Merge branch 'upstream' into regression-tests

cmake/CMakeLists.txt

@@ -204,7 +204,7 @@ option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
 # Support using clang-tidy for C++ files with selected options
 set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
 if(ENABLE_CLANG_TIDY)
-  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
 else()
   unset(CMAKE_CXX_CLANG_TIDY CACHE)
 endif()
@@ -306,6 +306,7 @@ set(STANDARD_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK
@@ -410,6 +411,7 @@ pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
 pkg_depends(MESONT MOLECULE)
+pkg_depends(RHEO BPM)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -550,7 +552,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -940,6 +942,7 @@ message(STATUS "<<< Compilers and Flags: >>>
 -- C++ Compiler:     ${CMAKE_CXX_COMPILER}
       Type:          ${CMAKE_CXX_COMPILER_ID}
       Version:       ${CMAKE_CXX_COMPILER_VERSION}
+      C++ Standard:  ${CMAKE_CXX_STANDARD}
       C++ Flags:    ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
       Defines:       ${DEFINES}")
 get_target_property(OPTIONS lammps COMPILE_OPTIONS)

cmake/Modules/Packages/ML-QUIP.cmake

@@ -27,7 +27,7 @@ if(DOWNLOAD_QUIP)
   else()
     message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
   endif()
-  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")

cmake/Modules/Packages/RHEO.cmake

@@ -0,0 +1,2 @@
+find_package(GSL 2.7 REQUIRED)
+target_link_libraries(lammps PRIVATE GSL::gsl)

cmake/Modules/Testing.cmake

@@ -102,9 +102,9 @@ endif()
 #######################################
 # select code sanitizer options
 #######################################
-set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, hwaddress, leak, thread, undefined)")
 mark_as_advanced(ENABLE_SANITIZER)
-set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set(ENABLE_SANITIZER_VALUES none address hwaddress leak thread undefined)
 set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
 validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
 string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)

cmake/presets/all_off.cmake

@@ -82,6 +82,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/all_on.cmake

@@ -84,6 +84,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK

doc/src/Build_development.rst

@@ -88,8 +88,8 @@ on recording all commands required to do the compilation.
 
 .. _sanitizer:
 
-Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
+Address, Leak, Undefined Behavior, and Thread Sanitizer Support (CMake only)
-----------------------------------------------------------------------
+----------------------------------------------------------------------------
 
 Compilers such as GCC and Clang support generating instrumented binaries
 which use different sanitizer libraries to detect problems in the code
@@ -110,6 +110,7 @@ compilation and linking stages.  This is done through setting the
 
    -D ENABLE_SANITIZER=none       # no sanitizer active (default)
    -D ENABLE_SANITIZER=address    # enable address sanitizer / memory leak checker
+   -D ENABLE_SANITIZER=hwaddress  # enable hardware assisted address sanitizer / memory leak checker
    -D ENABLE_SANITIZER=leak       # enable memory leak checker (only)
    -D ENABLE_SANITIZER=undefined  # enable undefined behavior sanitizer
    -D ENABLE_SANITIZER=thread     # enable thread sanitizer

doc/src/Build_extras.rst

@@ -59,6 +59,7 @@ This is the list of packages that may require additional steps.
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
    * :ref:`QMMM <qmmm>`
+   * :ref:`RHEO <rheo>`
    * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`
@@ -1566,10 +1567,11 @@ LAMMPS build.
    .. tab:: CMake build
 
       When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
-      command you must ensure that GSL is installed in locations that
+      command you must ensure that `the GNU Scientific Library (GSL)
-      are specified in your environment.  There are then two additional
+      <https://www.gnu.org/software/gsl/>` is installed in locations
-      variables that control the manner in which PLUMED is obtained and
+      that are accessible in your environment.  There are then two
-      linked into LAMMPS.
+      additional variables that control the manner in which PLUMED is
+      obtained and linked into LAMMPS.
 
       .. code-block:: bash
 
@@ -2040,6 +2042,36 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
 ----------
 
+.. _rheo:
+
+RHEO package
+------------
+
+To build with this package you must have the `GNU Scientific Library
+(GSL) <https://www.gnu.org/software/gsl/>` installed in locations that
+are accessible in your environment.  The GSL library should be at least
+version 2.7.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      If CMake cannot find the GSL library or include files, you can set:
+
+      .. code-block:: bash
+
+         -D GSL_ROOT_DIR=path    # path to root of GSL installation
+
+   .. tab:: Traditional make
+
+      LAMMPS will try to auto-detect the GSL compiler and linker flags
+      from the corresponding ``pkg-config`` file (``gsl.pc``), otherwise
+      you can edit the file ``lib/rheo/Makefile.lammps``
+      to specify the paths and library names where indicated by comments.
+      This must be done **before** the package is installed.
+
+----------
+
 .. _scafacos:
 
 SCAFACOS package

doc/src/Build_link.rst

@@ -45,8 +45,8 @@ executable code from the library is copied into the calling executable.
 
       .. code-block:: bash
 
-         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+         mpicc -c -O $(pkg-config --cflags liblammps) caller.c
-         mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
+         mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
 
    .. tab:: Traditional make
 
@@ -155,8 +155,8 @@ POEMS package installed becomes:
 
       .. code-block:: bash
 
-         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+         mpicc -c -O $(pkg-config --cflags liblammps) caller.c
-         mpicxx -o caller caller.o -$(pkgconf --libs)
+         mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
 
    .. tab:: Traditional make
 

doc/src/Build_package.rst

@@ -62,6 +62,7 @@ packages:
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
    * :ref:`QMMM <qmmm>`
+   * :ref:`RHEO <rheo>`
    * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`

doc/src/Commands_bond.rst

@@ -54,6 +54,7 @@ OPT.
    * :doc:`oxdna2/fene <bond_oxdna>`
    * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`rheo/shell <bond_rheo_shell>`
    * :doc:`special <bond_special>`
    * :doc:`table (o) <bond_table>`
 

doc/src/Commands_compute.rst

@@ -126,6 +126,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`
    * :doc:`reduce/region <compute_reduce>`
+   * :doc:`rheo/property/atom <compute_rheo_property_atom>`
    * :doc:`rigid/local <compute_rigid_local>`
    * :doc:`saed <compute_saed>`
    * :doc:`slcsa/atom <compute_slcsa_atom>`

doc/src/Commands_fix.rst

@@ -28,6 +28,7 @@ OPT.
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
+   * :doc:`add/heat <fix_add_heat>`
    * :doc:`addtorque <fix_addtorque>`
    * :doc:`alchemy <fix_alchemy>`
    * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
@@ -204,6 +205,11 @@ OPT.
    * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
+   * :doc:`rheo <fix_rheo>`
+   * :doc:`rheo/oxidation <fix_rheo_oxidation>`
+   * :doc:`rheo/pressure <fix_rheo_pressure>`
+   * :doc:`rheo/thermal <fix_rheo_thermal>`
+   * :doc:`rheo/viscosity <fix_rheo_viscosity>`
    * :doc:`rhok <fix_rhok>`
    * :doc:`rigid (o) <fix_rigid>`
    * :doc:`rigid/meso <fix_rigid_meso>`

doc/src/Commands_pair.rst

@@ -35,6 +35,10 @@ OPT.
    *
    *
    *
+   *
+   *
+   *
+   *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@@ -260,6 +264,8 @@ OPT.
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`rebomos (o) <pair_rebomos>`
    * :doc:`resquared (go) <pair_resquared>`
+   * :doc:`rheo <pair_rheo>`
+   * :doc:`rheo/solid <pair_rheo_solid>`
    * :doc:`saip/metal (t) <pair_saip_metal>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
    * :doc:`smatb <pair_smatb>`

doc/src/Examples.rst

@@ -134,6 +134,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | rerun       | use of rerun and read_dump commands                              |
 +-------------+------------------------------------------------------------------+
+| rheo        | RHEO simulations of fluid flows and phase transitions            |
++-------------+------------------------------------------------------------------+
 | rigid       | rigid bodies modeled as independent or coupled                   |
 +-------------+------------------------------------------------------------------+
 | shear       | sideways shear applied to 2d solid, with and without a void      |

doc/src/Howto.rst

@@ -89,6 +89,7 @@ Packages howto
    Howto_drude2
    Howto_peri
    Howto_manifold
+   Howto_rheo
    Howto_spins
 
 Tutorials howto

doc/src/Howto_chunk.rst

@@ -1,7 +1,7 @@
 Use chunks to calculate system properties
 =========================================
 
-In LAMMS, "chunks" are collections of atoms, as defined by the
+In LAMMPS, "chunks" are collections of atoms, as defined by the
 :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns
 each atom to a chunk ID (or to no chunk at all).  The number of chunks
 and the assignment of chunk IDs to atoms can be static or change over
@@ -148,14 +148,14 @@ Example calculations with chunks
 Here are examples using chunk commands to calculate various
 properties:
 
-(1) Average velocity in each of 1000 2d spatial bins:
+1. Average velocity in each of 1000 2d spatial bins:
 
 .. code-block:: LAMMPS
 
    compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
    fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
 
-(2) Temperature in each spatial bin, after subtracting a flow
+2. Temperature in each spatial bin, after subtracting a flow
 velocity:
 
 .. code-block:: LAMMPS
@@ -164,7 +164,7 @@ velocity:
    compute vbias all temp/profile 1 0 0 y 10
    fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
 
-(3) Center of mass of each molecule:
+3. Center of mass of each molecule:
 
 .. code-block:: LAMMPS
 
@@ -172,7 +172,7 @@ velocity:
    compute myChunk all com/chunk cc1
    fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
 
-(4) Total force on each molecule and ave/max across all molecules:
+4. Total force on each molecule and ave/max across all molecules:
 
 .. code-block:: LAMMPS
 
@@ -183,7 +183,7 @@ velocity:
    thermo 1000
    thermo_style custom step temp v_xave v_xmax
 
-(5) Histogram of cluster sizes:
+5. Histogram of cluster sizes:
 
 .. code-block:: LAMMPS
 
@@ -192,16 +192,16 @@ velocity:
    compute size all property/chunk cc1 count
    fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
 
-(6) An example for using a per-chunk value to apply per-atom forces to
+6. An example for using a per-chunk value to apply per-atom forces to
 compress individual polymer chains (molecules) in a mixture, is
 explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
 
-(7) An example for using one set of per-chunk values for molecule
+7. An example for using one set of per-chunk values for molecule
 chunks, to create a second set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the
 :doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page.
 
-(8) An example for using one set of per-chunk values (dipole moment
+8. An example for using one set of per-chunk values (dipole moment
 vectors) for molecule chunks, spreading the values to each atom in
 each chunk, then defining a second set of chunks as spatial bins, and
 using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an

doc/src/Howto_lammps_gui.rst

@@ -571,11 +571,12 @@ General Settings:
   size for the text editor and log font of the application can be set.
 - *GUI update interval:* Allows to set the time interval between GUI
   and data updates during a LAMMPS run in milliseconds. The default is
-  to update the GUI every 100 milliseconds. This is good for most cases.
+  to update the GUI every 10 milliseconds. This is good for most cases.
-  For LAMMPS runs that run very fast, however, data may be missed and
+  For LAMMPS runs that run *very* fast, however, data may be missed and
   through lowering this interval, this can be corrected. However, this
   will make the GUI use more resources, which may be a problem on some
-  computers with slower CPUs. The default value is 100 milliseconds.
+  computers with slower CPUs and a small number of CPU cores. This
+  setting may be changed to a value between 1 and 1000 milliseconds.
 
 Accelerators:
 ^^^^^^^^^^^^^

doc/src/Howto_rheo.rst

@@ -0,0 +1,116 @@
+Reproducing hydrodynamics and elastic objects (RHEO)
+====================================================
+
+The RHEO package is a hybrid implementation of smoothed particle
+hydrodynamics (SPH) for fluid flow, which can couple to the :doc:`BPM package
+<Howto_bpm>` to model solid elements. RHEO combines these methods to enable
+mesh-free modeling of multi-phase material systems. Its SPH solver supports
+many advanced options including reproducing kernels, particle shifting, free
+surface identification, and solid surface reconstruction. To model fluid-solid
+systems, the status of particles can dynamically change between a fluid and
+solid state, e.g. during melting/solidification, which determines how they
+interact and their physical behavior. The package is designed with modularity
+in mind, so one can easily turn various features on/off, adjust physical
+details of the system, or develop new capabilities. For instance, the numerics
+associated with calculating gradients, reproducing kernels, etc. are separated
+into distinctclasses to simplify the development of new integration schemes
+which can call these calculations. Additional numerical details can be found in
+:ref:`(Palermo) <howto_rheo_palermo>` and
+:ref:`(Clemmer) <howto_rheo_clemmer>`.
+
+Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
+<PKG-SPH>` package is likely better suited for your application. It has fewer advanced
+features and therefore benefits from improved performance. The :ref:`MACHDYN
+<PKG-MACHDYN>` package for solids may also be relevant for fluid-solid problems.
+
+----------
+
+At the core of the package is :doc:`fix rheo <fix_rheo>` which integrates
+particle trajectories and controls many optional features (e.g. the use
+of reproducing kernels). In conjunction to fix rheo, one must specify an
+instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
+of state and viscosity model, respectively. Optionally, one can model
+a heat equation with :doc:`fix rheo/thermal <fix_rheo_thermal>`, which also
+allows the user to specify equations for a particle's thermal conductivity,
+specific heat, latent heat, and melting temperature. The ordering of these
+fixes in an an input script matters. Fix rheo must be defined prior to all
+other RHEO fixes.
+
+Typically, RHEO requires atom style rheo. In addition to typical atom
+properties like positions and forces, particles store a local density,
+viscosity, pressure, and status. If thermal evolution is modeled, one must
+use atom style rheo/thermal which also includes a local energy, temperature, and
+conductivity. Note that the temperature is always derived from the energy.
+This implies the *temperature* attribute of :doc:`the set command <set>` does not
+affect particles. Instead, one should use the *sph/e* attribute.
+
+The status variable uses bit-masking to track various properties of a particle
+such as its current state of matter (fluid or solid) and its location relative
+to a surface. Some of these properties (and others) can be accessed using
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status*
+attribute in :doc:`the set command <set>` only allows control over the first bit
+which sets the state of matter, 0 is fluid and 1 is solid.
+
+Fluid interactions, including pressure forces, viscous forces, and heat exchange,
+are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
+pair rheo ignores the :doc:`special bond <special_bonds>` settings. Instead,
+it determines whether to calculate forces based on the status of particles: e.g.,
+hydrodynamic forces are only calculated if a fluid particle is involved.
+
+----------
+
+To model elastic objects, there are currently two mechanisms in RHEO, one designed
+for bulk solid bodies and the other for thin shells. Both mechanisms rely on
+introducing bonded forces between particles and therefore require a hybrid of atom
+style bond and rheo (or rheo/thermal).
+
+To create an elastic solid body, one has to (a) change the status of constituent
+particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
+bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
+more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
+apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
+pair rheo/solid considers a particles fluid/solid phase to determine whether to
+apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
+settings such that contact forces do not have to be calculated between two bonded
+solid particles in the same elastic body.
+
+In systems with thermal evolution, fix rheo/thermal can optionally set a
+melting/solidification temperature allowing particles to dynamically swap their
+state between fluid and solid when the temperature exceeds or drops below the
+critical temperature, respectively. Using the *react* option, one can specify a maximum
+bond length and a bond type. Then, when solidifying, particles will search their
+local neighbors and automatically create bonds with any neighboring solid particles
+in range. For BPM bond styles, bonds will then use the immediate position of the two
+particles to calculate a reference state. When melting, particles will delete any
+bonds of the specified type when reverting to a fluid state. Special bonds are updated
+as bonds are created/broken.
+
+The other option for elastic objects is an elastic shell that is nominally much
+thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
+on the surface of a fluid. Currently, this is implemented using
+:doc:`fix rheo/oxidation <fix_rheo_oxidation>` and bond style
+:doc:`rheo/shell <bond_rheo_shell>`. Essentially, fix rheo/oxidation creates candidate
+bonds of a specified type between surface fluid particles within a specified distance.
+a newly created rheo/shell bond will then start a timer. While the timer is counting
+down, the bond will delete itself if particles move too far apart or move away from the
+surface. However, if the timer reaches a user-defined threshold, then the bond will
+activate and apply additional forces to the fluid particles. Bond style rheo/shell
+then operates very similarly to a BPM bond style, storing a reference length and
+breaking if stretched too far. Unlike the above method, this option does not remove
+the underlying fluid interactions (although particle shifting is turned off) and does
+not modify special bond settings of particles.
+
+While these two options are not expected to be appropriate for every system,
+either framework can be modified to create more suitable models (e.g. by changing the
+criteria for creating/deleting a bond or altering force calculations).
+
+----------
+
+.. _howto_rheo_palermo:
+
+**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
+
+.. _howto_rheo_clemmer:
+
+**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

doc/src/Packages_details.rst

@@ -8,12 +8,12 @@ info on how to download or build any extra library it requires.  It also
 gives links to documentation, example scripts, and pictures/movies (if
 available) that illustrate use of the package.
 
-The majority of packages can be included in a LAMMPS build with a
+The majority of packages can be included in a LAMMPS build with a single
-single setting (``-D PKG_<NAME>=on`` for CMake) or command
+setting (``-D PKG_<NAME>=on`` for CMake) or command (``make yes-<name>``
-(``make yes-<name>`` for make).  See the :doc:`Build package <Build_package>`
+for make).  See the :doc:`Build package <Build_package>` page for more
-page for more info.  A few packages may require additional steps;
+info.  A few packages may require additional steps; this is indicated in
-this is indicated in the descriptions below.  The :doc:`Build extras <Build_extras>`
+the descriptions below.  The :doc:`Build extras <Build_extras>` page
-page gives those details.
+gives those details.
 
 .. note::
 
@@ -103,6 +103,7 @@ page gives those details.
    * :ref:`QEQ <PKG-QEQ>`
    * :ref:`QMMM <PKG-QMMM>`
    * :ref:`QTB <PKG-QTB>`
+   * :ref:`RHEO <PKG-RHEO>`
    * :ref:`REACTION <PKG-REACTION>`
    * :ref:`REAXFF <PKG-REAXFF>`
    * :ref:`REPLICA <PKG-REPLICA>`
@@ -1323,18 +1324,19 @@ KSPACE package
 
 **Contents:**
 
-A variety of long-range Coulombic solvers, as well as pair styles
+A variety of long-range Coulombic solvers, as well as pair styles which
-which compute the corresponding short-range pairwise Coulombic
+compute the corresponding short-range pairwise Coulombic interactions.
-interactions.  These include Ewald, particle-particle particle-mesh
+These include Ewald, particle-particle particle-mesh (PPPM), and
-(PPPM), and multilevel summation method (MSM) solvers.
+multilevel summation method (MSM) solvers.
 
 **Install:**
 
-Building with this package requires a 1d FFT library be present on
+Building with this package requires a 1d FFT library be present on your
-your system for use by the PPPM solvers.  This can be the KISS FFT
+system for use by the PPPM solvers.  This can be the KISS FFT library
-library provided with LAMMPS, third party libraries like FFTW, or a
+provided with LAMMPS, third party libraries like FFTW, or a
-vendor-supplied FFT library.  See the :doc:`Build settings <Build_settings>` page for details on how to select
+vendor-supplied FFT library.  See the :doc:`Build settings
-different FFT options for your LAMPMS build.
+<Build_settings>` page for details on how to select different FFT
+options for your LAMMPS build.
 
 **Supporting info:**
 
@@ -2621,6 +2623,45 @@ another set.
 
 ----------
 
+.. _PKG-RHEO:
+
+RHEO package
+------------
+
+**Contents:**
+
+Pair styles, bond styles, fixes, and computes for reproducing
+hydrodynamics and elastic objects. See the :doc:`Howto rheo
+<Howto_rheo>` page for an overview.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <rheo>` on the :doc:`Build extras <Build_extras>` page.
+
+**Authors:** Joel T. Clemmer (Sandia National Labs),
+Thomas C. O'Connor (Carnegie Mellon University)
+
+.. versionadded:: TBD
+
+**Supporting info:**
+
+* src/RHEO filenames -> commands
+* :doc:`Howto_rheo <Howto_rheo>`
+* :doc:`atom_style rheo <atom_style>`
+* :doc:`atom_style rheo/thermal <atom_style>`
+* :doc:`bond_style rheo/shell <bond_rheo_shell>`
+* :doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+* :doc:`fix rheo <fix_rheo>`
+* :doc:`fix rheo/oxidation <fix_rheo_oxidation>`
+* :doc:`fix rheo/pressure <fix_rheo_pressure>`
+* :doc:`fix rheo/thermal <fix_rheo_thermal>`
+* :doc:`fix rheo/viscosity <fix_rheo_viscosity>`
+* :doc:`pair_style rheo <pair_rheo>`
+* :doc:`pair_style rheo/solid <pair_rheo_solid>`
+* examples/rheo
+
+----------
+
 .. _PKG-RIGID:
 
 RIGID package

doc/src/Packages_list.rst

@@ -413,6 +413,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>`
      - qtb
      - no
+   * - :ref:`RHEO <PKG-RHEO>`
+     - reproducing hydrodynamics and elastic objects
+     - :doc:`Howto rheo <Howto_rheo>`
+     - rheo
+     - no
    * - :ref:`REACTION <PKG-REACTION>`
      - chemical reactions in classical MD
      - :doc:`fix bond/react <fix_bond_react>`

doc/src/Tools.rst

@@ -1329,7 +1329,7 @@ for Tcl with:
 .. code-block:: bash
 
    swig -tcl -module tcllammps lammps.i
-   gcc -fPIC -shared $(pkgconf --cflags tcl) -o tcllammps.so \
+   gcc -fPIC -shared $(pkg-config tcl --cflags) -o tcllammps.so \
                lammps_wrap.c -L ../src/ -llammps
    tclsh
 
@@ -1340,8 +1340,8 @@ functions included with:
 
    swig -tcl -module tcllmps lammps_shell.i
    gcc -o tcllmpsh lammps_wrap.c -Xlinker -export-dynamic \
-            -DHAVE_CONFIG_H $(pkgconf --cflags tcl) \
+            -DHAVE_CONFIG_H $(pkg-config tcl --cflags) \
-            $(pkgconf --libs tcl) -L ../src -llammps
+            $(pkg-config tcl --libs) -L ../src -llammps
 
 In both cases it is assumed that the LAMMPS library was compiled
 as a shared library in the ``src`` folder. Otherwise the last

doc/src/atom_modify.rst

@@ -190,7 +190,7 @@ Default
 By default, *id* is yes.  By default, atomic systems (no bond topology
 info) do not use a map.  For molecular systems (with bond topology
 info), the default is to use a map of either *array* or *hash* style
-depending on the size of the sustem, as explained above for the *map
+depending on the size of the system, as explained above for the *map
 yes* keyword/value option.  By default, a *first* group is not
 defined.  By default, sorting is enabled with a frequency of 1000 and
 a binsize of 0.0, which means the neighbor cutoff will be used to set

doc/src/atom_style.rst

@@ -189,6 +189,14 @@ the Additional Information section below.
      - *atomic* + molecule, radius, rmass + "smd data"
      - :ref:`MACHDYN <PKG-MACHDYN>`
      - Smooth Mach Dynamics models
+   * - *rheo*
+     - *atomic* + rho, status
+     - :ref:`RHEO <PKG-RHEO>`
+     - solid and fluid RHEO particles
+   * - *rheo/thermal*
+     - *atomic* + rho, status, energy, temperature
+     - :ref:`RHEO <PKG-RHEO>`
+     - RHEO particles with temperature
    * - *sph*
      - *atomic* + "sph data"
      - :ref:`SPH <PKG-SPH>`

doc/src/bond_rheo_shell.rst

@@ -0,0 +1,188 @@
+.. index:: bond_style rheo/shell
+
+bond_style rheo/shell command
+=============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style rheo/shell keyword value attribute1 attribute2 ...
+
+* required keyword = *t/form*
+* optional keyword = *store/local*
+
+  .. parsed-literal::
+
+       *t/form* value = formation time for a bond (time units)
+
+       *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)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style rheo/shell t/form 10.0
+   bond_coeff 1 1.0 0.05 0.1
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+The *rheo/shell* bond style is designed to work with
+:doc:`fix rheo/oxidation <fix_rheo_oxidation>` which creates candidate
+bonds between eligible surface or near-surface particles. When a bond
+is first created, it computes no forces and starts a timer. Forces are
+not computed until the timer reaches the specified bond formation time,
+*t/form*, and the bond is enabled and applies forces. If the two particles
+move outside of the maximum bond distance or move into the bulk before
+the timer reaches *t/form*, the bond automatically deletes itself. This
+deletion is not recorded as a broken bond in the optional *store/local* fix.
+
+Before bonds are enabled, they are still treated as regular bonds by
+all other parts of LAMMPS. This means they are written to data files
+and counted in computes such as :doc:`nbond/atom <compute_nbond_atom>`.
+To only count enabled bonds, use the *nbond/shell* attribute in
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`.
+
+When enabled, the bond then computes forces based on deviations from
+the initial reference state of the two atoms much like a BPM style
+bond (as further discussed in the :doc:`BPM howto page <Howto_bpm>`).
+The reference state is stored by each bond when it is first enabled.
+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 or the timer.
+
+This bond style is based on a model described in
+:ref:`(Clemmer) <rheo_clemmer>`. The force has a magnitude of
+
+.. math::
+
+   F = 2 k (r - r_0) + \frac{2 k}{r_0^2 \epsilon_c^2} (r - r_0)^3
+
+where :math:`k` is a stiffness, :math:`r` is the current distance
+and :math:`r_0` is the initial distance between the two particles, and
+:math:`\epsilon_c` is maximum strain beyond which a bond breaks. This
+is done by setting the bond type to 0 such that forces are no longer
+computed.
+
+A damping force proportional to the difference in the normal velocity
+of particles is also applied to bonded particles:
+
+.. math::
+
+   F_D = - \gamma w (\hat{r} \bullet \vec{v})
+
+where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
+displacement normal vector, and :math:`\vec{v}` is the velocity difference
+between the two particles.
+
+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)
+
+Unlike other BPM-style bonds, this bond style does not update special
+bond settings when bonds are created or deleted. This bond style also
+does not enforce specific :doc:`special_bonds <special_bonds>` settings.
+This behavior is purposeful such :doc:`RHEO pair <pair_rheo>` forces
+and heat flows are still calculated.
+
+If the *store/local* keyword is used, an internal 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 this optional
+keyword, 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 restore bonds. However, the reference state is NOT
+written to data files. Therefore reading a data file will not
+restore bonds and will cause their reference states to be redefined.
+
+If the *store/local* option is used, an internal fix will calculate
+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, broken bonds.  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.
+
+The single() function of this bond style returns 0.0 for the energy
+of a bonded interaction, since energy is not conserved in these
+dissipative potentials.  The single() function also calculates two
+extra bond quantities, the initial distance :math:`r_0` and a time.
+These extra quantities can be accessed by the
+:doc:`compute bond/local <compute_bond_local>` command as *b1* and *b2*\ .
+
+Restrictions
+""""""""""""
+
+This bond style is part of the RHEO 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:`bond_coeff <bond_coeff>`, :doc:`fix rheo/oxidation <fix_rheo_oxidation>`
+
+Default
+"""""""
+
+NA
+
+----------
+
+.. _rheo_clemmer:
+
+**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

doc/src/bond_style.rst

@@ -105,6 +105,7 @@ accelerated styles exist.
 * :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
 * :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
 * :doc:`quartic <bond_quartic>` - breakable quartic bond
+* :doc:`rheo/shell <bond_rheo_shell>` - shell bond for oxidation modeling in RHEO
 * :doc:`special <bond_special>` - enable special bond exclusions for 1-5 pairs and beyond
 * :doc:`table <bond_table>` - tabulated by bond length
 

doc/src/compute.rst

@@ -290,6 +290,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
 * :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
 * :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
+* :doc:`rheo/property/atom <compute_rheo_property_atom>` - convert atom attributes in RHEO package to per-atom vectors/arrays
 * :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
 * :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
 * :doc:`slcsa/atom <compute_slcsa_atom>` - perform Supervised Learning Crystal Structure Analysis (SL-CSA)

doc/src/compute_nbond_atom.rst

@@ -8,10 +8,17 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   compute ID group-ID nbond/atom
+   compute ID group-ID nbond/atom keyword value
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * nbond/atom = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *bond/type*
+
+  .. parsed-literal::
+
+       *bond/type* value = *btype*
+         *btype* = bond type included in count
 
 Examples
 """"""""
@@ -19,6 +26,7 @@ Examples
 .. code-block:: LAMMPS
 
    compute 1 all nbond/atom
+   compute 1 all nbond/atom bond/type 2
 
 Description
 """""""""""
@@ -31,6 +39,9 @@ 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.
 
+If the keyword *bond/type* is specified, only bonds of *btype* are
+counted.
+
 Output info
 """""""""""
 

doc/src/compute_rheo_property_atom.rst

@@ -0,0 +1,143 @@
+.. index:: compute rheo/property/atom
+
+compute rheo/property/atom command
+==================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID rheo/property/atom input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* rheo/property/atom = style name of this compute command
+* input = one or more atom attributes
+
+  .. parsed-literal::
+
+       possible attributes = phase, surface, surface/r,
+                             surface/divr, surface/n/a, coordination,
+                             shift/v/a, energy, temperature, heatflow,
+                             conductivity, cv, viscosity, pressure, rho,
+                             grad/v/ab, stress/v/ab, stress/t/ab, nbond/shell
+
+  .. parsed-literal::
+
+           *phase* = atom phase state
+           *surface* = atom surface status
+           *surface/r* = atom distance from the surface
+           *surface/divr* = divergence of position at atom position
+           *surface/n/a* = a-component of surface normal vector
+           *coordination* = coordination number
+           *shift/v/a* = a-component of atom shifting velocity
+           *energy* = atom energy
+           *temperature* = atom temperature
+           *heatflow* = atom heat flow
+           *conductivity* = atom conductivity
+           *cv* = atom specific heat
+           *viscosity* = atom viscosity
+           *pressure* = atom pressure
+           *rho* = atom density
+           *grad/v/ab* = ab-component of atom velocity gradient tensor
+           *stress/v/ab* = ab-component of atom viscous stress tensor
+           *stress/t/ab* = ab-component of atom total stress tensor (pressure and viscous)
+           *nbond/shell* = number of oxide bonds
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all rheo/property/atom phase surface/r surface/n/* pressure
+   compute 2 all rheo/property/atom shift/v/x grad/v/xx stress/v/*
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Define a computation that stores atom attributes specific to the RHEO
+package for each atom in the group.  This is useful so that the values
+can be used by other :doc:`output commands <Howto_output>` that take
+computes as inputs. See for example, the
+:doc:`compute reduce <compute_reduce>`,
+:doc:`fix ave/atom <fix_ave_atom>`,
+:doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`fix ave/chunk <fix_ave_chunk>`, and
+:doc:`atom-style variable <variable>` commands.
+
+For vector attributes, e.g. *shift/v/*:math:`\alpha`, one must specify
+:math:`\alpha` as the *x*, *y*, or *z* component, e.g. *shift/v/x*.
+Alternatively, a wild card \* will include all components, *x* and *y* in
+2D or *x*, *y*, and *z* in 3D.
+
+For tensor attributes, e.g. *grad/v/*:math:`\alpha \beta`, one must specify
+both :math:`\alpha` and :math:`\beta` as  *x*, *y*, or *z*, e.g. *grad/v/xy*.
+Alternatively, a wild card \* will include all components. In 2D, this
+includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
+*yx*, *yy*, *yz*, *zx*, *zy*, and *zz*.
+
+Many properties require their respective fixes, listed below in related
+commands, be defined. For instance, the *viscosity* attribute is the
+viscosity of a particle calculated by
+:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
+properties is described below.
+
+The *phase* property indicates whether the particle is in a fluid state,
+a value of 0, or a solid state, a value of 1.
+
+The *surface* property indicates the surface designation produced by
+the *interface/reconstruct* option of :doc:`fix rheo <fix_rheo>`. Bulk
+particles have a value of 0, surface particles have a value of 1, and
+splash particles have a value of 2. The *surface/r* property is the
+distance from the surface, up to the kernel cutoff length. Surface particles
+have a value of 0. The *surface/n/*:math:`\alpha` properties are the
+components of the surface normal vector.
+
+The *shift/v/*:math:`\alpha` properties are the components of the shifting
+velocity produced by the *shift* option of :doc:`fix rheo <fix_rheo>`.
+
+The *nbond/shell* property is the number of shell bonds that have been
+activated from :doc:`bond style rheo/shell <bond_rheo_shell>`.
+
+The values are stored in a per-atom vector or array as discussed
+below.  Zeroes are stored for atoms not in the specified group or for
+quantities that are not defined for a particular particle in the group
+
+Output info
+"""""""""""
+
+This compute calculates a per-atom vector or per-atom array depending
+on the number of input values.  Generally, if a single input is specified,
+a per-atom vector is produced.  If two or more inputs are specified, a
+per-atom array is produced where the number of columns = the number of
+inputs. However, if a wild card \* is used for a vector or tensor, then
+the number of inputs is considered to be incremented by the dimension or
+the dimension squared, respectively. The vector or array can be accessed
+by any command that uses per-atom 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 in whatever :doc:`units <units>` the
+corresponding attribute is in (e.g., density units for *rho*).
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`,
+:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`fix rheo/pressure <fix_rheo_pressure>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`fix rheo/oxdiation <fix_rheo_oxidation>`,
+:doc:`fix rheo <fix_rheo>`
+
+Default
+"""""""
+
+none

doc/src/fix.rst

@@ -193,6 +193,7 @@ accelerated styles exist.
 * :doc:`adapt <fix_adapt>` - change a simulation parameter over time
 * :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
 * :doc:`addforce <fix_addforce>` - add a force to each atom
+* :doc:`add/heat <fix_add_heat>` - add a heat flux to each atom
 * :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
 * :doc:`alchemy <fix_alchemy>` - perform an "alchemical transformation" between two partitions
 * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
@@ -369,6 +370,11 @@ accelerated styles exist.
 * :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information
 * :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
 * :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
+* :doc:`rheo <fix_rheo>` - integrator for the RHEO package
+* :doc:`rheo/thermal <fix_rheo_thermal>` - thermal integrator for the RHEO package
+* :doc:`rheo/oxidation <fix_rheo_oxidation>` - create oxidation bonds for the RHEO package
+* :doc:`rheo/pressure <fix_rheo_pressure>` - pressure calculation for the RHEO package
+* :doc:`rheo/viscosity <fix_rheo_pressure>` - viscosity calculation for the RHEO package
 * :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems
 * :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
 * :doc:`rigid/meso <fix_rigid_meso>` - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body

doc/src/fix_add_heat.rst

@@ -0,0 +1,111 @@
+.. index:: fix add/heat
+
+fix add/heat command
+====================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID add/heat style args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* add/heat = style name of this fix command
+* style = *constant* or *linear* or *quartic*
+
+  .. parsed-literal::
+
+       *constant* args = *rate*
+         *rate* = rate of heat flow (energy/time units)
+       *linear* args = :math:`T_{target}` *k*
+         :math:`T_{target}` = target temperature (temperature units)
+         *k* = prefactor (energy/(time*temperature) units)
+       *quartic* args = :math:`T_{target}` *k*
+         :math:`T_{target}` = target temperature (temperature units)
+         *k* = prefactor (energy/(time*temperature^4) units)
+
+* zero or more keyword/value pairs may be appended to args
+* keyword = *overwrite*
+
+  .. parsed-literal::
+
+       *overwrite* value = *yes* or *no*
+         *yes* = sets current heat flow of particle
+         *no* = adds to current heat flow of particle
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all add/heat constant v_heat
+   fix 1 all add/heat linear 10.0 1.0 overwrite yes
+
+Description
+"""""""""""
+
+This fix adds heat to particles with the temperature attribute every timestep.
+Note that this is an internal temperature of a particle intended for use with
+non-atomistic models like the discrete element method.
+
+For the *constant* style, heat is added at the specified rate. For the *linear* style,
+heat is added at a rate of :math:`k (T_{target} - T)` where :math:`k` is the
+specified prefactor, :math:`T_{target}` is the specified target temperature, and
+:math:`T` is the temperature of the atom. This may be more representative of a
+conductive process. For the *quartic* style, heat is added at a rate of
+:math:`k (T_{target}^4 - T^4)`, akin to radiative heat transfer.
+
+The rate or temperature can be can be specified as an equal-style or atom-style
+:doc:`variable <variable>`.  If the value is a variable, it should be
+specified as v_name, where name is the variable name.  In this case, the
+variable will be evaluated each time step, and its value will be used to
+determine the rate of heat added.
+
+Equal-style variables can specify formulas with various mathematical
+functions and include :doc:`thermo_style <thermo_style>` command
+keywords for the simulation box parameters, time step, and elapsed time
+to specify time-dependent heating.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates to specify spatially-dependent heating.
+
+If the *overwrite* keyword is set to *yes*, this fix will set the total
+heat flow on a particle every timestep, overwriting contributions from pair
+styles or other fixes. If *overwrite* is *no*, this fix will add heat on
+top of other contributions.
+
+----------
+
+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 pair style is part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
+
+This fix requires that atoms store temperature and heat flow
+as defined by the :doc:`fix property/atom <fix_property_atom>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix heat/flow <fix_heat_flow>`,
+:doc:`fix property/atom <fix_property_atom>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`
+
+Default
+"""""""
+
+The default for the *overwrite* keyword is *no*

doc/src/fix_deform.rst

@@ -4,9 +4,6 @@
 fix deform command
 ==================
 
-:doc:`fix deform/pressure <fix_deform_pressure>` command
-========================================================
-
 Accelerator Variants: *deform/kk*
 
 Syntax
@@ -14,12 +11,11 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   fix ID group-ID fix_style N parameter style args ... keyword value ...
+   fix ID group-ID deform N parameter style args ... keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* fix_style = *deform* or *deform/pressure*
 * N = perform box deformation every this many timesteps
-* one or more parameter/style/args sequences of arguments may be appended
+* one or more parameter/args sequences may be appended
 
   .. parsed-literal::
 
@@ -46,12 +42,6 @@ Syntax
            *variable* values = v_name1 v_name2
              v_name1 = variable with name1 for box length change as function of time
              v_name2 = variable with name2 for change rate as function of time
-           *pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-             target = target pressure (pressure units)
-             gain = proportional gain constant (1/(time * pressure) or 1/time units)
-           *pressure/mean* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-             target = target pressure (pressure units)
-             gain = proportional gain constant (1/(time * pressure) or 1/time units)
 
        *xy*, *xz*, *yz* args = style value
          style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable*
@@ -64,8 +54,6 @@ Syntax
                  effectively an engineering shear strain rate
            *erate* value = R
              R = engineering shear strain rate (1/time units)
-           *erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-             R = engineering shear strain rate (1/time units)
            *trate* value = R
              R = true shear strain rate (1/time units)
            *wiggle* values = A Tp
@@ -74,9 +62,6 @@ Syntax
            *variable* values = v_name1 v_name2
              v_name1 = variable with name1 for tilt change as function of time
              v_name2 = variable with name2 for change rate as function of time
-           *pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-             target = target pressure (pressure units)
-             gain = proportional gain constant (1/(time * pressure) or 1/time units)
 
 * zero or more keyword/value pairs may be appended
 * keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
@@ -92,15 +77,6 @@ Syntax
        *units* value = *lattice* or *box*
          lattice = distances are defined in lattice units
          box = distances are defined in simulation box units
-       *couple* value = *none* or *xyz* or *xy* or *yz* or *xz* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-         couple pressure values of various dimensions
-       *vol/balance/p* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-         Modifies the behavior of the *volume* option to try and balance pressures
-       *max/rate* value = *rate* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-         rate = maximum strain rate for pressure control
-       *normalize/pressure* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-         Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
-
 
 Examples
 """"""""
@@ -112,8 +88,6 @@ Examples
    fix 1 all deform 1 xy erate 0.001 remap v
    fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
 
-See examples for :doc:`fix deform/pressure <fix_deform_pressure>` on its doc page
-
 Description
 """""""""""
 
@@ -123,17 +97,13 @@ run.  Orthogonal simulation boxes have 3 adjustable parameters
 adjustable parameters (x,y,z,xy,xz,yz).  Any or all of them can be
 adjusted independently and simultaneously.
 
-The fix deform command allows use of all the arguments listed above,
+The :doc:`fix deform/pressure <fix_deform_pressure>` command extends
-except those flagged as available ONLY for the :doc:`fix
+this command with additional keywords and arguments.  The rest of this
-deform/pressure <fix_deform_pressure>` command, which are
+page explains the options common to both commands.  The :doc:`fix
-pressure-based controls.  The fix deform/pressure command allows use
+deform/pressure <fix_deform_pressure>` page explains the options
-of all the arguments listed above.
+available ONLY with the fix deform/pressure command.  Note that a
-
+simulation can define only a single deformation command: fix deform or
-The rest of this doc page explains the options common to both
+fix deform/pressure.
-commands.  The :doc:`fix deform/pressure <fix_deform_pressure>` doc
-page explains the options available ONLY with the fix deform/pressure
-command.  Note that a simulation can define only a single deformation
-command: fix deform or fix deform/pressure.
 
 Both these fixes can be used to perform non-equilibrium MD (NEMD)
 simulations of a continuously strained system.  See the :doc:`fix
@@ -143,6 +113,24 @@ simulation of a continuously extended system (extensional flow) can be
 modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix
 commands <fix_nh_uef>`.
 
+.. admonition:: Inconsistent trajectories due to image flags
+   :class: warning
+
+   When running long simulations while shearing the box or using a high
+   shearing rate, it is possible that the image flags used for storing
+   unwrapped atom positions will "wrap around".  When LAMMPS is compiled
+   with the default settings, case image flags are limited to a range of
+   :math:`-512 \le i \le 511`, which will overflow when atoms starting
+   at zero image flag value have passed through a periodic box dimension
+   more than 512 times.
+
+   Changing the :ref:`size of LAMMPS integer types <size>` to the
+   "bigbig" setting can make this overflow much less likely, since it
+   increases the image flag value range to :math:`- 1,048,576 \le i \le
+   1\,048\,575`
+
+----------
+
 For the *x*, *y*, *z* parameters, the associated dimension cannot be
 shrink-wrapped.  For the *xy*, *yz*, *xz* parameters, the associated
 second dimension cannot be shrink-wrapped.  Dimensions not varied by

doc/src/fix_deform_pressure.rst

@@ -13,29 +13,66 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * deform/pressure = style name of this fix command
 * N = perform box deformation every this many timesteps
-* one or more parameter/arg sequences may be appended
+* one or more parameter/args sequences may be appended
 
   .. parsed-literal::
 
      parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *box*
        *x*, *y*, *z* args = style value(s)
          style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
+           *final* values = lo hi
+             lo hi = box boundaries at end of run (distance units)
+           *delta* values = dlo dhi
+             dlo dhi = change in box boundaries at end of run (distance units)
+           *scale* values = factor
+             factor = multiplicative factor for change in box length at end of run
+           *vel* value = V
+             V = change box length at this velocity (distance/time units),
+                 effectively an engineering strain rate
+           *erate* value = R
+             R = engineering strain rate (1/time units)
+           *trate* value = R
+             R = true strain rate (1/time units)
+           *volume* value = none = adjust this dim to preserve volume of system
+           *wiggle* values = A Tp
+             A = amplitude of oscillation (distance units)
+             Tp = period of oscillation (time units)
+           *variable* values = v_name1 v_name2
+             v_name1 = variable with name1 for box length change as function of time
+             v_name2 = variable with name2 for change rate as function of time
            *pressure* values = target gain
              target = target pressure (pressure units)
              gain = proportional gain constant (1/(time * pressure) or 1/time units)
            *pressure/mean* values = target gain
              target = target pressure (pressure units)
              gain = proportional gain constant (1/(time * pressure) or 1/time units)
-           NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
 
        *xy*, *xz*, *yz* args = style value
          style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale*
+           *final* value = tilt
+             tilt = tilt factor at end of run (distance units)
+           *delta* value = dtilt
+             dtilt = change in tilt factor at end of run (distance units)
+           *vel* value = V
+             V = change tilt factor at this velocity (distance/time units),
+                 effectively an engineering shear strain rate
+           *erate* value = R
+             R = engineering shear strain rate (1/time units)
+           *erate/rescale* value = R
+             R = engineering shear strain rate (1/time units)
+           *trate* value = R
+             R = true shear strain rate (1/time units)
+           *wiggle* values = A Tp
+             A = amplitude of oscillation (distance units)
+             Tp = period of oscillation (time units)
+           *variable* values = v_name1 v_name2
+             v_name1 = variable with name1 for tilt change as function of time
+             v_name2 = variable with name2 for change rate as function of time
            *pressure* values = target gain
              target = target pressure (pressure units)
              gain = proportional gain constant (1/(time * pressure) or 1/time units)
            *erate/rescale* value = R
              R = engineering shear strain rate (1/time units)
-           NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
 
        *box* = style value
          style = *volume* or *pressure*
@@ -49,6 +86,15 @@ Syntax
 
   .. parsed-literal::
 
+       *remap* value = *x* or *v* or *none*
+         x = remap coords of atoms in group into deforming box
+         v = remap velocities of atoms in group when they cross periodic boundaries
+         none = no remapping of x or v
+       *flip* value = *yes* or *no*
+         allow or disallow box flips when it becomes highly skewed
+       *units* value = *lattice* or *box*
+         lattice = distances are defined in lattice units
+         box = distances are defined in simulation box units
        *couple* value = *none* or *xyz* or *xy* or *yz* or *xz*
          couple pressure values of various dimensions
        *vol/balance/p* value = *yes* or *no*
@@ -57,7 +103,6 @@ Syntax
          rate = maximum strain rate for pressure control
        *normalize/pressure* value = *yes* or *no*
          Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
-       NOTE: All other keywords are documented by the :doc:`fix deform <fix_deform>` command
 
 Examples
 """"""""
@@ -79,10 +124,26 @@ pressure-based controls implemented by this command.
 
 All arguments described on the :doc:`fix deform <fix_deform>` doc page
 also apply to this fix unless otherwise noted below.  The rest of this
-doc page explains the arguments specific to this fix.  Note that a
+page explains the arguments specific to this fix only.  Note that a
 simulation can define only a single deformation command: fix deform or
 fix deform/pressure.
 
+.. admonition:: Inconsistent trajectories due to image flags
+   :class: warning
+
+   When running long simulations while shearing the box or using a high
+   shearing rate, it is possible that the image flags used for storing
+   unwrapped atom positions will "wrap around".  When LAMMPS is compiled
+   with the default settings, case image flags are limited to a range of
+   :math:`-512 \le i \le 511`, which will overflow when atoms starting
+   at zero image flag value have passed through a periodic box dimension
+   more than 512 times.
+
+   Changing the :ref:`size of LAMMPS integer types <size>` to the
+   "bigbig" setting can make this overflow much less likely, since it
+   increases the image flag value range to :math:`- 1,048,576 \le i \le
+   1\,048\,575`
+
 ----------
 
 For the *x*, *y*, and *z* parameters, this is the meaning of the

doc/src/fix_electrode.rst

@@ -38,7 +38,7 @@ Syntax
        *electrode/thermo* args = potential eta *temp* values
             potential = electrode potential
             charge = electrode charge
-            eta = reciprocal width of electrode charge smearing
+            eta = reciprocal width of electrode charge smearing (can be NULL if eta keyword is used)
             *temp* values = T_v tau_v rng_v
                 T_v = temperature of thermo-potentiostat
                 tau_v = time constant of thermo-potentiostat
@@ -110,7 +110,7 @@ electrostatic configurations:
   :ref:`(Deissenbeck)<Deissenbeck>` between two electrodes
 
   * (resulting in changing charges and potentials with appropriate
-     average potential difference and thermal variance)
+    average potential difference and thermal variance)
 
 The first group-ID provided to each fix specifies the first electrode
 group, and more group(s) are added using the *couple* keyword for each
@@ -287,8 +287,18 @@ The *fix_modify tf* option enables the Thomas-Fermi metallicity model
    fix_modify ID tf type length voronoi
 
 
-If this option is used parameters must be set for all atom types of the
+If this option is used, these two parameters must be set for
-electrode.
+all atom types of the electrode:
+
+* `tf` is the Thomas-Fermi length :math:`l_{TF}`
+* `voronoi` is the Voronoi volume per atom in units of length cubed
+
+Different types may have different `tf` and `voronoi` values.
+The following self-energy term is then added for all electrode atoms:
+
+.. math::
+
+  A_{ii} += \frac{1}{4 \pi \epsilon_0} \times \frac{4 \pi l_{TF}^2}{\mathrm{Voronoi volume}}
 
 The *fix_modify timer* option turns on (off) additional timer outputs in the log
 file, for code developers to track optimization.
@@ -321,9 +331,11 @@ The global array has *N* rows and *2N+1* columns, where the fix manages
 array, the elements are:
 
 * array[I][1] = total charge that group *I* would have had *if it were
-  at 0 V applied potential* * array[I][2 to *N* + 1] = the *N* entries
+  at 0 V applied potential*
+* array[I][2 to *N* + 1] = the *N* entries
   of the *I*-th row of the electrode capacitance matrix (definition
-  follows) * array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
+  follows)
+* array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
   *I*-th row of the electrode elastance matrix (the inverse of the
   electrode capacitance matrix)
 

doc/src/fix_heat_flow.rst

@@ -1,7 +1,7 @@
 .. index:: fix heat/flow
 
 fix heat/flow command
-==========================
+=====================
 
 Syntax
 """"""
@@ -56,13 +56,19 @@ not invoked during :doc:`energy minimization <minimize>`.
 Restrictions
 """"""""""""
 
+This pair style is part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
+
 This fix requires that atoms store temperature and heat flow
 as defined by the :doc:`fix property/atom <fix_property_atom>` command.
 
 Related commands
 """"""""""""""""
 
-:doc:`pair granular <pair_granular>`, :doc:`fix property/atom <fix_property_atom>`
+:doc:`pair granular <pair_granular>`,
+:doc:`fix add/heat <fix_add_heat>`,
+:doc:`fix property/atom <fix_property_atom>`
 
 Default
 """""""

doc/src/fix_indent.rst

@@ -68,10 +68,10 @@ material or as an obstacle in a flow.  Alternatively, it can be used as a
 constraining wall around a simulation; see the discussion of the
 *side* keyword below.
 
-The *gstyle* geometry of the indenter can either be a sphere, a
+The *gstyle* keyword selects the geometry of the indenter and it can
-cylinder, a cone, or a plane.
+either have the value of *sphere*, *cylinder*, *cone*, or *plane*\ .
 
-A spherical indenter exerts a force of magnitude
+A spherical indenter (*gstyle* = *sphere*) exerts a force of magnitude
 
 .. math::
 
@@ -82,13 +82,16 @@ distance from the atom to the center of the indenter, and *R* is the
 radius of the indenter.  The force is repulsive and F(r) = 0 for *r* >
 *R*\ .
 
-A cylindrical indenter exerts the same force, except that *r* is the
+A cylindrical indenter (*gstyle* = *cylinder*) follows the same formula
-distance from the atom to the center axis of the cylinder.  The
+for the force as a sphere, except that *r* is defined the distance
-cylinder extends infinitely along its axis.
+from the atom to the center axis of the cylinder.  The cylinder extends
+infinitely along its axis.
 
-A conical indenter is similar to a cylindrical indenter except that it
+.. versionadded:: 17April2024
-has a finite length (between *lo* and *hi*), and that two different
+
-radii (one at each end, *radlo* and *radhi*) can be defined.
+A conical indenter (*gstyle* = *cone*) is similar to a cylindrical indenter
+except that it has a finite length (between *lo* and *hi*), and that two
+different radii (one at each end, *radlo* and *radhi*) can be defined.
 
 Spherical, cylindrical, and conical indenters account for periodic
 boundaries in two ways.  First, the center point of a spherical
@@ -101,15 +104,15 @@ or axis accounts for periodic boundaries.  Both of these mean that an
 indenter can effectively move through and straddle one or more
 periodic boundaries.
 
-A planar indenter is really an axis-aligned infinite-extent wall
+A planar indenter (*gstyle* = *plane*) behaves like an axis-aligned
-exerting the same force on atoms in the system, where *R* is the
+infinite-extent wall with the same force expression on atoms in the
-position of the plane and *r-R* is the distance from the plane.  If
+system as before, but where *R* is the position of the plane and *r-R*
-the *side* parameter of the plane is specified as *lo* then it will
+is the distance of an from the plane.  If the *side* parameter of the
-indent from the lo end of the simulation box, meaning that atoms with
+plane is specified as *lo* then it will indent from the lo end of the
-a coordinate less than the plane's current position will be pushed
+simulation box, meaning that atoms with a coordinate less than the
-towards the hi end of the box and atoms with a coordinate higher than
+plane's current position will be pushed towards the hi end of the box
-the plane's current position will feel no force.  Vice versa if *side*
+and atoms with a coordinate higher than the plane's current position
-is specified as *hi*\ .
+will feel no force.  Vice versa if *side* is specified as *hi*\ .
 
 Any of the 4 quantities defining a spherical indenter's geometry can
 be specified as an equal-style :doc:`variable <variable>`, namely *x*,

doc/src/fix_rheo.rst

@@ -0,0 +1,180 @@
+.. index:: fix rheo
+
+fix rheo command
+================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo cut kstyle zmin keyword values...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo = style name of this fix command
+* cut = cutoff for the kernel (distance)
+* kstyle = *quintic* or *RK0* or *RK1* or *RK2*
+* zmin = minimal number of neighbors for reproducing kernels
+* zero or more keyword/value pairs may be appended to args
+* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
+            *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
+
+  .. parsed-literal::
+
+       *thermal* values = none, turns on thermal evolution
+       *interface/reconstruct* values = none, reconstructs interfaces with solid particles
+       *surface/detection* values = *sdstyle* *limit* *limit/splash*
+         *sdstyle* = *coordination* or *divergence*
+         *limit* = threshold for surface particles
+         *limit/splash* = threshold for splash particles
+       *shift* values = none, turns on velocity shifting
+       *rho/sum* values = none, uses the kernel to compute the density of particles
+       *self/mass* values = none, a particle uses its own mass in a rho summation
+       *density* values = *rho01*, ... *rho0N* (density)
+       *speed/sound* values = *cs0*, ... *csN* (velocity)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo 3.0 quintic 0 thermal density 0.1 0.1 speed/sound 10.0 1.0
+   fix 1 all rheo 3.0 RK1 10 shift surface/detection coordination 40
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Perform time integration for RHEO particles, updating positions, velocities,
+and densities. For a detailed breakdown of the integration timestep and
+numerical details, see :ref:`(Palermo) <rheo_palermo>`. For an
+overview of other features available in the RHEO package, see
+:doc:`the RHEO howto <Howto_rheo>`.
+
+The type of kernel is specified using *kstyle* and the cutoff is *cut*. Four
+kernels are currently available. The *quintic* kernel is a standard quintic
+spline function commonly used in SPH. The other options, *RK0*, *RK1*, and
+*RK2*, are zeroth, first, and second order reproducing. To generate a
+reproducing kernel, a particle must have sufficient neighbors inside the
+kernel cutoff distance (a coordination number) to accurately calculate
+moments. This threshold is set by *zmin*. If reproducing kernels are
+requested but a particle has fewer neighbors, then it will revert to a
+non-reproducing quintic kernel until it gains more neighbors.
+
+To model temperature evolution, one must specify the *thermal* keyword,
+define a separate instance of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
+and use atom style rheo/thermal.
+
+By default, the density of solid RHEO particles does not evolve and forces
+with fluid particles are calculated using the current velocity of the solid
+particle. If the *interface/reconstruct* keyword is used, then the density
+and velocity of solid particles are alternatively reconstructed for every
+fluid-solid interaction to ensure no-slip and pressure-balanced boundaries.
+This is done by estimating the location of the fluid-solid interface and
+extrapolating fluid particle properties across the interface to calculate a
+temporary apparent density and velocity for a solid particle. The numerical
+details are the same as those described in
+:ref:`(Palermo) <howto_rheo_palermo>` except there is an additional
+restriction that the reconstructed solid density cannot be less than the
+equilibrium density. This prevents fluid particles from sticking to solid
+surfaces.
+
+A modified form of Fickian particle shifting can be enabled with the
+*shift* keyword. This effectively shifts particle positions to generate a
+more uniform spatial distribution. Shifting currently does not consider the
+type of a particle and therefore may be inappropriate in systems consisting
+of multiple fluid phases.
+
+In systems with free surfaces, the *surface/detection* keyword can be used
+to classify the location of particles as being within the bulk fluid, on a
+free surface, or isolated from other particles in a splash or droplet.
+Shifting is then disabled in the normal direction away from the free surface
+to prevent particles from diffusing away. Surface detection can also be used
+to control surface-nucleated effects like oxidation when used in combination
+with :doc:`fix rheo/oxidation <fix_rheo_oxidation>`. Surface detection is not
+performed on solid bodies.
+
+The *surface/detection* keyword takes three arguments: *sdstyle*, *limit*,
+and *limit/splash*. The first, *sdstyle*, specifies whether surface particles
+are identified using a coordination number (*coordination*) or the divergence
+of the local particle positions (*divergence*). The threshold value for a
+surface particle for either of these criteria is set by the numerical value
+of *limit*. Additionally, if a particle's coordination number is too low,
+i.e. if it has separated off from the bulk in a droplet, it is not possible
+to define surfaces and the particle is classified as a splash. The coordination
+threshold for this classification is set by the numerical value of
+*limit/splash*.
+
+By default, RHEO integrates particles' densities using a mass diffusion
+equation. Alternatively, one can update densities every timestep by performing
+a kernel summation of the masses of neighboring particles by specifying the *rho/sum*
+keyword.
+
+The *self/mass* keyword modifies the behavior of the density summation in *rho/sum*.
+Typically, the density :math:`\rho` of a particle is calculated as the sum over neighbors
+
+.. math::
+   \rho_i = \sum_{j} W_{ij} M_j
+
+where :math:`W_{ij}` is the kernel, and :math:`M_j` is the mass of particle :math:`j`.
+The *self/mass* keyword augments this expression by replacing :math:`M_j` with
+:math:`M_i`. This may be useful in simulations of multiple fluid phases with large
+differences in density, :ref:`(Hu) <fix_rheo_hu>`.
+
+The *density* keyword is used to specify the equilibrium density of each of the N
+particle types. It must be followed by N numerical values specifying each type's
+equilibrium density *rho0*.
+
+The *speed/sound* keyword is used to specify the speed of sound of each of the
+N particle types. It must be followed by N numerical values specifying each type's
+speed of sound *cs*.
+
+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 must be used with atom style rheo or rheo/thermal. This fix must
+be used in conjunction with :doc:`fix rheo/pressure <fix_rheo_pressure>`.
+and :doc:`fix rheo/viscosity <fix_rheo_viscosity>`. If the *thermal* setting
+is used, there must also be an instance of
+:doc:`fix rheo/thermal <fix_rheo_thermal>`. The fix group must be set to all.
+Only one instance of fix rheo may be defined and it  must be defined prior
+to all other RHEO fixes in the input script.
+
+This fix is part of the RHEO 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:`fix rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`fix rheo/pressure <fix_rheo_pressure>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`pair rheo <pair_rheo>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+*rho0* and *cs* are set to 1.0 for all atom types.
+
+----------
+
+.. _rheo_palermo:
+
+**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
+
+.. _fix_rheo_hu:
+
+**(Hu)** Hu, and Adams J. Comp. Physics, 213, 844-861 (2006).

doc/src/fix_rheo_oxidation.rst

@@ -0,0 +1,85 @@
+.. index:: fix rheo/oxidation
+
+fix rheo/oxidation command
+==========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo/oxidation cut btype rsurf
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo/oxidation = style name of this fix command
+* cut = maximum bond length (distance units)
+* btype = type of bonds created
+* rsurf = distance from surface to create bonds (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo/oxidation 1.5 2 0.0
+   fix 1 all rheo/oxidation 1.0 1 2.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix dynamically creates bonds on the surface of fluids to
+represent physical processes such as oxidation. It is intended
+for use with bond style :doc:`bond rheo/shell <bond_rheo_shell>`.
+
+Every timestep, particles check neighbors within a distance of *cut*.
+This distance must be smaller than the kernel length defined in
+:doc:`fix rheo <fix_rheo>`. Bonds of type *btype* are created between
+a fluid particle and either a fluid or solid neighbor. The fluid particles
+must also be on the fluid surface, or within a distance of *rsurf* from
+the surface. This process is further described in
+:ref:`(Clemmer) <howto_rheo_clemmer2>`.
+
+If used in conjunction with solid bodies, such as those generated
+by the *react* option of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
+it is recommended to use a :doc:`hybrid bond style <bond_hybrid>`
+with different bond types for solid and oxide bonds.
+
+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 must be used with the bond style :doc:`rheo/shell <bond_rheo_shell>`
+and :doc:`fix rheo <fix_rheo>` with surface detection enabled.
+
+This fix is part of the RHEO 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:`fix rheo <fix_rheo>`,
+:doc:`bond rheo/shell <bond_rheo_shell>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _howto_rheo_clemmer2:
+
+**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

doc/src/fix_rheo_pressure.rst

@@ -0,0 +1,106 @@
+.. index:: fix rheo/pressure
+
+fix rheo/pressure command
+=========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo/pressure type1 pstyle1 args1 ... typeN pstyleN argsN
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo/pressure = style name of this fix command
+* one or more types and pressure styles must be appended
+* types = lists of types (see below)
+* pstyle = *linear* or *taitwater* or *cubic*
+
+  .. parsed-literal::
+
+       *linear* args = none
+       *taitwater* args = none
+       *cubic* args = cubic prefactor :math:`A_3` (pressure/density\^2)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo/pressure * linear
+   fix 1 all rheo/pressure 1 linear 2 cubic 10.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix defines a pressure equation of state for RHEO particles. One can
+define different equations of state for different atom types. An equation
+must be specified for every atom type.
+
+One first defines the atom *types*. A wild-card asterisk can be used in place
+of or in conjunction with the *types* argument to set the coefficients for
+multiple pairs of atom types.  This takes the form "\*" or "\*n" or "m\*"
+or "m\*n".  If :math:`N` is the number of atom types, then an asterisk with
+no numeric values means all types from 1 to :math:`N`.  A leading asterisk
+means all types from 1 to n (inclusive).  A trailing asterisk means all types
+from m to :math:`N` (inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The *types* definition is followed by the pressure style, *pstyle*. Current
+options *linear*, *taitwater*, and *cubic*. Style *linear* is a linear
+equation of state with a particle pressure :math:`P` calculated as
+
+.. math::
+
+   P = c (\rho - \rho_0)
+
+where :math:`c` is the speed of sound, :math:`\rho_0` is the equilibrium density,
+and :math:`\rho` is the current density of a particle. The numerical values of
+:math:`c` and :math:`\rho_0` are set in :doc:`fix rheo <fix_rheo>`. Style *cubic*
+is a cubic equation of state which has an extra argument :math:`A_3`,
+
+.. math::
+
+   P = c ((\rho - \rho_0) + A_3 (\rho - \rho_0)^3) .
+
+Style *taitwater* is Tait's equation of state:
+
+.. math::
+
+   P = \frac{c^2 \rho_0}{7} \biggl[\left(\frac{\rho}{\rho_0}\right)^{7} - 1\biggr].
+
+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 must be used with an atom style that includes density
+such as atom_style rheo or rheo/thermal. This fix must be used in
+conjunction with :doc:`fix rheo <fix_rheo>`. The fix group must be
+set to all. Only one instance of fix rheo/pressure can be defined.
+
+This fix is part of the RHEO 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:`fix rheo <fix_rheo>`,
+:doc:`pair rheo <pair_rheo>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+none

doc/src/fix_rheo_thermal.rst

@@ -0,0 +1,128 @@
+.. index:: fix rheo/thermal
+
+fix rheo/thermal command
+========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo/thermal attribute values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo/thermal = style name of this fix command
+* one or more attributes may be appended
+* attribute = *conductivity* or *specific/heat* or *latent/heat* or *Tfreeze* or *react*
+
+  .. parsed-literal::
+
+       *conductivity* args = types style args
+         types = lists of types (see below)
+         style = *constant*
+           *constant* arg = conductivity (power/temperature)
+       *specific/heat* args = types style args
+         types = lists of types (see below)
+         style = *constant*
+           *constant* arg = specific heat (energy/(mass*temperature))
+       *latent/heat* args = types style args
+         types = lists of types (see below)
+         style = *constant*
+           *constant* arg = latent heat (energy/mass)
+       *Tfreeze* args = types style args
+         types = lists of types (see below)
+         style = *constant*
+           *constant* arg = freezing temperature (temperature)
+       *react* args = cut type
+         cut = maximum bond distance
+         type = bond type
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo/thermal conductivity * constant 1.0 specific/heat * constant 1.0 Tfreeze * constant 1.0
+   fix 1 all rheo/pressure conductivity 1*2 constant 1.0 conductivity 3*4 constant 2.0 specific/heat * constant 1.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix performs time integration of temperature for atom style rheo/thermal.
+In addition, it defines multiple thermal properties of particles and handles
+melting/solidification, if applicable. For more details on phase transitions
+in RHEO, see :doc:`the RHEO howto <Howto_rheo>`.
+
+Note that the temperature of a particle is always derived from the energy.
+This implies the *temperature* attribute of :doc:`the set command <set>` does
+not affect particles. Instead, one should use the *sph/e* attribute.
+
+For each atom type, one can define expressions for the *conductivity*,
+*specific/heat*, *latent/heat*, and critical temperature (*Tfreeze*).
+The conductivity and specific heat must be defined for all atom types.
+The latent heat and critical temperature are optional. However, a
+critical temperature must be defined to specify a latent heat.
+
+Note, if shifting is turned on in :doc:`fix rheo <fix_rheo>`, the gradient
+of the energy is used to shift energies. This may be inappropriate in systems
+with multiple atom types with different specific heats.
+
+For each property, one must first define a list of atom types. A wild-card
+asterisk can be used in place of or in conjunction with the *types* argument
+to set the coefficients for multiple pairs of atom types.  This takes the
+form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is the number of atom
+types, then an asterisk with no numeric values means all types from 1 to
+:math:`N`.  A leading asterisk means all types from 1 to n (inclusive).
+A trailing asterisk means all types from m to :math:`N` (inclusive).  A
+middle asterisk means all types from m to n (inclusive).
+
+The *types* definition for each property is followed by the style. Currently,
+the only option is *constant*. Style *constant* simply applies a constant value
+of respective property to each particle of the assigned type.
+
+The *react* keyword controls whether bonds are created/deleted when particles
+transition between a fluid and solid state. This option only applies to atom
+types that have a defined value of *Tfreeze*. When a fluid particle's
+temperature drops below *Tfreeze*, bonds of type *btype* are created between
+nearby solid particles within a distance of *cut*. The particle's status also
+swaps to a solid state. When a solid particle's temperature rises above
+*Tfreeze*, all bonds of type *btype* are broken and the particle's status swaps
+to a fluid state.
+
+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 must be used with an atom style that includes temperature,
+heatflow, and conductivity such as atom_style rheo/thermal This fix
+must be used in conjunction with :doc:`fix rheo <fix_rheo>` with the
+*thermal* setting. The fix group must be set to all. Only one
+instance of fix rheo/pressure can be defined.
+
+This fix is part of the RHEO 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:`fix rheo <fix_rheo>`,
+:doc:`pair rheo <pair_rheo>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`,
+:doc:`fix add/heat <fix_add_heat>`
+
+Default
+"""""""
+
+none

doc/src/fix_rheo_viscosity.rst

@@ -0,0 +1,117 @@
+.. index:: fix rheo/viscosity
+
+fix rheo/viscosity command
+==========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo/viscosity type1 pstyle1 args1 ... typeN pstyleN argsN
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo/viscosity = style name of this fix command
+* one or more types and viscosity styles must be appended
+* types = lists of types (see below)
+* vstyle = *constant* or *power*
+
+  .. parsed-literal::
+
+       *constant* args = *eta*
+         *eta* = viscosity
+
+       *power* args = *eta*, *gd0*, *K*, *n*
+         *eta* = viscosity
+         *gd0* = critical strain rate
+         *K* = consistency index
+         *n* = power-law exponent
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo/viscosity * constant 1.0
+   fix 1 all rheo/viscosity 1 constant 1.0 2 power 0.1 5e-4 0.001 0.5
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix defines a viscosity for RHEO particles. One can define different
+viscosities for different atom types, but a viscosity must be specified for
+every atom type.
+
+One first defines the atom *types*. A wild-card asterisk can be used in place
+of or in conjunction with the *types* argument to set the coefficients for
+multiple pairs of atom types.  This takes the form "\*" or "\*n" or "m\*"
+or "m\*n".  If :math:`N` is the number of atom types, then an asterisk with
+no numeric values means all types from 1 to :math:`N`.  A leading asterisk
+means all types from 1 to n (inclusive).  A trailing asterisk means all types
+from m to :math:`N` (inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The *types* definition is followed by the viscosity style, *vstyle*. Two
+options are available, *constant* and *power*. Style *constant* simply
+applies a constant value of the viscosity *eta* to each particle of the
+assigned type. Style *power* is a Hershchel-Bulkley constitutive equation
+for the stress :math:`\tau`
+
+.. math::
+
+   \tau = \left(\frac{\tau_0}{\dot{\gamma}} + K \dot{\gamma}^{n - 1}\right) \dot{\gamma}, \tau \ge \tau_0
+
+where :math:`\dot{\gamma}` is the strain rate and :math:`\tau_0` is the critical
+yield stress, below which :math:`\dot{\gamma} = 0.0`. To avoid divergences, this
+expression is regularized by defining a critical strain rate *gd0*. If the local
+strain rate on a particle falls below this limit, a constant viscosity of *eta*
+is assigned. This implies a value of
+
+.. math::
+   \tau_0 = \eta \dot{\gamma}_0 - K \dot{\gamma}_0^N
+
+as further discussed in :ref:`(Palermo) <rheo_palermo2>`.
+
+
+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 must be used with an atom style that includes viscosity
+such as atom_style rheo or rheo/thermal. This fix must be used in
+conjunction with :doc:`fix rheo <fix_rheo>`. The fix group must be
+set to all. Only one instance of fix rheo/viscosity can be defined.
+
+This fix is part of the RHEO 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:`fix rheo <fix_rheo>`,
+:doc:`pair rheo <pair_rheo>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _rheo_palermo2:
+
+**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.

doc/src/fix_store_force.rst

@@ -23,11 +23,12 @@ Examples
 Description
 """""""""""
 
-Store the forces on atoms in the group at the point during each
+Store the forces on atoms in the group at the point during each timestep
-timestep when the fix is invoked, as described below.  This is useful
+when the fix is invoked, as described below.  This is useful for storing
-for storing forces before constraints or other boundary conditions are
+forces before constraints or other boundary conditions are computed
-computed which modify the forces, so that unmodified forces can be
+which modify the forces, so that unmodified forces can be :doc:`written
-:doc:`written to a dump file <dump>` or accessed by other :doc:`output commands <Howto_output>` that use per-atom quantities.
+to a dump file <dump>` or accessed by other :doc:`output commands
+<Howto_output>` that use per-atom quantities.
 
 This fix is invoked at the point in the velocity-Verlet timestepping
 immediately after :doc:`pair <pair_style>`, :doc:`bond <bond_style>`,
@@ -36,12 +37,13 @@ immediately after :doc:`pair <pair_style>`, :doc:`bond <bond_style>`,
 forces have been calculated.  It is the point in the timestep when
 various fixes that compute constraint forces are calculated and
 potentially modify the force on each atom.  Examples of such fixes are
-:doc:`fix shake <fix_shake>`, :doc:`fix wall <fix_wall>`, and :doc:`fix indent <fix_indent>`.
+:doc:`fix shake <fix_shake>`, :doc:`fix wall <fix_wall>`, and :doc:`fix
+indent <fix_indent>`.
 
 .. note::
 
-   The order in which various fixes are applied which operate at
+   The order in which various fixes are applied which operate at the
-   the same point during the timestep, is the same as the order they are
+   same point during the timestep, is the same as the order they are
    specified in the input script.  Thus normally, if you want to store
    per-atom forces due to force field interactions, before constraints
    are applied, you should list this fix first within that set of fixes,
@@ -52,8 +54,9 @@ potentially modify the force on each atom.  Examples of such fixes are
 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
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.
 
 This fix produces a per-atom array which can be accessed by various
 :doc:`output commands <Howto_output>`.  The number of columns for each
@@ -61,7 +64,8 @@ atom is 3, and the columns store the x,y,z forces on each atom.  The
 per-atom values be accessed on any timestep.
 
 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>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/pair_coul.rst

@@ -2,6 +2,8 @@
 .. index:: pair_style coul/cut/gpu
 .. index:: pair_style coul/cut/kk
 .. index:: pair_style coul/cut/omp
+.. index:: pair_style coul/cut/global
+.. index:: pair_style coul/cut/global/omp
 .. index:: pair_style coul/debye
 .. index:: pair_style coul/debye/gpu
 .. index:: pair_style coul/debye/kk
@@ -11,8 +13,6 @@
 .. index:: pair_style coul/dsf/kk
 .. index:: pair_style coul/dsf/omp
 .. index:: pair_style coul/exclude
-.. index:: pair_style coul/cut/global
-.. index:: pair_style coul/cut/global/omp
 .. index:: pair_style coul/long
 .. index:: pair_style coul/long/omp
 .. index:: pair_style coul/long/kk
@@ -33,6 +33,11 @@ pair_style coul/cut command
 
 Accelerator Variants: *coul/cut/gpu*, *coul/cut/kk*, *coul/cut/omp*
 
+pair_style coul/cut/global command
+==================================
+
+Accelerator Variants: *coul/cut/omp*
+
 pair_style coul/debye command
 =============================
 
@@ -46,11 +51,6 @@ Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp*
 pair_style coul/exclude command
 ===============================
 
-pair_style coul/cut/global command
-==================================
-
-Accelerator Variants: *coul/cut/omp*
-
 pair_style coul/long command
 ============================
 
@@ -79,16 +79,17 @@ pair_style tip4p/long command
 
 Accelerator Variants: *tip4p/long/omp*
 
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
    pair_style coul/cut cutoff
+   pair_style coul/cut/global cutoff
    pair_style coul/debye kappa cutoff
    pair_style coul/dsf alpha cutoff
    pair_style coul/exclude cutoff
-   pair_style coul/cut/global cutoff
    pair_style coul/long cutoff
    pair_style coul/wolf alpha cutoff
    pair_style coul/streitz cutoff keyword alpha
@@ -152,6 +153,11 @@ the 2 atoms, and :math:`\epsilon` is the dielectric constant which can be set
 by the :doc:`dielectric <dielectric>` command.  The cutoff :math:`r_c` truncates
 the interaction distance.
 
+Pair style *coul/cut/global* computes the same Coulombic interactions
+as style *coul/cut* except that it allows only a single global cutoff
+and thus makes it compatible for use in combination with long-range
+coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
+
 ----------
 
 Style *coul/debye* adds an additional exp() damping factor to the
@@ -262,11 +268,6 @@ Streitz-Mintmire parameterization for the material being modeled.
 
 ----------
 
-Pair style *coul/cut/global* computes the same Coulombic interactions
-as style *coul/cut* except that it allows only a single global cutoff
-and thus makes it compatible for use in combination with long-range
-coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
-
 Pair style *coul/exclude* computes Coulombic interactions like *coul/cut*
 but **only** applies them to excluded pairs using a scaling factor
 of :math:`\gamma - 1.0` with :math:`\gamma` being the factor assigned

doc/src/pair_rheo.rst

@@ -0,0 +1,102 @@
+.. index:: pair_style rheo
+
+pair_style rheo command
+=======================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rheo cutoff keyword values
+
+* cutoff = global cutoff for kernel (distance units)
+* zero or more keyword/value pairs may be appended to args
+* keyword = *rho/damp* or *artificial/visc* or *harmonic/means*
+
+.. parsed-literal::
+
+     *rho/damp* args = density damping prefactor :math:`\xi`
+     *artificial/visc* args = artificial viscosity prefactor :math:`\zeta`
+     *harmonic/means* args = none
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rheo 3.0 rho/damp 1.0 artificial/visc 2.0
+   pair_coeff * *
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Pair style *rheo* computes pressure and viscous forces between particles
+in the :doc:`rheo package <Howto_rheo>`. If thermal evolution is turned
+on in :doc:`fix rheo <fix_rheo>`, then the pair style also calculates
+heat exchanged between particles.
+
+The *artificial/viscosity* keyword is used to specify the magnitude
+:math:`\zeta` of an optional artificial viscosity contribution to forces.
+This factor can help stabilize simulations by smoothing out small length
+scale variations in velocity fields. Artificial viscous forces typically
+are only exchanged by fluid particles. However, if interfaces are not
+reconstructed in fix rheo, fluid particles will also exchange artificial
+viscous forces with solid particles to improve stability.
+
+The *rho/damp* keyword is used to specify the magnitude :math:`\xi` of
+an optional pairwise damping term between the density of particles. This
+factor can help stabilize simulations by smoothing out small length
+scale variations in density fields. However, in systems that develop
+a density gradient in equilibrium (e.g. in a hydrostatic column underlying
+gravity), this option may be inappropriate.
+
+If particles have different viscosities or conductivities, the
+*harmonic/means* keyword changes how they are averaged before calculating
+pairwise forces or heat exchanges. By default, an arithmetic averaged is
+used, however, a harmonic mean may improve stability in systems with multiple
+fluid phases with large disparities in viscosities.
+
+No coefficients are defined for each pair of atoms types via the
+:doc:`pair_coeff <pair_coeff>` command as in the examples
+above.
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.
+Thus, you need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This 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
+""""""""""""
+
+This fix is part of the RHEO 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:`fix rheo <fix_rheo>`,
+:doc:`fix rheo/pressure <fix_rheo_pressure>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+Density damping and artificial viscous forces are not calculated.
+Arithmetic means are used for mixing particle properties.

doc/src/pair_rheo_solid.rst

@@ -0,0 +1,112 @@
+.. index:: pair_style rheo/solid
+
+pair_style rheo/solid command
+=============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rheo/solid
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rheo/solid
+   pair_coeff * * 1.0 1.5 1.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Style *rheo/solid* is effectively a copy of pair style
+:doc:`bpm/spring <pair_bpm_spring>` except it only applies forces
+between solid RHEO particles, determined by checking the status of
+each pair of neighboring particles before calculating forces.
+
+The style 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
+displacement 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 .
+
+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
+""""""""""""
+
+This pair style is part of the RHEO 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:`fix rheo <fix_rheo>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`pair bpm/spring <pair_bpm_spring>`
+
+Default
+"""""""
+
+none

doc/src/pair_style.rst

@@ -337,6 +337,8 @@ accelerated styles exist.
 * :doc:`reaxff <pair_reaxff>` - ReaxFF potential
 * :doc:`rebo <pair_airebo>` - Second generation REBO potential of Brenner
 * :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
+* :doc:`rheo <pair_rheo>` - fluid interactions in RHEO package
+* :doc:`rheo/solid <pair_rheo_solid>` - solid interactions in RHEO package
 * :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
 * :doc:`saip/metal <pair_saip_metal>` - Interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
 * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - Smoothed dissipative particle dynamics for water at isothermal conditions

doc/src/read_data.rst

@@ -12,7 +12,7 @@ Syntax
 
 * file = name of data file to read in
 * zero or more keyword/arg pairs may be appended
-* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *group* or *nocoeff* or *fix*
+* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* or *group* or *nocoeff* or *fix*
 
   .. parsed-literal::
 
@@ -859,6 +859,10 @@ of analysis.
      - atom-ID molecule-ID atom-type x y z
    * - peri
      - atom-ID atom-type volume density x y z
+   * - rheo
+     - atom-ID atom-type status rho x y z
+   * - rheo/thermal
+     - atom-ID atom-type status rho energy x y z
    * - smd
      - atom-ID atom-type molecule volume mass kradius cradius x0 y0 z0 x y z
    * - sph

doc/src/reset_atoms.rst

@@ -32,7 +32,7 @@ Syntax
 
   .. code-block:: LAMMPS
 
-     reset atoms mol group-ID keyword value ...
+     reset_atoms mol group-ID keyword value ...
 
   * group-ID = ID of group of atoms whose molecule IDs will be reset
   * zero or more keyword/value pairs can be appended
@@ -66,16 +66,16 @@ Description
 .. versionadded:: 22Dec2022
 
 The *reset_atoms* command resets the values of a specified atom
-property.  In contrast to the set command, it does this in a
+property.  In contrast to the *set* command, it does this in a
 collective manner which resets the values for many atoms in a
-self-consistent way.  This is often useful when the simulated system
+self-consistent way.  This command is often useful when the simulated
-has undergone significant modifications like adding or removing atoms
+system has undergone significant modifications like adding or removing
-or molecules, joining data files, changing bonds, or large-scale
+atoms or molecules, joining data files, changing bonds, or large-scale
 diffusion.
 
 The new values can be thought of as a *reset*, similar to values atoms
 would have if a new data file were being read or a new simulation
-performed.  Note that the set command also resets atom properties to
+performed.  Note that the *set* command also resets atom properties to
 new values, but it treats each atom independently.
 
 The *property* setting can be *id* or *image* or *mol*.  For *id*, the
@@ -90,7 +90,7 @@ keyword/value settings are given below.
 
 ----------
 
-*Property id*
+Property: *id*
 
 Reset atom IDs for the entire system, including all the global IDs
 stored for bond, angle, dihedral, improper topology data.  This will
@@ -146,7 +146,7 @@ processor have consecutive IDs, as the :doc:`create_atoms
 
 ----------
 
-*Property image*
+Property: *image*
 
 Reset the image flags of atoms so that at least one atom in each
 molecule has an image flag of 0.  Molecular topology is respected so
@@ -191,7 +191,7 @@ flags.
 
 ----------
 
-*Property mol*
+Property: *mol*
 
 Reset molecule IDs for a specified group of atoms based on current
 bond connectivity.  This will typically create a new set of molecule
@@ -203,7 +203,7 @@ For purposes of this operation, molecules are identified by the current
 bond connectivity in the system, which may or may not be consistent with
 the current molecule IDs.  A molecule in this context is a set of atoms
 connected to each other with explicit bonds.  The specific algorithm
-used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`
+used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`.
 Once the molecules are identified and a new molecule ID computed for
 each, this command will update the current molecule ID for all atoms in
 the group with the new molecule ID.  Note that if the group excludes
@@ -266,7 +266,7 @@ The *image* property can only be used when the atom style supports bonds.
 Related commands
 """"""""""""""""
 
-:doc:`compute fragment/atom <compute_cluster_atom>`
+:doc:`compute fragment/atom <compute_cluster_atom>`,
 :doc:`fix bond/react <fix_bond_react>`,
 :doc:`fix bond/create <fix_bond_create>`,
 :doc:`fix bond/break <fix_bond_break>`,

doc/src/set.rst

@@ -120,6 +120,8 @@ Syntax
        *angle* value = numeric angle type or angle type label, for all angles between selected atoms
        *dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
        *improper* value = numeric improper type or improper type label, for all impropers between selected atoms
+       *rheo/rho* value = density of RHEO particles (mass/distance\^3)
+       *rheo/status* value = status or phase of RHEO particles (unitless)
        *sph/e* value = energy of SPH particles (need units)
          value can be an atom-style variable (see below)
        *sph/cv* value = heat capacity of SPH particles (need units)
@@ -506,6 +508,10 @@ by the *bond types* (\ *angle types*, etc) field in the header of the
 data file read by the :doc:`read_data <read_data>` command.  These
 keywords do not allow use of an atom-style variable.
 
+Keywords *rheo/rho* and *rheo/status* set the density and the status of
+rheo particles. In particular, one can only set the phase in the status
+as described by the :doc:`RHEO howto page <Howto_rheo>`.
+
 Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
 and density of smoothed particle hydrodynamics (SPH) particles.  See
 `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.

doc/utils/sphinx-config/conf.py.in

@@ -41,7 +41,7 @@ sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'utils', 'sphinx-config', '_themes'
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = '5.2.0'
+needs_sphinx = '5.3.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -69,7 +69,7 @@ images_config = {
 templates_path = ['_templates']
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = {'.rst': 'restructuredtext'}
 
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'

doc/utils/sphinx-config/false_positives.txt

@@ -393,6 +393,7 @@ buf
 builtin
 Bulacu
 Bulatov
+Bulkley
 Bureekaew
 burlywood
 Bussi
@@ -564,6 +565,7 @@ cond
 conda
 Conda
 Condens
+conductivities
 conf
 config
 configfile
@@ -1440,6 +1442,7 @@ henrich
 Henrich
 Hermitian
 Herrmann
+Hershchel
 Hertizian
 hertzian
 Hertzsch
@@ -1831,6 +1834,7 @@ Kspace
 KSpace
 KSpaceStyle
 Kspring
+kstyle
 kT
 kTequil
 kth
@@ -2271,6 +2275,7 @@ modelled
 modelling
 Modelling
 Modine
+modularity
 moduli
 mofff
 MOFFF
@@ -2488,6 +2493,7 @@ Neumann
 Nevent
 nevery
 Nevery
+Nevins
 newfile
 Newns
 newtype
@@ -3067,6 +3073,7 @@ quatw
 queryargs
 Queteschiner
 quickmin
+quintic
 qw
 qx
 qy
@@ -3078,6 +3085,7 @@ radialscreenedspin
 radialspin
 radian
 radians
+radiative
 radj
 Rafferty
 rahman
@@ -3181,6 +3189,7 @@ rg
 Rg
 Rhaphson
 Rhe
+rheo
 rheological
 rheology
 rhodo
@@ -3268,6 +3277,7 @@ rsort
 rsq
 rst
 rstyle
+rsurf
 Rubensson
 Rubia
 Rud
@@ -3651,6 +3661,7 @@ Telsa
 tempCorrCoeff
 templated
 Templeton
+Tencer
 Tequil
 ters
 tersoff
@@ -3997,6 +4008,7 @@ Vries
 Vsevolod
 Vsmall
 Vstream
+vstyle
 vtarget
 vtk
 VTK

examples/PACKAGES/electrode/madelung/.gitignore

@@ -1,2 +1,3 @@
 *.csv
 *.txt
+*.lammpstrj

examples/PACKAGES/electrode/madelung/eval.py

@@ -17,14 +17,22 @@ q_ref = float(ref_line[3])
 inv11_ref = float(ref_line[4])
 inv12_ref = float(ref_line[5])
 b1_ref = float(ref_line[6])
+felec1_ref = float(ref_line[8])
+felyt1_ref = float(ref_line[10])
+press_ref = float(ref_line[12])
 
 # out.csv
 with open(sys.argv[2]) as f:
     out_line = f.readlines()[-1].split(", ")
 e_out = float(out_line[0])
 q_out = float(out_line[1])
+press_out = float(out_line[2])
 
-out_lines = [("energy", e_ref, e_out), ("charge", q_ref, q_out)]
+out_lines = [
+    ("energy", e_ref, e_out),
+    ("charge", q_ref, q_out),
+    ("pressure", press_ref, press_out),
+]
 
 # vec.csv
 vec_file = "vec.csv"
@@ -44,6 +52,14 @@ if op.isfile(inv_file):
     inv12_out = float(inv_line[1])
     out_lines.append(("inv11", inv11_ref, inv11_out))
 
+# forces.lammpstrj
+force_file = "forces.lammpstrj"
+with open(force_file) as f:
+    lines = f.readlines()[9:]
+    for name, i, f_ref in [("felec1", "1", felec1_ref), ("felyt1", "3", felyt1_ref)]:
+        f_out = next(float(y[3]) for x in lines if (y := x.split()) and y[0] == i)
+        out_lines.append((name, f_ref, f_out))
+
 lines = []
 for label, ref, out in out_lines:
     error = rel_error(out, ref)

examples/PACKAGES/electrode/madelung/in.eta_cg

@@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
 fix feta all property/atom d_eta ghost on
 set group bot d_eta 0.5
 set group top d_eta 3.0
-fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
+fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta algo cg 1e-6
 
 run 0
 

examples/PACKAGES/electrode/madelung/in.eta_mix

@@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
 fix feta all property/atom d_eta ghost on
 set group bot d_eta 0.5
 set group top d_eta 3.0
-fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
+fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
 
 run 0
 

examples/PACKAGES/electrode/madelung/plate_cap.py

@@ -1,12 +1,17 @@
 #!/usr/bin/env python3
 
+import time
+
 import numpy as np
 from scipy.special import erf
 
 SQRT2 = np.sqrt(2)
+SQRTPI_INV = 1 / np.sqrt(np.pi)
 COULOMB = 332.06371  #  Coulomb constant in Lammps 'real' units
 QE2F = 23.060549
+NKTV2P = 68568.415  # pressure in 'real' units
 LENGTH = 10000  # convergence parameter
+LZ = 20
 
 
 def lattice(length):
@@ -26,6 +31,25 @@ def b_element(r, q, eta):
     return q * erf(eta * r) / r
 
 
+def force_gauss(r, qq, eta):
+    etar = eta * r
+    return (qq / np.square(r)) * (
+        erf(etar) - 2 * etar * SQRTPI_INV * np.exp(-np.square(etar))
+    )
+
+
+def force_point(r, qq):
+    return qq / np.square(r)
+
+
+def force_component(dx, d, qq, eta=None):
+    if eta:
+        return np.sum(dx / d * force_gauss(d, qq, eta))
+    else:
+        return np.sum(dx / d * force_point(d, qq))
+
+
+time_start = time.perf_counter()
 a = 1  # nearest neighbor distance i.e. lattice constant / sqrt(2)
 x_elec = [-2, 2]
 x_elyt = [-1, 1]
@@ -36,8 +60,20 @@ v = np.array([-0.5, 0.5]) * (QE2F / COULOMB)
 # distances to images within electrode and to opposite electrode
 distances = a * np.linalg.norm(lattice(LENGTH), axis=1)
 opposite_distances = np.sqrt(np.square(distances) + distance_plates**2)
+image_distances = []
+for x in x_elec:
+    image_distances.append([])
+    for y in x_elyt:
+        image_distances[-1].append(np.sqrt(np.square(distances) + np.abs(y - x) ** 2))
+image_elyt_distances = [[None for _ in range(len(x_elyt))] for _ in range(len(x_elyt))]
+for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
+    for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
+        image_elyt_distances[i][j] = np.sqrt(
+            np.square(distances) + np.abs(xj - xi) ** 2
+        )
 
 for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
+    # for name, eta_elec in [("", [2.0, 2.0])]:
     eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec)))
     # self interaction and within original box
     A_11 = np.sqrt(2 / np.pi) * eta_elec[0]
@@ -55,22 +91,18 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
 
     # electrode-electrolyte interaction
     b = []
-    for x, eta in zip(x_elec, eta_elec):
+    for i, (x, eta) in enumerate(zip(x_elec, eta_elec)):
         bi = 0
-        for y, q in zip(x_elyt, q_elyt):
+        for j, (y, q) in enumerate(zip(x_elyt, q_elyt)):
-            d = abs(y - x)
+            bi += b_element(np.abs(y - x), q, eta)
-            bi += b_element(d, q, eta)
+            bi += 4 * np.sum(b_element(image_distances[i][j], q, eta))
-            image_distances = np.sqrt(np.square(distances) + d**2)
-            bi += 4 * np.sum(b_element(image_distances, q, eta))
         b.append(bi)
     b = np.array(b)
 
     # electrolyte-electrolyte energy
     elyt_11 = 4 * np.sum(1 / distances)
     distance_elyt = x_elyt[1] - x_elyt[0]
-    elyt_12 = 1 / distance_elyt + 4 * np.sum(
+    elyt_12 = 1 / distance_elyt + 4 * np.sum(1 / image_elyt_distances[0][1])
-        1 / np.sqrt(np.square(distances) + distance_elyt**2)
-    )
     elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]])
     energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt))
 
@@ -78,9 +110,48 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
     q = np.dot(inv, v - b)
     energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt)
 
+    # forces in out-of-plane direction
+    f_elec = np.zeros(len(x_elec))
+    f_elyt = np.zeros(len(x_elyt))
+    # electrode-electrode
+    dx = x_elec[1] - x_elec[0]
+    fij_box = force_component(dx, np.abs(dx), q[0] * q[1], eta_mix)
+    fij_img = 4 * force_component(dx, opposite_distances, q[0] * q[1], eta_mix)
+    f_elec[0] -= fij_box + fij_img
+    f_elec[1] += fij_box + fij_img
+    # electrode-electrolyte
+    for i, (xi, qi, etai) in enumerate(zip(x_elec, q, eta_elec)):
+        for j, (xj, qj) in enumerate(zip(x_elyt, q_elyt)):
+            dx = xj - xi
+            fij_box = force_component(dx, np.abs(dx), qi * qj, etai)
+            fij_img = 4 * force_component(dx, image_distances[i][j], qi * qj, etai)
+            f_elec[i] -= fij_box + fij_img
+            f_elyt[j] += fij_box + fij_img
+    # electrolyte-electrolyte
+    for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
+        for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
+            dx = xj - xi
+            fij_box = force_component(dx, np.abs(dx), qi * qj)
+            fij_img = 4 * force_component(dx, image_elyt_distances[i][j], qi * qj)
+            f_elyt[i] -= fij_img + fij_box
+            f_elyt[j] += fij_img + fij_box
+    # force units
+    assert np.abs(np.sum(f_elec) + np.sum(f_elyt)) < 1e-8
+    f_elec *= COULOMB
+    f_elyt *= COULOMB
+
+    # Virial
+    volume = a**2 * LZ
+    virial = 0.0
+    for x, f in [(x_elec, f_elec), (x_elyt, f_elyt)]:
+        virial += np.dot(x, f)
+    pressure = NKTV2P * virial / volume
+
     with open(f"plate_cap{name}.csv", "w") as f:
         f.write(
-            "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A\n"
+            "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A"
+            + ", b1 / e/A, b2 / e/A, felec1 / kcal/mol/A, felec2 / kcal/mol/A"
+            + ", felyt1 / kcal/mol/A, felyt2 / kcal/mol/A, press\n"
         )
         f.write(
             ", ".join(
@@ -93,7 +164,14 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
                     f"{inv[0, 1]:.10f}",
                     f"{b[0]:.8f}",
                     f"{b[1]:.8f}",
+                    f"{f_elec[0]:.5f}",
+                    f"{f_elec[1]:.5f}",
+                    f"{f_elyt[0]:.5f}",
+                    f"{f_elyt[1]:.5f}",
+                    f"{pressure:.2f}",
                 ]
             )
             + "\n"
         )
+time_end = time.perf_counter()
+print(f"{time_end - time_start:0.4f} seconds")

examples/PACKAGES/electrode/madelung/settings.mod

@@ -19,4 +19,8 @@ compute qtop top reduce sum v_q
 compute compute_pe all pe
 variable vpe equal c_compute_pe
 variable charge equal c_qtop
-fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
+compute press all pressure NULL virial
+variable p3 equal c_press[3]
+fix fxprint all print 1 "${vpe}, ${charge}, ${p3}" file "out.csv"
+
+dump dump_forces all custom 1 forces.lammpstrj id fx fy fz

examples/PACKAGES/electrode/piston/in.piston

@@ -42,7 +42,11 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
 
 # equilibrate z-coordinate of upper electrode while keeping the electrode rigid
 fix fxforce_wa wall setforce 0.0 0.0 NULL
-fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
+variable atm equal 1/68568.415 # 1/force->nktv2p
+variable area equal (xhi-xlo)*(yhi-ylo)
+variable wall_force equal -v_atm*v_area/count(wall)
+print "Wall force per atom: ${wall_force}"
+fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
 fix fxdrag     wall viscous 100
 fix fxrigid    wall rigid/nve single
 

examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.1

@@ -1,4 +1,5 @@
-LAMMPS (3 Nov 2022)
+LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
+  using 1 OpenMP thread(s) per MPI task
 # The intention is to find the average position of one wall at atmospheric
 # pressure.  The output is the wall position over time which can be used to
 # find the average position for a run with fixed wall position.
@@ -40,8 +41,8 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-3 neighbors
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
-  special bonds CPU = 0.001 seconds
+  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.011 seconds
+  read_data CPU = 0.012 seconds
 
 # ----------------- Settings Section -----------------
 
@@ -77,7 +78,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
 
 # equilibrate z-coordinate of upper electrode while keeping the electrode rigid
 fix fxforce_wa wall setforce 0.0 0.0 NULL
-fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
+variable atm equal 1/68568.415 # 1/force->nktv2p
+variable area equal (xhi-xlo)*(yhi-ylo)
+variable wall_force equal -v_atm*v_area/count(wall)
+print "Wall force per atom: ${wall_force}"
+Wall force per atom: -0.000109285996244287
+fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
+fix fxpressure wall aveforce 0 0 -0.000109285996244287 
 fix fxdrag     wall viscous 100
 fix fxrigid    wall rigid/nve single
   1 rigid bodies with 48 atoms
@@ -134,7 +141,7 @@ PPPM/electrode initialization ...
   stencil order = 5
   estimated absolute RMS force accuracy = 0.02930901
   estimated relative force accuracy = 8.8263214e-05
-  using double precision MKL FFT
+  using double precision FFTW3
   3d grid and FFT values/proc = 15884 6480
 Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
 Neighbor list info ...
@@ -157,54 +164,54 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
    Step     c_temp_mobile      c_qwa          c_qau        v_top_wall  
          0   303.38967     -0.042963484    0.042963484    21.4018      
-      5000   285.08828     -0.26105255     0.26105255     25.155629    
+      5000   311.85363      0.03543775    -0.03543775     24.79665     
-     10000   323.19176     -0.26264003     0.26264003     24.541676    
+     10000   285.91321     -0.16873703     0.16873703     23.103088    
-     15000   310.479       -0.27318148     0.27318148     23.141522    
+     15000   295.39476     -0.44424612     0.44424612     23.767107    
-     20000   295.18544     -0.11313444     0.11313444     23.828735    
+     20000   296.12969     -0.14120993     0.14120993     23.96361     
-     25000   295.38607     -0.25433086     0.25433086     23.673314    
+     25000   306.59629     -0.29333182     0.29333182     23.884488    
-     30000   288.0613      -0.30099901     0.30099901     23.438086    
+     30000   297.98559     -0.10749684     0.10749684     23.73316     
-     35000   278.5591      -0.15823576     0.15823576     24.311915    
+     35000   297.98503     -0.11809975     0.11809975     23.984669    
-     40000   303.95751     -0.19941381     0.19941381     23.69594     
+     40000   300.26292     -0.32784184     0.32784184     23.462748    
-     45000   279.026       -0.1659962      0.1659962      23.588604    
+     45000   295.68441     -0.25940165     0.25940165     23.516403    
-     50000   298.79278     -0.28866703     0.28866703     23.372508    
+     50000   315.12883     -0.36037614     0.36037614     23.627879    
-     55000   301.03353     -0.078370381    0.078370381    23.192985    
+     55000   290.55151     -0.0032838106   0.0032838106   23.684931    
-     60000   306.77965     -0.12807205     0.12807205     23.968574    
+     60000   316.4625      -0.17245368     0.17245368     24.126883    
-     65000   309.86008     -0.27162663     0.27162663     23.616704    
+     65000   296.79343     -0.054061851    0.054061851    23.695094    
-     70000   287.31116     -0.029751882    0.029751882    23.667495    
+     70000   305.99923     -0.11363801     0.11363801     23.55476     
-     75000   312.48654     -0.10759866     0.10759866     23.504105    
+     75000   297.40131     -0.27054153     0.27054153     23.928994    
-     80000   309.94267     -0.2558548      0.2558548      23.810576    
+     80000   306.54811     -0.25409719     0.25409719     23.869448    
-     85000   328.04389     -0.1575471      0.1575471      24.013437    
+     85000   303.95231     -0.17895561     0.17895561     23.658833    
-     90000   302.9806      -0.032002164    0.032002164    24.264432    
+     90000   313.43739     -0.059036514    0.059036514    23.36056     
-     95000   294.20804     -0.27797238     0.27797238     23.291758    
+     95000   290.3077      -0.31394478     0.31394478     23.885538    
-    100000   307.63019     -0.19047448     0.19047448     23.632147    
+    100000   297.5156      -0.30730083     0.30730083     23.511674    
-Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms
+Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms
 
-Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s
+Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 190.47     | 190.47     | 190.47     |   0.0 | 35.88
+Pair    | 460.91     | 460.91     | 460.91     |   0.0 | 29.06
-Bond    | 0.10754    | 0.10754    | 0.10754    |   0.0 |  0.02
+Bond    | 0.047873   | 0.047873   | 0.047873   |   0.0 |  0.00
-Kspace  | 73.179     | 73.179     | 73.179     |   0.0 | 13.79
+Kspace  | 341.4      | 341.4      | 341.4      |   0.0 | 21.53
-Neigh   | 24.209     | 24.209     | 24.209     |   0.0 |  4.56
+Neigh   | 52.868     | 52.868     | 52.868     |   0.0 |  3.33
-Comm    | 1.6857     | 1.6857     | 1.6857     |   0.0 |  0.32
+Comm    | 5.2321     | 5.2321     | 5.2321     |   0.0 |  0.33
-Output  | 0.0016861  | 0.0016861  | 0.0016861  |   0.0 |  0.00
+Output  | 0.00099102 | 0.00099102 | 0.00099102 |   0.0 |  0.00
-Modify  | 240.23     | 240.23     | 240.23     |   0.0 | 45.26
+Modify  | 724.63     | 724.63     | 724.63     |   0.0 | 45.69
-Other   |            | 0.9595     |            |       |  0.18
+Other   |            | 0.9741     |            |       |  0.06
 
 Nlocal:            726 ave         726 max         726 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           2335 ave        2335 max        2335 min
+Nghost:           2336 ave        2336 max        2336 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:         120271 ave      120271 max      120271 min
+Neighs:         120321 ave      120321 max      120321 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 120271
+Total # of neighbors = 120321
-Ave neighs/atom = 165.66253
+Ave neighs/atom = 165.7314
 Ave special neighs/atom = 1.7355372
-Neighbor list builds = 7722
+Neighbor list builds = 7670
 Dangerous builds = 0
 write_data "data.piston.final"
 System init for write_data ...
@@ -213,11 +220,11 @@ PPPM/electrode initialization ...
   G vector (1/distance) = 0.32814871
   grid = 12 15 36
   stencil order = 5
-  estimated absolute RMS force accuracy = 0.029311365
+  estimated absolute RMS force accuracy = 0.029311329
-  estimated relative force accuracy = 8.8270304e-05
+  estimated relative force accuracy = 8.8270197e-05
-  using double precision MKL FFT
+  using double precision FFTW3
   3d grid and FFT values/proc = 15884 6480
 Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
 
 Average conjugate gradient steps: 1.981
-Total wall time: 0:08:50
+Total wall time: 0:26:26

examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.4

@@ -1,4 +1,5 @@
-LAMMPS (3 Nov 2022)
+LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
+  using 1 OpenMP thread(s) per MPI task
 # The intention is to find the average position of one wall at atmospheric
 # pressure.  The output is the wall position over time which can be used to
 # find the average position for a run with fixed wall position.
@@ -41,8 +42,8 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-3 neighbors
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
-  special bonds CPU = 0.001 seconds
+  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.017 seconds
+  read_data CPU = 0.012 seconds
 
 # ----------------- Settings Section -----------------
 
@@ -66,7 +67,7 @@ Finding SHAKE clusters ...
        0 = # of size 3 clusters
        0 = # of size 4 clusters
      210 = # of frozen angles
-  find clusters CPU = 0.002 seconds
+  find clusters CPU = 0.000 seconds
 pair_modify mix arithmetic
 
 # ----------------- Run Section -----------------
@@ -78,7 +79,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
 
 # equilibrate z-coordinate of upper electrode while keeping the electrode rigid
 fix fxforce_wa wall setforce 0.0 0.0 NULL
-fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
+variable atm equal 1/68568.415 # 1/force->nktv2p
+variable area equal (xhi-xlo)*(yhi-ylo)
+variable wall_force equal -v_atm*v_area/count(wall)
+print "Wall force per atom: ${wall_force}"
+Wall force per atom: -0.000109285996244287
+fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
+fix fxpressure wall aveforce 0 0 -0.000109285996244287 
 fix fxdrag     wall viscous 100
 fix fxrigid    wall rigid/nve single
   1 rigid bodies with 48 atoms
@@ -135,7 +142,7 @@ PPPM/electrode initialization ...
   stencil order = 5
   estimated absolute RMS force accuracy = 0.02930901
   estimated relative force accuracy = 8.8263214e-05
-  using double precision MKL FFT
+  using double precision FFTW3
   3d grid and FFT values/proc = 8512 2880
 Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
 Neighbor list info ...
@@ -158,54 +165,54 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.22 | 10.41 Mbytes
    Step     c_temp_mobile      c_qwa          c_qau        v_top_wall  
          0   303.38967     -0.042963484    0.042963484    21.4018      
-      5000   292.03027     -0.19040435     0.19040435     24.581338    
+      5000   291.6303      -0.1820085      0.1820085      24.641399    
-     10000   309.52764     -0.48308301     0.48308301     23.776985    
+     10000   299.42886     -0.19823095     0.19823095     23.820522    
-     15000   295.00243     -0.16591109     0.16591109     23.672038    
+     15000   288.23071     -0.065261869    0.065261869    23.360845    
-     20000   293.5536      -0.086669084    0.086669084    23.426455    
+     20000   299.4644      -0.042993777    0.042993777    23.987554    
-     25000   303.0079      -0.16488112     0.16488112     23.862966    
+     25000   304.26497     -0.15665293     0.15665293     23.729006    
-     30000   306.31463     -0.23192653     0.23192653     23.819882    
+     30000   292.29674     -0.25142779     0.25142779     23.960725    
-     35000   303.66268     -0.2317907      0.2317907      23.495344    
+     35000   295.57492     -0.01269228     0.01269228     23.445383    
-     40000   301.39435     -0.34661329     0.34661329     23.657835    
+     40000   303.38438     -0.13941727     0.13941727     23.517483    
-     45000   291.61205     -0.30539427     0.30539427     23.437303    
+     45000   302.211       -0.19589892     0.19589892     23.704043    
-     50000   298.65319     -0.096107034    0.096107034    23.57809     
+     50000   281.64939     -0.18057298     0.18057298     23.542137    
-     55000   282.65069     -0.14943539     0.14943539     23.823728    
+     55000   274.90565     -0.15453379     0.15453379     23.734347    
-     60000   310.64182     -0.17418813     0.17418813     23.286959    
+     60000   290.70459     -0.27977436     0.27977436     23.835365    
-     65000   308.47141     -0.02075662     0.02075662     23.91313     
+     65000   293.42241     -0.2454241      0.2454241      23.59269     
-     70000   292.5186      -0.080163162    0.080163162    23.96283     
+     70000   295.20229     -0.041314995    0.041314995    23.73856     
-     75000   270.13928     -0.029528648    0.029528648    23.488972    
+     75000   297.79519     -0.11231755     0.11231755     23.57262     
-     80000   322.10914      0.030761045   -0.030761045    23.47592     
+     80000   285.17858     -0.070796508    0.070796508    23.817135    
-     85000   310.60347     -0.24069996     0.24069996     23.987091    
+     85000   311.71609     -0.068920177    0.068920177    23.861127    
-     90000   294.35695     -0.070458235    0.070458235    23.397929    
+     90000   287.80446     -0.19183387     0.19183387     23.369393    
-     95000   308.69043     -0.2652581      0.2652581      23.473813    
+     95000   309.43345     -0.15238671     0.15238671     23.597792    
-    100000   318.71883      0.024035956   -0.024035956    23.449863    
+    100000   294.12422     -0.14284353     0.14284353     23.526286    
-Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms
+Loop time of 876.546 on 4 procs for 100000 steps with 726 atoms
 
-Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s
+Performance: 19.714 ns/day, 1.217 hours/ns, 114.084 timesteps/s, 82.825 katom-step/s
-72.5% CPU use with 4 MPI tasks x no OpenMP threads
+98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 57.391     | 75.867     | 96.292     | 212.1 | 12.85
+Pair    | 123.63     | 171.23     | 215.73     | 336.6 | 19.53
-Bond    | 0.10177    | 0.11042    | 0.12415    |   2.7 |  0.02
+Bond    | 0.068261   | 0.075883   | 0.081822   |   1.9 |  0.01
-Kspace  | 102.79     | 123.16     | 141.5      | 165.7 | 20.87
+Kspace  | 187.59     | 231.71     | 279.01     | 287.1 | 26.43
-Neigh   | 12.808     | 12.895     | 12.982     |   2.3 |  2.18
+Neigh   | 29.28      | 29.462     | 29.637     |   2.5 |  3.36
-Comm    | 18.885     | 19.973     | 21.064     |  24.0 |  3.38
+Comm    | 12.544     | 13.731     | 14.929     |  29.1 |  1.57
-Output  | 0.0022573  | 0.0022749  | 0.0023225  |   0.1 |  0.00
+Output  | 0.0010182  | 0.0014585  | 0.0016071  |   0.7 |  0.00
-Modify  | 355.89     | 356.74     | 357.61     |   4.2 | 60.44
+Modify  | 428.74     | 429.25     | 429.74     |   2.3 | 48.97
-Other   |            | 1.478      |            |       |  0.25
+Other   |            | 1.092      |            |       |  0.12
 
-Nlocal:          181.5 ave         207 max         169 min
+Nlocal:          181.5 ave         195 max         166 min
-Histogram: 2 0 1 0 0 0 0 0 0 1
+Histogram: 1 1 0 0 0 0 0 0 0 2
-Nghost:         1961.5 ave        1984 max        1926 min
+Nghost:         1955.5 ave        1978 max        1931 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
+Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs:          30051 ave       41646 max       20775 min
+Neighs:          30343 ave       39847 max       20428 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
+Histogram: 2 0 0 0 0 0 0 0 0 2
 
-Total # of neighbors = 120204
+Total # of neighbors = 121372
-Ave neighs/atom = 165.57025
+Ave neighs/atom = 167.17906
 Ave special neighs/atom = 1.7355372
-Neighbor list builds = 7663
+Neighbor list builds = 7698
 Dangerous builds = 0
 write_data "data.piston.final"
 System init for write_data ...
@@ -214,11 +221,11 @@ PPPM/electrode initialization ...
   G vector (1/distance) = 0.32814871
   grid = 12 15 36
   stencil order = 5
-  estimated absolute RMS force accuracy = 0.029311028
+  estimated absolute RMS force accuracy = 0.029310954
-  estimated relative force accuracy = 8.8269289e-05
+  estimated relative force accuracy = 8.8269069e-05
-  using double precision MKL FFT
+  using double precision FFTW3
   3d grid and FFT values/proc = 8512 2880
 Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
 
-Average conjugate gradient steps: 1.982
+Average conjugate gradient steps: 1.981
-Total wall time: 0:09:50
+Total wall time: 0:14:36

examples/rheo/balloon/in.rheo.balloon

@@ -0,0 +1,75 @@
+# ------ 2D water balloon ------ #
+
+dimension          2
+units              lj
+atom_style         hybrid rheo bond
+boundary           m m p
+comm_modify        vel yes
+newton             off
+
+region             box block -40 40 0 80 -0.01 0.01 units box
+create_box         1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
+
+region             fluid sphere -10 40 0 30 units box side in
+lattice            hex 1.0
+create_atoms       1 region fluid
+
+region             shell sphere -10 40 0 27 units box side out
+group              shell region shell
+
+set                group shell rheo/status 1
+set                group all vx 0.005 vy -0.04
+
+# ------ Model parameters ------#
+
+variable           cut equal 3.0
+variable           n equal 1.0
+variable           rho0 equal 1.0
+variable           cs equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           zeta equal 0.05
+variable           kappa equal 0.01*${rho0}/${mp}
+variable           dt_max equal 0.1*${cut}/${cs}/3
+variable           eta equal 0.05
+variable           Cv equal 1.0
+variable           L equal 1.0
+variable           Tf equal 1.0
+
+mass               * ${mp}
+timestep           0.1
+
+pair_style         hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
+pair_coeff         * * rheo
+pair_coeff         * * rheo/solid 1.0 1.0 1.0
+
+special_bonds      lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+create_bonds       many shell shell 1 0 1.5
+special_bonds      lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+bond_style         bpm/spring
+bond_coeff         1 1.0 1.0 1.0
+
+# A lower critical strain allows the balloon to pop
+#bond_coeff         1 1.0 0.05 1.0
+
+# ------ Drop balloon ------#
+
+fix             1 all rheo ${cut} quintic 0 &
+                           shift &
+                           surface/detection coordination 22 8
+fix             2 all rheo/viscosity * constant ${eta}
+fix             3 all rheo/pressure * linear
+fix             4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
+fix             5 all enforce2d
+
+compute         rho all rheo/property/atom rho
+compute         phase all rheo/property/atom phase
+compute         nbond all nbond/atom
+
+# ------ Output & Run ------ #
+
+thermo          200
+thermo_style    custom step time ke press atoms
+
+#dump            1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
+run             30000

examples/rheo/balloon/log.17Apr2024.balloon.g++.4

@@ -0,0 +1,382 @@
+LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
+# ------ 2D water balloon ------ #
+
+dimension          2
+units              lj
+atom_style         hybrid rheo bond
+boundary           m m p
+comm_modify        vel yes
+newton             off
+
+region             box block -40 40 0 80 -0.01 0.01 units box
+create_box         1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
+Created orthogonal box = (-40 0 -0.01) to (40 80 0.01)
+  2 by 2 by 1 MPI processor grid
+
+region             fluid sphere -10 40 0 30 units box side in
+lattice            hex 1.0
+Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
+create_atoms       1 region fluid
+Created 2830 atoms
+  using lattice units in orthogonal box = (-40 0 -0.01) to (40 80 0.01)
+  create_atoms CPU = 0.001 seconds
+
+region             shell sphere -10 40 0 27 units box side out
+group              shell region shell
+544 atoms in group shell
+
+set                group shell rheo/status 1
+Setting atom values ...
+  544 settings made for rheo/status
+set                group all vx 0.005 vy -0.04
+Setting atom values ...
+  2830 settings made for vx
+  2830 settings made for vy
+
+# ------ Model parameters ------#
+
+variable           cut equal 3.0
+variable           n equal 1.0
+variable           rho0 equal 1.0
+variable           cs equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           mp equal 1/${n}
+variable           mp equal 1/1
+variable           zeta equal 0.05
+variable           kappa equal 0.01*${rho0}/${mp}
+variable           kappa equal 0.01*1/${mp}
+variable           kappa equal 0.01*1/1
+variable           dt_max equal 0.1*${cut}/${cs}/3
+variable           dt_max equal 0.1*3/${cs}/3
+variable           dt_max equal 0.1*3/1/3
+variable           eta equal 0.05
+variable           Cv equal 1.0
+variable           L equal 1.0
+variable           Tf equal 1.0
+
+mass               * ${mp}
+mass               * 1
+timestep           0.1
+
+pair_style         hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
+pair_style         hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
+pair_style         hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
+pair_coeff         * * rheo
+pair_coeff         * * rheo/solid 1.0 1.0 1.0
+
+special_bonds      lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        1        1       
+     0 = max # of 1-2 neighbors
+   101 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+create_bonds       many shell shell 1 0 1.5
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 49 49 1
+  3 neighbor lists, perpetual/occasional/extra = 2 1 0
+  (1) command create_bonds, occasional
+      attributes: full, newton off
+      pair build: full/bin
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair rheo, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: full/bin/2d
+      bin: standard
+  (3) pair rheo/solid, perpetual, trim from (2)
+      attributes: half, newton off, cut 1.3
+      pair build: trim
+      stencil: none
+      bin: none
+Added 1263 bonds, new total = 1263
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        1        1       
+     6 = max # of 1-2 neighbors
+   101 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+special_bonds      lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+bond_style         bpm/spring
+bond_coeff         1 1.0 1.0 1.0
+
+# A lower critical strain allows the balloon to pop
+#bond_coeff         1 1.0 0.05 1.0
+
+# ------ Drop balloon ------#
+
+fix             1 all rheo ${cut} quintic 0                            shift                            surface/detection coordination 22 8
+fix             1 all rheo 3 quintic 0                            shift                            surface/detection coordination 22 8
+fix             2 all rheo/viscosity * constant ${eta}
+fix             2 all rheo/viscosity * constant 0.05
+fix             3 all rheo/pressure * linear
+fix             4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
+fix             5 all enforce2d
+
+compute         rho all rheo/property/atom rho
+compute         phase all rheo/property/atom phase
+compute         nbond all nbond/atom
+
+# ------ Output & Run ------ #
+
+thermo          200
+thermo_style    custom step time ke press atoms
+
+dump            1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
+run             30000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- BPM bond style: doi:10.1039/D3SM01373A
+
+@Article{Clemmer2024,
+ author =  {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
+ title =   {A soft departure from jamming: the compaction of deformable
+            granular matter under high pressures},
+ journal = {Soft Matter},
+ year =    2024,
+ volume =  20,
+ number =  8,
+ pages =   {1702--1718}
+}
+
+- @article{PalermoInPrep,
+ journal = {in prep},
+ title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
+ year = {2024},
+ author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 49 49 1
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair rheo, perpetual, half/full from (3)
+      attributes: half, newton off
+      pair build: halffull/newtoff
+      stencil: none
+      bin: none
+  (2) pair rheo/solid, perpetual, trim from (1)
+      attributes: half, newton off, cut 1.3
+      pair build: trim
+      stencil: none
+      bin: none
+  (3) compute RHEO/KERNEL, perpetual
+      attributes: full, newton off
+      pair build: full/bin
+      stencil: full/bin/2d
+      bin: standard
+  (4) compute RHEO/GRAD, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) compute RHEO/VSHIFT, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) compute RHEO/SURFACE, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 17.63 | 17.64 | 17.65 Mbytes
+   Step          Time          KinEng         Press         Atoms   
+         0   0              0.0008125      0.00035927734       2830 
+       200   20             0.0008125      0.00035927734       2830 
+       400   40             0.0008125      0.00035927734       2830 
+       600   60             0.0008125      0.00035927734       2830 
+       800   80             0.0008125      0.00035927734       2830 
+      1000   100            0.0008125      0.00035927734       2830 
+      1200   120            0.0008125      0.00035927734       2830 
+      1400   140            0.0008125      0.00035927734       2830 
+      1600   160            0.0008125      0.00035927734       2830 
+      1800   180            0.0008125      0.00035927734       2830 
+      2000   200            0.0008125      0.00035927734       2830 
+      2200   220            0.0008125      0.00035927734       2830 
+      2400   240            0.00079033569  0.00043037861       2830 
+      2600   260            0.0007549229   0.00045188383       2830 
+      2800   280            0.00072808836  0.00031695003       2830 
+      3000   300            0.0007017958   1.6121754e-05       2830 
+      3200   320            0.00067479047 -0.00015725514       2830 
+      3400   340            0.00064762254 -0.00023361314       2830 
+      3600   360            0.00061960255 -0.00033837679       2830 
+      3800   380            0.0005857206  -0.00051770716       2830 
+      4000   400            0.00055061733 -0.00070309251       2830 
+      4200   420            0.00051884719 -0.0008247795        2830 
+      4400   440            0.00049022236 -0.00099918413       2830 
+      4600   460            0.00046060011 -0.0010923159        2830 
+      4800   480            0.00042900173 -0.0011524571        2830 
+      5000   500            0.00039751503 -0.0012586358        2830 
+      5200   520            0.00036620054 -0.0013973543        2830 
+      5400   540            0.00033130023 -0.0015185231        2830 
+      5600   560            0.00030565892 -0.0016159836        2830 
+      5800   580            0.00028209836 -0.0016925198        2830 
+      6000   600            0.00024695044 -0.0017796892        2830 
+      6200   620            0.00021190635 -0.0018706272        2830 
+      6400   640            0.0001947093  -0.0019146643        2830 
+      6600   660            0.00018903936 -0.0019146199        2830 
+      6800   680            0.00017753371 -0.0019390155        2830 
+      7000   700            0.00015170593 -0.0020247472        2830 
+      7200   720            0.00011509692 -0.0021222209        2830 
+      7400   740            7.9861785e-05 -0.0022033181        2830 
+      7600   760            6.1350463e-05 -0.0022511971        2830 
+      7800   780            6.5269523e-05 -0.0022222806        2830 
+      8000   800            8.5709569e-05 -0.0021089664        2830 
+      8200   820            0.00011746348 -0.0019351493        2830 
+      8400   840            0.00015698134 -0.0017079928        2830 
+      8600   860            0.00019758065 -0.0014618965        2830 
+      8800   880            0.00023338199 -0.0012365832        2830 
+      9000   900            0.00026282353 -0.0010348527        2830 
+      9200   920            0.00028604776 -0.00085287884       2830 
+      9400   940            0.00030388767 -0.000681122         2830 
+      9600   960            0.000317589   -0.00052203521       2830 
+      9800   980            0.00032716728 -0.00037501187       2830 
+     10000   1000           0.00033270692 -0.00025576132       2830 
+     10200   1020           0.00033485986 -0.00016554207       2830 
+     10400   1040           0.00033476763 -9.8525417e-05       2830 
+     10600   1060           0.00033351922 -5.1166347e-05       2830 
+     10800   1080           0.00033161645 -2.0773965e-05       2830 
+     11000   1100           0.00032913022  2.2384421e-07       2830 
+     11200   1120           0.00032618376  1.2304773e-05       2830 
+     11400   1140           0.00032310409  1.3725982e-05       2830 
+     11600   1160           0.0003202128   9.0431945e-06       2830 
+     11800   1180           0.00031760386 -5.3537879e-07       2830 
+     12000   1200           0.00031518884 -1.331708e-05        2830 
+     12200   1220           0.00031283958 -3.0838612e-05       2830 
+     12400   1240           0.0003104901  -5.0038548e-05       2830 
+     12600   1260           0.00030811597 -6.9699925e-05       2830 
+     12800   1280           0.00030555782 -8.9972287e-05       2830 
+     13000   1300           0.00030256671 -0.00011712941       2830 
+     13200   1320           0.00029907961 -0.00015495826       2830 
+     13400   1340           0.00029504656 -0.00020292633       2830 
+     13600   1360           0.0002905184  -0.00024892421       2830 
+     13800   1380           0.00028564542 -0.000295085         2830 
+     14000   1400           0.00028073246 -0.00034571956       2830 
+     14200   1420           0.00027611457 -0.00039341977       2830 
+     14400   1440           0.00027217382 -0.0004281012        2830 
+     14600   1460           0.00026919129 -0.00045342545       2830 
+     14800   1480           0.00026727674 -0.00047323419       2830 
+     15000   1500           0.0002663482  -0.00048423944       2830 
+     15200   1520           0.00026616663 -0.0004816085        2830 
+     15400   1540           0.00026634862 -0.00047573486       2830 
+     15600   1560           0.0002664314  -0.00046803192       2830 
+     15800   1580           0.00026603348 -0.00045753668       2830 
+     16000   1600           0.00026511015 -0.00044676105       2830 
+     16200   1620           0.00026373403 -0.00044075794       2830 
+     16400   1640           0.00026217342 -0.00043684036       2830 
+     16600   1660           0.0002607038  -0.00042774771       2830 
+     16800   1680           0.00025951097 -0.00041603026       2830 
+     17000   1700           0.00025869088 -0.00040302996       2830 
+     17200   1720           0.00025825588 -0.00038415247       2830 
+     17400   1740           0.00025818373 -0.00035742127       2830 
+     17600   1760           0.00025843381 -0.00032854722       2830 
+     17800   1780           0.00025897836 -0.00029821183       2830 
+     18000   1800           0.00025981472 -0.00026108907       2830 
+     18200   1820           0.00026095775 -0.00021731058       2830 
+     18400   1840           0.00026239688 -0.00017030825       2830 
+     18600   1860           0.00026404432 -0.00011868778       2830 
+     18800   1880           0.00026574247 -5.9556286e-05       2830 
+     19000   1900           0.00026729563  2.3014881e-06       2830 
+     19200   1920           0.00026852418  6.2100169e-05       2830 
+     19400   1940           0.00026929086  0.00012090325       2830 
+     19600   1960           0.0002695407   0.00017904223       2830 
+     19800   1980           0.00026929677  0.00023112254       2830 
+     20000   2000           0.00026863577  0.0002756697        2830 
+     20200   2020           0.00026765699  0.0003158399        2830 
+     20400   2040           0.00026646841  0.00035200747       2830 
+     20600   2060           0.00026516938  0.00038018442       2830 
+     20800   2080           0.00026383495  0.00040179111       2830 
+     21000   2100           0.00026252489  0.00042030921       2830 
+     21200   2120           0.00026128616  0.00043466976       2830 
+     21400   2140           0.00026014896  0.00044221445       2830 
+     21600   2160           0.00025912325  0.00044531883       2830 
+     21800   2180           0.00025821515  0.00044661709       2830 
+     22000   2200           0.00025742576  0.00044409089       2830 
+     22200   2220           0.00025674938  0.00043634999       2830 
+     22400   2240           0.00025617111  0.00042630344       2830 
+     22600   2260           0.0002556791   0.00041561603       2830 
+     22800   2280           0.00025525963  0.00040166735       2830 
+     23000   2300           0.00025489538  0.00038430419       2830 
+     23200   2320           0.00025456861  0.0003669402        2830 
+     23400   2340           0.00025426747  0.00034972373       2830 
+     23600   2360           0.00025398353  0.0003302242        2830 
+     23800   2380           0.00025370842  0.00030993088       2830 
+     24000   2400           0.00025344084  0.00029143258       2830 
+     24200   2420           0.00025318683  0.00027421708       2830 
+     24400   2440           0.0002529591   0.00025603123       2830 
+     24600   2460           0.0002527713   0.00023950245       2830 
+     24800   2480           0.00025264228  0.00022644812       2830 
+     25000   2500           0.00025259021  0.00021540748       2830 
+     25200   2520           0.00025262892  0.00020544201       2830 
+     25400   2540           0.00025276229  0.00019845807       2830 
+     25600   2560           0.0002529876   0.00019449958       2830 
+     25800   2580           0.00025329374  0.00019082606       2830 
+     26000   2600           0.00025366066  0.00018700064       2830 
+     26200   2620           0.00025406164  0.00018426061       2830 
+     26400   2640           0.00025446737  0.00018098339       2830 
+     26600   2660           0.00025484714  0.00017471869       2830 
+     26800   2680           0.00025516604  0.00016565557       2830 
+     27000   2700           0.00025538911  0.00015493626       2830 
+     27200   2720           0.00025548177  0.00014075592       2830 
+     27400   2740           0.00025541168  0.00012205573       2830 
+     27600   2760           0.00025514889  0.00010039772       2830 
+     27800   2780           0.00025467547  7.7069215e-05       2830 
+     28000   2800           0.0002539915   5.1158042e-05       2830 
+     28200   2820           0.00025312083  2.3468384e-05       2830 
+     28400   2840           0.00025211323 -3.2184465e-06       2830 
+     28600   2860           0.00025104366 -2.7726301e-05       2830 
+     28800   2880           0.00025000263 -5.0202987e-05       2830 
+     29000   2900           0.00024907814 -6.9244776e-05       2830 
+     29200   2920           0.00024833815 -8.2874516e-05       2830 
+     29400   2940           0.0002478155  -9.1854992e-05       2830 
+     29600   2960           0.00024750313 -9.766055e-05        2830 
+     29800   2980           0.00024735538 -9.9681291e-05       2830 
+     30000   3000           0.00024730191 -9.818759e-05        2830 
+Loop time of 177.982 on 4 procs for 30000 steps with 2830 atoms
+
+Performance: 1456330.235 tau/day, 168.557 timesteps/s, 477.016 katom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 22.913     | 27.061     | 34.594     |  87.2 | 15.20
+Bond    | 0.22386    | 0.26159    | 0.30792    |   6.0 |  0.15
+Neigh   | 0.84412    | 0.84509    | 0.8462     |   0.1 |  0.47
+Comm    | 0.50015    | 0.55579    | 0.60346    |   5.2 |  0.31
+Output  | 0.65854    | 0.69412    | 0.72473    |   2.8 |  0.39
+Modify  | 133.13     | 136        | 137.38     |  14.5 | 76.41
+Other   |            | 12.57      |            |       |  7.06
+
+Nlocal:          707.5 ave        1576 max          53 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Nghost:         164.75 ave         239 max          94 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:        12307.8 ave       27380 max         983 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+FullNghs:        23517 ave       53040 max        1502 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 94068
+Ave neighs/atom = 33.239576
+Ave special neighs/atom = 0.89257951
+Neighbor list builds = 783
+Dangerous builds = 0
+Total wall time: 0:02:58

examples/rheo/dam-break/in.rheo.dam.break

@@ -0,0 +1,76 @@
+# ------ 2D dam break ------ #
+
+dimension          2
+units              lj
+atom_style         rheo
+boundary           f s p
+comm_modify        vel yes
+newton             off
+
+# ------ Create simulation box ------ #
+
+variable           n equal 1.0
+variable           cut equal 2.2
+variable           dx equal 3.0
+
+region             box block -1 150 -1 80 -0.1 0.1 units box
+create_box         2 box
+lattice            hex ${n}
+
+region             fluid block $(xlo+v_dx+1.0) $(xlo+40.0) $(ylo+v_dx+1.0) $(yhi-20.0) EDGE EDGE units box
+region             walls1 block $(xlo+v_dx) $(xhi-v_dx) $(ylo+v_dx) $(yhi-v_dx) EDGE EDGE side out units box
+region             walls2 block EDGE EDGE EDGE $(yhi-v_dx) EDGE EDGE side in units box
+region             walls intersect 2 walls1 walls2
+
+create_atoms       1 region fluid
+create_atoms       2 region walls
+
+group              fluid type 1
+group              rig type 2
+
+# ------ Model parameters ------ #
+
+variable           rho0 equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           cs equal 1.0
+variable           zeta equal 0.1
+variable           dt_max equal  0.1*${cut}/${cs}/3
+variable           eta equal 0.1
+variable           Dr equal 0.1
+
+mass               1 ${mp}
+mass               2 $(2*v_mp)
+set                group all rheo/rho ${rho0}
+
+set                group all rheo/status 0
+set                group rig rheo/status 1
+
+timestep           ${dt_max}
+
+pair_style         rheo ${cut} artificial/visc ${zeta} #rho/damp ${Dr}
+pair_coeff         * *
+
+# ------ Fixes & computes ------ #
+
+fix                1 all rheo ${cut} quintic 10 &
+                              surface/detection coordination 22 8 &
+                              rho/sum
+fix                2 all rheo/viscosity * constant ${eta}
+fix                3 all rheo/pressure * linear
+fix                4 all gravity 1e-3 vector 0 -1 0
+fix                5 rig setforce 0.0 0.0 0.0
+fix                6 all enforce2d
+
+compute            rho all rheo/property/atom rho
+compute            p all rheo/property/atom pressure
+compute            surf all rheo/property/atom surface
+compute            sn all rheo/property/atom surface/n/x surface/n/y
+
+# ------ Output & Run ------ #
+
+thermo             20
+thermo_style       custom step time ke press
+
+#dump               1 all custom 200 atomDump id type x y vx vy fx fy c_rho c_surf c_p c_sn[*]
+
+run                30000

examples/rheo/ice-cubes/in.rheo.ice.cubes

@@ -0,0 +1,82 @@
+# ------ 2D Ice Cube Pour ------ #
+
+dimension          2
+units              lj
+atom_style         hybrid rheo/thermal bond
+boundary           m m p
+comm_modify        vel yes
+newton             off
+special_bonds      lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+region             box block -25 25 0 100 -0.01 0.01 units box
+create_box         1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
+
+region             fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
+lattice            sq 1.0
+create_atoms       1 region fluid
+
+set                group all sph/e 8.0
+
+# ------ Model parameters ------#
+
+variable           cut equal 3.0
+variable           n equal 1.0
+variable           rho0 equal 1.0
+variable           cs equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           zeta equal 0.05
+variable           kappa equal 0.01*${rho0}/${mp}
+variable           dt_max equal 0.1*${cut}/${cs}/3
+variable           eta equal 0.05
+variable           Cv equal 1.0
+variable           L equal 1.0
+variable           Tf equal 1.0
+
+mass               * ${mp}
+timestep           0.1
+
+pair_style         hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
+pair_coeff         * * rheo
+pair_coeff         * * rheo/solid 1.0 1.0 1.0
+
+bond_style         bpm/spring
+bond_coeff         1 1.0 1.0 1.0
+
+# ------ Pour particles ------#
+
+molecule        my_mol "square.mol"
+
+# Wall region extends far enough in z to avoid contact
+region          wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
+region          drop block -16 16 70 90 EDGE EDGE side in units box
+
+fix             1 all rheo ${cut} quintic 0 &
+                           thermal &
+                           shift &
+                           surface/detection coordination 22 8
+fix             2 all rheo/viscosity * constant ${eta}
+fix             3 all rheo/pressure * linear
+fix             4 all rheo/thermal conductivity * constant ${kappa} &
+                                   specific/heat * constant ${Cv} &
+                                   Tfreeze * constant ${Tf} &
+                                   latent/heat * constant ${L} &
+                                   react 1.5 1
+fix             5 all wall/region wall harmonic 1.0 1.0 1.0
+fix             6 all gravity 5e-4 vector 0 -1 0
+fix             7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
+fix             8 all enforce2d
+
+compute         rho all rheo/property/atom rho
+compute         phase all rheo/property/atom phase
+compute         temp all rheo/property/atom temperature
+compute         eng all rheo/property/atom energy
+compute         nbond all nbond/atom
+
+# ------ Output & Run ------ #
+
+thermo          200
+thermo_style    custom step time ke press atoms
+
+#dump            1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
+
+run             30000

examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4

@@ -0,0 +1,379 @@
+LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
+# ------ 2D Ice Cube Pour ------ #
+
+dimension          2
+units              lj
+atom_style         hybrid rheo/thermal bond
+boundary           m m p
+comm_modify        vel yes
+newton             off
+special_bonds      lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+region             box block -25 25 0 100 -0.01 0.01 units box
+create_box         1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
+Created orthogonal box = (-25 0 -0.01) to (25 100 0.01)
+  2 by 2 by 1 MPI processor grid
+
+region             fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
+region             fluid block -24 $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
+region             fluid block -24 24 $(ylo+1) $(ylo+30) EDGE EDGE units box
+region             fluid block -24 24 1 $(ylo+30) EDGE EDGE units box
+region             fluid block -24 24 1 30 EDGE EDGE units box
+lattice            sq 1.0
+Lattice spacing in x,y,z = 1 1 1
+create_atoms       1 region fluid
+Created 1470 atoms
+  using lattice units in orthogonal box = (-25 0 -0.01) to (25 100 0.01)
+  create_atoms CPU = 0.001 seconds
+
+set                group all sph/e 8.0
+Setting atom values ...
+  1470 settings made for sph/e
+
+# ------ Model parameters ------#
+
+variable           cut equal 3.0
+variable           n equal 1.0
+variable           rho0 equal 1.0
+variable           cs equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           mp equal 1/${n}
+variable           mp equal 1/1
+variable           zeta equal 0.05
+variable           kappa equal 0.01*${rho0}/${mp}
+variable           kappa equal 0.01*1/${mp}
+variable           kappa equal 0.01*1/1
+variable           dt_max equal 0.1*${cut}/${cs}/3
+variable           dt_max equal 0.1*3/${cs}/3
+variable           dt_max equal 0.1*3/1/3
+variable           eta equal 0.05
+variable           Cv equal 1.0
+variable           L equal 1.0
+variable           Tf equal 1.0
+
+mass               * ${mp}
+mass               * 1
+timestep           0.1
+
+pair_style         hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
+pair_style         hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
+pair_style         hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
+pair_coeff         * * rheo
+pair_coeff         * * rheo/solid 1.0 1.0 1.0
+
+bond_style         bpm/spring
+bond_coeff         1 1.0 1.0 1.0
+
+# ------ Pour particles ------#
+
+molecule        my_mol "square.mol"
+Read molecule template my_mol:
+#Made with create_mol.py
+  1 molecules
+  0 fragments
+  100 atoms with max type 1
+  342 bonds with max type 1
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+
+# Wall region extends far enough in z to avoid contact
+region          wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
+region          drop block -16 16 70 90 EDGE EDGE side in units box
+
+fix             1 all rheo ${cut} quintic 0                            thermal                            shift                            surface/detection coordination 22 8
+fix             1 all rheo 3 quintic 0                            thermal                            shift                            surface/detection coordination 22 8
+fix             2 all rheo/viscosity * constant ${eta}
+fix             2 all rheo/viscosity * constant 0.05
+fix             3 all rheo/pressure * linear
+fix             4 all rheo/thermal conductivity * constant ${kappa}                                    specific/heat * constant ${Cv}                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
+fix             4 all rheo/thermal conductivity * constant 0.01                                    specific/heat * constant ${Cv}                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
+fix             4 all rheo/thermal conductivity * constant 0.01                                    specific/heat * constant 1                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
+fix             4 all rheo/thermal conductivity * constant 0.01                                    specific/heat * constant 1                                    Tfreeze * constant 1                                    latent/heat * constant ${L}                                    react 1.5 1
+fix             4 all rheo/thermal conductivity * constant 0.01                                    specific/heat * constant 1                                    Tfreeze * constant 1                                    latent/heat * constant 1                                    react 1.5 1
+fix             5 all wall/region wall harmonic 1.0 1.0 1.0
+fix             6 all gravity 5e-4 vector 0 -1 0
+fix             7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
+WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1881)
+fix             8 all enforce2d
+
+compute         rho all rheo/property/atom rho
+compute         phase all rheo/property/atom phase
+compute         temp all rheo/property/atom temperature
+compute         eng all rheo/property/atom energy
+compute         nbond all nbond/atom
+
+# ------ Output & Run ------ #
+
+thermo          200
+thermo_style    custom step time ke press atoms
+
+dump            1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
+
+run             30000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- BPM bond style: doi:10.1039/D3SM01373A
+
+@Article{Clemmer2024,
+ author =  {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
+ title =   {A soft departure from jamming: the compaction of deformable
+            granular matter under high pressures},
+ journal = {Soft Matter},
+ year =    2024,
+ volume =  20,
+ number =  8,
+ pages =   {1702--1718}
+}
+
+- @article{PalermoInPrep,
+ journal = {in prep},
+ title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
+ year = {2024},
+ author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
+}
+
+- @article{ApplMathModel.130.310,
+ title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
+ journal = {Applied Mathematical Modelling},
+ volume = {130},
+ pages = {310-326},
+ year = {2024},
+ issn = {0307-904X},
+ doi = {https://doi.org/10.1016/j.apm.2024.02.027},
+ author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 31 61 1
+  7 neighbor lists, perpetual/occasional/extra = 6 1 0
+  (1) pair rheo, perpetual, half/full from (3)
+      attributes: half, newton off
+      pair build: halffull/newtoff
+      stencil: none
+      bin: none
+  (2) pair rheo/solid, perpetual, trim from (4)
+      attributes: half, newton off, cut 1.3
+      pair build: trim
+      stencil: none
+      bin: none
+  (3) compute RHEO/KERNEL, perpetual
+      attributes: full, newton off
+      pair build: full/bin
+      stencil: full/bin/2d
+      bin: standard
+  (4) compute RHEO/GRAD, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) compute RHEO/VSHIFT, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) compute RHEO/SURFACE, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (7) fix rheo/thermal, occasional, trim from (4)
+      attributes: half, newton off, cut 3
+      pair build: trim
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 15.53 | 15.61 | 15.69 Mbytes
+   Step          Time          KinEng         Press         Atoms   
+         0   0              0              0                   1470 
+       200   20             5.6002982e-05  3.4434234e-05       1570 
+       400   40             8.2173099e-05  8.6171768e-05       1570 
+       600   60             8.019018e-05   0.00010750355       1570 
+       800   80             0.00013866953  0.00010265608       1570 
+      1000   100            0.00018965028  8.1985605e-05       1570 
+      1200   120            0.00022033242  7.4736443e-05       1670 
+      1400   140            0.00030767062  0.00011264333       1670 
+      1600   160            0.00040770127  0.00018779992       1670 
+      1800   180            0.00047476332  0.00023153009       1670 
+      2000   200            0.00059116774  0.00027200445       1670 
+      2200   220            0.0007151733   0.0002919963        1770 
+      2400   240            0.00083392135  0.00029757889       1770 
+      2600   260            0.00099653466  0.00036547269       1770 
+      2800   280            0.0011964069   0.00045983458       1770 
+      3000   300            0.0013716953   0.00055013647       1770 
+      3200   320            0.0015174096   0.00064203572       1870 
+      3400   340            0.0016539743   0.00086671622       1870 
+      3600   360            0.0015887858   0.00066353749       1870 
+      3800   380            0.0016451684   0.00070551483       1870 
+      4000   400            0.0017330971   0.00080722283       1870 
+      4200   420            0.001812193    0.00073573903       1970 
+      4400   440            0.001755871    0.0010621909        1970 
+      4600   460            0.0016190772   0.00072913706       1970 
+      4800   480            0.0015741931   0.00073524088       1970 
+      5000   500            0.0016488815   0.00088684275       1970 
+      5200   520            0.0017213288   0.00077042378       2070 
+      5400   540            0.0018509598   0.0010219434        2070 
+      5600   560            0.0020251064   0.00083182483       2070 
+      5800   580            0.0022473255   0.00095076144       2070 
+      6000   600            0.0024843519   0.0011247014        2070 
+      6200   620            0.0022282321   0.0018105932        2170 
+      6400   640            0.0020289063   0.0014158497        2170 
+      6600   660            0.002145241    0.0011359383        2170 
+      6800   680            0.0024313937   0.0016475504        2170 
+      7000   700            0.0021000599   0.0020983745        2170 
+      7200   720            0.0019137235   0.0010439152        2270 
+      7400   740            0.0018801367   0.00095436448       2270 
+      7600   760            0.0017979449   0.0011184039        2270 
+      7800   780            0.0018005205   0.0009243205        2270 
+      8000   800            0.0017827073   0.0013671228        2270 
+      8200   820            0.0018387108   0.0015426012        2270 
+      8400   840            0.0016000788   0.0016751514        2270 
+      8600   860            0.0013954964   0.0016884335        2270 
+      8800   880            0.0013283728   0.0012399398        2270 
+      9000   900            0.001389385    0.0012968496        2270 
+      9200   920            0.0012295438   0.0012995821        2270 
+      9400   940            0.0010522655   0.00082245528       2270 
+      9600   960            0.00097085496  0.00053833131       2270 
+      9800   980            0.0009398987   0.00063467387       2270 
+     10000   1000           0.00092710392  0.00059494446       2270 
+     10200   1020           0.00095545471  0.00074560644       2270 
+     10400   1040           0.0009645841   0.00085429807       2270 
+     10600   1060           0.00064037148  0.0017222246        2270 
+     10800   1080           0.00046790978  0.00088204234       2270 
+     11000   1100           0.00030106229  0.00074950209       2270 
+     11200   1120           0.00027746016  0.00052831745       2270 
+     11400   1140           0.0002533348   0.0006272715        2270 
+     11600   1160           0.00021825085  0.00029691552       2270 
+     11800   1180           0.0001451308   0.00015037478       2270 
+     12000   1200           0.0001314823   0.00017227174       2270 
+     12200   1220           0.00013693632  0.00017791384       2270 
+     12400   1240           0.00014987347  0.0002286677        2270 
+     12600   1260           0.00015092598  0.0003698436        2270 
+     12800   1280           0.0001291653   0.00047229532       2270 
+     13000   1300           0.00011949988  0.00049560375       2270 
+     13200   1320           0.00011694665  0.00057542084       2270 
+     13400   1340           9.6164519e-05  0.00062714755       2270 
+     13600   1360           8.4517591e-05  0.00044156913       2270 
+     13800   1380           0.00019140516  0.0003264745        2270 
+     14000   1400           0.00013868599  0.00037753497       2270 
+     14200   1420           9.3701636e-05  0.00031517848       2270 
+     14400   1440           6.7389077e-05  0.0002946861        2270 
+     14600   1460           5.3640086e-05  0.00026650711       2270 
+     14800   1480           4.2699992e-05  0.00023789279       2270 
+     15000   1500           5.3012016e-05  0.00019933234       2270 
+     15200   1520           5.8834197e-05  0.00022407007       2270 
+     15400   1540           5.0899982e-05  0.00029695531       2270 
+     15600   1560           3.0476742e-05  0.00039119066       2270 
+     15800   1580           1.6633264e-05  0.00033770401       2270 
+     16000   1600           1.098906e-05   0.00036684894       2270 
+     16200   1620           1.464848e-05   0.00036449759       2270 
+     16400   1640           1.9598429e-05  0.00021056689       2270 
+     16600   1660           1.2644955e-05  0.00020781781       2270 
+     16800   1680           8.8428553e-06  0.000165            2270 
+     17000   1700           8.8971439e-06  0.00012266475       2270 
+     17200   1720           1.7032781e-05  0.00019873443       2270 
+     17400   1740           1.9448563e-05  0.00025661663       2270 
+     17600   1760           1.3714713e-05  0.000324022         2270 
+     17800   1780           9.1326468e-06  0.00031392513       2270 
+     18000   1800           9.2464802e-06  0.00029729527       2270 
+     18200   1820           1.5553042e-05  0.00027488475       2270 
+     18400   1840           1.4132933e-05  0.00019565459       2270 
+     18600   1860           9.4734832e-06  0.00016716988       2270 
+     18800   1880           5.5115145e-06  0.00013728033       2270 
+     19000   1900           8.268812e-06   0.00015119605       2270 
+     19200   1920           1.2470136e-05  0.00020222131       2270 
+     19400   1940           9.9387775e-06  0.00024503373       2270 
+     19600   1960           5.4241999e-06  0.00026921858       2270 
+     19800   1980           2.7987348e-06  0.00026201267       2270 
+     20000   2000           6.272538e-06   0.00025626323       2270 
+     20200   2020           8.0157781e-06  0.000220139         2270 
+     20400   2040           6.1652093e-06  0.00017089058       2270 
+     20600   2060           2.9967592e-06  0.00014582864       2270 
+     20800   2080           3.016678e-06   0.000148629         2270 
+     21000   2100           7.287645e-06   0.00016486102       2270 
+     21200   2120           8.6905277e-06  0.00020276916       2270 
+     21400   2140           6.8453018e-06  0.00023156153       2270 
+     21600   2160           3.3853799e-06  0.0002432462        2270 
+     21800   2180           4.1241209e-06  0.00022829024       2270 
+     22000   2200           7.0802396e-06  0.00020784823       2270 
+     22200   2220           7.3361691e-06  0.00018114134       2270 
+     22400   2240           5.0764593e-06  0.00014351106       2270 
+     22600   2260           2.7487537e-06  0.00012919872       2270 
+     22800   2280           4.620167e-06   0.00013746218       2270 
+     23000   2300           6.9819357e-06  0.00015985102       2270 
+     23200   2320           6.8923916e-06  0.00018713045       2270 
+     23400   2340           4.1795088e-06  0.00019846682       2270 
+     23600   2360           2.2871028e-06  0.00021068421       2270 
+     23800   2380           3.862046e-06   0.00019553306       2270 
+     24000   2400           5.2448555e-06  0.00017398041       2270 
+     24200   2420           4.7565441e-06  0.00015008142       2270 
+     24400   2440           2.2952135e-06  0.00012747106       2270 
+     24600   2460           2.1575617e-06  0.00012516996       2270 
+     24800   2480           4.1777868e-06  0.0001331902        2270 
+     25000   2500           5.5679133e-06  0.00015504562       2270 
+     25200   2520           4.5758741e-06  0.00017146032       2270 
+     25400   2540           2.3403277e-06  0.00017611666       2270 
+     25600   2560           2.7029302e-06  0.00016850788       2270 
+     25800   2580           4.3601102e-06  0.00015884642       2270 
+     26000   2600           5.2244249e-06  0.00013793898       2270 
+     26200   2620           3.4577672e-06  0.00012395875       2270 
+     26400   2640           2.361577e-06   0.00011600057       2270 
+     26600   2660           2.8515644e-06  0.00011277063       2270 
+     26800   2680           4.0851213e-06  0.0001290832        2270 
+     27000   2700           4.2579644e-06  0.0001476495        2270 
+     27200   2720           2.6593858e-06  0.00015977745       2270 
+     27400   2740           1.990115e-06   0.00015612787       2270 
+     27600   2760           2.6756835e-06  0.00014913772       2270 
+     27800   2780           3.9032806e-06  0.00014014763       2270 
+     28000   2800           3.2729446e-06  0.00012216846       2270 
+     28200   2820           1.9357278e-06  0.00011078621       2270 
+     28400   2840           1.7094832e-06  0.00010910509       2270 
+     28600   2860           2.8731406e-06  0.00011179644       2270 
+     28800   2880           3.7062354e-06  0.00012254091       2270 
+     29000   2900           2.7844262e-06  0.00013060331       2270 
+     29200   2920           1.7680655e-06  0.00013797514       2270 
+     29400   2940           1.706873e-06   0.0001350685        2270 
+     29600   2960           2.8764562e-06  0.00012428508       2270 
+     29800   2980           3.1502029e-06  0.00011456718       2270 
+     30000   3000           2.1833409e-06  0.00010317469       2270 
+Loop time of 165.611 on 4 procs for 30000 steps with 2270 atoms
+
+Performance: 1565111.240 tau/day, 181.147 timesteps/s, 411.204 katom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.63183    | 21.226     | 42.266     | 444.6 | 12.82
+Bond    | 0.095073   | 0.17799    | 0.27877    |  17.0 |  0.11
+Neigh   | 2.0745     | 2.0781     | 2.0822     |   0.2 |  1.25
+Comm    | 0.32024    | 0.38703    | 0.45564    |   8.1 |  0.23
+Output  | 0.60459    | 0.76798    | 0.93724    |  18.6 |  0.46
+Modify  | 119.85     | 140.76     | 161.36     | 172.2 | 85.00
+Other   |            | 0.2124     |            |       |  0.13
+
+Nlocal:          567.5 ave        1139 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:           75.5 ave         152 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:        9238.25 ave       18490 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:        17945 ave       35917 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 71780
+Ave neighs/atom = 31.621145
+Ave special neighs/atom = 0.22026432
+Neighbor list builds = 2071
+Dangerous builds = 0
+
+Total wall time: 0:02:45

examples/rheo/ice-cubes/square.mol

@@ -0,0 +1,658 @@
+#Made with create_mol.py
+
+100 atoms 
+342 bonds 
+
+Coords
+#ID x y z
+1 -4 -4 0
+2 -3 -4 0
+3 -2 -4 0
+4 -1 -4 0
+5 0 -4 0
+6 1 -4 0
+7 2 -4 0
+8 3 -4 0
+9 4 -4 0
+10 5 -4 0
+11 -4 -3 0
+12 -3 -3 0
+13 -2 -3 0
+14 -1 -3 0
+15 0 -3 0
+16 1 -3 0
+17 2 -3 0
+18 3 -3 0
+19 4 -3 0
+20 5 -3 0
+21 -4 -2 0
+22 -3 -2 0
+23 -2 -2 0
+24 -1 -2 0
+25 0 -2 0
+26 1 -2 0
+27 2 -2 0
+28 3 -2 0
+29 4 -2 0
+30 5 -2 0
+31 -4 -1 0
+32 -3 -1 0
+33 -2 -1 0
+34 -1 -1 0
+35 0 -1 0
+36 1 -1 0
+37 2 -1 0
+38 3 -1 0
+39 4 -1 0
+40 5 -1 0
+41 -4 0 0
+42 -3 0 0
+43 -2 0 0
+44 -1 0 0
+45 0 0 0
+46 1 0 0
+47 2 0 0
+48 3 0 0
+49 4 0 0
+50 5 0 0
+51 -4 1 0
+52 -3 1 0
+53 -2 1 0
+54 -1 1 0
+55 0 1 0
+56 1 1 0
+57 2 1 0
+58 3 1 0
+59 4 1 0
+60 5 1 0
+61 -4 2 0
+62 -3 2 0
+63 -2 2 0
+64 -1 2 0
+65 0 2 0
+66 1 2 0
+67 2 2 0
+68 3 2 0
+69 4 2 0
+70 5 2 0
+71 -4 3 0
+72 -3 3 0
+73 -2 3 0
+74 -1 3 0
+75 0 3 0
+76 1 3 0
+77 2 3 0
+78 3 3 0
+79 4 3 0
+80 5 3 0
+81 -4 4 0
+82 -3 4 0
+83 -2 4 0
+84 -1 4 0
+85 0 4 0
+86 1 4 0
+87 2 4 0
+88 3 4 0
+89 4 4 0
+90 5 4 0
+91 -4 5 0
+92 -3 5 0
+93 -2 5 0
+94 -1 5 0
+95 0 5 0
+96 1 5 0
+97 2 5 0
+98 3 5 0
+99 4 5 0
+100 5 5 0
+
+Types
+#ID type
+1 1
+2 1
+3 1
+4 1
+5 1
+6 1
+7 1
+8 1
+9 1
+10 1
+11 1
+12 1
+13 1
+14 1
+15 1
+16 1
+17 1
+18 1
+19 1
+20 1
+21 1
+22 1
+23 1
+24 1
+25 1
+26 1
+27 1
+28 1
+29 1
+30 1
+31 1
+32 1
+33 1
+34 1
+35 1
+36 1
+37 1
+38 1
+39 1
+40 1
+41 1
+42 1
+43 1
+44 1
+45 1
+46 1
+47 1
+48 1
+49 1
+50 1
+51 1
+52 1
+53 1
+54 1
+55 1
+56 1
+57 1
+58 1
+59 1
+60 1
+61 1
+62 1
+63 1
+64 1
+65 1
+66 1
+67 1
+68 1
+69 1
+70 1
+71 1
+72 1
+73 1
+74 1
+75 1
+76 1
+77 1
+78 1
+79 1
+80 1
+81 1
+82 1
+83 1
+84 1
+85 1
+86 1
+87 1
+88 1
+89 1
+90 1
+91 1
+92 1
+93 1
+94 1
+95 1
+96 1
+97 1
+98 1
+99 1
+100 1
+
+Masses
+#ID mass
+1 1
+2 1
+3 1
+4 1
+5 1
+6 1
+7 1
+8 1
+9 1
+10 1
+11 1
+12 1
+13 1
+14 1
+15 1
+16 1
+17 1
+18 1
+19 1
+20 1
+21 1
+22 1
+23 1
+24 1
+25 1
+26 1
+27 1
+28 1
+29 1
+30 1
+31 1
+32 1
+33 1
+34 1
+35 1
+36 1
+37 1
+38 1
+39 1
+40 1
+41 1
+42 1
+43 1
+44 1
+45 1
+46 1
+47 1
+48 1
+49 1
+50 1
+51 1
+52 1
+53 1
+54 1
+55 1
+56 1
+57 1
+58 1
+59 1
+60 1
+61 1
+62 1
+63 1
+64 1
+65 1
+66 1
+67 1
+68 1
+69 1
+70 1
+71 1
+72 1
+73 1
+74 1
+75 1
+76 1
+77 1
+78 1
+79 1
+80 1
+81 1
+82 1
+83 1
+84 1
+85 1
+86 1
+87 1
+88 1
+89 1
+90 1
+91 1
+92 1
+93 1
+94 1
+95 1
+96 1
+97 1
+98 1
+99 1
+100 1
+
+Bonds
+#ID type atom1 atom2
+1 1 1 2
+2 1 1 11
+3 1 1 12
+4 1 2 3
+5 1 2 11
+6 1 2 12
+7 1 2 13
+8 1 3 4
+9 1 3 12
+10 1 3 13
+11 1 3 14
+12 1 4 5
+13 1 4 13
+14 1 4 14
+15 1 4 15
+16 1 5 6
+17 1 5 14
+18 1 5 15
+19 1 5 16
+20 1 6 7
+21 1 6 15
+22 1 6 16
+23 1 6 17
+24 1 7 8
+25 1 7 16
+26 1 7 17
+27 1 7 18
+28 1 8 9
+29 1 8 17
+30 1 8 18
+31 1 8 19
+32 1 9 10
+33 1 9 18
+34 1 9 19
+35 1 9 20
+36 1 10 19
+37 1 10 20
+38 1 11 21
+39 1 11 12
+40 1 11 22
+41 1 12 21
+42 1 12 13
+43 1 12 22
+44 1 12 23
+45 1 13 22
+46 1 13 23
+47 1 13 14
+48 1 13 24
+49 1 14 23
+50 1 14 24
+51 1 14 15
+52 1 14 25
+53 1 15 24
+54 1 15 16
+55 1 15 25
+56 1 15 26
+57 1 16 25
+58 1 16 26
+59 1 16 17
+60 1 16 27
+61 1 17 26
+62 1 17 18
+63 1 17 27
+64 1 17 28
+65 1 18 27
+66 1 18 28
+67 1 18 19
+68 1 18 29
+69 1 19 28
+70 1 19 29
+71 1 19 20
+72 1 19 30
+73 1 20 29
+74 1 20 30
+75 1 21 22
+76 1 21 31
+77 1 21 32
+78 1 22 23
+79 1 22 31
+80 1 22 32
+81 1 22 33
+82 1 23 24
+83 1 23 32
+84 1 23 33
+85 1 23 34
+86 1 24 25
+87 1 24 33
+88 1 24 34
+89 1 24 35
+90 1 25 26
+91 1 25 34
+92 1 25 35
+93 1 25 36
+94 1 26 27
+95 1 26 35
+96 1 26 36
+97 1 26 37
+98 1 27 28
+99 1 27 36
+100 1 27 37
+101 1 27 38
+102 1 28 29
+103 1 28 37
+104 1 28 38
+105 1 28 39
+106 1 29 30
+107 1 29 38
+108 1 29 39
+109 1 29 40
+110 1 30 39
+111 1 30 40
+112 1 31 32
+113 1 31 41
+114 1 31 42
+115 1 32 33
+116 1 32 41
+117 1 32 42
+118 1 32 43
+119 1 33 34
+120 1 33 42
+121 1 33 43
+122 1 33 44
+123 1 34 35
+124 1 34 43
+125 1 34 44
+126 1 34 45
+127 1 35 36
+128 1 35 44
+129 1 35 45
+130 1 35 46
+131 1 36 37
+132 1 36 45
+133 1 36 46
+134 1 36 47
+135 1 37 38
+136 1 37 46
+137 1 37 47
+138 1 37 48
+139 1 38 39
+140 1 38 47
+141 1 38 48
+142 1 38 49
+143 1 39 40
+144 1 39 48
+145 1 39 49
+146 1 39 50
+147 1 40 49
+148 1 40 50
+149 1 41 51
+150 1 41 42
+151 1 41 52
+152 1 42 51
+153 1 42 43
+154 1 42 52
+155 1 42 53
+156 1 43 52
+157 1 43 53
+158 1 43 44
+159 1 43 54
+160 1 44 53
+161 1 44 54
+162 1 44 45
+163 1 44 55
+164 1 45 54
+165 1 45 46
+166 1 45 55
+167 1 45 56
+168 1 46 55
+169 1 46 56
+170 1 46 47
+171 1 46 57
+172 1 47 56
+173 1 47 48
+174 1 47 57
+175 1 47 58
+176 1 48 57
+177 1 48 58
+178 1 48 49
+179 1 48 59
+180 1 49 58
+181 1 49 59
+182 1 49 50
+183 1 49 60
+184 1 50 59
+185 1 50 60
+186 1 51 52
+187 1 51 61
+188 1 51 62
+189 1 52 53
+190 1 52 61
+191 1 52 62
+192 1 52 63
+193 1 53 54
+194 1 53 62
+195 1 53 63
+196 1 53 64
+197 1 54 55
+198 1 54 63
+199 1 54 64
+200 1 54 65
+201 1 55 56
+202 1 55 64
+203 1 55 65
+204 1 55 66
+205 1 56 57
+206 1 56 65
+207 1 56 66
+208 1 56 67
+209 1 57 58
+210 1 57 66
+211 1 57 67
+212 1 57 68
+213 1 58 59
+214 1 58 67
+215 1 58 68
+216 1 58 69
+217 1 59 60
+218 1 59 68
+219 1 59 69
+220 1 59 70
+221 1 60 69
+222 1 60 70
+223 1 61 71
+224 1 61 62
+225 1 61 72
+226 1 62 71
+227 1 62 63
+228 1 62 72
+229 1 62 73
+230 1 63 72
+231 1 63 73
+232 1 63 64
+233 1 63 74
+234 1 64 73
+235 1 64 74
+236 1 64 65
+237 1 64 75
+238 1 65 74
+239 1 65 66
+240 1 65 75
+241 1 65 76
+242 1 66 75
+243 1 66 76
+244 1 66 67
+245 1 66 77
+246 1 67 76
+247 1 67 68
+248 1 67 77
+249 1 67 78
+250 1 68 77
+251 1 68 78
+252 1 68 69
+253 1 68 79
+254 1 69 78
+255 1 69 79
+256 1 69 70
+257 1 69 80
+258 1 70 79
+259 1 70 80
+260 1 71 72
+261 1 71 81
+262 1 71 82
+263 1 72 73
+264 1 72 81
+265 1 72 82
+266 1 72 83
+267 1 73 74
+268 1 73 82
+269 1 73 83
+270 1 73 84
+271 1 74 75
+272 1 74 83
+273 1 74 84
+274 1 74 85
+275 1 75 76
+276 1 75 84
+277 1 75 85
+278 1 75 86
+279 1 76 77
+280 1 76 85
+281 1 76 86
+282 1 76 87
+283 1 77 78
+284 1 77 86
+285 1 77 87
+286 1 77 88
+287 1 78 79
+288 1 78 87
+289 1 78 88
+290 1 78 89
+291 1 79 80
+292 1 79 88
+293 1 79 89
+294 1 79 90
+295 1 80 89
+296 1 80 90
+297 1 81 82
+298 1 81 91
+299 1 81 92
+300 1 82 83
+301 1 82 91
+302 1 82 92
+303 1 82 93
+304 1 83 84
+305 1 83 92
+306 1 83 93
+307 1 83 94
+308 1 84 85
+309 1 84 93
+310 1 84 94
+311 1 84 95
+312 1 85 86
+313 1 85 94
+314 1 85 95
+315 1 85 96
+316 1 86 87
+317 1 86 95
+318 1 86 96
+319 1 86 97
+320 1 87 88
+321 1 87 96
+322 1 87 97
+323 1 87 98
+324 1 88 89
+325 1 88 97
+326 1 88 98
+327 1 88 99
+328 1 89 90
+329 1 89 98
+330 1 89 99
+331 1 89 100
+332 1 90 99
+333 1 90 100
+334 1 91 92
+335 1 92 93
+336 1 93 94
+337 1 94 95
+338 1 95 96
+339 1 96 97
+340 1 97 98
+341 1 98 99
+342 1 99 100

examples/rheo/oxidation/in.rheo.oxidation

@@ -0,0 +1,102 @@
+# ------ 2D oxidizing bar ------ #
+
+dimension          2
+units              lj
+atom_style         hybrid rheo/thermal bond
+boundary           m m p
+comm_modify        vel yes
+newton             off
+
+region             box block -60 60 0 80 -0.01 0.01 units box
+create_box         3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
+
+region             lbar block -15 0 3 80 EDGE EDGE units box
+region             rbar block 0 15 3 80 EDGE EDGE units box
+region             bar union 2 lbar rbar
+region             floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
+
+lattice            hex 1.0
+create_atoms       1 region bar
+create_atoms       3 region floor
+
+set                region rbar type 2
+group              bar type 1 2
+group              rbar type 2
+group              floor type 3
+
+set                group all sph/e 0.0
+set                group all rheo/status 1
+
+# ------ Model parameters ------#
+
+variable           cut equal 3.0
+variable           n equal 1.0
+variable           rho0 equal 1.0
+variable           cs equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           zeta equal 0.05
+variable           kappa equal 0.1*${rho0}/${mp}
+variable           dt_max equal 0.1*${cut}/${cs}/3
+variable           eta equal 0.05
+variable           Cv equal 1.0
+variable           L equal 0.1
+variable           Tf equal 1.0
+
+mass               * ${mp}
+timestep           0.1
+
+pair_style         hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
+pair_coeff         * * rheo
+pair_coeff         * * rheo/solid 1.0 1.0 1.0
+
+special_bonds      lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+create_bonds       many bar bar 1 0 1.5
+special_bonds      lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+bond_style         hybrid bpm/spring rheo/shell t/form 100
+bond_coeff         1 bpm/spring 1.0 1.0 1.0
+bond_coeff         2 rheo/shell 0.2 0.2 0.1
+
+# ------ Apply dynamics ------#
+
+# Note: surface detection is not performed on solid bodies, so cannot use surface property
+compute         coord all rheo/property/atom coordination
+variable        surf atom c_coord<22
+group           surf dynamic all var surf every 10
+
+fix             1 all rheo ${cut} quintic 0 &
+                           thermal &
+                           shift &
+                           surface/detection coordination 22 8
+fix             2 all rheo/viscosity * constant ${eta}
+fix             3 all rheo/pressure * linear
+fix             4 all rheo/thermal conductivity * constant ${kappa} &
+                                   specific/heat * constant ${Cv} &
+                                   Tfreeze * constant ${Tf} &
+                                   latent/heat * constant ${L} &
+                                   react 1.5 1
+
+fix             5 rbar rheo/oxidation 1.5 2 1.0
+fix             6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
+fix             7 all gravity 5e-5 vector 0 -1 0
+fix             8 floor setforce 0.0 0.0 0.0
+fix             9 surf add/heat linear 1.1 0.05
+fix             10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
+fix             11 all enforce2d
+
+compute         surf all rheo/property/atom surface
+compute         rho all rheo/property/atom rho
+compute         phase all rheo/property/atom phase
+compute         temp all rheo/property/atom temperature
+compute         eng all rheo/property/atom energy
+compute         nbond_shell all rheo/property/atom nbond/shell
+compute         nbond_solid all nbond/atom bond/type 1
+
+# ------ Output & Run ------ #
+
+thermo          200
+thermo_style    custom step time ke press atoms
+
+#dump            1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf
+
+run             40000

examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4

@@ -0,0 +1,488 @@
+LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
+# ------ 2D oxidizing bar ------ #
+
+dimension          2
+units              lj
+atom_style         hybrid rheo/thermal bond
+boundary           m m p
+comm_modify        vel yes
+newton             off
+
+region             box block -60 60 0 80 -0.01 0.01 units box
+create_box         3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
+Created orthogonal box = (-60 0 -0.01) to (60 80 0.01)
+  2 by 2 by 1 MPI processor grid
+
+region             lbar block -15 0 3 80 EDGE EDGE units box
+region             rbar block 0 15 3 80 EDGE EDGE units box
+region             bar union 2 lbar rbar
+region             floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
+
+lattice            hex 1.0
+Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
+create_atoms       1 region bar
+Created 2255 atoms
+  using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
+  create_atoms CPU = 0.001 seconds
+create_atoms       3 region floor
+Created 446 atoms
+  using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
+  create_atoms CPU = 0.000 seconds
+
+set                region rbar type 2
+Setting atom values ...
+  1148 settings made for type
+group              bar type 1 2
+2255 atoms in group bar
+group              rbar type 2
+1148 atoms in group rbar
+group              floor type 3
+446 atoms in group floor
+
+set                group all sph/e 0.0
+Setting atom values ...
+  2701 settings made for sph/e
+set                group all rheo/status 1
+Setting atom values ...
+  2701 settings made for rheo/status
+
+# ------ Model parameters ------#
+
+variable           cut equal 3.0
+variable           n equal 1.0
+variable           rho0 equal 1.0
+variable           cs equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           mp equal 1/${n}
+variable           mp equal 1/1
+variable           zeta equal 0.05
+variable           kappa equal 0.1*${rho0}/${mp}
+variable           kappa equal 0.1*1/${mp}
+variable           kappa equal 0.1*1/1
+variable           dt_max equal 0.1*${cut}/${cs}/3
+variable           dt_max equal 0.1*3/${cs}/3
+variable           dt_max equal 0.1*3/1/3
+variable           eta equal 0.05
+variable           Cv equal 1.0
+variable           L equal 0.1
+variable           Tf equal 1.0
+
+mass               * ${mp}
+mass               * 1
+timestep           0.1
+
+pair_style         hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
+pair_style         hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
+pair_style         hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
+pair_coeff         * * rheo
+pair_coeff         * * rheo/solid 1.0 1.0 1.0
+
+special_bonds      lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        1        1       
+     0 = max # of 1-2 neighbors
+   101 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+create_bonds       many bar bar 1 0 1.5
+Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 73 49 1
+  3 neighbor lists, perpetual/occasional/extra = 2 1 0
+  (1) command create_bonds, occasional
+      attributes: full, newton off
+      pair build: full/bin
+      stencil: full/bin/2d
+      bin: standard
+  (2) pair rheo, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: full/bin/2d
+      bin: standard
+  (3) pair rheo/solid, perpetual, trim from (2)
+      attributes: half, newton off, cut 1.3
+      pair build: trim
+      stencil: none
+      bin: none
+Added 6547 bonds, new total = 6547
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        1        1       
+  special bond factors coul:  0        1        1       
+     6 = max # of 1-2 neighbors
+   101 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+special_bonds      lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+bond_style         hybrid bpm/spring rheo/shell t/form 100
+bond_coeff         1 bpm/spring 1.0 1.0 1.0
+bond_coeff         2 rheo/shell 0.2 0.2 0.1
+
+# ------ Apply dynamics ------#
+
+# Note: surface detection is not performed on solid bodies, so cannot use surface property
+compute         coord all rheo/property/atom coordination
+variable        surf atom c_coord<22
+group           surf dynamic all var surf every 10
+dynamic group surf defined
+
+fix             1 all rheo ${cut} quintic 0                            thermal                            shift                            surface/detection coordination 22 8
+fix             1 all rheo 3 quintic 0                            thermal                            shift                            surface/detection coordination 22 8
+fix             2 all rheo/viscosity * constant ${eta}
+fix             2 all rheo/viscosity * constant 0.05
+fix             3 all rheo/pressure * linear
+fix             4 all rheo/thermal conductivity * constant ${kappa}                                    specific/heat * constant ${Cv}                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
+fix             4 all rheo/thermal conductivity * constant 0.1                                    specific/heat * constant ${Cv}                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
+fix             4 all rheo/thermal conductivity * constant 0.1                                    specific/heat * constant 1                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
+fix             4 all rheo/thermal conductivity * constant 0.1                                    specific/heat * constant 1                                    Tfreeze * constant 1                                    latent/heat * constant ${L}                                    react 1.5 1
+fix             4 all rheo/thermal conductivity * constant 0.1                                    specific/heat * constant 1                                    Tfreeze * constant 1                                    latent/heat * constant 0.1                                    react 1.5 1
+
+fix             5 rbar rheo/oxidation 1.5 2 1.0
+fix             6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
+fix             7 all gravity 5e-5 vector 0 -1 0
+fix             8 floor setforce 0.0 0.0 0.0
+fix             9 surf add/heat linear 1.1 0.05
+fix             10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
+fix             11 all enforce2d
+
+compute         surf all rheo/property/atom surface
+compute         rho all rheo/property/atom rho
+compute         phase all rheo/property/atom phase
+compute         status all rheo/property/atom status
+compute         temp all rheo/property/atom temperature
+compute         eng all rheo/property/atom energy
+compute         nbond_shell all rheo/property/atom nbond/shell
+compute         nbond_solid all nbond/atom bond/type 1
+
+# ------ Output & Run ------ #
+
+thermo          200
+thermo_style    custom step time ke press atoms
+
+dump            1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status
+
+run             40000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- BPM bond style: doi:10.1039/D3SM01373A
+
+@Article{Clemmer2024,
+ author =  {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
+ title =   {A soft departure from jamming: the compaction of deformable
+            granular matter under high pressures},
+ journal = {Soft Matter},
+ year =    2024,
+ volume =  20,
+ number =  8,
+ pages =   {1702--1718}
+}
+
+- @article{PalermoInPrep,
+ journal = {in prep},
+ title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
+ year = {2024},
+ author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
+}
+
+- @article{ApplMathModel.130.310,
+ title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
+ journal = {Applied Mathematical Modelling},
+ volume = {130},
+ pages = {310-326},
+ year = {2024},
+ issn = {0307-904X},
+ doi = {https://doi.org/10.1016/j.apm.2024.02.027},
+ author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 73 49 1
+  8 neighbor lists, perpetual/occasional/extra = 7 1 0
+  (1) pair rheo, perpetual, half/full from (3)
+      attributes: half, newton off
+      pair build: halffull/newtoff
+      stencil: none
+      bin: none
+  (2) pair rheo/solid, perpetual, trim from (4)
+      attributes: half, newton off, cut 1.3
+      pair build: trim
+      stencil: none
+      bin: none
+  (3) compute RHEO/KERNEL, perpetual
+      attributes: full, newton off
+      pair build: full/bin
+      stencil: full/bin/2d
+      bin: standard
+  (4) compute RHEO/GRAD, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) compute RHEO/VSHIFT, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) compute RHEO/SURFACE, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (7) fix rheo/thermal, occasional, trim from (4)
+      attributes: half, newton off, cut 3
+      pair build: trim
+      stencil: none
+      bin: none
+  (8) fix rheo/oxidation, perpetual, trim from (3)
+      attributes: full, newton off, cut 1.8
+      pair build: trim
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes
+   Step          Time          KinEng         Press         Atoms   
+         0   0              0              0                   2701 
+       200   20             4.1743799e-07  1.1743617e-07       2701 
+       400   40             1.6697519e-06  4.6974469e-07       2701 
+       600   60             3.7127333e-06  1.0646825e-05       2701 
+       800   80             4.6683656e-06  0.00015182605       2701 
+      1000   100            4.7368707e-06  0.00028128761       2701 
+      1200   120            3.4384322e-06  0.00045913378       2701 
+      1400   140            1.4119866e-06  0.00055627091       2701 
+      1600   160            4.4114517e-07  0.00058247308       2701 
+      1800   180            4.8289229e-07  0.0005510948        2701 
+      2000   200            1.8494183e-06  0.00048386222       2701 
+      2200   220            3.3319816e-06  0.00037903264       2701 
+      2400   240            3.8128922e-06  0.00024115906       2701 
+      2600   260            3.1943401e-06  9.727407e-05        2701 
+      2800   280            1.6172816e-06 -2.632162e-05        2701 
+      3000   300            3.6100709e-07 -8.5761867e-05       2701 
+      3200   320            1.4745502e-07 -5.9204127e-05       2701 
+      3400   340            8.3369782e-07  8.8312464e-07       2701 
+      3600   360            2.0484052e-06  5.8521477e-05       2701 
+      3800   380            3.1639387e-06  0.0001685663        2701 
+      4000   400            3.1692907e-06  0.00026875988       2701 
+      4200   420            2.391933e-06   0.00038621787       2701 
+      4400   440            1.1964404e-06  0.00048901286       2701 
+      4600   460            4.0508824e-07  0.00051863639       2701 
+      4800   480            5.4908507e-07  0.00049263754       2701 
+      5000   500            1.3139665e-06  0.00041984264       2701 
+      5200   520            2.1939161e-06  0.00033095351       2701 
+      5400   540            2.3687031e-06  0.00022422981       2701 
+      5600   560            1.8280882e-06  0.00011544328       2701 
+      5800   580            8.8610517e-07  2.9307791e-05       2701 
+      6000   600            2.0989359e-07 -1.7340941e-05       2701 
+      6200   620            2.8658301e-07 -8.1237835e-06       2701 
+      6400   640            9.7636239e-07  4.3755922e-05       2701 
+      6600   660            1.891303e-06   0.0001185719        2701 
+      6800   680            2.4149904e-06  0.00020830273       2701 
+      7000   700            2.3174953e-06  0.00030114767       2701 
+      7200   720            1.7918612e-06  0.00037821537       2701 
+      7400   740            1.2114987e-06  0.0004233475        2701 
+      7600   760            9.9661553e-07  0.00042958263       2701 
+      7800   780            1.1552559e-06  0.00039944618       2701 
+      8000   800            1.5249138e-06  0.00034034478       2701 
+      8200   820            1.7453861e-06  0.00026826463       2701 
+      8400   840            1.6259021e-06  0.00019131768       2701 
+      8600   860            1.2612805e-06  0.0001162957        2701 
+      8800   880            8.6964518e-07  7.1771506e-05       2701 
+      9000   900            7.6892472e-07  5.6170687e-05       2701 
+      9200   920            1.0780045e-06  7.1925995e-05       2701 
+      9400   940            1.6514902e-06  0.00011635293       2701 
+      9600   960            2.1891377e-06  0.00017599885       2701 
+      9800   980            2.4551701e-06  0.00024127934       2701 
+     10000   1000           2.4277051e-06  0.00029918622       2701 
+     10200   1020           2.2655987e-06  0.00034067996       2701 
+     10400   1040           2.1767207e-06  0.00035598133       2701 
+     10600   1060           2.2796719e-06  0.00034359076       2701 
+     10800   1080           2.4884225e-06  0.00030749714       2701 
+     11000   1100           2.6387215e-06  0.00025725198       2701 
+     11200   1120           2.5968908e-06  0.00020170699       2701 
+     11400   1140           2.4108931e-06  0.00015185858       2701 
+     11600   1160           2.2375166e-06  0.00011800349       2701 
+     11800   1180           2.2407196e-06  0.00010646971       2701 
+     12000   1200           2.4845263e-06  0.00011817498       2701 
+     12200   1220           2.8733204e-06  0.00015013186       2701 
+     12400   1240           3.2437087e-06  0.00019211975       2701 
+     12600   1260           3.4732728e-06  0.00023620276       2701 
+     12800   1280           3.5836611e-06  0.00027352269       2701 
+     13000   1300           3.6592211e-06  0.00029533734       2701 
+     13200   1320           3.782506e-06   0.00030032559       2701 
+     13400   1340           3.9807086e-06  0.00028395722       2701 
+     13600   1360           4.2023176e-06  0.00025390325       2701 
+     13800   1380           4.3559781e-06  0.00021794236       2701 
+     14000   1400           4.4273371e-06  0.00018026034       2701 
+     14200   1420           4.49867e-06    0.0001526569        2701 
+     14400   1440           4.6591574e-06  0.00013707051       2701 
+     14600   1460           4.9589583e-06  0.00013803875       2701 
+     14800   1480           5.3859375e-06  0.00015455425       2701 
+     15000   1500           5.8639557e-06  0.00017954785       2701 
+     15200   1520           6.3075561e-06  0.0002084257        2701 
+     15400   1540           6.7022179e-06  0.0002347669        2701 
+     15600   1560           7.0789688e-06  0.00025020766       2701 
+     15800   1580           7.4734777e-06  0.00025394845       2701 
+     16000   1600           7.8884743e-06  0.00024571725       2701 
+     16200   1620           8.3224059e-06  0.00022706648       2701 
+     16400   1640           8.7337783e-06  0.00020320706       2701 
+     16600   1660           9.1454649e-06  0.00017824346       2701 
+     16800   1680           9.5948793e-06  0.00015961835       2701 
+     17000   1700           1.0106407e-05  0.00015135471       2701 
+     17200   1720           1.0707273e-05  0.00015166884       2701 
+     17400   1740           1.1392597e-05  0.0001645916        2701 
+     17600   1760           1.2118829e-05  0.00018119729       2701 
+     17800   1780           1.2846056e-05  0.0002003616        2701 
+     18000   1800           1.3555288e-05  0.00021585952       2701 
+     18200   1820           1.4301024e-05  0.00022290158       2701 
+     18400   1840           1.5089217e-05  0.00021970192       2701 
+     18600   1860           1.5902351e-05  0.00020911128       2701 
+     18800   1880           1.6753175e-05  0.00019278718       2701 
+     19000   1900           1.7602996e-05  0.00017584076       2701 
+     19200   1920           1.8479378e-05  0.00016206226       2701 
+     19400   1940           1.9421603e-05  0.00015575677       2701 
+     19600   1960           2.0477421e-05  0.00015687558       2701 
+     19800   1980           2.1617288e-05  0.00016424998       2701 
+     20000   2000           2.2814347e-05  0.00017466664       2701 
+     20200   2020           2.4029097e-05  0.00018647149       2701 
+     20400   2040           2.5255953e-05  0.00019516077       2701 
+     20600   2060           2.649418e-05   0.00019906384       2701 
+     20800   2080           2.7755897e-05  0.00019630586       2701 
+     21000   2100           2.9067854e-05  0.00018674721       2701 
+     21200   2120           3.0396477e-05  0.0001758048        2701 
+     21400   2140           3.1759719e-05  0.00016782801       2701 
+     21600   2160           3.3193597e-05  0.00016324138       2701 
+     21800   2180           3.4729384e-05  0.00016124274       2701 
+     22000   2200           3.6367594e-05  0.00016437457       2701 
+     22200   2220           3.8095131e-05  0.00017015573       2701 
+     22400   2240           3.9867003e-05  0.00017649465       2701 
+     22600   2260           4.169511e-05   0.00018111374       2701 
+     22800   2280           4.3566134e-05  0.00018104136       2701 
+     23000   2300           4.5461538e-05  0.00017822707       2701 
+     23200   2320           4.7377333e-05  0.00017285066       2701 
+     23400   2340           4.9354403e-05  0.00016826524       2701 
+     23600   2360           5.1399791e-05  0.00016517913       2701 
+     23800   2380           5.3510931e-05  0.00016299649       2701 
+     24000   2400           5.5681048e-05  0.00016256674       2701 
+     24200   2420           5.7902429e-05  0.00016513449       2701 
+     24400   2440           6.0216049e-05  0.00016895109       2701 
+     24600   2460           6.270982e-05   0.00016946227       2701 
+     24800   2480           6.5390117e-05  0.00016589426       2701 
+     25000   2500           6.8121899e-05  0.00016241676       2701 
+     25200   2520           7.0947331e-05  0.00015624292       2701 
+     25400   2540           7.4304148e-05  0.0001449537        2701 
+     25600   2560           7.7745077e-05  0.00013179658       2701 
+     25800   2580           8.0739829e-05  0.00013098838       2701 
+     26000   2600           8.3827874e-05  0.00014278841       2701 
+     26200   2620           8.7060677e-05  0.00015381649       2701 
+     26400   2640           9.0266508e-05  0.00016130999       2701 
+     26600   2660           9.3339049e-05  0.00016908268       2701 
+     26800   2680           9.6347013e-05  0.00016771087       2701 
+     27000   2700           9.9294711e-05  0.00016577315       2701 
+     27200   2720           0.00010230007  0.0001670893        2701 
+     27400   2740           0.00010547172  0.00016569077       2701 
+     27600   2760           0.00010872426  0.00016506303       2701 
+     27800   2780           0.00011201844  0.00016482702       2701 
+     28000   2800           0.00011532129  0.00016694886       2701 
+     28200   2820           0.00011869854  0.00016163005       2701 
+     28400   2840           0.00012209747  0.00015339281       2701 
+     28600   2860           0.00012549322  0.00014765883       2701 
+     28800   2880           0.00012898685  0.00014241765       2701 
+     29000   2900           0.00013259039  0.00014215724       2701 
+     29200   2920           0.00013628209  0.00014881155       2701 
+     29400   2940           0.00014001213  0.00015671333       2701 
+     29600   2960           0.00014379216  0.00016446215       2701 
+     29800   2980           0.00014764687  0.0001639602        2701 
+     30000   3000           0.00015142301  0.00015664816       2701 
+     30200   3020           0.00015496407  0.00015545099       2701 
+     30400   3040           0.00015797338  0.00015368625       2701 
+     30600   3060           0.00016042141  0.00015679918       2701 
+     30800   3080           0.00016244716  0.00016093678       2701 
+     31000   3100           0.00016202247  0.00016066954       2701 
+     31200   3120           0.0001613312   0.00015932059       2701 
+     31400   3140           0.00016274961  0.00015988567       2701 
+     31600   3160           0.00016541518  0.00015724809       2701 
+     31800   3180           0.00016809362  0.00015498827       2701 
+     32000   3200           0.00017067801  0.00014830489       2701 
+     32200   3220           0.00017333906  0.00014371345       2701 
+     32400   3240           0.0001759011   0.00014421259       2701 
+     32600   3260           0.00017849952  0.00014228443       2701 
+     32800   3280           0.00017801812  0.00014117391       2701 
+     33000   3300           0.00017718857  0.00014644675       2701 
+     33200   3320           0.00017833666  0.0001291286        2701 
+     33400   3340           0.000178576    0.00014878558       2701 
+     33600   3360           0.00017846711  0.00013905481       2701 
+     33800   3380           0.00017822937  0.00015535996       2701 
+     34000   3400           0.00017899663  0.00016094303       2701 
+     34200   3420           0.00017924661  0.00015017553       2701 
+     34400   3440           0.00018024855  0.00014723549       2701 
+     34600   3460           0.00018143865  0.00013903131       2701 
+     34800   3480           0.00018258173  0.00013722112       2701 
+     35000   3500           0.00018404873  0.00014675949       2701 
+     35200   3520           0.00018538521  0.00015108242       2701 
+     35400   3540           0.00018669649  0.00014564852       2701 
+     35600   3560           0.00018814608  0.00013762161       2701 
+     35800   3580           0.00018967415  0.00014602307       2701 
+     36000   3600           0.00019146735  0.000126909         2701 
+     36200   3620           0.00019414036  0.00012384379       2701 
+     36400   3640           0.00019613057  0.00011059573       2701 
+     36600   3660           0.00019897104  0.00013621801       2701 
+     36800   3680           0.00020169688  0.00013665462       2701 
+     37000   3700           0.00020447655  0.00013929258       2701 
+     37200   3720           0.00020711105  0.0001363895        2701 
+     37400   3740           0.00021077854  0.00013610672       2701 
+     37600   3760           0.00021303084  0.00015051235       2701 
+     37800   3780           0.00021619561  0.00012664801       2701 
+     38000   3800           0.0002194018   0.00012808247       2701 
+     38200   3820           0.00022242646  0.0001360174        2701 
+     38400   3840           0.00022531568  0.00013311221       2701 
+     38600   3860           0.00022821731  0.00013523939       2701 
+     38800   3880           0.000231228    0.00014090695       2701 
+     39000   3900           0.00023404038  0.00013661835       2701 
+     39200   3920           0.00023755044  0.00013659469       2701 
+     39400   3940           0.00024009059  0.00012097907       2701 
+     39600   3960           0.0002432098   9.7877876e-05       2701 
+     39800   3980           0.00024475294  0.0001164688        2701 
+     40000   4000           0.00024171274  0.00012432219       2701 
+Loop time of 192.659 on 4 procs for 40000 steps with 2701 atoms
+
+Performance: 1793840.118 tau/day, 207.620 timesteps/s, 560.783 katom-step/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 16.881     | 24.402     | 30.74      | 114.6 | 12.67
+Bond    | 1.1126     | 1.8917     | 2.6935     |  43.3 |  0.98
+Neigh   | 35.387     | 35.508     | 35.625     |   1.5 | 18.43
+Comm    | 1.5499     | 1.6694     | 1.8006     |   7.4 |  0.87
+Output  | 0.99755    | 1.0072     | 1.0165     |   0.8 |  0.52
+Modify  | 120.6      | 127.43     | 135.54     |  54.8 | 66.14
+Other   |            | 0.7553     |            |       |  0.39
+
+Nlocal:         675.25 ave        1373 max           7 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:            103 ave         163 max          50 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:          10509 ave       21592 max         126 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:        20367 ave       41981 max         141 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 81468
+Ave neighs/atom = 30.162162
+Ave special neighs/atom = 1.6593854
+Neighbor list builds = 39932
+Dangerous builds = 0
+
+Total wall time: 0:03:12

examples/rheo/poiseuille/in.rheo.poiseuille

@@ -0,0 +1,75 @@
+# ------ 2D Poiseuille flow ------ #
+
+dimension          2
+units              lj
+atom_style         rheo
+boundary           p p p
+comm_modify        vel yes
+
+# ------ Create simulation box ------ #
+
+variable           n equal 1.0
+variable           cut equal 3.0
+
+region             box block 0 20 -10 10 -0.01 0.01
+create_box         2 box
+lattice            sq ${n}
+
+region             inner   block INF INF -7.5 7.5 INF INF units box
+region             walls   block INF INF -7.5 7.5 INF INF units box side out
+
+create_atoms       2 region walls
+create_atoms       1 region inner
+
+group              fluid type 1
+group              rig type 2
+
+displace_atoms     fluid random 0.1 0.1 0 135414 units box
+
+# ------ Model parameters ------ #
+
+variable           rho0 equal 1.0
+variable           cs equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           zeta equal 1.0
+variable	       kappa equal 1.0*${rho0}/${mp}
+variable           fext equal 1e-4/${n}
+variable           dt_max equal  0.1*${cut}/${cs}/3
+variable           Dr equal 0.05*${cut}*${cs}
+
+variable           eta equal 0.1
+variable           gd0 equal 5e-4
+variable           npow equal 0.5
+variable           K equal 0.001
+
+mass               * ${mp}
+set                group all rheo/rho ${rho0}
+set                group all rheo/status 0
+set                group rig rheo/status 1
+
+timestep           ${dt_max}
+
+pair_style         rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
+pair_coeff         * *
+
+# ------ Fixes & computes ------ #
+
+fix                1 all rheo ${cut} quintic 0 shift
+fix                2 all rheo/viscosity * constant ${eta}
+#fix                2 all rheo/viscosity * power ${eta} ${gd0} ${K} ${npow}
+fix                3 all rheo/pressure * linear
+fix                4 rig setforce 0.0 0.0 0.0
+fix                5 fluid addforce ${fext} 0.0 0.0
+fix                6 all enforce2d
+
+compute            rho all rheo/property/atom rho
+
+# ------ Output & Run ------ #
+
+thermo             200
+thermo_style       custom step time ke press
+
+#dump               1 all custom 200 atomDump id type x y vx vy fx fy c_rho
+
+run                20000
+

examples/rheo/poiseuille/log.17Apr2024.poiseuille.g++.4

@@ -0,0 +1,288 @@
+LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
+# ------ 2D Poiseuille flow ------ #
+
+dimension          2
+units              lj
+atom_style         rheo
+boundary           p p p
+comm_modify        vel yes
+
+# ------ Create simulation box ------ #
+
+variable           n equal 1.0
+variable           cut equal 3.0
+
+region             box block 0 20 -10 10 -0.01 0.01
+create_box         2 box
+Created orthogonal box = (0 -10 -0.01) to (20 10 0.01)
+  2 by 2 by 1 MPI processor grid
+lattice            sq ${n}
+lattice            sq 1
+Lattice spacing in x,y,z = 1 1 1
+
+region             inner   block INF INF -7.5 7.5 INF INF units box
+region             walls   block INF INF -7.5 7.5 INF INF units box side out
+
+create_atoms       2 region walls
+Created 100 atoms
+  using lattice units in orthogonal box = (0 -10 -0.01) to (20 10 0.01)
+  create_atoms CPU = 0.000 seconds
+create_atoms       1 region inner
+Created 300 atoms
+  using lattice units in orthogonal box = (0 -10 -0.01) to (20 10 0.01)
+  create_atoms CPU = 0.000 seconds
+
+group              fluid type 1
+300 atoms in group fluid
+group              rig type 2
+100 atoms in group rig
+
+displace_atoms     fluid random 0.1 0.1 0 135414 units box
+Displacing atoms ...
+
+# ------ Model parameters ------ #
+
+variable           rho0 equal 1.0
+variable           cs equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           mp equal 1/${n}
+variable           mp equal 1/1
+variable           zeta equal 1.0
+variable	       kappa equal 1.0*${rho0}/${mp}
+variable	       kappa equal 1.0*1/${mp}
+variable	       kappa equal 1.0*1/1
+variable           fext equal 1e-4/${n}
+variable           fext equal 1e-4/1
+variable           dt_max equal  0.1*${cut}/${cs}/3
+variable           dt_max equal  0.1*3/${cs}/3
+variable           dt_max equal  0.1*3/1/3
+variable           Dr equal 0.05*${cut}*${cs}
+variable           Dr equal 0.05*3*${cs}
+variable           Dr equal 0.05*3*1
+
+variable           eta equal 0.1
+variable           gd0 equal 5e-4
+variable           npow equal 0.5
+variable           K equal 0.001
+
+mass               * ${mp}
+mass               * 1
+set                group all rheo/rho ${rho0}
+set                group all rheo/rho 1
+Setting atom values ...
+  400 settings made for rheo/rho
+set                group all rheo/status 0
+Setting atom values ...
+  400 settings made for rheo/status
+set                group rig rheo/status 1
+Setting atom values ...
+  100 settings made for rheo/status
+
+timestep           ${dt_max}
+timestep           0.1
+
+pair_style         rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
+pair_style         rheo 3 artificial/visc ${zeta} rho/damp ${Dr}
+pair_style         rheo 3 artificial/visc 1 rho/damp ${Dr}
+pair_style         rheo 3 artificial/visc 1 rho/damp 0.15
+pair_coeff         * *
+
+# ------ Fixes & computes ------ #
+
+fix                1 all rheo ${cut} quintic 0 shift
+fix                1 all rheo 3 quintic 0 shift
+fix                2 all rheo/viscosity * constant ${eta}
+fix                2 all rheo/viscosity * constant 0.1
+#fix                2 all rheo/viscosity * power ${eta} ${gd0} ${K} ${npow}
+fix                3 all rheo/pressure * linear
+fix                4 rig setforce 0.0 0.0 0.0
+fix                5 fluid addforce ${fext} 0.0 0.0
+fix                5 fluid addforce 0.0001 0.0 0.0
+fix                6 all enforce2d
+
+compute            rho all rheo/property/atom rho
+
+# ------ Output & Run ------ #
+
+thermo             200
+thermo_style       custom step time ke press
+
+dump               1 all custom 200 atomDump id type x y vx vy fx fy c_rho
+
+run                20000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- @article{PalermoInPrep,
+ journal = {in prep},
+ title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
+ year = {2024},
+ author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 13 13 1
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair rheo, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) compute RHEO/KERNEL, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (3) compute RHEO/GRAD, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) compute RHEO/VSHIFT, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 5.693 | 5.693 | 5.693 Mbytes
+   Step          Time          KinEng         Press     
+         0   0              0              0            
+       200   20             1.2220462e-06  3.7383146e-05
+       400   40             4.345762e-06   7.5866885e-05
+       600   60             8.8559433e-06  0.00011353743
+       800   80             1.4370506e-05  0.00015135634
+      1000   100            2.0576198e-05  0.00018903722
+      1200   120            2.721926e-05   0.00022533997
+      1400   140            3.4099653e-05  0.00026016069
+      1600   160            4.1064175e-05  0.00029445207
+      1800   180            4.8001225e-05  0.00032893763
+      2000   200            5.4832849e-05  0.00036402396
+      2200   220            6.1508431e-05  0.00039945249
+      2400   240            6.8000141e-05  0.00043534411
+      2600   260            7.430136e-05   0.00046943441
+      2800   280            8.0415328e-05  0.00049807225
+      3000   300            8.6335032e-05  0.00051815375
+      3200   320            9.2021626e-05  0.00052618224
+      3400   340            9.7387936e-05  0.00051877918
+      3600   360            0.00010231526  0.00048650828
+      3800   380            0.00010676617  0.00044578079
+      4000   400            0.00011080098  0.00044777126
+      4200   420            0.00011448127  0.00047047629
+      4400   440            0.00011787852  0.00050280249
+      4600   460            0.00012106805  0.0005397213 
+      4800   480            0.00012412056  0.00057885539
+      5000   500            0.0001271078   0.00061396896
+      5200   520            0.00013006637  0.00063981812
+      5400   540            0.00013295039  0.00065094073
+      5600   560            0.00013561487  0.00063918847
+      5800   580            0.00013791796  0.00059087656
+      6000   600            0.00013983422  0.00052171998
+      6200   620            0.00014144833  0.00050658002
+      6400   640            0.00014286538  0.0005248626 
+      6600   660            0.00014417734  0.00055826606
+      6800   680            0.00014546931  0.00060063748
+      7000   700            0.00014682553  0.00064421411
+      7200   720            0.0001482833   0.00068252242
+      7400   740            0.00014977996  0.00070671308
+      7600   760            0.00015114829  0.00069774026
+      7800   780            0.0001522719   0.00064408311
+      8000   800            0.00015312897  0.00055977044
+      8200   820            0.00015375669  0.0005225573 
+      8400   840            0.00015425683  0.00053833691
+      8600   860            0.00015471278  0.00057447427
+      8800   880            0.0001552059   0.00061980921
+      9000   900            0.00015581593  0.0006659836 
+      9200   920            0.0001565564   0.00070813532
+      9400   940            0.00015733573  0.00073378551
+      9600   960            0.00015802107  0.00071560835
+      9800   980            0.00015855339  0.00065636189
+     10000   1000           0.00015890743  0.0005699855 
+     10200   1020           0.00015908095  0.00053138971
+     10400   1040           0.00015915523  0.00054790708
+     10600   1060           0.00015921254  0.00058899454
+     10800   1080           0.00015934193  0.00063964906
+     11000   1100           0.00015959891  0.00069241358
+     11200   1120           0.0001599636   0.00073734651
+     11400   1140           0.00016036526  0.00074477329
+     11600   1160           0.00016075471  0.00071047555
+     11800   1180           0.00016109516  0.00064173183
+     12000   1200           0.00016131524  0.00055500553
+     12200   1220           0.00016136366  0.0005290215 
+     12400   1240           0.0001613025   0.00055124296
+     12600   1260           0.00016123023  0.00059758627
+     12800   1280           0.00016123043  0.00065488735
+     13000   1300           0.00016132935  0.0007140876 
+     13200   1320           0.00016152165  0.00074795629
+     13400   1340           0.00016180372  0.00074730778
+     13600   1360           0.00016216585  0.00071370995
+     13800   1380           0.0001625339   0.00065176323
+     14000   1400           0.00016274999  0.00057515371
+     14200   1420           0.00016271295  0.00055878258
+     14400   1440           0.00016249768  0.00058448193
+     14600   1460           0.00016223675  0.00063096229
+     14800   1480           0.00016201846  0.00068639548
+     15000   1500           0.00016190593  0.00072444357
+     15200   1520           0.00016194466  0.00073830636
+     15400   1540           0.00016216164  0.00072773256
+     15600   1560           0.00016253174  0.00069215481
+     15800   1580           0.00016290895  0.00063239408
+     16000   1600           0.00016306463  0.00057466273
+     16200   1620           0.00016292218  0.00057951567
+     16400   1640           0.00016261117  0.00061504156
+     16600   1660           0.00016225906  0.00066066637
+     16800   1680           0.00016197993  0.00069751908
+     17000   1700           0.0001618568   0.00072202303
+     17200   1720           0.00016194264  0.00073255034
+     17400   1740           0.00016225911  0.0007231031 
+     17600   1760           0.00016270465  0.00068931224
+     17800   1780           0.00016304053  0.00062934836
+     18000   1800           0.00016302624  0.00058060272
+     18200   1820           0.00016274847  0.00058859513
+     18400   1840           0.00016236893  0.00061804803
+     18600   1860           0.00016202777  0.00065393237
+     18800   1880           0.0001618184   0.00068747094
+     19000   1900           0.0001618044   0.00071352541
+     19200   1920           0.00016204402  0.00072351769
+     19400   1940           0.00016249999  0.00071330322
+     19600   1960           0.00016297924  0.00067984167
+     19800   1980           0.00016317435  0.00061634142
+     20000   2000           0.00016301186  0.00057234115
+Loop time of 15.6198 on 4 procs for 20000 steps with 400 atoms
+
+Performance: 11062881.511 tau/day, 1280.426 timesteps/s, 512.170 katom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.1979     | 2.4473     | 2.6992     |  15.7 | 15.67
+Neigh   | 0.024709   | 0.027006   | 0.029223   |   1.3 |  0.17
+Comm    | 0.4657     | 0.71686    | 0.9662     |  29.0 |  4.59
+Output  | 0.033698   | 0.036781   | 0.039359   |   1.1 |  0.24
+Modify  | 12.306     | 12.313     | 12.319     |   0.2 | 78.83
+Other   |            | 0.07916    |            |       |  0.51
+
+Nlocal:            100 ave         107 max          93 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:          185.5 ave         192 max         179 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:           1712 ave        1848 max        1598 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+FullNghs:         3424 ave        3682 max        3174 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 13696
+Ave neighs/atom = 34.24
+Neighbor list builds = 331
+Dangerous builds = 0
+
+
+Total wall time: 0:00:15

examples/rheo/taylor-green/in.rheo.taylor.green

@@ -0,0 +1,65 @@
+# ------ 2D Taylor Green vortex ------ #
+
+dimension          2
+units              lj
+atom_style         rheo
+boundary           p p p
+comm_modify        vel yes
+newton off
+
+# ------ Create simulation box ------ #
+
+variable           n equal 1.0
+variable           cut equal 3.0
+
+region             box block 0 40 0 40 -0.01 0.01
+create_box         1 box
+lattice            sq ${n}
+
+create_atoms       1 region box
+
+displace_atoms     all random 0.1 0.1 0 135414 units box
+
+# ------ Model parameters ------ #
+
+variable           rho0 equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           cs equal 1.0
+variable           eta equal 0.05
+variable           zeta equal 1
+variable           dt_max equal 0.1*${cut}/${cs}/3
+variable           Dr equal 0.1*${cut}*${cs}
+
+mass               * ${mp}
+set                group all rheo/rho ${rho0}
+set                group all rheo/status 0
+
+variable           u0 equal 0.05
+variable           uy atom  ${u0}*sin(2*PI*x/lx)*cos(2*PI*y/ly)
+variable           ux atom -${u0}*sin(2*PI*y/ly)*cos(2*PI*x/ly)
+variable           d0 atom ${rho0}-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
+
+velocity           all set v_ux v_uy 0.0 units box
+
+timestep           ${dt_max}
+
+pair_style         rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
+pair_coeff         * *
+
+# ------ Fixes & computes ------ #
+
+fix                1 all rheo ${cut} RK1 8 shift
+fix                2 all rheo/viscosity * constant ${eta}
+fix                3 all rheo/pressure * linear
+fix                4 all enforce2d
+
+compute            rho all rheo/property/atom rho
+
+# ------ Output & Run ------ #
+
+thermo             200
+thermo_style       custom step time ke press
+
+#dump               1 all custom 200 atomDump id type x y vx vy fx fy c_rho
+
+run 10000

examples/rheo/taylor-green/log.17Apr2024.taylor.green.g++.4

@@ -0,0 +1,224 @@
+LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
+# ------ 2D Taylor Green vortex ------ #
+
+dimension          2
+units              lj
+atom_style         rheo
+boundary           p p p
+comm_modify        vel yes
+newton off
+
+# ------ Create simulation box ------ #
+
+variable           n equal 1.0
+variable           cut equal 3.0
+
+region             box block 0 40 0 40 -0.01 0.01
+create_box         1 box
+Created orthogonal box = (0 0 -0.01) to (40 40 0.01)
+  2 by 2 by 1 MPI processor grid
+lattice            sq ${n}
+lattice            sq 1
+Lattice spacing in x,y,z = 1 1 1
+
+create_atoms       1 region box
+Created 1600 atoms
+  using lattice units in orthogonal box = (0 0 -0.01) to (40 40 0.01)
+  create_atoms CPU = 0.001 seconds
+
+displace_atoms     all random 0.1 0.1 0 135414 units box
+Displacing atoms ...
+
+# ------ Model parameters ------ #
+
+variable           rho0 equal 1.0
+variable           mp equal ${rho0}/${n}
+variable           mp equal 1/${n}
+variable           mp equal 1/1
+variable           cs equal 1.0
+variable           eta equal 0.05
+variable           zeta equal 1
+variable           dt_max equal 0.1*${cut}/${cs}/3
+variable           dt_max equal 0.1*3/${cs}/3
+variable           dt_max equal 0.1*3/1/3
+variable           Dr equal 0.1*${cut}*${cs}
+variable           Dr equal 0.1*3*${cs}
+variable           Dr equal 0.1*3*1
+
+mass               * ${mp}
+mass               * 1
+set                group all rheo/rho ${rho0}
+set                group all rheo/rho 1
+Setting atom values ...
+  1600 settings made for rheo/rho
+set                group all rheo/status 0
+Setting atom values ...
+  1600 settings made for rheo/status
+
+variable           u0 equal 0.05
+variable           uy atom  ${u0}*sin(2*PI*x/lx)*cos(2*PI*y/ly)
+variable           uy atom  0.05*sin(2*PI*x/lx)*cos(2*PI*y/ly)
+variable           ux atom -${u0}*sin(2*PI*y/ly)*cos(2*PI*x/ly)
+variable           ux atom -0.05*sin(2*PI*y/ly)*cos(2*PI*x/ly)
+variable           d0 atom ${rho0}-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
+variable           d0 atom 1-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
+variable           d0 atom 1-0.05*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
+variable           d0 atom 1-0.05*0.05*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
+variable           d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
+variable           d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/1/${cs}
+variable           d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/1/1
+
+velocity           all set v_ux v_uy 0.0 units box
+
+timestep           ${dt_max}
+timestep           0.1
+
+pair_style         rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
+pair_style         rheo 3 artificial/visc ${zeta} rho/damp ${Dr}
+pair_style         rheo 3 artificial/visc 1 rho/damp ${Dr}
+pair_style         rheo 3 artificial/visc 1 rho/damp 0.3
+pair_coeff         * *
+
+# ------ Fixes & computes ------ #
+
+fix                1 all rheo ${cut} RK1 8 shift
+fix                1 all rheo 3 RK1 8 shift
+fix                2 all rheo/viscosity * constant ${eta}
+fix                2 all rheo/viscosity * constant 0.05
+fix                3 all rheo/pressure * linear
+fix                4 all enforce2d
+
+compute            rho all rheo/property/atom rho
+
+# ------ Output & Run ------ #
+
+thermo             200
+thermo_style       custom step time ke press
+
+dump               1 all custom 200 atomDump id type x y vx vy fx fy c_rho
+
+run 10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- @article{PalermoInPrep,
+ journal = {in prep},
+ title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
+ year = {2024},
+ author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 25 25 1
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair rheo, perpetual, half/full from (2)
+      attributes: half, newton off
+      pair build: halffull/newtoff
+      stencil: none
+      bin: none
+  (2) compute RHEO/KERNEL, perpetual
+      attributes: full, newton off
+      pair build: full/bin/atomonly
+      stencil: full/bin/2d
+      bin: standard
+  (3) compute RHEO/GRAD, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) compute RHEO/VSHIFT, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 6.835 | 6.835 | 6.835 Mbytes
+   Step          Time          KinEng         Press     
+         0   0              0.00062497276  0.00062607301
+       200   20             0.00056200647  0.00056633785
+       400   40             0.00050570968  0.00051098771
+       600   60             0.00045586684  0.00046081672
+       800   80             0.00041124523  0.00041549607
+      1000   100            0.00037065341  0.00037412741
+      1200   120            0.00033391585  0.00033580899
+      1400   140            0.00030078316  0.00030057307
+      1600   160            0.00027093231  0.00026842603
+      1800   180            0.00024403239  0.00023839026
+      2000   200            0.0002197865   0.00021148941
+      2200   220            0.0001979269   0.00018659386
+      2400   240            0.00017822267  0.00016430442
+      2600   260            0.00016047141  0.00014408514
+      2800   280            0.00014448504  0.00012574125
+      3000   300            0.00013009159  0.00010869938
+      3200   320            0.00011713578  9.414951e-05 
+      3400   340            0.00010547564  8.1900579e-05
+      3600   360            9.4982139e-05  7.1285649e-05
+      3800   380            8.5538983e-05  6.1571123e-05
+      4000   400            7.7040171e-05  5.3462572e-05
+      4200   420            6.9390317e-05  4.6338308e-05
+      4400   440            6.2503763e-05  3.9697323e-05
+      4600   460            5.6303766e-05  3.4234465e-05
+      4800   480            5.0721595e-05  3.0841338e-05
+      5000   500            4.5695301e-05  2.7788566e-05
+      5200   520            4.1169161e-05  2.5744409e-05
+      5400   540            3.7093059e-05  2.3912739e-05
+      5600   560            3.3421819e-05  2.2494185e-05
+      5800   580            3.0114735e-05  2.1594384e-05
+      6000   600            2.7135224e-05  2.1164421e-05
+      6200   620            2.4450446e-05  2.0979349e-05
+      6400   640            2.2030925e-05  2.0858567e-05
+      6600   660            1.9850196e-05  2.098115e-05 
+      6800   680            1.7884553e-05  2.1134827e-05
+      7000   700            1.6112763e-05  2.1242242e-05
+      7200   720            1.4515783e-05  2.1312763e-05
+      7400   740            1.3076456e-05  2.1370947e-05
+      7600   760            1.1779327e-05  2.1332126e-05
+      7800   780            1.0610469e-05  2.1156562e-05
+      8000   800            9.5573298e-06  2.0898126e-05
+      8200   820            8.6085799e-06  2.0517958e-05
+      8400   840            7.7539888e-06  1.9841551e-05
+      8600   860            6.9843033e-06  1.9114769e-05
+      8800   880            6.2911575e-06  1.8362959e-05
+      9000   900            5.6669785e-06  1.7473404e-05
+      9200   920            5.1049208e-06  1.6452745e-05
+      9400   940            4.5987908e-06  1.5578629e-05
+      9600   960            4.1429972e-06  1.4427274e-05
+      9800   980            3.7324962e-06  1.3169649e-05
+     10000   1000           3.3627455e-06  1.1938723e-05
+Loop time of 38.2006 on 4 procs for 10000 steps with 1600 atoms
+
+Performance: 2261743.875 tau/day, 261.776 timesteps/s, 418.841 katom-step/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.2958     | 8.7273     | 9.3582     |  15.2 | 22.85
+Neigh   | 0.034282   | 0.035689   | 0.037115   |   0.7 |  0.09
+Comm    | 0.16788    | 0.17018    | 0.17278    |   0.4 |  0.45
+Output  | 0.066977   | 0.06882    | 0.071704   |   0.7 |  0.18
+Modify  | 28.483     | 28.793     | 28.962     |   3.6 | 75.37
+Other   |            | 0.4053     |            |       |  1.06
+
+Nlocal:            400 ave         402 max         399 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:         307.25 ave         308 max         305 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs:        7618.25 ave        7697 max        7564 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+FullNghs:        13343 ave       13497 max       13258 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 53372
+Ave neighs/atom = 33.3575
+Neighbor list builds = 123
+Dangerous builds = 0
+Total wall time: 0:00:38

lib/qmmm/Makefile.gfortran-cmake

@@ -46,8 +46,8 @@ QELIBS +=  -lgfortran -lmpi_mpifh
 
 # part 3: add-on libraries and main library for LAMMPS
 sinclude ../../src/Makefile.package
-LAMMPSFLAGS = $(shell pkgconf liblammps --cflags)
+LAMMPSFLAGS = $(shell pkg-config --cflags liblammps)
-LAMMPSLIB   = $(shell pkgconf liblammps --libs)
+LAMMPSLIB   = $(shell pkg-config --libs liblammps)
 
 # part 4: local QM/MM library and progams
 SRC=pwqmmm.c libqmmm.c

lib/qmmm/README

@@ -101,7 +101,7 @@ Makefile.gfortran-cmake and make adjustments to the makefile variables
 according to the comments in the file.  You probably need to adjust
 the QETOPDIR variable to point to the location of your QE
 compilation/installation.
-Please also check that the command "pkgconf liblammps --libs" works.
+Please also check that the command "pkg-config --libs liblammps" works.
 Then you should be able to compile the QM/MM executable with:
 
   make -f Makefile.gfortran-cmake pwqmmm.x

lib/rheo/Makefile.lammps

@@ -0,0 +1,14 @@
+# Settings that the LAMMPS build will import when this package is installed
+
+ifeq ($(strip $(shell pkg-config --version)),)
+  # manual configuration w/o pkg-config/pkgconf
+  # change this to -I/path/to/your/lib/gsl/include/
+  rheo_SYSINC = -I../../lib/rheo/gsl/include/
+
+  # change this to -L/path/to/your/lib/gsl/lib/
+  rheo_SYSLIB = -L../../lib/rheo/gsl/lib/ -lgsl -lgslcblas
+else
+  # autodetect GSL settings from pkg-config/pkgconf
+  rheo_SYSINC = $(shell pkg-config --cflags gsl)
+  rheo_SYSLIB = $(shell pkg-config --libs gsl)
+endif

lib/rheo/README

@@ -0,0 +1,7 @@
+This directory has a Makefile.lammps file with settings that allows LAMMPS to
+dynamically link to the GSL library.  This is required to use the RHEO package
+in a LAMMPS input script.  If you have the pkg-config command available, it
+will automatically import the GSL settings. Otherwise they will have to be
+added manually.
+
+See the header of Makefile.lammps for more info.

src/.gitignore

@@ -245,6 +245,9 @@
 /pair_tdpd.cpp
 /pair_tdpd.h
 
+/*rheo*.cpp
+/*rheo*.h
+
 /compute_grid.cpp
 /compute_grid.h
 /compute_grid_local.cpp
@@ -790,6 +793,8 @@
 /fix_acks2_reaxff.h
 /fix_adapt_fep.cpp
 /fix_adapt_fep.h
+/fix_add_heat.cpp
+/fix_add_heat.h
 /fix_addtorque.cpp
 /fix_addtorque.h
 /fix_append_atoms.cpp

src/BPM/bond_bpm.cpp

@@ -18,6 +18,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
+#include "fix.h"
 #include "fix_bond_history.h"
 #include "fix_store_local.h"
 #include "fix_update_special_bonds.h"
@@ -53,10 +54,14 @@ BondBPM::BondBPM(LAMMPS *_lmp) :
     pack_choice(nullptr), output_data(nullptr)
 {
   overlay_flag = 0;
+  ignore_special_flag = 0;
   prop_atom_flag = 0;
   break_flag = 1;
   nvalues = 0;
 
+  nhistory = 0;
+  update_flag = 0;
+
   r0_max_estimate = 0.0;
   max_stretch = 1.0;
 
@@ -64,10 +69,10 @@ BondBPM::BondBPM(LAMMPS *_lmp) :
   // 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");
+  id_fix_dummy = utils::strdup(fmt::format("BPM_DUMMY_{}", instance_total));
   modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy));
 
-  id_fix_dummy2 = utils::strdup("BPM_DUMMY2");
+  id_fix_dummy2 = utils::strdup(fmt::format("BPM_DUMMY2_{}", instance_total));
   modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy2));
 
   if (lmp->citeme) lmp->citeme->add(cite_bpm);
@@ -82,7 +87,7 @@ BondBPM::~BondBPM()
   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 (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);
 
@@ -109,39 +114,46 @@ void BondBPM::init_style()
     fix_store_local->nvalues = nvalues;
   }
 
-  if (overlay_flag) {
+  if (!ignore_special_flag) {
-    if (force->special_lj[1] != 1.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
+    if (overlay_flag) {
-        force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
+      if (force->special_lj[1] != 1.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
-      error->all(FLERR,
+          force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
-                 "With overlay/pair yes, BPM bond styles require a value of 1.0 for all special_bonds weights");
+        error->all(FLERR,
-    if (id_fix_update) {
+                   "With overlay/pair yes, BPM bond styles require a value of 1.0 for all special_bonds weights");
-      modify->delete_fix(id_fix_update);
+      if (id_fix_update) {
-      delete[] id_fix_update;
+        modify->delete_fix(id_fix_update);
-      id_fix_update = nullptr;
+        delete[] id_fix_update;
-    }
+        id_fix_update = nullptr;
-  } else {
+      }
-    // Require atoms know about all of their bonds and if they break
+    } else {
-    if (force->newton_bond && break_flag)
+      // Require atoms know about all of their bonds and if they break
-      error->all(FLERR, "With overlay/pair no, or break yes, BPM bond styles require Newton bond off");
+      if (force->newton_bond && break_flag)
+        error->all(FLERR, "With overlay/pair no, or break yes, BPM bond styles require Newton bond off");
 
-    // special lj must be 0 1 1 to censor pair forces between bonded particles
+      // special lj must be 0 1 1 to censor pair forces between bonded particles
-    if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
+      if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
-      error->all(FLERR,
+        error->all(FLERR,
-                 "With overlay/pair no, BPM bond styles require special LJ weights = 0,1,1");
+                   "With overlay/pair no, BPM bond styles require special LJ weights = 0,1,1");
-    // if bonds can break, special coulomb must be 1 1 1 to ensure all pairs are included in the
+      // if bonds can break, 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
+      //    neighbor list and 1-3 and 1-4 special bond lists are skipped
-    if (break_flag && (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
+      if (break_flag && (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
-        force->special_coul[3] != 1.0))
+          force->special_coul[3] != 1.0))
-      error->all(FLERR,
+        error->all(FLERR,
-                 "With overlay/pair no, and break yes, BPM bond styles requires special Coulomb weights = 1,1,1");
+                   "With overlay/pair no, and break yes, BPM bond styles requires special Coulomb weights = 1,1,1");
 
-    if (id_fix_dummy && break_flag) {
+      if (id_fix_dummy && break_flag) {
-      id_fix_update = utils::strdup("BPM_UPDATE_SPECIAL_BONDS");
+        id_fix_update = utils::strdup("BPM_UPDATE_SPECIAL_BONDS");
-      fix_update_special_bonds = dynamic_cast<FixUpdateSpecialBonds *>(modify->replace_fix(
+        fix_update_special_bonds = dynamic_cast<FixUpdateSpecialBonds *>(modify->replace_fix(
-          id_fix_dummy, fmt::format("{} all UPDATE_SPECIAL_BONDS", id_fix_update), 1));
+            id_fix_dummy, fmt::format("{} all UPDATE_SPECIAL_BONDS", id_fix_update), 1));
-      delete[] id_fix_dummy;
+        delete[] id_fix_dummy;
-      id_fix_dummy = nullptr;
+        id_fix_dummy = nullptr;
+      }
     }
+
+    // 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");
   }
 
   if (force->angle || force->dihedral || force->improper)
@@ -149,10 +161,16 @@ void BondBPM::init_style()
   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
+  // find all instances of bond history to delete/shift data
-  if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 || force->special_coul[2] != 1.0 ||
+  // (bond hybrid may create multiple)
-      force->special_coul[3] != 1.0)
+  histories = modify->get_fix_by_style("BOND_HISTORY");
-    error->all(FLERR, "Bond style bpm requires 1-3 and 1-4 special weights of 1.0");
+  n_histories = histories.size();
+
+  // If a bond type isn't set, must be using bond style hybrid
+  hybrid_flag = 0;
+  for (int i = 1; i <= atom->nbondtypes; i++)
+    if (!setflag[i]) hybrid_flag = 1;
+  fix_bond_history->setflag = setflag;
 }
 
 /* ----------------------------------------------------------------------
@@ -269,6 +287,14 @@ void BondBPM::settings(int narg, char **arg)
       }
     }
   }
+
+  // Set up necessary history fix
+  if (!fix_bond_history) {
+    fix_bond_history = dynamic_cast<FixBondHistory *>(modify->replace_fix(
+        id_fix_dummy2, fmt::format("{} all BOND_HISTORY {} {}", id_fix_bond_history, update_flag, nhistory), 1));
+    delete[] id_fix_dummy2;
+    id_fix_dummy2 = nullptr;
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -385,12 +411,15 @@ void BondBPM::process_broken(int i, int j)
 
   if (i < nlocal) {
     for (m = 0; m < num_bond[i]; m++) {
-      if (bond_atom[i][m] == tag[j]) {
+      if (bond_atom[i][m] == tag[j] && setflag[bond_type[i][m]]) {
         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);
+        for (auto &ihistory: histories) {
-        fix_bond_history->delete_history(i, n - 1);
+          auto fix_bond_history2 = dynamic_cast<FixBondHistory *>  (ihistory);
+          fix_bond_history2->shift_history(i, m, n - 1);
+          fix_bond_history2->delete_history(i, n - 1);
+        }
         num_bond[i]--;
         break;
       }
@@ -399,12 +428,15 @@ void BondBPM::process_broken(int i, int j)
 
   if (j < nlocal) {
     for (m = 0; m < num_bond[j]; m++) {
-      if (bond_atom[j][m] == tag[i]) {
+      if (bond_atom[j][m] == tag[i] && setflag[bond_type[j][m]]) {
         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);
+        for (auto &ihistory: histories) {
-        fix_bond_history->delete_history(j, n - 1);
+          auto fix_bond_history2 = dynamic_cast<FixBondHistory *>  (ihistory);
+          fix_bond_history2->shift_history(j, m, n - 1);
+          fix_bond_history2->delete_history(j, n - 1);
+        }
         num_bond[j]--;
         break;
       }

src/BPM/bond_bpm.h

@@ -16,8 +16,12 @@
 
 #include "bond.h"
 
+#include <vector>
+
 namespace LAMMPS_NS {
 
+class Fix;
+
 class BondBPM : public Bond {
  public:
   BondBPM(class LAMMPS *);
@@ -34,7 +38,7 @@ class BondBPM : public Bond {
  protected:
   double r0_max_estimate;
   double max_stretch;
-  int store_local_freq;
+  int store_local_freq, nhistory, update_flag, hybrid_flag;
 
   std::vector<int> leftover_iarg;
 
@@ -50,9 +54,12 @@ class BondBPM : public Bond {
   FnPtrPack *pack_choice;    // ptrs to pack functions
   double *output_data;
 
-  int prop_atom_flag, nvalues, overlay_flag, break_flag;
+  int prop_atom_flag, nvalues, overlay_flag, break_flag, ignore_special_flag;
   int index_x_ref, index_y_ref, index_z_ref;
 
+  int n_histories;
+  std::vector<Fix *> histories;
+
   void pack_id1(int, int, int);
   void pack_id2(int, int, int);
   void pack_time(int, int, int);

src/BPM/bond_bpm_rotational.cpp

@@ -52,6 +52,9 @@ BondBPMRotational::BondBPMRotational(LAMMPS *_lmp) :
   smooth_flag = 1;
   normalize_flag = 0;
 
+  nhistory = 4;
+  id_fix_bond_history = utils::strdup("HISTORY_BPM_ROTATIONAL");
+
   single_extra = 7;
   svector = new double[7];
 }
@@ -458,6 +461,9 @@ void BondBPMRotational::compute(int eflag, int vflag)
     store_data();
   }
 
+  if (hybrid_flag)
+    fix_bond_history->compress_history();
+
   int i1, i2, itmp, n, type;
   double r[3], r0[3], rhat[3];
   double rsq, r0_mag, r_mag, r_mag_inv;
@@ -563,6 +569,9 @@ void BondBPMRotational::compute(int eflag, int vflag)
       ev_tally_xyz(i1, i2, nlocal, newton_bond, 0.0, -force1on2[0] * smooth, -force1on2[1] * smooth,
                    -force1on2[2] * smooth, r[0], r[1], r[2]);
   }
+
+  if (hybrid_flag)
+    fix_bond_history->uncompress_history();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -652,14 +661,6 @@ void BondBPMRotational::init_style()
 
   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;
-  }
 }
 
 /* ---------------------------------------------------------------------- */

src/BPM/bond_bpm_spring.cpp

@@ -39,6 +39,9 @@ BondBPMSpring::BondBPMSpring(LAMMPS *_lmp) :
   smooth_flag = 1;
   normalize_flag = 0;
 
+  nhistory = 1;
+  id_fix_bond_history = utils::strdup("HISTORY_BPM_SPRING");
+
   single_extra = 1;
   svector = new double[1];
 }
@@ -137,6 +140,9 @@ void BondBPMSpring::compute(int eflag, int vflag)
     store_data();
   }
 
+  if (hybrid_flag)
+    fix_bond_history->compress_history();
+
   int i1, i2, itmp, n, type;
   double delx, dely, delz, delvx, delvy, delvz;
   double e, rsq, r, r0, rinv, smooth, fbond, dot;
@@ -226,6 +232,9 @@ void BondBPMSpring::compute(int eflag, int vflag)
 
     if (evflag) ev_tally(i1, i2, nlocal, newton_bond, 0.0, fbond, delx, dely, delz);
   }
+
+  if (hybrid_flag)
+    fix_bond_history->uncompress_history();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -283,14 +292,6 @@ void BondBPMSpring::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;
-  }
 }
 
 /* ---------------------------------------------------------------------- */

src/BPM/compute_nbond_atom.cpp

@@ -14,7 +14,9 @@
 #include "compute_nbond_atom.h"
 
 #include "atom.h"
+#include "atom_vec.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "memory.h"
 
@@ -27,6 +29,21 @@ ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) :
 {
   if (narg < 3) utils::missing_cmd_args(FLERR, "compute nbond/atom", error);
 
+  if (atom->avec->bonds_allow == 0)
+    error->all(FLERR,"Compute nbond/atom used in system without bonds");
+
+  btype = -1;
+  int iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "bond/type") == 0) {
+      if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "compute nbond/atom bond/type", error);
+      btype = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
+      iarg += 2;
+    } else {
+      error->all(FLERR, "Unknown compute nbond/atom command {}", arg[iarg]);
+    }
+  }
+
   peratom_flag = 1;
   size_peratom_cols = 0;
   comm_reverse = 1;
@@ -77,6 +94,7 @@ void ComputeNBondAtom::compute_peratom()
   for (i = 0; i < nlocal; i++) {
     for (j = 0; j < num_bond[i]; j++) {
       if (bond_type[i][j] <= 0) continue;
+      if (btype != -1 && bond_type[i][j] != btype) continue;
 
       k = atom->map(bond_atom[i][j]);
       if (k < 0) continue;

src/BPM/compute_nbond_atom.h

@@ -35,7 +35,7 @@ class ComputeNBondAtom : public Compute {
   double memory_usage() override;
 
  private:
-  int nmax;
+  int nmax, btype;
   double *nbond;
 };
 

src/BPM/fix_update_special_bonds.cpp

@@ -90,11 +90,13 @@ void FixUpdateSpecialBonds::pre_exchange()
   for (auto const &it : broken_pairs) {
     tagi = it.first;
     tagj = it.second;
+
     i = atom->map(tagi);
     j = atom->map(tagj);
 
     // remove i from special bond list for atom j and vice versa
     // ignore n2, n3 since 1-3, 1-4 special factors required to be 1.0
+    // assume ghosts don't need special information
     if (i < nlocal) {
       slist = special[i];
       n1 = nspecial[i][0];
@@ -126,19 +128,24 @@ void FixUpdateSpecialBonds::pre_exchange()
 
     // add i to special bond list for atom j and vice versa
     // ignore n2, n3 since 1-3, 1-4 special factors required to be 1.0
-    n1 = nspecial[i][0];
+    // assume ghosts don't need special information
-    if (n1 >= atom->maxspecial)
+    if (i < nlocal) {
-      error->one(FLERR, "Special list size exceeded in fix update/special/bond");
+      n1 = nspecial[i][0];
-    special[i][n1] = tagj;
+      if (n1 >= atom->maxspecial)
-    nspecial[i][0] += 1;
+        error->one(FLERR, "Special list size exceeded for atom {}", tagi);
-    nspecial[i][1] = nspecial[i][2] = nspecial[i][0];
+      special[i][n1] = tagj;
+      nspecial[i][0] += 1;
+      nspecial[i][1] = nspecial[i][2] = nspecial[i][0];
+    }
 
-    n1 = nspecial[j][0];
+    if (j < nlocal) {
-    if (n1 >= atom->maxspecial)
+      n1 = nspecial[j][0];
-      error->one(FLERR, "Special list size exceeded in fix update/special/bond");
+      if (n1 >= atom->maxspecial)
-    special[j][n1] = tagi;
+        error->one(FLERR, "Special list size exceeded for atom {}", tagj);
-    nspecial[j][0] += 1;
+      special[j][n1] = tagi;
-    nspecial[j][1] = nspecial[j][2] = nspecial[j][0];
+      nspecial[j][0] += 1;
+      nspecial[j][1] = nspecial[j][2] = nspecial[j][0];
+    }
   }
 
   broken_pairs.clear();
@@ -162,7 +169,7 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
   tagint *tag = atom->tag;
 
   // In theory could communicate a list of broken bonds to neighboring processors here
-  // to remove restriction that users use Newton bond off
+  // to remove restriction on Newton bond off
 
   for (int ilist = 0; ilist < neighbor->nlist; ilist++) {
     list = neighbor->lists[ilist];

src/ELECTRODE/fix_electrode_conp.cpp

@@ -79,6 +79,9 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
     potential_i(nullptr), potential_iele(nullptr)
 {
   if (lmp->citeme) lmp->citeme->add(cite_fix_electrode);
+  if (atom->map_style == Atom::MAP_NONE)
+    error->all(FLERR, "Fix {} requires an atom map, see atom_modify", style);
+
   // fix.h output flags
   scalar_flag = 1;
   vector_flag = 1;
@@ -86,6 +89,9 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
   extvector = 0;
   extarray = 0;
 
+  virial_global_flag = 1;    // use virials of this fix
+  thermo_virial = 1;         // set vflags for v_tally
+
   bool default_algo = true;
   algo = Algo::MATRIX_INV;
   matrix_algo = true;
@@ -123,7 +129,8 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
   } else
     group_psi_const[0] = utils::numeric(FLERR, arg[3], false, lmp);
   char *eta_str = arg[4];
-  eta = utils::numeric(FLERR, eta_str, false, lmp);
+  bool etanull = (strcmp(eta_str, "NULL") == 0);
+  if (!etanull) eta = utils::numeric(FLERR, eta_str, false, lmp);
   int iarg = 5;
   while (iarg < narg) {
     if ((strcmp(arg[iarg], "couple") == 0)) {
@@ -214,7 +221,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
         qtotal_var_style = VarStyle::CONST;
       }
     } else if ((strcmp(arg[iarg], "eta") == 0)) {
-      if (iarg + 2 > narg) error->all(FLERR, "Need two arguments after eta command");
+      if (iarg + 2 > narg) error->all(FLERR, "Need one argument after eta command");
       etaflag = true;
       int is_double, cols, ghost;
       eta_index = atom->find_custom_ghost(arg[++iarg] + 2, is_double, cols, ghost);
@@ -240,6 +247,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
   if (qtotal_var_style != VarStyle::UNSET) {
     if (symm) error->all(FLERR, "{} cannot use qtotal keyword with symm on", this->style);
   }
+  if (etanull && !etaflag) error->all(FLERR, "If eta is NULL the eta keyword must be used");
 
   // computatonal potential
   group_psi = std::vector<double>(groups.size());
@@ -346,7 +354,7 @@ int FixElectrodeConp::modify_param(int narg, char **arg)
     MPI_Allreduce(MPI_IN_PLACE, &in_ele, 1, MPI_INT, MPI_SUM, world);
     if (in_ele == 0) error->all(FLERR, "No atoms of type in electrode");
     MPI_Allreduce(MPI_IN_PLACE, &not_in_ele, 1, MPI_INT, MPI_SUM, world);
-    if (not_in_ele)
+    if (not_in_ele && (comm->me == 0))
       error->warning(FLERR,
                      "Not all atoms of type in electrode; Thomas-Fermi parameters will be ignored "
                      "for electrolyte");
@@ -427,12 +435,11 @@ void FixElectrodeConp::init()
     }
     if (comm->me == 0)
       for (char *fix_id : integrate_ids)
-        error->warning(
+        error->warning(FLERR,
-            FLERR,
+                       "Electrode atoms are integrated by fix {}, but fix electrode is using a "
-            "Electrode atoms are integrated by fix {}, but fix electrode is using a matrix method. "
+                       "matrix method. For mobile electrodes use the conjugate gradient algorithm "
-            "For "
+                       "without matrix ('algo cg').",
-            "mobile electrodes use the conjugate gradient algorithm without matrix ('algo cg').",
+                       fix_id);
-            fix_id);
   }
 
   // check for package intel
@@ -478,7 +485,7 @@ void FixElectrodeConp::post_constructor()
   input->variable->set(fmt::format("{} equal f_{}[{}]", var_vtop, fixname, 1 + top_group));
   input->variable->set(fmt::format("{} equal (v_{}-v_{})/lz", var_efield, var_vbot, var_vtop));
   // check for other efields and warn if found
-  if (modify->get_fix_by_style("^efield").size() > 0 && comm->me == 0)
+  if ((modify->get_fix_by_style("^efield").size() > 0) && (comm->me == 0))
     error->warning(FLERR, "Other efield fixes found -- please make sure this is intended!");
   // call fix command:
   // fix [varstem]_efield all efield 0.0 0.0 [var_vdiff]/lz
@@ -638,13 +645,14 @@ void FixElectrodeConp::setup_post_neighbor()
 
 /* ---------------------------------------------------------------------- */
 
-void FixElectrodeConp::setup_pre_reverse(int eflag, int /*vflag*/)
+void FixElectrodeConp::setup_pre_reverse(int eflag, int vflag)
 {
+  if (pair->did_tally_callback() && (comm->me == 0))
+    error->warning(FLERR, "Computation of virials in fix {} is incompatible with TALLY package", style);
   // correct forces for initial timestep
-  gausscorr(eflag, true);
+  ev_init(eflag, vflag);
+  gausscorr(eflag, vflag, true);
   self_energy(eflag);
-  // potential_energy(eflag); // not always part of the energy, depending on ensemble, therefore
-  // removed
 }
 
 /* ---------------------------------------------------------------------- */
@@ -674,7 +682,7 @@ void FixElectrodeConp::invert()
 void FixElectrodeConp::symmetrize()
 {
   // S matrix to enforce charge neutrality constraint
-  if (read_inv && comm->me == 0)
+  if (read_inv && (comm->me == 0))
     error->warning(FLERR,
                    "Symmetrizing matrix from file. Make sure the provided matrix has not been "
                    "symmetrized yet.");
@@ -755,11 +763,11 @@ void FixElectrodeConp::setup_pre_exchange()    // create_taglist
   // if memory_usage > 0.5 GiB, warn with expected usage
   double mem_needed = memory_usage();
   mem_needed /= (1024 * 1024 * 1024);    // convert to GiB
-  if (mem_needed > 0.5 && comm->me == 0)
+  if ((mem_needed > 0.5) && (comm->me == 0))
     error->warning(FLERR,
-                   "Please ensure there is sufficient memory for fix electrode "
+                   "Please ensure there is sufficient memory for fix {} "
                    "(anticipated usage is at least {:.1f} GiB per proc)",
-                   mem_needed);
+                   style, mem_needed);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -771,12 +779,11 @@ void FixElectrodeConp::pre_force(int)
 
 /* ---------------------------------------------------------------------- */
 
-void FixElectrodeConp::pre_reverse(int eflag, int /*vflag*/)
+void FixElectrodeConp::pre_reverse(int eflag, int vflag)
 {
-  gausscorr(eflag, true);
+  ev_init(eflag, vflag);
+  gausscorr(eflag, vflag, true);
   self_energy(eflag);
-  //potential_energy(eflag); // not always part of the energy, depending on ensemble, therefore
-  // removed
 }
 
 /* ---------------------------------------------------------------------- */
@@ -924,7 +931,7 @@ void FixElectrodeConp::update_charges()
       dot_old = dot_new;
     }
     recompute_potential(std::move(b), q_local);
-    if (delta > cg_threshold && comm->me == 0) error->warning(FLERR, "CG threshold not reached");
+    if ((delta > cg_threshold) && (comm->me == 0)) error->warning(FLERR, "CG threshold not reached");
   } else {
     error->all(FLERR, "This algorithm is not implemented, yet");
   }
@@ -1224,11 +1231,10 @@ double FixElectrodeConp::self_energy(int eflag)
 
 /* ---------------------------------------------------------------------- */
 
-double FixElectrodeConp::gausscorr(int eflag, bool fflag)
+double FixElectrodeConp::gausscorr(int eflag, int vflag, bool fflag)
 {
   // correction to short range interaction due to eta
 
-  int evflag = pair->evflag;
   double const qqrd2e = force->qqrd2e;
   int const nlocal = atom->nlocal;
   int *mask = atom->mask;
@@ -1294,13 +1300,11 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag)
             f[j][2] -= delz * fpair;
           }
         }
-
+        if (eflag) {
-        double ecoul = 0.;
+          double ecoul = -prefactor * erfc_etar;
-        if (eflag) ecoul = -prefactor * erfc_etar;
+          force->pair->ev_tally(i, j, nlocal, newton_pair, 0., ecoul, 0., 0., 0., 0.);
-
-        if (evflag) {
-          force->pair->ev_tally(i, j, nlocal, newton_pair, 0., ecoul, fpair, delx, dely, delz);
         }
+        if (vflag) v_tally(i, j, nlocal, newton_pair, fpair, delx, dely, delz);
       }
     }
   }
@@ -1621,3 +1625,70 @@ void FixElectrodeConp::unpack_forward_comm(int n, int first, double *buf)
   int const last = first + n;
   for (int i = first, m = 0; i < last; i++) atom->q[i] = buf[m++];
 }
+
+/* ----------------------------------------------------------------------
+   Tally virial of pair interactions in pre_reverse. This cannot be done with pair->ev_tally()
+   because compute_fdotr is called before pre_reverse, i.e. Virials need to be tallied even if fdotr
+   is used.
+------------------------------------------------------------------------- */
+
+void FixElectrodeConp::v_tally(int i, int j, int nlocal, int newton_pair, double fpair, double delx,
+                               double dely, double delz)
+{
+  double v[6];
+  if (vflag_either) {
+    v[0] = delx * delx * fpair;
+    v[1] = dely * dely * fpair;
+    v[2] = delz * delz * fpair;
+    v[3] = delx * dely * fpair;
+    v[4] = delx * delz * fpair;
+    v[5] = dely * delz * fpair;
+
+    if (vflag_global) {
+      if (newton_pair) {
+        virial[0] += v[0];
+        virial[1] += v[1];
+        virial[2] += v[2];
+        virial[3] += v[3];
+        virial[4] += v[4];
+        virial[5] += v[5];
+      } else {
+        if (i < nlocal) {
+          virial[0] += 0.5 * v[0];
+          virial[1] += 0.5 * v[1];
+          virial[2] += 0.5 * v[2];
+          virial[3] += 0.5 * v[3];
+          virial[4] += 0.5 * v[4];
+          virial[5] += 0.5 * v[5];
+        }
+        if (j < nlocal) {
+          virial[0] += 0.5 * v[0];
+          virial[1] += 0.5 * v[1];
+          virial[2] += 0.5 * v[2];
+          virial[3] += 0.5 * v[3];
+          virial[4] += 0.5 * v[4];
+          virial[5] += 0.5 * v[5];
+        }
+      }
+    }
+
+    if (vflag_atom) {
+      if (newton_pair || i < nlocal) {
+        vatom[i][0] += 0.5 * v[0];
+        vatom[i][1] += 0.5 * v[1];
+        vatom[i][2] += 0.5 * v[2];
+        vatom[i][3] += 0.5 * v[3];
+        vatom[i][4] += 0.5 * v[4];
+        vatom[i][5] += 0.5 * v[5];
+      }
+      if (newton_pair || j < nlocal) {
+        vatom[j][0] += 0.5 * v[0];
+        vatom[j][1] += 0.5 * v[1];
+        vatom[j][2] += 0.5 * v[2];
+        vatom[j][3] += 0.5 * v[3];
+        vatom[j][4] += 0.5 * v[4];
+        vatom[j][5] += 0.5 * v[5];
+      }
+    }
+  }
+}

src/ELECTRODE/fix_electrode_conp.h

@@ -119,10 +119,11 @@ class FixElectrodeConp : public Fix {
   void create_taglist();
   void invert();
   void symmetrize();
-  double gausscorr(int, bool);
+  double gausscorr(int, int, bool);
   void update_charges();
   double potential_energy();
   double self_energy(int);
+  void v_tally(int, int, int, int, double, double, double, double);
   void write_to_file(FILE *, const std::vector<tagint> &, const std::vector<std::vector<double>> &);
   void read_from_file(const std::string &input_file, double **, const std::string &);
   void compute_sd_vectors();

src/GRANULAR/fix_add_heat.cpp

@@ -0,0 +1,161 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Joel Clemmer (SNL)
+------------------------------------------------------------------------- */
+
+#include "fix_add_heat.h"
+
+#include "atom.h"
+#include "error.h"
+#include "input.h"
+#include "memory.h"
+#include "update.h"
+#include "variable.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+enum { CONSTANT, EQUAL, ATOM };
+enum { ADD, LINEAR, QUARTIC };
+
+/* ---------------------------------------------------------------------- */
+
+FixAddHeat::FixAddHeat(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg), varstr(nullptr), vatom(nullptr)
+{
+  if (narg < 5) utils::missing_cmd_args(FLERR, "fix add/heat", error);
+  dynamic_group_allow = 1;
+  overwrite_flag = 0;
+
+  if (strcmp(arg[3], "constant") == 0) {
+    style = ADD;
+  } else if (strcmp(arg[3], "linear") == 0) {
+    style = LINEAR;
+  } else if (strcmp(arg[3], "quartic") == 0) {
+    style = QUARTIC;
+  } else {
+    error->all(FLERR, "Invalid option {}", arg[3]);
+  }
+
+  if (utils::strmatch(arg[4], "^v_")) {
+    varstr = utils::strdup(arg[4] + 2);
+  } else {
+    value = utils::numeric(FLERR, arg[4], false, lmp);
+    vstyle = CONSTANT;
+  }
+
+  int iarg = 5;
+  if (style != ADD) {
+    if (narg != 6) utils::missing_cmd_args(FLERR, "fix add/heat", error);
+    prefactor = utils::numeric(FLERR, arg[5], false, lmp);
+    iarg = 6;
+  }
+
+  // optional args
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "overwrite") == 0) {
+      if (iarg + 1 >= narg) utils::missing_cmd_args(FLERR, "fix add/heat", error);
+      overwrite_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
+      iarg += 2;
+    } else {
+      error->all(FLERR, "Illegal fix add/heat command, invalid argument {}", arg[iarg]);
+    }
+  }
+
+  maxatom = -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixAddHeat::~FixAddHeat()
+{
+  delete[] varstr;
+  memory->destroy(vatom);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixAddHeat::setmask()
+{
+  int mask = 0;
+  mask |= POST_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAddHeat::init()
+{
+  if (!atom->temperature_flag)
+    error->all(FLERR, "Fix add/heat requires atom style with temperature property");
+  if (!atom->heatflow_flag)
+    error->all(FLERR, "Fix add/heat requires atom style with heatflow property");
+
+  // check variable
+
+  if (varstr) {
+    var = input->variable->find(varstr);
+    if (var < 0) error->all(FLERR, "Variable {} for fix addforce does not exist", varstr);
+    if (input->variable->equalstyle(var))
+      vstyle = EQUAL;
+    else if (input->variable->atomstyle(var))
+      vstyle = ATOM;
+    else
+      error->all(FLERR, "Variable {} for fix addforce is invalid style", varstr);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAddHeat::post_force(int /*vflag*/)
+{
+  int *mask = atom->mask;
+  double *heatflow = atom->heatflow;
+  double *temperature = atom->temperature;
+  double dtinv = 1.0 / update->dt;
+
+  if (vstyle == ATOM) {
+    if (atom->nmax > maxatom) {
+      maxatom = atom->nmax;
+      memory->destroy(vatom);
+      memory->create(vatom, maxatom, "addheat:vatom");
+    }
+
+    input->variable->compute_atom(var, igroup, &vatom[0], 1, 0);
+  }
+
+  if (overwrite_flag)
+    for (int i = 0; i < atom->nlocal; i++)
+      if (mask[i] & groupbit)
+        heatflow[i] = 0.0;
+
+  double vtmp, dt;
+  if (vstyle == CONSTANT) vtmp = value;
+  if (vstyle == EQUAL) vtmp = input->variable->compute_equal(var);
+  for (int i = 0; i < atom->nlocal; i++) {
+    if (mask[i] & groupbit) {
+      if (vstyle == ATOM) vtmp = vatom[i];
+
+      if (style == ADD) {
+        heatflow[i] += dtinv * vtmp;
+      } else if (style == LINEAR) {
+        heatflow[i] += dtinv * prefactor * (vtmp - temperature[i]);
+      } else if (style == QUARTIC) {
+        heatflow[i] += dtinv * prefactor * (pow(vtmp, 4.0) - pow(temperature[i], 4.0));
+      }
+    }
+  }
+}

src/GRANULAR/fix_add_heat.h

@@ -0,0 +1,45 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   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(add/heat,FixAddHeat);
+// clang-format on
+#else
+
+#ifndef LMP_FIX_ADD_HEAT_H
+#define LMP_FIX_ADD_HEAT_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixAddHeat : public Fix {
+ public:
+  FixAddHeat(class LAMMPS *, int, char **);
+  ~FixAddHeat() override;
+  int setmask() override;
+  void init() override;
+  void post_force(int) override;
+
+ protected:
+  double value, prefactor;
+  int var, vstyle, maxatom, style, overwrite_flag;
+  char *varstr;
+  double *vatom;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/Makefile

@@ -124,6 +124,7 @@ PACKAGE = \
 	reaction \
 	reaxff \
 	replica \
+	rheo \
 	rigid \
 	scafacos \
 	shock \
@@ -233,6 +234,7 @@ PACKLIB = \
 	plumed \
 	qmmm \
 	ml-quip \
+	rheo \
 	scafacos \
 	machdyn \
 	vtk \
@@ -254,6 +256,7 @@ PACKEXT = \
 	netcdf \
 	plumed \
 	qmmm \
+	rheo \
 	scafacos \
 	voronoi \
 	vtk \

src/PYTHON/fix_python_invoke.cpp

@@ -105,6 +105,13 @@ void FixPythonInvoke::end_of_step()
 
 /* ---------------------------------------------------------------------- */
 
+void FixPythonInvoke::setup(int vflag)
+{
+  if (selected_callback == POST_FORCE) post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
 void FixPythonInvoke::post_force(int vflag)
 {
   if (update->ntimestep % nevery != 0) return;

src/PYTHON/fix_python_invoke.h

@@ -30,6 +30,7 @@ class FixPythonInvoke : public Fix {
   FixPythonInvoke(class LAMMPS *, int, char **);
   ~FixPythonInvoke() override;
   int setmask() override;
+  void setup(int) override;
   void end_of_step() override;
   void post_force(int) override;
 

src/REAXFF/fix_reaxff_bonds.cpp

@@ -44,6 +44,7 @@ FixReaxFFBonds::FixReaxFFBonds(LAMMPS *lmp, int narg, char **arg) :
   ntypes = atom->ntypes;
   nmax = atom->nmax;
   compressed = 0;
+  first_flag = true;
 
   nevery = utils::inumeric(FLERR,arg[3],false,lmp);
 
@@ -94,7 +95,10 @@ int FixReaxFFBonds::setmask()
 
 void FixReaxFFBonds::setup(int /*vflag*/)
 {
-  end_of_step();
+  // only print output during setup() at the very beginning
+  // to avoid duplicate outputs when using multiple run statements
+  if (first_flag) end_of_step();
+  first_flag = false;
 }
 
 /* ---------------------------------------------------------------------- */

src/REAXFF/fix_reaxff_bonds.h

@@ -40,6 +40,7 @@ class FixReaxFFBonds : public Fix {
   tagint **neighid;
   double **abo;
   FILE *fp;
+  bool first_flag;
 
   void allocate();
   void destroy();
@@ -50,7 +51,6 @@ class FixReaxFFBonds : public Fix {
   int nint(const double &);
   double memory_usage() override;
 
-  bigint nvalid, nextvalid();
   struct _reax_list *lists;
   class PairReaxFF *reaxff;
   class NeighList *list;

src/RHEO/Install.sh

@@ -0,0 +1,70 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+# arg1 = file, arg2 = file it depends on
+
+action () {
+  if (test $mode = 0) then
+    rm -f ../$1
+  elif (! cmp -s $1 ../$1) then
+    if (test -z "$2" || test -e ../$2) then
+      cp $1 ..
+      if (test $mode = 2) then
+        echo "  updating src/$1"
+      fi
+    fi
+  elif (test -n "$2") then
+    if (test ! -e ../$2) then
+      rm -f ../$1
+    fi
+  fi
+}
+
+# some styles in RHEO have base classes in BPM
+
+if (test $1 = 1) then
+  if (test ! -e ../bond_bpm.cpp) then
+    echo "Must install BPM package with RHEO"
+    exit 1
+  fi
+fi
+
+for file in *.cpp *.h; do
+    action ${file}
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*rheo[^ \t]* //' ../Makefile.package
+    sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(rheo_SYSINC) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(rheo_SYSLIB) |' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^[ \t]*include.*rheo.*$/d' ../Makefile.package.settings
+    # multiline form needed for BSD sed on Macs
+    sed -i -e '4 i \
+include ..\/..\/lib\/rheo\/Makefile.lammps
+' ../Makefile.package.settings
+  fi
+
+elif (test $1 = 0) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*rheo[^ \t]* //' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^[ \t]*include.*rheo.*$/d' ../Makefile.package.settings
+  fi
+
+fi

src/RHEO/README

@@ -0,0 +1,10 @@
+RHEO or Reproducing Hydrodynamics and Elastic Objects is a package to model
+multiphase fluid systems. The authors include Joel Clemmer (Sandia), Thomas
+O'Connor (Carnegie Mellon), and Eric Palermo (Carnegie Mellon).
+
+Bond style rheo/shell, compute style rheo/property/atom, and fix style
+rheo/temperature all depend on the BPM package.
+
+This package requires the GNU scientific library (GSL). We recommend version
+2.7 or later. To build this package, one must first separately install GSL in
+a location that can be found by your environment.

src/RHEO/atom_vec_rheo.cpp

@@ -0,0 +1,174 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors:
+   Joel Clemmer (SNL)
+----------------------------------------------------------------------- */
+
+#include "atom_vec_rheo.h"
+
+#include "atom.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecRHEO::AtomVecRHEO(LAMMPS *lmp) : AtomVec(lmp)
+{
+  molecular = Atom::ATOMIC;
+  mass_type = PER_TYPE;
+  forceclearflag = 1;
+
+  atom->rheo_status_flag = 1;
+  atom->pressure_flag = 1;
+  atom->rho_flag = 1;
+  atom->viscosity_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
+
+  fields_grow = {"rheo_status", "rho", "drho", "pressure", "viscosity"};
+  fields_copy = {"rheo_status", "rho", "drho", "pressure", "viscosity"};
+  fields_comm = {"rheo_status", "rho"};
+  fields_comm_vel = {"rheo_status", "rho"};
+  fields_reverse = {"drho"};
+  fields_border = {"rheo_status", "rho"};
+  fields_border_vel = {"rheo_status", "rho"};
+  fields_exchange = {"rheo_status", "rho"};
+  fields_restart = {"rheo_status", "rho"};
+  fields_create = {"rheo_status", "rho", "drho", "pressure", "viscosity"};
+  fields_data_atom = {"id", "type", "rheo_status", "rho", "x"};
+  fields_data_vel = {"id", "v"};
+
+  setup_fields();
+}
+
+/* ----------------------------------------------------------------------
+   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 AtomVecRHEO::grow_pointers()
+{
+  rheo_status = atom->rheo_status;
+  pressure = atom->pressure;
+  rho = atom->rho;
+  drho = atom->drho;
+  viscosity = atom->viscosity;
+}
+
+/* ----------------------------------------------------------------------
+   clear extra forces starting at atom N
+   nbytes = # of bytes to clear for a per-atom vector
+------------------------------------------------------------------------- */
+
+void AtomVecRHEO::force_clear(int n, size_t nbytes)
+{
+  memset(&drho[n], 0, nbytes);
+}
+
+/* ----------------------------------------------------------------------
+   initialize non-zero atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecRHEO::create_atom_post(int ilocal)
+{
+  rho[ilocal] = 1.0;
+}
+
+/* ----------------------------------------------------------------------
+   modify what AtomVec::data_atom() just unpacked
+   or initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecRHEO::data_atom_post(int ilocal)
+{
+  drho[ilocal] = 0.0;
+  pressure[ilocal] = 0.0;
+  viscosity[ilocal] = 0.0;
+}
+
+/* ----------------------------------------------------------------------
+   assign an index to named atom property and return index
+   return -1 if name is unknown to this atom style
+------------------------------------------------------------------------- */
+
+int AtomVecRHEO::property_atom(const std::string &name)
+{
+  if (name == "rheo_status") return 0;
+  if (name == "pressure") return 1;
+  if (name == "rho") return 2;
+  if (name == "drho") return 3;
+  if (name == "viscosity") return 4;
+  return -1;
+}
+
+/* ----------------------------------------------------------------------
+   pack per-atom data into buf for ComputePropertyAtom
+   index maps to data specific to this atom style
+------------------------------------------------------------------------- */
+
+void AtomVecRHEO::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
+{
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  int n = 0;
+
+  if (index == 0) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = rheo_status[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 1) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = pressure[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 2) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = rho[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 3) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = drho[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 4) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = viscosity[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  }
+}

src/RHEO/atom_vec_rheo.h

@@ -0,0 +1,46 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   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(rheo,AtomVecRHEO);
+// clang-format on
+#else
+
+#ifndef LMP_ATOM_VEC_RHEO_H
+#define LMP_ATOM_VEC_RHEO_H
+
+#include "atom_vec.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecRHEO : virtual public AtomVec {
+ public:
+  AtomVecRHEO(class LAMMPS *);
+
+  void grow_pointers() override;
+  void force_clear(int, size_t) override;
+  void create_atom_post(int) override;
+  void data_atom_post(int) override;
+  int property_atom(const std::string &) override;
+  void pack_property_atom(int, double *, int, int) override;
+
+ private:
+  int *rheo_status;
+  double *pressure, *rho, *drho, *viscosity;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/RHEO/atom_vec_rheo_thermal.cpp

@@ -0,0 +1,222 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors:
+   Joel Clemmer (SNL)
+----------------------------------------------------------------------- */
+
+#include "atom_vec_rheo_thermal.h"
+
+#include "atom.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecRHEOThermal::AtomVecRHEOThermal(LAMMPS *lmp) : AtomVec(lmp)
+{
+  molecular = Atom::ATOMIC;
+  mass_type = PER_TYPE;
+  forceclearflag = 1;
+
+  atom->rheo_status_flag = 1;
+  atom->conductivity_flag = 1;
+  atom->temperature_flag = 1;
+  atom->esph_flag = 1;
+  atom->heatflow_flag = 1;
+  atom->pressure_flag = 1;
+  atom->rho_flag = 1;
+  atom->viscosity_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
+
+  fields_grow = {"rheo_status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"};
+  fields_copy = {"rheo_status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"};
+  fields_comm = {"rheo_status", "rho", "esph"};
+  fields_comm_vel = {"rheo_status", "rho", "esph"};
+  fields_reverse = {"drho", "heatflow"};
+  fields_border = {"rheo_status", "rho", "esph"};
+  fields_border_vel = {"rheo_status", "rho", "esph"};
+  fields_exchange = {"rheo_status", "rho", "esph"};
+  fields_restart = {"rheo_status", "rho", "esph"};
+  fields_create = {"rheo_status", "rho", "drho", "temperature", "esph", "heatflow", "conductivity", "pressure", "viscosity"};
+  fields_data_atom = {"id", "type", "rheo_status", "rho", "esph", "x"};
+  fields_data_vel = {"id", "v"};
+
+  setup_fields();
+}
+
+/* ----------------------------------------------------------------------
+   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 AtomVecRHEOThermal::grow_pointers()
+{
+  rheo_status = atom->rheo_status;
+  conductivity = atom->conductivity;
+  temperature = atom->temperature;
+  esph = atom->esph;
+  heatflow = atom->heatflow;
+  pressure = atom->pressure;
+  rho = atom->rho;
+  drho = atom->drho;
+  viscosity = atom->viscosity;
+}
+
+/* ----------------------------------------------------------------------
+   clear extra forces starting at atom N
+   nbytes = # of bytes to clear for a per-atom vector
+------------------------------------------------------------------------- */
+
+void AtomVecRHEOThermal::force_clear(int n, size_t nbytes)
+{
+  memset(&drho[n], 0, nbytes);
+  memset(&heatflow[n], 0, nbytes);
+}
+
+/* ----------------------------------------------------------------------
+   initialize non-zero atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecRHEOThermal::create_atom_post(int ilocal)
+{
+  rho[ilocal] = 1.0;
+}
+
+/* ----------------------------------------------------------------------
+   modify what AtomVec::data_atom() just unpacked
+   or initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecRHEOThermal::data_atom_post(int ilocal)
+{
+  drho[ilocal] = 0.0;
+  heatflow[ilocal] = 0.0;
+  temperature[ilocal] = 0.0;
+  pressure[ilocal] = 0.0;
+  viscosity[ilocal] = 0.0;
+  conductivity[ilocal] = 0.0;
+}
+
+/* ----------------------------------------------------------------------
+   assign an index to named atom property and return index
+   return -1 if name is unknown to this atom style
+------------------------------------------------------------------------- */
+
+int AtomVecRHEOThermal::property_atom(const std::string &name)
+{
+  if (name == "rheo_status") return 0;
+  if (name == "rho") return 1;
+  if (name == "drho") return 2;
+  if (name == "temperature") return 3;
+  if (name == "esph") return 4;
+  if (name == "heatflow") return 5;
+  if (name == "conductivity") return 6;
+  if (name == "pressure") return 7;
+  if (name == "viscosity") return 8;
+  return -1;
+}
+
+/* ----------------------------------------------------------------------
+   pack per-atom data into buf for ComputePropertyAtom
+   index maps to data specific to this atom style
+------------------------------------------------------------------------- */
+
+void AtomVecRHEOThermal::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
+{
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  int n = 0;
+
+  if (index == 0) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = rheo_status[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 1) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = rho[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 2) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = drho[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 3) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = temperature[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 4) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = esph[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 5) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = heatflow[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 6) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = conductivity[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 7) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = pressure[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  } else if (index == 8) {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit)
+        buf[n] = viscosity[i];
+      else
+        buf[n] = 0.0;
+      n += nvalues;
+    }
+  }
+}