
+void FixMDIAimd::init()
+{
+  if (mdicomm != MDI_COMM_NULL) return;
+
+  // one-time auto-detect whether engine is stand-alone code or plugin library
+  // also initializes mdicomm
+  // plugin = 0/1 for engine = stand-alone code vs plugin library
+
+  MDI_Get_communicator(&mdicomm, 0);
+
+  if (mdicomm == MDI_COMM_NULL) {
+    plugin = 0;
+    MDI_Accept_communicator(&mdicomm);
+    if (mdicomm == MDI_COMM_NULL) error->all(FLERR, "MDI unable to connect to stand-alone engine");
+  } else {
+    plugin = 1;
+    int method;
+    MDI_Get_method(&method, mdicomm);
+    if (method != MDI_PLUGIN) error->all(FLERR, "MDI internal error for plugin engine");
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
 void FixMDIAimd::setup(int vflag)
 {
   post_force(vflag);

src/MDI/fix_mdi_aimd.h

@@ -27,14 +27,11 @@ namespace LAMMPS_NS {
 
 class FixMDIAimd : public Fix {
  public:
-  // MDI communicator, public so that LAMMPS can work with a plugin
-
-  MDI_Comm mdicomm;
-
   FixMDIAimd(class LAMMPS *, int, char **);
   ~FixMDIAimd();
   int setmask();
 
+  void init();
   void setup(int);
   void setup_pre_reverse(int, int);
   void pre_reverse(int, int);
@@ -46,6 +43,8 @@ class FixMDIAimd : public Fix {
   int nprocs;
   int plugin;
 
+  MDI_Comm mdicomm;
+
   int eflag_caller;
   double engine_energy;
   int lmpunits;

src/MDI/mdi_engine.cpp

@@ -601,7 +601,8 @@ void MDIEngine::mdi_md()
   // delete the instance before this method returns
 
   modify->add_fix("MDI_ENGINE_INTERNAL all MDI/ENGINE");
-  FixMDIEngine *mdi_fix = dynamic_cast<FixMDIEngine *>( modify->get_fix_by_id("MDI_ENGINE_INTERNAL"));
+  FixMDIEngine *mdi_fix =
+      dynamic_cast<FixMDIEngine *>(modify->get_fix_by_id("MDI_ENGINE_INTERNAL"));
   mdi_fix->mdi_engine = this;
 
   // initialize LAMMPS and setup() the simulation
@@ -723,7 +724,8 @@ void MDIEngine::mdi_optg()
   // delete the instance before this method returns
 
   modify->add_fix("MDI_ENGINE_INTERNAL all MDI/ENGINE");
-  FixMDIEngine *mdi_fix = dynamic_cast<FixMDIEngine *>( modify->get_fix_by_id("MDI_ENGINE_INTERNAL"));
+  FixMDIEngine *mdi_fix =
+      dynamic_cast<FixMDIEngine *>(modify->get_fix_by_id("MDI_ENGINE_INTERNAL"));
   mdi_fix->mdi_engine = this;
 
   // initialize LAMMPS and setup() the simulation
@@ -956,7 +958,8 @@ void MDIEngine::create_system()
   // optionally set charges if specified by ">CHARGES"
 
   if (flag_velocities)
-    lammps_create_atoms(lmp, sys_natoms, nullptr, sys_types, sys_coords, sys_velocities, nullptr, 1);
+    lammps_create_atoms(lmp, sys_natoms, nullptr, sys_types, sys_coords, sys_velocities, nullptr,
+                        1);
   else
     lammps_create_atoms(lmp, sys_natoms, nullptr, sys_types, sys_coords, nullptr, nullptr, 1);
 

src/MDI/mdi_plugin.cpp

@@ -92,11 +92,6 @@ MDIPlugin::MDIPlugin(LAMMPS *_lmp, int narg, char **arg) : Pointers(_lmp)
     strcat(plugin_args, extra_arg);
   }
 
-  // find FixMDIAimd instance so can reset its mdicomm
-  // NOTE: this is a kludge - need better way to handle this
-
-  fixptr = modify->get_fix_by_style("mdi/aimd")[0];
-
   // launch the MDI plugin library
   // path for lib was specified in -mdi command-line arg when LAMMPS started
   // this calls back to plugin_wrapper, which must issue MDI EXIT at end
@@ -108,8 +103,7 @@ MDIPlugin::MDIPlugin(LAMMPS *_lmp, int narg, char **arg) : Pointers(_lmp)
 
 /* ----------------------------------------------------------------------
    callback function from MDI_Launch_plugin()
-   this function must wrap entire interaction of LAMMPS as a driver
+   this function wraps entire interaction of LAMMPS driver with the plugin
-     with the plugin
 ---------------------------------------------------------------------- */
 
 int MDIPlugin::plugin_wrapper(void * /*pmpicomm*/, MDI_Comm mdicomm, void *vptr)
@@ -118,11 +112,6 @@ int MDIPlugin::plugin_wrapper(void * /*pmpicomm*/, MDI_Comm mdicomm, void *vptr)
   LAMMPS *lammps = ptr->lmp;
   char *lammps_command = ptr->lammps_command;
 
-  // set FixMDIAimd mdicomm to driver's mdicomm passed to this callback
-
-  auto aimdptr = dynamic_cast<FixMDIAimd *> (ptr->fixptr);
-  aimdptr->mdicomm = mdicomm;
-
   // invoke the specified LAMMPS command
   // that operation will issue MDI commands to the plugin engine
 

src/MDI/mdi_plugin.h

@@ -25,7 +25,6 @@ class MDIPlugin : protected Pointers {
 
  private:
   char *lammps_command;
-  class Fix *fixptr;
 
   static int plugin_wrapper(void *, MDI_Comm, void *);
 };

src/MISC/fix_pair_tracker.cpp

@@ -1,350 +0,0 @@
-/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
-
-   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-   certain rights in this software.  This software is distributed under
-   the GNU General Public License.
-
-   See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "fix_pair_tracker.h"
-
-#include "atom.h"
-#include "error.h"
-#include "memory.h"
-#include "tokenizer.h"
-#include "update.h"
-
-#include <cstring>
-
-using namespace LAMMPS_NS;
-using namespace FixConst;
-
-#define DELTA 1000
-
-/* ---------------------------------------------------------------------- */
-
-FixPairTracker::FixPairTracker(LAMMPS *lmp, int narg, char **arg) :
-    Fix(lmp, narg, arg), nvalues(0), vector(nullptr), array(nullptr), pack_choice(nullptr)
-{
-  if (narg < 3) error->all(FLERR, "Illegal fix pair/tracker command");
-  local_flag = 1;
-
-  nevery = utils::inumeric(FLERR, arg[3], false, lmp);
-  if (nevery <= 0) error->all(FLERR, "Illegal fix pair/tracker command");
-  local_freq = nevery;
-
-  // If optional arguments included, this will be oversized
-  nvalues = narg - 4;
-  pack_choice = new FnPtrPack[nvalues];
-
-  tmin = -1;
-  type_filter = nullptr;
-  int iarg = 4;
-  nvalues = 0;
-  while (iarg < narg) {
-    if (strcmp(arg[iarg], "id1") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_id1;
-    } else if (strcmp(arg[iarg], "id2") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_id2;
-
-    } else if (strcmp(arg[iarg], "time/created") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_time_created;
-    } else if (strcmp(arg[iarg], "time/broken") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_time_broken;
-    } else if (strcmp(arg[iarg], "time/total") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_time_total;
-
-    } else if (strcmp(arg[iarg], "x") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_x;
-    } else if (strcmp(arg[iarg], "y") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_y;
-    } else if (strcmp(arg[iarg], "z") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_z;
-
-    } else if (strcmp(arg[iarg], "r/min") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_rmin;
-    } else if (strcmp(arg[iarg], "r/ave") == 0) {
-      pack_choice[nvalues++] = &FixPairTracker::pack_rave;
-
-    } else if (strcmp(arg[iarg], "time/min") == 0) {
-      if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in fix pair/tracker command");
-      tmin = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
-      iarg++;
-
-    } else if (strcmp(arg[iarg], "type/include") == 0) {
-      if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in fix pair/tracker command");
-      int ntypes = atom->ntypes;
-      int i, j, itype, jtype;
-      int inlo, inhi, jnlo, jnhi;
-
-      if (!type_filter) {
-        memory->create(type_filter, ntypes + 1, ntypes + 1, "fix/pair/tracker:type_filter");
-
-        for (i = 0; i <= ntypes; i++) {
-          for (j = 0; j <= ntypes; j++) type_filter[i][j] = 0;
-        }
-      }
-
-      auto iwords = Tokenizer(arg[iarg + 1], ",").as_vector();
-      auto jwords = Tokenizer(arg[iarg + 2], ",").as_vector();
-
-      for (const auto &ifield : iwords) {
-        utils::bounds(FLERR, ifield, 1, ntypes, inlo, inhi, error);
-        for (const auto &jfield : jwords) {
-          utils::bounds(FLERR, jfield, 1, ntypes, jnlo, jnhi, error);
-
-          for (itype = inlo; itype <= inhi; itype++) {
-            for (jtype = jnlo; jtype <= jnhi; jtype++) {
-              type_filter[itype][jtype] = 1;
-              type_filter[jtype][itype] = 1;
-            }
-          }
-        }
-      }
-      iarg += 2;
-
-    } else
-      error->all(FLERR, "Invalid keyword in fix pair/tracker command");
-
-    iarg++;
-  }
-
-  if (nvalues == 1)
-    size_local_cols = 0;
-  else
-    size_local_cols = nvalues;
-
-  nmax = 0;
-  ncount = 0;
-  vector = nullptr;
-  array = nullptr;
-}
-
-/* ---------------------------------------------------------------------- */
-
-FixPairTracker::~FixPairTracker()
-{
-  delete[] pack_choice;
-
-  memory->destroy(vector);
-  memory->destroy(array);
-  memory->destroy(type_filter);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int FixPairTracker::setmask()
-{
-  int mask = 0;
-  mask |= POST_FORCE;
-  return mask;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::init()
-{
-  // Set size of array/vector
-  ncount = 0;
-
-  if (ncount > nmax) reallocate(ncount);
-
-  size_local_rows = ncount;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::lost_contact(int i, int j, double time_tmp, double nstep_tmp, double rsum_tmp,
-                                  double rmin_tmp)
-{
-
-  double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
-  if ((time - time_tmp) < tmin) return;
-
-  if (type_filter) {
-    int *type = atom->type;
-    if (type_filter[type[i]][type[j]] == 0) return;
-  }
-
-  int *mask = atom->mask;
-  if (!(mask[i] & groupbit)) return;
-  if (!(mask[j] & groupbit)) return;
-
-  if (ncount == nmax) reallocate(ncount);
-
-  index_i = i;
-  index_j = j;
-
-  rmin = rmin_tmp;
-  rsum = rsum_tmp;
-  time_initial = time_tmp;
-  nstep_initial = nstep_tmp;
-
-  // fill vector or array with local values
-  if (nvalues == 1) {
-    (this->*pack_choice[0])(0);
-  } else {
-    for (int k = 0; k < nvalues; k++) { (this->*pack_choice[k])(k); }
-  }
-
-  ncount += 1;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::post_force(int /*vflag*/)
-{
-  if (update->ntimestep % nevery == 0) {
-    size_local_rows = ncount;
-    ncount = 0;
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::reallocate(int n)
-{
-  // grow vector or array
-  while (nmax <= n) nmax += DELTA;
-
-  if (nvalues == 1) {
-    memory->grow(vector, nmax, "fix_pair_tracker:vector");
-    vector_local = vector;
-  } else {
-    memory->grow(array, nmax, nvalues, "fix_pair_tracker:array");
-    array_local = array;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   memory usage of local data
-------------------------------------------------------------------------- */
-
-double FixPairTracker::memory_usage()
-{
-  double bytes = nmax * (double) nvalues * sizeof(double);
-  bytes += nmax * 2 * sizeof(int);
-  return bytes;
-}
-
-/* ----------------------------------------------------------------------
-   one method for every keyword fix pair/tracker can output
-   the atom property is packed into a local vector or array
-------------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_time_created(int n)
-{
-  if (nvalues == 1)
-    vector[ncount] = time_initial;
-  else
-    array[ncount][n] = time_initial;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_time_broken(int n)
-{
-  double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
-  if (nvalues == 1)
-    vector[ncount] = time;
-  else
-    array[ncount][n] = time;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_time_total(int n)
-{
-  double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
-  if (nvalues == 1)
-    vector[ncount] = time - time_initial;
-  else
-    array[ncount][n] = time - time_initial;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_id1(int n)
-{
-  tagint *tag = atom->tag;
-
-  if (nvalues == 1)
-    vector[ncount] = tag[index_i];
-  else
-    array[ncount][n] = tag[index_i];
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_id2(int n)
-{
-  tagint *tag = atom->tag;
-
-  if (nvalues == 1)
-    vector[ncount] = tag[index_j];
-  else
-    array[ncount][n] = tag[index_j];
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_x(int n)
-{
-  double **x = atom->x;
-
-  if (nvalues == 1)
-    vector[ncount] = (x[index_i][0] + x[index_j][0]) / 2;
-  else
-    array[ncount][n] = (x[index_i][0] + x[index_j][0]) / 2;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_y(int n)
-{
-  double **x = atom->x;
-
-  if (nvalues == 1)
-    vector[ncount] = (x[index_i][1] + x[index_j][1]) / 2;
-  else
-    array[ncount][n] = (x[index_i][1] + x[index_j][1]) / 2;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_z(int n)
-{
-  double **x = atom->x;
-
-  if (nvalues == 1)
-    vector[ncount] = (x[index_i][2] + x[index_j][2]) / 2;
-  else
-    array[ncount][n] = (x[index_i][2] + x[index_j][2]) / 2;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_rmin(int n)
-{
-  if (nvalues == 1)
-    vector[ncount] = rmin;
-  else
-    array[ncount][n] = rmin;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixPairTracker::pack_rave(int n)
-{
-  if (nvalues == 1)
-    vector[ncount] = rsum / (update->ntimestep - nstep_initial);
-  else
-    array[ncount][n] = rsum / (update->ntimestep - nstep_initial);
-}

src/MISC/pair_tracker.cpp

@@ -19,39 +19,41 @@
 #include "fix.h"
 #include "fix_dummy.h"
 #include "fix_neigh_history.h"
-#include "fix_pair_tracker.h"
+#include "fix_store_local.h"
 #include "force.h"
 #include "memory.h"
 #include "modify.h"
 #include "neigh_list.h"
 #include "neighbor.h"
+#include "tokenizer.h"
 #include "update.h"
+#include "utils.h"
 
-#include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairTracker::PairTracker(LAMMPS *lmp) : Pair(lmp)
+PairTracker::PairTracker(LAMMPS *lmp) :
+    Pair(lmp), onerad_dynamic(nullptr), onerad_frozen(nullptr), maxrad_dynamic(nullptr),
+    maxrad_frozen(nullptr), id_fix_store_local(nullptr), fix_dummy(nullptr), fix_history(nullptr),
+    fix_store_local(nullptr), type_filter(nullptr), output_data(nullptr), pack_choice(nullptr)
 {
   single_enable = 1;
   no_virial_fdotr_compute = 1;
 
   neighprev = 0;
   history = 1;
-  size_history = 4;
+  size_history = 3;
   nondefault_history_transfer = 1;
 
   finitecutflag = 0;
+  tmin = -1;
 
   // create dummy fix as placeholder for FixNeighHistory
   // this is so final order of Modify:fix will conform to input script
-
+  fix_dummy = dynamic_cast<FixDummy *>(modify->add_fix("NEIGH_HISTORY_TRACK_DUMMY all DUMMY"));
-  fix_history = nullptr;
-  modify->add_fix("NEIGH_HISTORY_TRACK_DUMMY all DUMMY");
-  fix_dummy = dynamic_cast<FixDummy *>( modify->fix[modify->nfix - 1]);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -62,6 +64,7 @@ PairTracker::~PairTracker()
     modify->delete_fix("NEIGH_HISTORY_TRACK_DUMMY");
   else
     modify->delete_fix("NEIGH_HISTORY_TRACK");
+  if (id_fix_store_local) modify->delete_fix(id_fix_store_local);
 
   if (allocated) {
     memory->destroy(setflag);
@@ -73,6 +76,12 @@ PairTracker::~PairTracker()
     delete[] maxrad_dynamic;
     delete[] maxrad_frozen;
   }
+
+  delete[] pack_choice;
+  delete[] id_fix_store_local;
+
+  memory->destroy(output_data);
+  memory->destroy(type_filter);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -80,7 +89,7 @@ PairTracker::~PairTracker()
 void PairTracker::compute(int eflag, int vflag)
 {
   int i, j, ii, jj, inum, jnum, itype, jtype;
-  double xtmp, ytmp, ztmp, delx, dely, delz, time;
+  double xtmp, ytmp, ztmp, delx, dely, delz;
   double radi, radj, radsum, rsq, r;
   int *ilist, *jlist, *numneigh, **firstneigh;
   int *touch, **firsttouch;
@@ -131,27 +140,23 @@ void PairTracker::compute(int eflag, int vflag)
         if (rsq >= radsum * radsum) {
 
           data = &alldata[size_history * jj];
-          if (touch[jj] == 1) {
+          if (touch[jj] == 1) process_data(i, j, data);
-            fix_pair_tracker->lost_contact(i, j, data[0], data[1], data[2], data[3]);
+
-          }
           touch[jj] = 0;
-          data[0] = 0.0;    // initial time
+          data[0] = 0.0;    // initial timestep
-          data[1] = 0.0;    // initial timestep
+          data[1] = 0.0;    // sum of r, may be inaccurate over long times
-          data[2] = 0.0;    // sum of r, may overflow
+          data[2] = 0.0;    // min of r
-          data[3] = 0.0;    // min of r
 
         } else {
 
           data = &alldata[size_history * jj];
           if (touch[jj] == 0) {
-            time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
+            data[0] = (double) update->ntimestep;
-            data[0] = time;
+            data[1] = r;
-            data[1] = (double) update->ntimestep;
             data[2] = r;
-            data[3] = r;
           } else if (updateflag) {
-            data[2] += r;
+            data[1] += r;
-            if (data[3] > r) data[3] = r;
+            if (data[2] > r) data[2] = r;
           }
           touch[jj] = 1;
         }
@@ -160,28 +165,23 @@ void PairTracker::compute(int eflag, int vflag)
         if (rsq >= cutsq[itype][jtype]) {
 
           data = &alldata[size_history * jj];
-          if (touch[jj] == 1) {
+          if (touch[jj] == 1) process_data(i, j, data);
-            fix_pair_tracker->lost_contact(i, j, data[0], data[1], data[2], data[3]);
-          }
 
           touch[jj] = 0;
-          data[0] = 0.0;    // initial time
+          data[0] = 0.0;    // initial timestep
-          data[1] = 0.0;    // initial timestep
+          data[1] = 0.0;    // sum of r, may be inaccurate over long times
-          data[2] = 0.0;    // sum of r, may overflow
+          data[2] = 0.0;    // min of r
-          data[3] = 0.0;    // min of r
 
         } else {
 
           data = &alldata[size_history * jj];
           if (touch[jj] == 0) {
-            time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
+            data[0] = (double) update->ntimestep;
-            data[0] = time;
+            data[1] = r;
-            data[1] = (double) update->ntimestep;
             data[2] = r;
-            data[3] = r;
           } else if (updateflag) {
-            data[2] += r;
+            data[1] += r;
-            if (data[3] > r) data[3] = r;
+            if (data[2] > r) data[2] = r;
           }
           touch[jj] = 1;
         }
@@ -218,14 +218,89 @@ void PairTracker::allocate()
 
 void PairTracker::settings(int narg, char **arg)
 {
-  if (narg != 0 && narg != 1) error->all(FLERR, "Illegal pair_style command");
+  if (narg < 2) error->all(FLERR, "Illegal pair_style command");
 
-  if (narg == 1) {
+  id_fix_store_local = utils::strdup(arg[0]);
-    if (strcmp(arg[0], "finite") == 0)
+  store_local_freq = utils::inumeric(FLERR, arg[1], false, lmp);
+
+  // If optional arguments included, this will be oversized
+  pack_choice = new FnPtrPack[narg - 1];
+
+  nvalues = 0;
+  int iarg = 2;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "finite") == 0) {
       finitecutflag = 1;
-    else
+    } else if (strcmp(arg[iarg], "id1") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_id1;
+    } else if (strcmp(arg[iarg], "id2") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_id2;
+    } else if (strcmp(arg[iarg], "time/created") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_time_created;
+    } else if (strcmp(arg[iarg], "time/broken") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_time_broken;
+    } else if (strcmp(arg[iarg], "time/total") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_time_total;
+    } else if (strcmp(arg[iarg], "x") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_x;
+    } else if (strcmp(arg[iarg], "y") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_y;
+    } else if (strcmp(arg[iarg], "z") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_z;
+    } else if (strcmp(arg[iarg], "r/min") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_rmin;
+    } else if (strcmp(arg[iarg], "r/ave") == 0) {
+      pack_choice[nvalues++] = &PairTracker::pack_rave;
+    } else if (strcmp(arg[iarg], "time/min") == 0) {
+      if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in pair tracker command");
+      tmin = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
+      iarg++;
+
+    } else if (strcmp(arg[iarg], "type/include") == 0) {
+      if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in pair tracker command");
+      int ntypes = atom->ntypes;
+      int i, j, itype, jtype;
+      int inlo, inhi, jnlo, jnhi;
+
+      if (!type_filter) {
+        memory->create(type_filter, ntypes + 1, ntypes + 1, "pair/tracker:type_filter");
+
+        for (i = 0; i <= ntypes; i++) {
+          for (j = 0; j <= ntypes; j++) type_filter[i][j] = 0;
+        }
+      }
+
+      auto iwords = Tokenizer(arg[iarg + 1], ",").as_vector();
+      auto jwords = Tokenizer(arg[iarg + 2], ",").as_vector();
+
+      for (const auto &ifield : iwords) {
+        utils::bounds(FLERR, ifield, 1, ntypes, inlo, inhi, error);
+        for (const auto &jfield : jwords) {
+          utils::bounds(FLERR, jfield, 1, ntypes, jnlo, jnhi, error);
+
+          for (itype = inlo; itype <= inhi; itype++) {
+            for (jtype = jnlo; jtype <= jnhi; jtype++) {
+              type_filter[itype][jtype] = 1;
+              type_filter[jtype][itype] = 1;
+            }
+          }
+        }
+      }
+      iarg += 2;
+
+    } else {
       error->all(FLERR, "Illegal pair_style command");
     }
+    iarg++;
+  }
+
+  if (nvalues == 0) error->all(FLERR, "Must request at least one value to output");
+  memory->create(output_data, nvalues, "pair/tracker:output_data");
+
+  fix_store_local = dynamic_cast<FixStoreLocal *>(modify->get_fix_by_id(id_fix_store_local));
+  if (!fix_store_local)
+    fix_store_local = dynamic_cast<FixStoreLocal *>(modify->add_fix(
+        fmt::format("{} all STORE_LOCAL {} {}", id_fix_store_local, store_local_freq, nvalues)));
 }
 
 /* ----------------------------------------------------------------------
@@ -263,8 +338,6 @@ void PairTracker::coeff(int narg, char **arg)
 
 void PairTracker::init_style()
 {
-  int i;
-
   // error and warning checks
 
   if (!atom->radius_flag && finitecutflag)
@@ -283,44 +356,49 @@ void PairTracker::init_style()
   if (fix_history == nullptr) {
     modify->replace_fix("NEIGH_HISTORY_TRACK_DUMMY",
                         fmt::format("NEIGH_HISTORY_TRACK all NEIGH_HISTORY {}", size_history), 1);
-    fix_history = dynamic_cast<FixNeighHistory *>( modify->get_fix_by_id("NEIGH_HISTORY_TRACK"));
+    fix_history = dynamic_cast<FixNeighHistory *>(modify->get_fix_by_id("NEIGH_HISTORY_TRACK"));
     fix_history->pair = this;
     fix_history->use_bit_flag = 0;
   } else {
-    fix_history = dynamic_cast<FixNeighHistory *>( modify->get_fix_by_id("NEIGH_HISTORY_TRACK"));
+    fix_history = dynamic_cast<FixNeighHistory *>(modify->get_fix_by_id("NEIGH_HISTORY_TRACK"));
     if (!fix_history) error->all(FLERR, "Could not find pair fix neigh history ID");
   }
 
   if (finitecutflag) {
-
     if (force->pair->beyond_contact)
       error->all(FLERR,
                  "Pair tracker incompatible with granular pairstyles that extend beyond contact");
+
+    // check for FixFreeze and set freeze_group_bit
+
+    auto fixlist = modify->get_fix_by_style("^freeze");
+    if (fixlist.size() == 0)
+      freeze_group_bit = 0;
+    else if (fixlist.size() > 1)
+      error->all(FLERR, "Only one fix freeze command at a time allowed");
+    else
+      freeze_group_bit = fixlist.front()->groupbit;
+
     // check for FixPour and FixDeposit so can extract particle radii
 
-    int ipour;
+    auto pours = modify->get_fix_by_style("^pour");
-    for (ipour = 0; ipour < modify->nfix; ipour++)
+    auto deps = modify->get_fix_by_style("^deposit");
-      if (strcmp(modify->fix[ipour]->style, "pour") == 0) break;
-    if (ipour == modify->nfix) ipour = -1;
-
-    int idep;
-    for (idep = 0; idep < modify->nfix; idep++)
-      if (strcmp(modify->fix[idep]->style, "deposit") == 0) break;
-    if (idep == modify->nfix) idep = -1;
 
     // set maxrad_dynamic and maxrad_frozen for each type
     // include future FixPour and FixDeposit particles as dynamic
 
-    int itype;
+    int itype = 0;
-    for (i = 1; i <= atom->ntypes; i++) {
+    for (int i = 1; i <= atom->ntypes; i++) {
       onerad_dynamic[i] = onerad_frozen[i] = 0.0;
-      if (ipour >= 0) {
+      for (auto &ipour : pours) {
         itype = i;
-        onerad_dynamic[i] = *((double *) modify->fix[ipour]->extract("radius", itype));
+        double maxrad = *((double *) ipour->extract("radius", itype));
+        if (maxrad > 0.0) onerad_dynamic[i] = maxrad;
       }
-      if (idep >= 0) {
+      for (auto &idep : deps) {
         itype = i;
-        onerad_dynamic[i] = *((double *) modify->fix[idep]->extract("radius", itype));
+        double maxrad = *((double *) idep->extract("radius", itype));
+        if (maxrad > 0.0) onerad_dynamic[i] = maxrad;
       }
     }
 
@@ -329,7 +407,7 @@ void PairTracker::init_style()
     int *type = atom->type;
     int nlocal = atom->nlocal;
 
-    for (i = 0; i < nlocal; i++)
+    for (int i = 0; i < nlocal; i++)
       if (mask[i] & freeze_group_bit)
         onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]], radius[i]);
       else
@@ -338,11 +416,6 @@ void PairTracker::init_style()
     MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
     MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
   }
-
-  auto trackfixes = modify->get_fix_by_style("pair/tracker");
-  if (trackfixes.size() != 1)
-    error->all(FLERR, "Must use exactly one fix pair/tracker command with pair style tracker");
-  fix_pair_tracker = dynamic_cast<FixPairTracker *>( trackfixes.front());
 }
 
 /* ----------------------------------------------------------------------
@@ -354,8 +427,7 @@ double PairTracker::init_one(int i, int j)
   if (!allocated) allocate();
 
   // always mix prefactors geometrically
-
+  if (setflag[i][j] == 0) cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
-  if (setflag[i][j] == 0) { cut[i][j] = mix_distance(cut[i][i], cut[j][j]); }
 
   cut[j][i] = cut[i][j];
 
@@ -384,7 +456,7 @@ void PairTracker::write_restart(FILE *fp)
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
       fwrite(&setflag[i][j], sizeof(int), 1, fp);
-      if (setflag[i][j]) { fwrite(&cut[i][j], sizeof(double), 1, fp); }
+      if (setflag[i][j]) fwrite(&cut[i][j], sizeof(double), 1, fp);
     }
 }
 
@@ -404,7 +476,7 @@ void PairTracker::read_restart(FILE *fp)
       if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
       MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
       if (setflag[i][j]) {
-        if (me == 0) { utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); }
+        if (me == 0) utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
         MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
       }
     }
@@ -466,3 +538,91 @@ double PairTracker::radii2cut(double r1, double r2)
   double cut = r1 + r2;
   return cut;
 }
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::process_data(int i, int j, double *input_data)
+{
+  if ((update->ntimestep - input_data[0]) < tmin) return;
+
+  if (type_filter) {
+    int *type = atom->type;
+    if (type_filter[type[i]][type[j]] == 0) return;
+  }
+
+  for (int k = 0; k < nvalues; k++) (this->*pack_choice[k])(k, i, j, input_data);
+  fix_store_local->add_data(output_data, i, j);
+}
+
+/* ----------------------------------------------------------------------
+   one method for every keyword fix pair/tracker can output
+   the atom property is packed into a local vector or array
+------------------------------------------------------------------------- */
+
+void PairTracker::pack_time_created(int n, int /*i*/, int /*j*/, double *data)
+{
+  output_data[n] = data[0];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_time_broken(int n, int /*i*/, int /*j*/, double * /*data*/)
+{
+  output_data[n] = update->ntimestep;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_time_total(int n, int /*i*/, int /*j*/, double *data)
+{
+  output_data[n] = update->ntimestep - data[0];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_id1(int n, int i, int /*j*/, double * /*data*/)
+{
+  output_data[n] = atom->tag[i];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_id2(int n, int /*i*/, int j, double * /*data*/)
+{
+  output_data[n] = atom->tag[j];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_x(int n, int i, int j, double * /*data*/)
+{
+  output_data[n] = (atom->x[i][0] + atom->x[j][0]) * 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_y(int n, int i, int j, double * /*data*/)
+{
+  output_data[n] = (atom->x[i][1] + atom->x[j][1]) * 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_z(int n, int i, int j, double * /*data*/)
+{
+  output_data[n] = (atom->x[i][2] + atom->x[j][2]) * 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_rmin(int n, int /*i*/, int /*j*/, double *data)
+{
+  output_data[n] = data[2];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairTracker::pack_rave(int n, int /*i*/, int /*j*/, double *data)
+{
+  output_data[n] = data[1] / (update->ntimestep - data[0]);
+}

src/MISC/pair_tracker.h

@@ -40,6 +40,7 @@ class PairTracker : public Pair {
   double single(int, int, int, int, double, double, double, double &) override;
   double atom2cut(int) override;
   double radii2cut(double, double) override;
+  void transfer_history(double *, double *) override;
 
  protected:
   int sizeflag;
@@ -50,12 +51,33 @@ class PairTracker : public Pair {
   double *onerad_dynamic, *onerad_frozen;
   double *maxrad_dynamic, *maxrad_frozen;
   int freeze_group_bit;
+  int store_local_freq;
 
+  char *id_fix_store_local;
   class FixDummy *fix_dummy;
   class FixNeighHistory *fix_history;
-  class FixPairTracker *fix_pair_tracker;
+  class FixStoreLocal *fix_store_local;
 
-  void transfer_history(double *, double *) override;
+  int **type_filter;
+  double tmin;
+
+  int nvalues, ncount;
+  double *output_data;
+  typedef void (PairTracker::*FnPtrPack)(int, int, int, double *);
+  FnPtrPack *pack_choice;    // ptrs to pack functions
+
+  void pack_id1(int, int, int, double *);
+  void pack_id2(int, int, int, double *);
+  void pack_time_created(int, int, int, double *);
+  void pack_time_broken(int, int, int, double *);
+  void pack_time_total(int, int, int, double *);
+  void pack_x(int, int, int, double *);
+  void pack_y(int, int, int, double *);
+  void pack_z(int, int, int, double *);
+  void pack_rmin(int, int, int, double *);
+  void pack_rave(int, int, int, double *);
+
+  void process_data(int, int, double *);
   void allocate();
 };
 
@@ -72,20 +94,37 @@ Self-explanatory.  Check the input script syntax and compare to the
 documentation for the command.  You can use -echo screen as a
 command-line option when running LAMMPS to see the offending line.
 
+E: Invalid keyword in pair tracker command
+
+Self-explanatory.
+
 E: Incorrect args for pair coefficients
 
 Self-explanatory.  Check the input script or data file.
 
+E: Must request at least one value to output
+
+Must include at least one bond property to store in fix store/local
+
 E: Pair tracker requires atom attribute radius for finite cutoffs
 
 The atom style defined does not have these attributes.
 
+E: Pair tracker incompatible with granular pairstyles that extend beyond contact
+
+Self-explanatory.
+
 E: Could not find pair fix neigh history ID
 
 The associated fix neigh/history is missing
 
-E: Cannot use pair tracker without fix pair/tracker
+E: Cannot use pair tracker without fix store/local
 
-This pairstyle requires one to define a pair/tracker fix
+The associated fix store/local does not exist
+
+E: Inconsistent number of output variables in fix store/local
+
+The number of values specified in fix store/local disagrees with
+the number of values requested in pair tracker
 
 */