Merge branch 'kk_atom_vec' of github.com:stanmoore1/lammps into strip-style-suffix

.github/CODEOWNERS

@@ -37,6 +37,7 @@ src/MESONT/*          @iafoss
 src/ML-HDNNP/*        @singraber
 src/ML-IAP/*          @athomps
 src/ML-PACE/*         @yury-lysogorskiy
+src/ML-POD/*          @exapde @rohskopf
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka

.github/workflows/compile-msvc.yml

@@ -26,7 +26,7 @@ jobs:
     - name: Select Python version
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Building LAMMPS via CMake
       shell: bash
@@ -37,6 +37,8 @@ jobs:
         nuget install MSMPIDIST
         cmake -C cmake/presets/windows.cmake \
               -D PKG_PYTHON=on \
+              -D WITH_PNG=off \
+              -D WITH_JPEG=off \
               -S cmake -B build \
               -D BUILD_SHARED_LIBS=on \
               -D LAMMPS_EXCEPTIONS=on \

cmake/CMakeLists.txt

@@ -266,6 +266,7 @@ set(STANDARD_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-POD  
   MOFFF
   MOLECULE
   MOLFILE
@@ -432,7 +433,7 @@ if(BUILD_OMP)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
+if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
@@ -638,7 +639,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
   endif()
 endforeach()
 
-if(PKG_ELECTRODE)
+if(PKG_ELECTRODE OR PKG_ML-POD)
   target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
 endif()
 

cmake/presets/all_off.cmake

@@ -56,6 +56,7 @@ set(ALL_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP

cmake/presets/all_on.cmake

@@ -58,6 +58,7 @@ set(ALL_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP

cmake/presets/mingw-cross.cmake

@@ -47,6 +47,7 @@ set(WIN_PACKAGES
   MISC
   ML-HDNNP
   ML-IAP
+  ML-POD
   ML-RANN
   ML-SNAP
   MOFFF

cmake/presets/most.cmake

@@ -41,6 +41,7 @@ set(ALL_PACKAGES
   MEAM
   MISC
   ML-IAP
+  ML-POD
   ML-SNAP
   MOFFF
   MOLECULE

doc/src/Build_extras.rst

@@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
@@ -1411,6 +1412,49 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
 ----------
 
+.. _ml-pod:
+
+ML-POD package
+-----------------------------
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      No additional settings are needed besides ``-D PKG_ML-POD=yes``.
+
+   .. tab:: Traditional make
+
+      Before building LAMMPS, you must configure the ML-POD support
+      settings in ``lib/mlpod``.  You can do this manually, if you
+      prefer, or do it in one step from the ``lammps/src`` dir, using a
+      command like the following, which simply invoke the
+      ``lib/mlpod/Install.py`` script with the specified args:
+
+      .. code-block:: bash
+
+         $ make lib-mlpod                   # print help message
+         $ make lib-mlpod args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         $ make lib-mlpod args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         $ make lib-mlpod args="-m mpi -e linalg"   # same as above but use the bundled linalg lib
+
+      Note that the ``Makefile.lammps`` file has settings to use the BLAS
+      and LAPACK linear algebra libraries.  These can either exist on
+      your system, or you can use the files provided in ``lib/linalg``.
+      In the latter case you also need to build the library in
+      ``lib/linalg`` with a command like these:
+
+      .. code-block:: bash
+
+         $ make lib-linalg                     # print help message
+         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+
+      The package itself is activated with ``make yes-ML-POD``.
+
+----------
+
 .. _plumed:
 
 PLUMED package

doc/src/Commands_all.rst

@@ -89,8 +89,7 @@ table above.
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset_atom_ids <reset_atom_ids>`
+   * :doc:`reset_atoms <reset_atoms>`
-   * :doc:`reset_mol_ids <reset_mol_ids>`
    * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`
@@ -126,6 +125,7 @@ additional letter in parenthesis: k = KOKKOS.
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`kim <kim_commands>`
+   * :doc:`fitpod <fitpod_command>`
    * :doc:`mdi <mdi>`
    * :doc:`ndx2group <group2ndx>`
    * :doc:`neb <neb>`

doc/src/Commands_fix.rst

@@ -69,9 +69,9 @@ OPT.
    * :doc:`edpd/source <fix_dpd_source>`
    * :doc:`efield <fix_efield>`
    * :doc:`ehex <fix_ehex>`
-   * :doc:`electrode/conp (i) <fix_electrode_conp>`
+   * :doc:`electrode/conp (i) <fix_electrode>`
-   * :doc:`electrode/conq (i) <fix_electrode_conp>`
+   * :doc:`electrode/conq (i) <fix_electrode>`
-   * :doc:`electrode/thermo (i) <fix_electrode_conp>`
+   * :doc:`electrode/thermo (i) <fix_electrode>`
    * :doc:`electron/stopping <fix_electron_stopping>`
    * :doc:`electron/stopping/fit <fix_electron_stopping>`
    * :doc:`enforce2d (k) <fix_enforce2d>`

doc/src/Commands_pair.rst

@@ -237,6 +237,7 @@ OPT.
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
    * :doc:`pace/extrapolation <pair_pace>`
+   * :doc:`pod <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`

doc/src/Commands_removed.rst

@@ -26,10 +26,15 @@ Box command
 The *box* command has been removed and the LAMMPS code changed so it won't
 be needed.  If present, LAMMPS will ignore the command and print a warning.
 
-Reset_ids command
+Reset_ids, reset_atom_ids, reset_mol_ids commands
------------------
+-------------------------------------------------
 
-The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
+.. deprecated:: TBD
+
+The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
+been folded into the :doc:`reset_atoms <reset_atoms>` command.  If
+present, LAMMPS will replace the commands accordingly and print a
+warning.
 
 MEAM package
 ------------
@@ -39,18 +44,21 @@ The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
 Fortran code of MEAM into C++, which removes several restrictions
 (e.g. there can be multiple instances in hybrid pair styles) and allows
 for some optimizations leading to better performance.  The pair style
-:doc:`meam <pair_meam>` has the exact same syntax.
+:doc:`meam <pair_meam>` has the exact same syntax.  For a transition
+period the C++ version of MEAM was called USER-MEAMC so it could
+coexist with the Fortran version.
 
 REAX package
 ------------
 
 The REAX package has been removed since it was superseded by the
-:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF
+:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF package has been tested
-package has been tested to yield equivalent results to the REAX package,
+to yield equivalent results to the REAX package, offers better
-offers better performance, supports OpenMP multi-threading via OPENMP,
+performance, supports OpenMP multi-threading via OPENMP, and GPU and
-and GPU and threading parallelization through KOKKOS.  The new pair styles
+threading parallelization through KOKKOS.  The new pair styles are not
-are not syntax compatible with the removed reax pair style, so input
+syntax compatible with the removed reax pair style, so input files will
-files will have to be adapted.
+have to be adapted.  The REAXFF package was originally called
+USER-REAXC.
 
 USER-CUDA package
 -----------------
@@ -69,5 +77,6 @@ restart2data tool
 The functionality of the restart2data tool has been folded into the
 LAMMPS executable directly instead of having a separate tool.  A
 combination of the commands :doc:`read_restart <read_restart>` and
-:doc:`write_data <write_data>` can be used to the same effect.  For added
+:doc:`write_data <write_data>` can be used to the same effect.  For
-convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
+added convenience this conversion can also be triggered by
+:doc:`command line flags <Run_options>`

doc/src/Developer_code_design.rst

@@ -50,7 +50,7 @@ parallel each MPI process creates such an instance.  This can be seen
 in the ``main.cpp`` file where the core steps of running a LAMMPS
 simulation are the following 3 lines of code:
 
-.. code-block:: C++
+.. code-block:: c++
 
     LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
     lammps->input->file();
@@ -78,7 +78,7 @@ LAMMPS makes extensive use of the object oriented programming (OOP)
 principles of *compositing* and *inheritance*. Classes like the
 ``LAMMPS`` class are a **composite** containing pointers to instances
 of other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
-``Modify``, and so on.  Each of these classes implement certain
+``Modify``, and so on.  Each of these classes implements certain
 functionality by storing and manipulating data related to the
 simulation and providing member functions that trigger certain
 actions.  Some of those classes like ``Force`` are themselves
@@ -87,9 +87,9 @@ interactions.  Similarly the ``Modify`` class contains a list of
 ``Fix`` and ``Compute`` classes.  If the input commands that
 correspond to these classes include the word *style*, then LAMMPS
 stores only a single instance of that class.  E.g. *atom_style*,
-*comm_style*, *pair_style*, *bond_style*.  It the input command does
+*comm_style*, *pair_style*, *bond_style*.  If the input command does
-not include the word *style*, there can be many instances of that
+**not** include the word *style*, then there may be many instances of
-class defined.  E.g. *region*, *fix*, *compute*, *dump*.
+that class defined, for example *region*, *fix*, *compute*, *dump*.
 
 **Inheritance** enables creation of *derived* classes that can share
 common functionality in their base class while providing a consistent
@@ -232,7 +232,7 @@ macro ``PairStyle()`` will associate the style name "lj/cut"
 with a factory function creating an instance of the ``PairLJCut``
 class.
 
-.. code-block:: C++
+.. code-block:: c++
 
    // from force.h
    typedef Pair *(*PairCreator)(LAMMPS *);
@@ -360,7 +360,7 @@ characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
 argument type must be compatible or else the {fmt} formatting code will
 throw an exception. Some format string examples are given below:
 
-.. code-block:: C
+.. code-block:: c++
 
    auto mesg = fmt::format("  CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
    mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",

doc/src/Developer_notes.rst

@@ -105,7 +105,7 @@ list, where each pair of atoms is listed only once (except when the
 pairs straddling sub-domains or periodic boundaries will be listed twice).
 Thus these are the default settings when a neighbor list request is created in:
 
-.. code-block:: C++
+.. code-block:: c++
 
    void Pair::init_style()
    {
@@ -129,7 +129,7 @@ neighbor list request to the specific needs of a style an additional
 request flag is needed.  The :doc:`tersoff <pair_tersoff>` pair style,
 for example, needs a "full" neighbor list:
 
-.. code-block:: C++
+.. code-block:: c++
 
    void PairTersoff::init_style()
    {
@@ -141,7 +141,7 @@ When a pair style supports r-RESPA time integration with different cutoff region
 the request flag may depend on the corresponding r-RESPA settings. Here an example
 from pair style lj/cut:
 
-.. code-block:: C++
+.. code-block:: c++
 
    void PairLJCut::init_style()
    {
@@ -160,7 +160,7 @@ Granular pair styles need neighbor lists based on particle sizes and not cutoff
 and also may require to have the list of previous neighbors available ("history").
 For example with:
 
-.. code-block:: C++
+.. code-block:: c++
 
    if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
    else neighbor->add_request(this, NeighConst::REQ_SIZE);
@@ -170,7 +170,7 @@ settings each request can set an id which is then used in the corresponding
 ``init_list()`` function to assign it to the suitable pointer variable. This is
 done for example by the :doc:`pair style meam <pair_meam>`:
 
-.. code-block:: C++
+.. code-block:: c++
 
    void PairMEAM::init_style()
    {
@@ -189,7 +189,7 @@ just once) and this can also be indicated by a flag.  As an example here
 is the request from the ``FixPeriNeigh`` class which is created
 internally by :doc:`Peridynamics pair styles <pair_peri>`:
 
-.. code-block:: C++
+.. code-block:: c++
 
    neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
 
@@ -198,7 +198,7 @@ than what is usually inferred from the pair style settings (largest cutoff of
 all pair styles plus neighbor list skin).  The following is used in the
 :doc:`compute rdf <compute_rdf>` command implementation:
 
-.. code-block:: C++
+.. code-block:: c++
 
   if (cutflag)
     neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
@@ -212,7 +212,7 @@ for printing the neighbor list summary the name of the requesting command
 should be set.  Below is the request from the :doc:`delete atoms <delete_atoms>`
 command:
 
-.. code-block:: C++
+.. code-block:: c++
 
    neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
 

doc/src/Developer_plugins.rst

@@ -95,7 +95,7 @@ a class ``PairMorse2`` in the files ``pair_morse2.h`` and
 ``pair_morse2.cpp`` with the factory function and initialization
 function would look like this:
 
-.. code-block:: C++
+.. code-block:: c++
 
   #include "lammpsplugin.h"
   #include "version.h"
@@ -141,7 +141,7 @@ list of argument strings), then the pointer type is ``lammpsplugin_factory2``
 and it must be assigned to the *creator.v2* member of the plugin struct.
 Below is an example for that:
 
-.. code-block:: C++
+.. code-block:: c++
 
   #include "lammpsplugin.h"
   #include "version.h"
@@ -176,7 +176,7 @@ demonstrated in the following example, which also shows that the
 implementation of the plugin class may be within the same source
 file as the plugin interface code:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "lammpsplugin.h"
 

doc/src/Developer_unittest.rst

@@ -194,7 +194,7 @@ macro. These tests operate by capturing the screen output when executing
 the failing command and then comparing that with a provided regular
 expression string pattern.  Example:
 
-.. code-block:: C++
+.. code-block:: c++
 
    TEST_F(SimpleCommandsTest, UnknownCommand)
    {
@@ -226,9 +226,9 @@ The following test programs are currently available:
    * - ``test_kim_commands.cpp``
      - KimCommands
      - Tests for several commands from the :ref:`KIM package <PKG-KIM>`
-   * - ``test_reset_ids.cpp``
+   * - ``test_reset_atoms.cpp``
-     - ResetIDs
+     - ResetAtoms
-     - Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
+     - Tests to validate the :doc:`reset_atoms <reset_atoms>` sub-commands
 
 
 Tests for the C-style library interface
@@ -249,7 +249,7 @@ MPI support.  These include tests where LAMMPS is run in multi-partition
 mode or only on a subset of the MPI world communicator.  The CMake
 script code for adding this kind of test looks like this:
 
-.. code-block:: CMake
+.. code-block:: cmake
 
    if (BUILD_MPI)
      add_executable(test_library_mpi test_library_mpi.cpp)

doc/src/Developer_updating.rst

@@ -61,7 +61,7 @@ header file needs to be updated accordingly.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
    {
@@ -75,7 +75,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
    {
@@ -112,14 +112,14 @@ Example from a pair style:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    if (eflag || vflag) ev_setup(eflag, vflag);
    else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    ev_init(eflag, vflag);
 
@@ -142,14 +142,14 @@ when they are called from only one or a subset of the MPI processes.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
     val = force->numeric(FLERR, arg[1]);
     num = force->inumeric(FLERR, arg[2]);
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
     val = utils::numeric(FLERR, true, arg[1], lmp);
     num = utils::inumeric(FLERR, false, arg[2], lmp);
@@ -183,14 +183,14 @@ copy them around for simulations.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    fp = force->open_potential(filename);
    fp = fopen(filename, "r");
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    fp = utils::open_potential(filename, lmp);
 
@@ -207,7 +207,7 @@ Example:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    if (fptr == NULL) {
      char str[128];
@@ -217,7 +217,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    if (fptr == nullptr)
      error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
@@ -237,7 +237,7 @@ an example from the ``FixWallReflect`` class:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    FixWallReflect(class LAMMPS *, int, char **);
    virtual ~FixWallReflect();
@@ -247,7 +247,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    FixWallReflect(class LAMMPS *, int, char **);
    ~FixWallReflect() override;
@@ -271,7 +271,7 @@ the type of the "this" pointer argument.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    comm->forward_comm_pair(this);
    comm->forward_comm_fix(this);
@@ -284,7 +284,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    comm->forward_comm(this);
    comm->reverse_comm(this);
@@ -304,7 +304,7 @@ requests can be :doc:`found here <Developer_notes>`. Example from the
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int irequest = neighbor->request(this,instance_me);
    neighbor->requests[irequest]->pair = 0;
@@ -317,7 +317,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
    if (cutflag) req->set_cutoff(mycutneigh);
@@ -340,7 +340,7 @@ these are internal fixes, there is no user visible change.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "fix_store.h"
 
@@ -351,7 +351,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "fix_store_peratom.h"
 
@@ -362,7 +362,7 @@ New:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "fix_store.h"
 
@@ -373,7 +373,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "fix_store_global.h"
 
@@ -396,7 +396,7 @@ the dump directly.  Example:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int idump = output->find_dump(arg[iarg+1]);
    if (idump < 0)
@@ -412,7 +412,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    auto idump = output->get_dump_by_id(arg[iarg+1]);
    if (!idump) error->all(FLERR,"Dump ID {} in hyper command does not exist", arg[iarg+1]);

doc/src/Developer_utils.rst

@@ -320,7 +320,7 @@ are all "whitespace" characters, i.e. the space character, the tabulator
 character, the carriage return character, the linefeed character, and
 the form feed character.
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: Tokenizer class example listing entries of the PATH environment variable
 
    #include "tokenizer.h"
@@ -352,7 +352,7 @@ tokenizer into a ``try`` / ``catch`` block to handle errors.  The
 when a (type of) number is requested as next token that is not
 compatible with the string representing the next word.
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: ValueTokenizer class example with exception handling
 
    #include "tokenizer.h"
@@ -430,7 +430,7 @@ one or two array indices "[<number>]" with numbers > 0.
 
 A typical code segment would look like this:
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: Usage example for ArgInfo class
 
    int nvalues = 0;
@@ -479,7 +479,7 @@ open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in
 case of failures to read or to convert numbers, so that LAMMPS will be
 aborted.
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: Use of PotentialFileReader class in pair style coul/streitz
 
     PotentialFileReader reader(lmp, file, "coul/streitz");
@@ -558,7 +558,7 @@ chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget()
 its size is registered later with :cpp:func:`MyPage::vgot()
 <LAMMPS_NS::MyPage::vgot>`.
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: Example of using :cpp:class:`MyPage <LAMMPS_NS::MyPage>`
 
       #include "my_page.h"

doc/src/Developer_write.rst

@@ -26,7 +26,7 @@ constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
 Every fix must be registered in LAMMPS by writing the following lines
 of code in the header before include guards:
 
-.. code-block:: c
+.. code-block:: c++
 
    #ifdef FIX_CLASS
    // clang-format off
@@ -47,7 +47,7 @@ keyword when it parses the input script.
 Let's write a simple fix which will print the average velocity at the end
 of each timestep. First of all, implement a constructor:
 
-.. code-block:: C++
+.. code-block:: c++
 
    FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
    : Fix(lmp, narg, arg)
@@ -72,7 +72,7 @@ in the Fix class called ``nevery`` which specifies how often the method
 
 The next method we need to implement is ``setmask()``:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int FixPrintVel::setmask()
    {
@@ -87,7 +87,7 @@ during execution. The constant ``END_OF_STEP`` corresponds to the
 are called during a timestep and the order in which they are called
 are shown in the previous section.
 
-.. code-block:: C++
+.. code-block:: c++
 
    void FixPrintVel::end_of_step()
    {
@@ -143,7 +143,7 @@ The group membership information of an atom is contained in the *mask*
 property of and atom and the bit corresponding to a given group is
 stored in the groupbit variable which is defined in Fix base class:
 
-.. code-block:: C++
+.. code-block:: c++
 
    for (int i = 0; i < nlocal; ++i) {
      if (atom->mask[i] & groupbit) {
@@ -174,7 +174,7 @@ to store positions of atoms from previous timestep, we need to add
 ``double** xold`` to the header file. Than add allocation code
 to the constructor:
 
-.. code-block:: C++
+.. code-block:: c++
 
    FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
    {
@@ -190,7 +190,7 @@ to the constructor:
 
 Implement the aforementioned methods:
 
-.. code-block:: C++
+.. code-block:: c++
 
    double FixSavePos::memory_usage()
    {

doc/src/Howto_pylammps.rst

@@ -152,14 +152,14 @@ Creating a new instance of PyLammps
 To create a PyLammps object you need to first import the class from the lammps
 module. By using the default constructor, a new *lammps* instance is created.
 
-.. code-block:: Python
+.. code-block:: python
 
    from lammps import PyLammps
    L = PyLammps()
 
 You can also initialize PyLammps on top of this existing *lammps* object:
 
-.. code-block:: Python
+.. code-block:: python
 
    from lammps import lammps, PyLammps
    lmp = lammps()
@@ -180,14 +180,14 @@ For instance, let's take the following LAMMPS command:
 In the original interface this command can be executed with the following
 Python code if *L* was a lammps instance:
 
-.. code-block:: Python
+.. code-block:: python
 
    L.command("region box block 0 10 0 5 -0.5 0.5")
 
 With the PyLammps interface, any command can be split up into arbitrary parts
 separated by white-space, passed as individual arguments to a region method.
 
-.. code-block:: Python
+.. code-block:: python
 
    L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
 
@@ -199,14 +199,14 @@ The benefit of this approach is avoiding redundant command calls and easier
 parameterization. In the original interface parameterization needed to be done
 manually by creating formatted strings.
 
-.. code-block:: Python
+.. code-block:: python
 
    L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
 
 In contrast, methods of PyLammps accept parameters directly and will convert
 them automatically to a final command string.
 
-.. code-block:: Python
+.. code-block:: python
 
    L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
 
@@ -256,7 +256,7 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface.
 
 To define a variable you can use the :doc:`variable <variable>` command:
 
-.. code-block:: Python
+.. code-block:: python
 
    L.variable("a index 2")
 
@@ -265,14 +265,14 @@ A dictionary of all variables is returned by L.variables
 you can access an individual variable by retrieving a variable object from the
 L.variables dictionary by name
 
-.. code-block:: Python
+.. code-block:: python
 
    a = L.variables['a']
 
 The variable value can then be easily read and written by accessing the value
 property of this object.
 
-.. code-block:: Python
+.. code-block:: python
 
    print(a.value)
    a.value = 4
@@ -284,7 +284,7 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The
 passed string parameter can be any expression containing global thermo values,
 variables, compute or fix data.
 
-.. code-block:: Python
+.. code-block:: python
 
    result = L.eval("ke") # kinetic energy
    result = L.eval("pe") # potential energy
@@ -298,7 +298,7 @@ All atoms in the current simulation can be accessed by using the L.atoms list.
 Each element of this list is an object which exposes its properties (id, type,
 position, velocity, force, etc.).
 
-.. code-block:: Python
+.. code-block:: python
 
    # access first atom
    L.atoms[0].id
@@ -311,7 +311,7 @@ position, velocity, force, etc.).
 
 Some properties can also be used to set:
 
-.. code-block:: Python
+.. code-block:: python
 
    # set position in 2D simulation
    L.atoms[0].position = (1.0, 0.0)
@@ -328,7 +328,7 @@ after a run via the L.runs list. This list contains a growing list of run data.
 The first element is the output of the first run, the second element that of
 the second run.
 
-.. code-block:: Python
+.. code-block:: python
 
    L.run(1000)
    L.runs[0] # data of first 1000 time steps
@@ -339,14 +339,14 @@ the second run.
 Each run contains a dictionary of all trajectories. Each trajectory is
 accessible through its thermo name:
 
-.. code-block:: Python
+.. code-block:: python
 
    L.runs[0].thermo.Step # list of time steps in first run
    L.runs[0].thermo.Ke   # list of kinetic energy values in first run
 
 Together with matplotlib plotting data out of LAMMPS becomes simple:
 
-.. code-block:: Python
+.. code-block:: python
 
    import matplotlib.plot as plt
    steps = L.runs[0].thermo.Step
@@ -406,7 +406,7 @@ Four atoms are placed in the simulation and the dihedral potential is applied on
 them using a datafile. Then one of the atoms is rotated along the central axis by
 setting its position from Python, which changes the dihedral angle.
 
-.. code-block:: Python
+.. code-block:: python
 
    phi = [d \* math.pi / 180 for d in range(360)]
 
@@ -439,7 +439,7 @@ Initially, a 2D system is created in a state with minimal energy.
 
 It is then disordered by moving each atom by a random delta.
 
-.. code-block:: Python
+.. code-block:: python
 
    random.seed(27848)
    deltaperturb = 0.2
@@ -458,7 +458,7 @@ It is then disordered by moving each atom by a random delta.
 Finally, the Monte Carlo algorithm is implemented in Python. It continuously
 moves random atoms by a random delta and only accepts certain moves.
 
-.. code-block:: Python
+.. code-block:: python
 
    estart = L.eval("pe")
    elast = estart
@@ -517,7 +517,7 @@ PyLammps can be run in parallel using mpi4py. This python package can be install
 The following is a short example which reads in an existing LAMMPS input file and
 executes it in parallel.  You can find in.melt in the examples/melt folder.
 
-.. code-block:: Python
+.. code-block:: python
 
    from mpi4py import MPI
    from lammps import PyLammps

doc/src/Howto_structured_data.rst

@@ -43,7 +43,7 @@ JSON
      "ke": $(ke)
    }""" file current_state.json screen no
 
-.. code-block:: JSON
+.. code-block:: json
    :caption: current_state.json
 
    {

doc/src/Library_config.rst

@@ -39,7 +39,7 @@ crashes within LAMMPS may be recovered from by enabling
 :ref:`exceptions <exceptions>`, avoiding them proactively is a safer
 approach.
 
-.. code-block:: C
+.. code-block:: c
    :caption: Example for using configuration settings functions
 
    #include "library.h"

doc/src/Library_create.rst

@@ -22,7 +22,7 @@ as the "handle" argument in subsequent function calls until that
 instance is destroyed by calling :cpp:func:`lammps_close`.  Here is a
 simple example demonstrating its use:
 
-.. code-block:: C
+.. code-block:: c
 
    #include "library.h"
    #include <stdio.h>

doc/src/Library_execute.rst

@@ -30,7 +30,7 @@ be included in the file or strings, and expansion of variables with
 ``${name}`` or ``$(expression)`` syntax is performed.
 Below is a short example using some of these functions.
 
-.. code-block:: C
+.. code-block:: c
 
    /* define to make the otherwise hidden prototype for "lammps_open()" visible */
    #define LAMMPS_LIB_MPI

doc/src/Library_properties.rst

@@ -32,7 +32,7 @@ indexed accordingly. Per-atom data can change sizes and ordering at
 every neighbor list rebuild or atom sort event as atoms migrate between
 sub-domains and processors.
 
-.. code-block:: C
+.. code-block:: c
 
    #include "library.h"
    #include <stdio.h>

doc/src/Modify_bond.rst

@@ -13,24 +13,65 @@ Here is a brief description of common methods you define in your
 new derived class.  See bond.h, angle.h, dihedral.h, and improper.h
 for details and specific additional methods.
 
-+-----------------------+---------------------------------------------------------------------------------------+
++-----------------------+---------------------------------------------------------------------+
-| init                  | check if all coefficients are set, calls *init_style* (optional)                      |
+| Required              | "pure" methods that *must* be overridden in a derived class         |
-+-----------------------+---------------------------------------------------------------------------------------+
++=======================+=====================================================================+
-| init_style            | check if style specific conditions are met (optional)                                 |
+| compute               | compute the molecular interactions for all listed items             |
-+-----------------------+---------------------------------------------------------------------------------------+
++-----------------------+---------------------------------------------------------------------+
-| compute               | compute the molecular interactions (required)                                         |
+| coeff                 | set coefficients for one type                                       |
-+-----------------------+---------------------------------------------------------------------------------------+
++-----------------------+---------------------------------------------------------------------+
-| settings              | apply global settings for all types (optional)                                        |
+| equilibrium_distance  | length of bond, used by SHAKE (bond styles only)                    |
-+-----------------------+---------------------------------------------------------------------------------------+
++-----------------------+---------------------------------------------------------------------+
-| coeff                 | set coefficients for one type (required)                                              |
+| equilibrium_angle     | opening of angle, used by SHAKE (angle styles only)                 |
-+-----------------------+---------------------------------------------------------------------------------------+
++-----------------------+---------------------------------------------------------------------+
-| equilibrium_distance  | length of bond, used by SHAKE (required, bond only)                                   |
+| write & read_restart  | writes/reads coeffs to restart files                                |
-+-----------------------+---------------------------------------------------------------------------------------+
++-----------------------+---------------------------------------------------------------------+
-| equilibrium_angle     | opening of angle, used by SHAKE (required, angle only)                                |
+| single                | force/r (bond styles only) and energy of a single bond or angle     |
-+-----------------------+---------------------------------------------------------------------------------------+
++-----------------------+---------------------------------------------------------------------+
-| write & read_restart  | writes/reads coeffs to restart files (required)                                       |
+
-+-----------------------+---------------------------------------------------------------------------------------+
+
-| single                | force (bond only) and energy of a single bond or angle (required, bond or angle only) |
++--------------------------------+----------------------------------------------------------------------+
-+-----------------------+---------------------------------------------------------------------------------------+
+| Optional                       | methods that have a default or dummy implementation                  |
-| memory_usage          | tally memory allocated by the style (optional)                                        |
++================================+======================================================================+
-+-----------------------+---------------------------------------------------------------------------------------+
+| init                           | check if all coefficients are set, calls init_style()                |
++--------------------------------+----------------------------------------------------------------------+
+| init_style                     | check if style specific conditions are met                           |
++--------------------------------+----------------------------------------------------------------------+
+| settings                       | apply global settings for all types                                  |
++--------------------------------+----------------------------------------------------------------------+
+| write & read_restart_settings  | writes/reads global style settings to restart files                  |
++--------------------------------+----------------------------------------------------------------------+
+| write_data                     | write corresponding Coeffs section(s) in data file                   |
++--------------------------------+----------------------------------------------------------------------+
+| memory_usage                   | tally memory allocated by the style                                  |
++--------------------------------+----------------------------------------------------------------------+
+| extract                        | provide access to internal data  (bond or angle styles only)         |
++--------------------------------+----------------------------------------------------------------------+
+| reinit                         | reset all type-based parameters, called by fix adapt (bonds only)    |
++--------------------------------+----------------------------------------------------------------------+
+| pack & unpack_forward_comm     | copy data to and from buffer in forward communication (bonds only)   |
++--------------------------------+----------------------------------------------------------------------+
+| pack & unpack_reverse_comm     | copy data to and from buffer in reverse communication (bonds only)   |
++--------------------------------+----------------------------------------------------------------------+
+
+Here is a list of flags or settings that should be set in the
+constructor of the derived class when they differ from the default
+setting.
+
++---------------------------------+------------------------------------------------------------------------------+---------+
+| Name of flag                    | Description                                                                  | default |
++=================================+==============================================================================+=========+
+| writedata                       | 1 if write_data() is implemented                                             | 1       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| single_extra                    | number of extra single values calculated (bond styles only)                  | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| partial_flag                    | 1 if bond type can be set to 0 and deleted (bond styles only)                | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| reinitflag                      | 1 if style has reinit() and is compatible with fix adapt                     | 1       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| comm_forward                    | size of buffer (in doubles) for forward communication  (bond styles only)    | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| comm_reverse                    | size of buffer (in doubles) for reverse communication  (bond styles only)    | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| comm_reverse_off                | size of buffer for reverse communication with newton off (bond styles only)  | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+

doc/src/Modify_pair.rst

@@ -1,35 +1,121 @@
 Pair styles
 ===========
 
-Classes that compute pairwise interactions are derived from the Pair
+Classes that compute pairwise non-bonded interactions are derived from
-class.  In LAMMPS, pairwise calculation include many-body potentials
+the Pair class.  In LAMMPS, pairwise calculation include many-body
-such as EAM or Tersoff where particles interact without a static bond
+potentials such as EAM, Tersoff, or ReaxFF where particles interact
-topology.  New styles can be created to add new pair potentials to
+without an explicit bond topology but include interactions beyond
-LAMMPS.
+pairwise non-bonded contributions.  New styles can be created to add
+support for additional pair potentials to LAMMPS.  When the
+modifications are small, sometimes it is more effective to derive from
+an existing pair style class.  This latter approach is also used by
+:doc:`Accelerator packages <Speed_packages>` where the accelerated style
+names differ from their base classes by an appended suffix.
 
-Pair_lj_cut.cpp is a simple example of a Pair class, though it
+The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a
-includes some optional methods to enable its use with rRESPA.
+very simple potential function.  It includes several optional methods to
+enable its use with :doc:`run_style respa <run_style>` and :doc:`compute
+group/group <compute_group_group>`.
 
-Here is a brief description of the class methods in pair.h:
+Here is a brief list of some the class methods in the Pair class that
+*must* be or *may* be overridden in a derived class.
 
 +---------------------------------+---------------------------------------------------------------------+
+| Required                        | "pure" methods that *must* be overridden in a derived class         |
++=================================+=====================================================================+
 | compute                         | workhorse routine that computes pairwise interactions               |
 +---------------------------------+---------------------------------------------------------------------+
-| settings                        | reads the input script line with arguments you define               |
+| settings                        | processes the arguments to the pair_style command                   |
 +---------------------------------+---------------------------------------------------------------------+
-| coeff                           | set coefficients for one i,j type pair                              |
+| coeff                           | set coefficients for one i,j type pair, called from pair_coeff      |
-+---------------------------------+---------------------------------------------------------------------+
-| init_one                        | perform initialization for one i,j type pair                        |
-+---------------------------------+---------------------------------------------------------------------+
-| init_style                      | initialization specific to this pair style                          |
-+---------------------------------+---------------------------------------------------------------------+
-| write & read_restart            | write/read i,j pair coeffs to restart files                         |
-+---------------------------------+---------------------------------------------------------------------+
-| write & read_restart_settings   | write/read global settings to restart files                         |
-+---------------------------------+---------------------------------------------------------------------+
-| single                          | force/r and energy of a single pairwise interaction between 2 atoms |
-+---------------------------------+---------------------------------------------------------------------+
-| compute_inner/middle/outer      | versions of compute used by rRESPA                                  |
 +---------------------------------+---------------------------------------------------------------------+
 
-The inner/middle/outer routines are optional.
++---------------------------------+----------------------------------------------------------------------+
+| Optional                        | methods that have a default or dummy implementation                  |
++=================================+======================================================================+
+| init_one                        | perform initialization for one i,j type pair                         |
++---------------------------------+----------------------------------------------------------------------+
+| init_style                      | style initialization: request neighbor list(s), error checks         |
++---------------------------------+----------------------------------------------------------------------+
+| init_list                       | Neighbor class callback function to pass neighbor list to pair style |
++---------------------------------+----------------------------------------------------------------------+
+| single                          | force/r and energy of a single pairwise interaction between 2 atoms  |
++---------------------------------+----------------------------------------------------------------------+
+| compute_inner/middle/outer      | versions of compute used by rRESPA                                   |
++---------------------------------+----------------------------------------------------------------------+
+| memory_usage                    | return estimated amount of memory used by the pair style             |
++---------------------------------+----------------------------------------------------------------------+
+| modify_params                   | process arguments to pair_modify command                             |
++---------------------------------+----------------------------------------------------------------------+
+| extract                         | provide access to internal scalar or per-type data like cutoffs      |
++---------------------------------+----------------------------------------------------------------------+
+| extract_peratom                 | provide access to internal per-atom data                             |
++---------------------------------+----------------------------------------------------------------------+
+| setup                           | initialization at the beginning of a run                             |
++---------------------------------+----------------------------------------------------------------------+
+| finish                          | called at the end of a run, e.g. to print                            |
++---------------------------------+----------------------------------------------------------------------+
+| write & read_restart            | write/read i,j pair coeffs to restart files                          |
++---------------------------------+----------------------------------------------------------------------+
+| write & read_restart_settings   | write/read global settings to restart files                          |
++---------------------------------+----------------------------------------------------------------------+
+| write_data                      | write Pair Coeffs section to data file                               |
++---------------------------------+----------------------------------------------------------------------+
+| write_data_all                  | write PairIJ Coeffs section to data file                             |
++---------------------------------+----------------------------------------------------------------------+
+| pack & unpack_forward_comm      | copy data to and from buffer if style uses forward communication     |
++---------------------------------+----------------------------------------------------------------------+
+| pack & unpack_reverse_comm      | copy data to and from buffer if style uses reverse communication     |
++---------------------------------+----------------------------------------------------------------------+
+| reinit                          | reset all type-based parameters, called by fix adapt for example     |
++---------------------------------+----------------------------------------------------------------------+
+| reset_dt                        | called when the time step is changed by timestep or fix reset/dt     |
++---------------------------------+----------------------------------------------------------------------+
+
+Here is a list of flags or settings that should be set in the
+constructor of the derived pair class when they differ from the default
+setting.
+
++---------------------------------+-------------------------------------------------------------+---------+
+| Name of flag                    | Description                                                 | default |
++=================================+=============================================================+=========+
+| single_enable                   | 1 if single() method is implemented, 0 if missing           | 1       |
++---------------------------------+-------------------------------------------------------------+---------+
+| respa_enable                    | 1 if pair style has compute_inner/middle/outer()            | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| restartinfo                     | 1 if pair style writes its settings to a restart            | 1       |
++---------------------------------+-------------------------------------------------------------+---------+
+| one_coeff                       | 1 if only a pair_coeff * * command is allowed               | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| manybody_flag                   | 1 if pair style is a manybody potential                     | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| unit_convert_flag               | value != 0 indicates support for unit conversion            | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| no_virial_fdotr_compute         | 1 if pair style does not call virial_fdotr_compute()        | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| writedata                       | 1 if write_data() and write_data_all() are implemented      | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| comm_forward                    | size of buffer (in doubles) for forward communication       | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| comm_reverse                    | size of buffer (in doubles) for reverse communication       | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| ghostneigh                      | 1 if cutghost is set and style uses neighbors of ghosts     | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| finitecutflag                   | 1 if cutoff depends on diameter of atoms                    | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| reinitflag                      | 1 if style has reinit() and is compatible with fix adapt    | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| ewaldflag                       | 1 if compatible with kspace_style ewald                     | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| pppmflag                        | 1 if compatible with kspace_style pppm                      | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| msmflag                         | 1 if compatible with kspace_style msm                       | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| dispersionflag                  | 1 if compatible with ewald/disp or pppm/disp                | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| tip4pflag                       | 1 if compatible with kspace_style pppm/tip4p                | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| dipoleflag                      | 1 if compatible with dipole kspace_style                    | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| spinflag                        | 1 if compatible with spin kspace_style                      | 0       |
++---------------------------------+-------------------------------------------------------------+---------+

doc/src/Packages_details.rst

@@ -80,6 +80,7 @@ page gives those details.
    * :ref:`ML-HDNNP <PKG-ML-HDNNP>`
    * :ref:`ML-IAP <PKG-ML-IAP>`
    * :ref:`ML-PACE <PKG-ML-PACE>`
+   * :ref:`ML-POD <PKG-ML-POD>`
    * :ref:`ML-QUIP <PKG-ML-QUIP>`
    * :ref:`ML-RANN <PKG-ML-RANN>`
    * :ref:`ML-SNAP <PKG-ML-SNAP>`
@@ -865,7 +866,7 @@ ELECTRODE package
 The ELECTRODE package allows the user to enforce a constant potential method for
 groups of atoms that interact with the remaining atoms as electrolyte.
 
-**Authors:** The ELECTRODE library is written and maintained by Ludwig
+**Authors:** The ELECTRODE package is written and maintained by Ludwig
 Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
 Robert Meissner (TUHH, Hamburg, Germany).
 
@@ -878,7 +879,7 @@ This package has :ref:`specific installation instructions <electrode>` on the
 
 **Supporting info:**
 
-* :doc:`fix electrode/conp <fix_electrode_conp>`
+* :doc:`fix electrode/conp <fix_electrode>`
 
 ----------
 
@@ -1796,6 +1797,39 @@ This package has :ref:`specific installation instructions <ml-pace>` on the
 
 ----------
 
+.. _PKG-ML-POD:
+
+ML-POD package
+-------------------
+
+**Contents:**
+
+A pair style and fitpod style for Proper Orthogonal Descriptors
+(POD). POD is a methodology for deriving descriptors based on the proper
+orthogonal decomposition. The ML-POD package provides an efficient
+implementation for running simulations with POD potentials, along with
+fitting the potentials natively in LAMMPS.
+
+**Authors:**
+
+Ngoc Cuong Nguyen (MIT), Andrew Rohskopf (Sandia)
+
+.. versionadded:: TBD
+
+**Install:**
+
+This package has :ref:`specific installation instructions <ml-pod>` on the
+:doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* src/ML-POD: filenames -> commands
+* :doc:`pair_style pod <pair_pod>`
+* :doc:`command_style fitpod <fitpod_command>`
+* examples/PACKAGES/pod
+
+----------
+
 .. _PKG-ML-QUIP:
 
 ML-QUIP package

doc/src/Packages_list.rst

@@ -155,7 +155,7 @@ whether an extra library is needed to build and use the package:
      - no
    * - :ref:`ELECTRODE <PKG-ELECTRODE>`
      - electrode charges to match potential
-     - :doc:`fix electrode/conp <fix_electrode_conp>`
+     - :doc:`fix electrode/conp <fix_electrode>`
      - PACKAGES/electrode
      - no
    * - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
@@ -298,6 +298,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`pair pace <pair_pace>`
      - PACKAGES/pace
      - ext
+   * - :ref:`ML-POD <PKG-ML-POD>`
+     - Proper orthogonal decomposition potentials
+     - :doc:`pair pod <pair_pod>`
+     - pod
+     - ext
    * - :ref:`ML-QUIP <PKG-ML-QUIP>`
      - QUIP/libatoms interface
      - :doc:`pair_style quip <pair_quip>`

doc/src/Python_atoms.rst

@@ -58,7 +58,7 @@ against invalid accesses.
       Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
       these objects provide access to their data (id, type, position, velocity, force, etc.):
 
-      .. code-block:: Python
+      .. code-block:: python
 
          # access first atom
          L.atoms[0].id
@@ -71,7 +71,7 @@ against invalid accesses.
 
       Some attributes can be changed:
 
-      .. code-block:: Python
+      .. code-block:: python
 
          # set position in 2D simulation
          L.atoms[0].position = (1.0, 0.0)

doc/src/Python_config.rst

@@ -4,7 +4,7 @@ Configuration information
 The following methods can be used to query the LAMMPS library
 about compile time settings and included packages and styles.
 
-.. code-block:: Python
+.. code-block:: python
    :caption: Example for using configuration settings functions
 
    from lammps import lammps

doc/src/Python_create.rst

@@ -74,7 +74,7 @@ Here are simple examples using all three Python interfaces:
       :py:class:`PyLammps <lammps.PyLammps>` objects can also be created on top of an existing
       :py:class:`lammps <lammps.lammps>` object:
 
-      .. code-block:: Python
+      .. code-block:: python
 
          from lammps import lammps, PyLammps
          ...
@@ -113,7 +113,7 @@ Here are simple examples using all three Python interfaces:
 
       You can also initialize IPyLammps on top of an existing :py:class:`lammps` or :py:class:`PyLammps` object:
 
-      .. code-block:: Python
+      .. code-block:: python
 
          from lammps import lammps, IPyLammps
          ...
@@ -142,7 +142,7 @@ the MPI and/or Kokkos environment if enabled and active.
 Note that you can create multiple LAMMPS objects in your Python
 script, and coordinate and run multiple simulations, e.g.
 
-.. code-block:: Python
+.. code-block:: python
 
    from lammps import lammps
    lmp1 = lammps()

doc/src/Python_error.rst

@@ -7,7 +7,7 @@ current Python process with an error message.  C++ exceptions allow capturing
 them on the C++ side and rethrowing them on the Python side. This way
 LAMMPS errors can be handled through the Python exception handling mechanism.
 
-.. code-block:: Python
+.. code-block:: python
 
    from lammps import lammps, MPIAbortException
 

doc/src/Python_execute.rst

@@ -60,7 +60,7 @@ it is possible to "compute" what the next LAMMPS command should be.
       can be executed using with the lammps API with the following Python code if ``lmp`` is an
       instance of :py:class:`lammps <lammps.lammps>`:
 
-      .. code-block:: Python
+      .. code-block:: python
 
          from lammps import lammps
 
@@ -73,7 +73,7 @@ it is possible to "compute" what the next LAMMPS command should be.
       The arguments of the command can be passed as one string, or
       individually.
 
-      .. code-block:: Python
+      .. code-block:: python
 
          from lammps import PyLammps
 
@@ -93,14 +93,14 @@ it is possible to "compute" what the next LAMMPS command should be.
       parameterization. In the lammps API parameterization needed to be done
       manually by creating formatted command strings.
 
-      .. code-block:: Python
+      .. code-block:: python
 
          lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
 
       In contrast, methods of PyLammps accept parameters directly and will convert
       them automatically to a final command string.
 
-      .. code-block:: Python
+      .. code-block:: python
 
          L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
 

doc/src/Python_launch.rst

@@ -56,7 +56,7 @@ and you should see the same output as if you had typed
 
 Note that without the mpi4py specific lines from ``test.py``
 
-.. code-block:: Python
+.. code-block:: python
 
    from lammps import lammps
    lmp = lammps()

doc/src/Python_objects.rst

@@ -76,7 +76,7 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
 
       To define a variable you can use the :doc:`variable <variable>` command:
 
-      .. code-block:: Python
+      .. code-block:: python
 
          L.variable("a index 2")
 
@@ -85,14 +85,14 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
       you can access an individual variable by retrieving a variable object from the
       ``L.variables`` dictionary by name
 
-      .. code-block:: Python
+      .. code-block:: python
 
          a = L.variables['a']
 
       The variable value can then be easily read and written by accessing the value
       property of this object.
 
-      .. code-block:: Python
+      .. code-block:: python
 
          print(a.value)
          a.value = 4

doc/src/Python_properties.rst

@@ -105,7 +105,7 @@ against invalid accesses.
       variables, compute or fix data (see :doc:`Howto_output`):
 
 
-      .. code-block:: Python
+      .. code-block:: python
 
          result = L.eval("ke") # kinetic energy
          result = L.eval("pe") # potential energy

doc/src/Python_scatter.rst

@@ -1,7 +1,7 @@
 Scatter/gather operations
 =========================
 
-.. code-block:: Python
+.. code-block:: python
 
    data = lmp.gather_atoms(name,type,count)  # return per-atom property of all atoms gathered into data, ordered by atom ID
                                              # name = "x", "charge", "type", etc
@@ -42,7 +42,7 @@ For the scatter methods, the array of coordinates passed to must be a
 ctypes vector of ints or doubles, allocated and initialized something
 like this:
 
-.. code-block:: Python
+.. code-block:: python
 
    from ctypes import c_double
    natoms = lmp.get_natoms()

doc/src/commands_list.rst

@@ -42,6 +42,7 @@ Commands
    echo
    fix
    fix_modify
+   fitpod_command
    group
    group2ndx
    hyper
@@ -89,8 +90,7 @@ Commands
    region
    replicate
    rerun
-   reset_atom_ids
+   reset_atoms
-   reset_mol_ids
    reset_timestep
    restart
    run

doc/src/compute_pair_local.rst

@@ -59,7 +59,7 @@ commands.
 The value *dist* is the distance between the pair of atoms.
 The values *dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the
 *distance* between the pair of atoms. This value is always the
-distance from the atom of lower to the one with the higher id.
+distance from the atom of higher to the one with the lower atom ID.
 
 The value *eng* is the interaction energy for the pair of atoms.
 

doc/src/delete_atoms.rst

@@ -135,7 +135,7 @@ number of atoms in the system.  Note that this is not done for
 molecular systems (see the :doc:`atom_style <atom_style>` command),
 regardless of the *compress* setting, since it would foul up the bond
 connectivity that has already been assigned.  However, the
-:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this
+:doc:`reset_atoms id <reset_atoms>` command can be used after this
 command to accomplish the same thing.
 
 Note that the re-assignment of IDs is not really a compression, where
@@ -203,7 +203,7 @@ using molecule template files via the :doc:`molecule <molecule>` and
 Related commands
 """"""""""""""""
 
-:doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>`
+:doc:`create_atoms <create_atoms>`, :doc:`reset_atoms id <reset_atoms>`
 
 Default
 """""""

doc/src/fitpod_command.rst

@@ -0,0 +1,745 @@
+.. index:: fitpod
+
+fitpod command
+======================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fitpod Ta_param.pod Ta_data.pod
+
+* fitpod = style name of this command
+* Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs)
+* Ta_data.pod = an input file that specifies DFT data used to fit a POD potential
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fitpod Ta_param.pod Ta_data.pod
+
+Description
+"""""""""""
+.. versionadded:: TBD
+
+Fit a machine-learning interatomic potential (ML-IAP) based on proper
+orthogonal descriptors (POD).  Two input files are required for this
+command. The first input file describes a POD potential parameter
+settings, while the second input file specifies the DFT data used for
+the fitting procedure.
+
+The table below has one-line descriptions of all the keywords that can
+be used in the first input file (i.e. ``Ta_param.pod`` in the example
+above):
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Keyword
+     - Default
+     - Type
+     - Description
+   * - species
+     - (none)
+     - STRING
+     - Chemical symbols for all elements in the system and have to match XYZ training files.
+   * - pbc
+     - 1 1 1
+     - INT
+     - three integer constants specify boundary conditions
+   * - rin
+     - 1.0
+     - REAL
+     - a real number specifies the inner cut-off radius
+   * - rcut
+     - 5.0
+     - REAL
+     - a real number specifies the outer cut-off radius
+   * - bessel_polynomial_degree
+     - 3
+     - INT
+     - the maximum degree of Bessel polynomials
+   * - inverse_polynomial_degree
+     - 6
+     - INT
+     - the maximum degree of inverse radial basis functions
+   * - onebody
+     - 1
+     - BOOL
+     - turns on/off one-body potential
+   * - twobody_number_radial_basis_functions
+     - 6
+     - INT
+     - number of radial basis functions for two-body potential
+   * - threebody_number_radial_basis_functions
+     - 5
+     - INT
+     - number of radial basis functions for three-body potential
+   * - threebody_number_angular_basis_functions
+     - 5
+     - INT
+     - number of angular basis functions for three-body potential
+   * - fourbody_snap_twojmax
+     - 0
+     - INT
+     - band limit for SNAP bispectrum components (0,2,4,6,8... allowed)
+   * - fourbody_snap_chemflag
+     - 0
+     - BOOL
+     - turns on/off the explicit multi-element variant of the SNAP bispectrum components
+   * - quadratic_pod_potential
+     - 0
+     - BOOL
+     - turns on/off quadratic POD potential
+
+All keywords except *species* have default values. If a keyword is not
+set in the input file, its default value is used.  The next table
+describes all keywords that can be used in the second input file
+(i.e. ``Ta_data.pod`` in the example above):
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Keyword
+     - Default
+     - Type
+     - Description
+   * - file_format
+     - extxyz
+     - STRING
+     - only the extended xyz format (extxyz) is currently supported
+   * - file_extension
+     - xyz
+     - STRING
+     - extension of the data files
+   * - path_to_training_data_set
+     - (none)
+     - STRING
+     - specifies the path to training data files in double quotes
+   * - path_to_test_data_set
+     - ""
+     - STRING
+     - specifies the path to test data files in double quotes
+   * - fraction_training_data_set
+     - 1.0
+     - REAL
+     - a real number (<= 1.0) specifies the fraction of the training set used to fit POD
+   * - randomize_training_data_set
+     - 0
+     - BOOL
+     - turns on/off randomization of the training set
+   * - fitting_weight_energy
+     - 100.0
+     - REAL
+     - a real constant specifies the weight for energy in the least-squares fit
+   * - fitting_weight_force
+     - 1.0
+     - REAL
+     - a real constant specifies the weight for force in the least-squares fit
+   * - fitting_regularization_parameter
+     - 1.0e-10
+     - REAL
+     - a real constant specifies the regularization parameter in the least-squares fit
+   * - error_analysis_for_training_data_set
+     - 0
+     - BOOL
+     - turns on/off error analysis for the training data set
+   * - error_analysis_for_test_data_set
+     - 0
+     - BOOL
+     - turns on/off error analysis for the test data set
+   * - basename_for_output_files
+     - pod
+     - STRING
+     - a basename string added to the output files
+   * - precision_for_pod_coefficients
+     - 8
+     - INT
+     - number of digits after the decimal points for numbers in the coefficient file
+
+All keywords except *path_to_training_data_set* have default values. If
+a keyword is not set in the input file, its default value is used.  After
+successful training, a number of output files are produced, if enabled:
+
+* ``<basename>_training_errors.pod``  reports the errors in energy and forces for the training data set
+* ``<basename>_training_analysis.pod`` reports detailed errors for all training configurations
+* ``<basename>_test_errors.pod`` reports errors for the test data set
+* ``<basename>_test_analysis.pod`` reports detailed errors for all test configurations
+* ``<basename>_coefficients.pod`` contains the coefficients of the POD potential
+
+After training the POD potential, ``Ta_param.pod`` and ``<basename>_coefficients.pod``
+are the two files needed to use the POD potential in LAMMPS. See
+:doc:`pair_style pod <pair_pod>` for using the POD potential. Examples
+about training and using POD potentials are found in the directory
+lammps/examples/PACKAGES/pod.
+
+Parameterized Potential Energy Surface
+""""""""""""""""""""""""""""""""""""""
+
+We consider a multi-element system of *N* atoms with :math:`N_{\rm e}`
+unique elements.  We denote by :math:`\boldsymbol r_n` and :math:`Z_n`
+position vector and type of an atom *n* in the system,
+respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e}
+\}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
+\boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1,
+Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The potential energy surface
+(PES) of the system can be expressed as a many-body expansion of the
+form
+
+.. math::
+
+    E(\boldsymbol R, \boldsymbol Z, \boldsymbol{\eta}, \boldsymbol{\mu}) \ = \ & \sum_{i} V^{(1)}(\boldsymbol r_i, Z_i, \boldsymbol \mu^{(1)} ) + \frac12 \sum_{i,j} V^{(2)}(\boldsymbol r_i, \boldsymbol r_j, Z_i, Z_j, \boldsymbol \eta, \boldsymbol \mu^{(2)})  \\
+    & + \frac16 \sum_{i,j,k} V^{(3)}(\boldsymbol r_i, \boldsymbol r_j, \boldsymbol r_k, Z_i, Z_j, Z_k, \boldsymbol \eta, \boldsymbol \mu^{(3)}) + \ldots
+
+where :math:`V^{(1)}` is the one-body potential often used for
+representing external field or energy of isolated elements, and the
+higher-body potentials :math:`V^{(2)}, V^{(3)}, \ldots` are symmetric,
+uniquely defined, and zero if two or more indices take identical values.
+The superscript on each potential denotes its body order. Each *q*-body
+potential :math:`V^{(q)}` depends on :math:`\boldsymbol \mu^{(q)}` which
+are sets of parameters to fit the PES. Note that :math:`\boldsymbol \mu`
+is a collection of all potential parameters :math:`\boldsymbol
+\mu^{(1)}`, :math:`\boldsymbol \mu^{(2)}`, :math:`\boldsymbol
+\mu^{(3)}`, etc, and that :math:`\boldsymbol \eta` is a set of
+hyper-parameters such as inner cut-off radius :math:`r_{\rm in}` and
+outer cut-off radius :math:`r_{\rm cut}`.
+
+Interatomic potentials rely on parameters to learn relationship between
+atomic environments and interactions.  Since interatomic potentials are
+approximations by nature, their parameters need to be set to some
+reference values or fitted against data by necessity.  Typically,
+potential fitting finds optimal parameters, :math:`\boldsymbol \mu^*`,
+to minimize a certain loss function of the predicted quantities and
+data. Since the fitted potential depends on the data set used to fit it,
+different data sets will yield different optimal parameters and thus
+different fitted potentials. When fitting the same functional form on
+*Q* different data sets, we would obtain *Q* different optimized
+potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta,
+\boldsymbol \mu_q^*), 1 \le q \le Q`.  Consequently, there exist many
+different sets of optimized parameters for empirical interatomic
+potentials.
+
+Instead of optimizing the potential parameters, inspired by the reduced
+basis method :ref:`(Grepl) <Grepl20072>` for parameterized partial
+differential equations, we view the parameterized PES as a parametric
+manifold of potential energies
+
+.. math::
+
+    \mathcal{M} = \{E(\boldsymbol R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu) \ | \  \boldsymbol \mu \in \Omega^{\boldsymbol \mu} \}
+
+where :math:`\Omega^{\boldsymbol \mu}` is a parameter domain in which
+:math:`\boldsymbol \mu` resides.  The parametric manifold
+:math:`\mathcal{M}` contains potential energy surfaces for all values of
+:math:`\boldsymbol \mu \in \Omega^{\boldsymbol \mu}`.  Therefore, the
+parametric manifold yields a much richer and more transferable atomic
+representation than any particular individual PES :math:`E(\boldsymbol
+R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu^*)`.
+
+We propose specific forms of the parameterized potentials for one-body,
+two-body, and three-body interactions. We apply the Karhunen-Loeve
+expansion to snapshots of the parameterized potentials to obtain sets of
+orthogonal basis functions. These basis functions are aggregated
+according to the chemical elements of atoms, thus leading to
+multi-element proper orthogonal descriptors.
+
+Proper Orthogonal Descriptors
+"""""""""""""""""""""""""""""
+
+Proper orthogonal descriptors are finger prints characterizing the
+radial and angular distribution of a system of atoms. The detailed
+mathematical definition is given in the paper by Nguyen and Rohskopf
+:ref:`(Nguyen) <Nguyen20222>`.
+
+The descriptors for the one-body interaction are used to capture energy
+of isolated elements and defined as follows
+
+.. math::
+
+    D_{ip}^{(1)} =  \left\{
+        \begin{array}{ll}
+        1, & \mbox{if } Z_i = p \\
+        0, & \mbox{if } Z_i \neq p
+        \end{array}
+    \right.
+
+for :math:`1 \le i \le N, 1 \le p \le N_{\rm e}`. The number of one-body
+descriptors per atom is equal to the number of elements. The one-body
+descriptors are independent of atom positions, but dependent on atom
+types. The one-body descriptors are active only when the keyword
+*onebody* is set to 1.
+
+We adopt the usual assumption that the direct interaction between two
+atoms vanishes smoothly when their distance is greater than the outer
+cutoff distance :math:`r_{\rm cut}`. Furthermore, we assume that two
+atoms can not get closer than the inner cutoff distance :math:`r_{\rm
+in}` due to the Pauli repulsion principle. Let :math:`r \in (r_{\rm in},
+r_{\rm cut})`, we introduce the following parameterized radial functions
+
+.. math::
+
+    \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta)  = \frac{\sin (\alpha \pi x) }{r - r_{\rm in}}, \qquad  \varphi(r, \gamma)  = \frac{1}{r^\gamma} ,
+
+where the scaled distance function :math:`x` is defined below to enrich the two-body manifold
+
+.. math::
+
+    x(r, r_{\rm in}, r_{\rm cut}, \beta) = \frac{e^{-\beta(r - r_{\rm in})/(r_{\rm cut} - r_{\rm in})} - 1}{e^{-\beta} - 1} .
+
+We introduce the following function as a convex combination of the two functions
+
+.. math::
+
+    \psi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta, \gamma, \kappa)  = \kappa \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) + (1- \kappa)  \varphi(r, \gamma) .
+
+We see that :math:`\psi` is a function of distance :math:`r`, cut-off
+distances :math:`r_{\rm in}` and :math:`r_{\rm cut}`, and parameters
+:math:`\alpha, \beta, \gamma, \kappa`. Together these parameters allow
+the function :math:`\psi` to characterize a diverse spectrum of two-body
+interactions within the cut-off interval :math:`(r_{\rm in}, r_{\rm
+cut})`.
+
+Next, we introduce the following parameterized potential
+
+.. math::
+
+    W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)})  = f_{\rm c}(r_{ij}, \boldsymbol \eta) \psi(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)})
+
+where :math:`\eta_1 = r_{\rm in}, \eta_2 = r_{\rm cut}, \mu_1^{(2)} =
+\alpha, \mu_2^{(2)} = \beta, \mu_3^{(2)} = \gamma`, and
+:math:`\mu_4^{(2)} = \kappa`. Here the cut-off function :math:`f_{\rm
+c}(r_{ij}, \boldsymbol \eta)` proposed in [refs] is used to ensure the
+smooth vanishing of the potential and its derivative for :math:`r_{ij}
+\ge r_{\rm cut}`:
+
+.. math::
+
+    f_{\rm c}(r_{ij},  r_{\rm in}, r_{\rm cut})  =  \exp \left(1 -\frac{1}{\sqrt{\left(1 - \frac{(r-r_{\rm in})^3}{(r_{\rm cut} - r_{\rm in})^3} \right)^2 + 10^{-6}}} \right)
+
+Based on the parameterized potential, we form a set of snapshots as
+follows.  We assume that we are given :math:`N_{\rm s}` parameter tuples
+:math:`\boldsymbol \mu^{(2)}_\ell, 1 \le \ell \le N_{\rm s}`. We
+introduce the following set of snapshots on :math:`(r_{\rm in}, r_{\rm
+cut})`:
+
+.. math::
+
+    \xi_\ell(r_{ij}, \boldsymbol \eta) =  W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}_\ell),  \quad \ell = 1, \ldots, N_{\rm s} .
+
+To ensure adequate sampling of the PES for different parameters, we
+choose :math:`N_{\rm s}` parameter points :math:`\boldsymbol
+\mu^{(2)}_\ell = (\alpha_\ell, \beta_\ell, \gamma_\ell, \kappa_\ell), 1
+\le \ell \le N_{\rm s}` as follows. The parameters :math:`\alpha \in [1,
+N_\alpha]` and :math:`\gamma \in [1, N_\gamma]` are integers, where
+:math:`N_\alpha` and :math:`N_\gamma` are the highest degrees for
+:math:`\alpha` and :math:`\gamma`, respectively. We next choose
+:math:`N_\beta` different values of :math:`\beta` in the interval
+:math:`[\beta_{\min}, \beta_{\max}]`, where :math:`\beta_{\min} = 0` and
+:math:`\beta_{\max} = 4`. The parameter :math:`\kappa` can be set either
+0 or 1.  Hence, the total number of parameter points is :math:`N_{\rm s}
+= N_\alpha N_\beta + N_\gamma`.  Although :math:`N_\alpha, N_\beta,
+N_\gamma` can be chosen conservatively large, we find that
+:math:`N_\alpha = 6, N_\beta = 3, N_\gamma = 8` are adequate for most
+problems.  Note that :math:`N_\alpha` and :math:`N_\gamma` correspond to
+*bessel_polynomial_degree* and *inverse_polynomial_degree*,
+respectively.
+
+We employ the Karhunen-Loeve (KL) expansion to generate an orthogonal
+basis set which is known to be optimal for representation of the
+snapshot family :math:`\{\xi_\ell\}_{\ell=1}^{N_{\rm s}}`. The two-body
+orthogonal basis functions are computed as follows
+
+.. math::
+
+    U^{(2)}_m(r_{ij}, \boldsymbol \eta) = \sum_{\ell = 1}^{N_{\rm s}} A_{\ell m}(\boldsymbol \eta) \,  \xi_\ell(r_{ij}, \boldsymbol \eta), \qquad m = 1, \ldots, N_{\rm 2b} ,
+
+where the matrix :math:`\boldsymbol A \in \mathbb{R}^{N_{\rm s} \times
+N_{\rm s}}` consists of eigenvectors of the eigenvalue problem
+
+.. math::
+
+    \boldsymbol C \boldsymbol a = \lambda \boldsymbol a
+
+with the entries of :math:`\boldsymbol C \in \mathbb{R}^{N_{\rm s} \times N_{\rm s}}` being given by
+
+.. math::
+
+    C_{ij}  = \frac{1}{N_{\rm s}} \int_{r_{\rm in}}^{r_{\rm cut}} \xi_i(x, \boldsymbol \eta) \xi_j(x, \boldsymbol \eta) dx, \quad 1 \le i, j \le N_{\rm s}
+
+Note that the eigenvalues :math:`\lambda_\ell, 1 \le \ell \le N_{\rm
+s}`, are ordered such that :math:`\lambda_1 \ge \lambda_2 \ge \ldots \ge
+\lambda_{N_{\rm s}}`, and that the matrix :math:`\boldsymbol A` is
+pe-computed and stored for any given :math:`\boldsymbol \eta`.  Owing to
+the rapid convergence of the KL expansion, only a small number of
+orthogonal basis functions is needed to obtain accurate
+approximation. The value of :math:`N_{\rm 2b}` corresponds to
+*twobody_number_radial_basis_functions*.
+
+The two-body proper orthogonal descriptors at each atom *i* are computed
+by summing the orthogonal basis functions over the neighbors of atom *i*
+and numerating on the atom types as follows
+
+.. math::
+
+    D^{(2)}_{im l(p, q) }(\boldsymbol \eta)  = \left\{
+    \begin{array}{ll}
+    \displaystyle \sum_{\{j | Z_j = q\}} U^{(2)}_m(r_{ij},  \boldsymbol \eta), & \mbox{if } Z_i = p \\
+    0, & \mbox{if } Z_i \neq p
+    \end{array}
+    \right.
+
+for :math:`1 \le i \le N, 1 \le m \le N_{\rm 2b}, 1 \le q, p \le N_{\rm
+e}`. Here :math:`l(p,q)` is a symmetric index mapping such that
+
+.. math::
+
+    l(p,q)  = \left\{
+    \begin{array}{ll}
+    q + (p-1) N_{\rm e} - p(p-1)/2, & \mbox{if } q \ge p \\
+    p + (q-1) N_{\rm e} - q(q-1)/2, & \mbox{if } q < p .
+    \end{array}
+    \right.
+
+The number of two-body descriptors per atom is thus :math:`N_{\rm 2b}
+N_{\rm e}(N_{\rm e}+1)/2`.
+
+It is important to note that the orthogonal basis functions do not
+depend on the atomic numbers :math:`Z_i` and :math:`Z_j`. Therefore, the
+cost of evaluating the basis functions and their derivatives with
+respect to :math:`r_{ij}` is independent of the number of elements
+:math:`N_{\rm e}`. Consequently, even though the two-body proper
+orthogonal descriptors depend on :math:`\boldsymbol Z`, their
+computational complexity is independent of :math:`N_{\rm e}`.
+
+In order to provide proper orthogonal descriptors for three-body
+interactions, we need to introduce a three-body parameterized
+potential. In particular, the three-body potential is defined as a
+product of radial and angular functions as follows
+
+.. math::
+
+    W^{(3)}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta, \boldsymbol \mu^{(3)})  =  \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}) \\
+    \psi(r_{ik}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ik}, r_{\rm min}, r_{\rm max}) \\
+    \cos (\sigma \theta_{ijk} + \zeta)
+
+where :math:`\sigma` is the periodic multiplicity, :math:`\zeta` is the
+equilibrium angle, :math:`\boldsymbol \mu^{(3)} = (\alpha, \beta,
+\gamma, \kappa, \sigma, \zeta)`. The three-body potential provides an
+angular fingerprint of the atomic environment through the bond angles
+:math:`\theta_{ijk}` formed with each pair of neighbors :math:`j` and
+:math:`k`.  Compared to the two-body potential, the three-body potential
+has two extra parameters :math:`(\sigma, \zeta)` associated with the
+angular component.
+
+Let :math:`\boldsymbol \varrho = (\alpha, \beta, \gamma, \kappa)`. We
+assume that we are given :math:`L_{\rm r}` parameter tuples
+:math:`\boldsymbol \varrho_\ell, 1 \le \ell \le L_{\rm r}`.  We
+introduce the following set of snapshots on :math:`(r_{\min},
+r_{\max})`:
+
+.. math::
+
+    \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ) =  \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \boldsymbol \varrho_\ell) f_{\rm c}(r_{ij}, r_{\rm min},  r_{\rm max}), \quad 1 \le \ell \le L_{\rm r} .
+
+We apply the Karhunen-Loeve (KL) expansion to this set of snapshots to
+obtain orthogonal basis functions as follows
+
+.. math::
+
+    U^{r}_m(r_{ij}, r_{\rm min}, r_{\rm max} ) = \sum_{\ell = 1}^{L_{\rm r}} A_{\ell m} \,  \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ), \qquad m = 1, \ldots, N_{\rm r} ,
+
+where the matrix :math:`\boldsymbol A \in \mathbb{R}^{L_{\rm r} \times L_{\rm r}}` consists
+of eigenvectors of the eigenvalue problem. For the parameterized angular function,
+we consider angular basis functions
+
+.. math::
+
+    U^{a}_n(\theta_{ijk}) = \cos ((n-1) \theta_{ijk}), \qquad  n = 1,\ldots, N_{\rm a},
+
+where :math:`N_{\rm a}` is the number of angular basis functions. The orthogonal
+basis functions for the parameterized potential are computed as follows
+
+.. math::
+
+    U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta) = U^{r}_m(r_{ij}, \boldsymbol \eta) U^{r}_m(r_{ik}, \boldsymbol \eta) U^{a}_n(\theta_{ijk}),
+
+for :math:`1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}`. The number of three-body
+orthogonal basis functions is equal to :math:`N_{\rm 3b} = N_{\rm r} N_{\rm a}` and
+independent of the number of elements. The value of :math:`N_{\rm r}` corresponds to
+*threebody_number_radial_basis_functions*, while that of :math:`N_{\rm a}` to
+*threebody_number_angular_basis_functions*.
+
+The three-body proper orthogonal descriptors at each atom *i*
+are obtained by summing over the neighbors *j* and *k* of atom *i* as
+
+.. math::
+
+    D^{(3)}_{imn \ell(p, q, s)}(\boldsymbol \eta)  = \left\{
+    \begin{array}{ll}
+    \displaystyle \sum_{\{j | Z_j = q\}} \sum_{\{k | Z_k = s\}} U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta), & \mbox{if } Z_i = p \\
+    0, & \mbox{if } Z_i \neq p
+    \end{array}
+    \right.
+
+for :math:`1 \le i \le N, 1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}, 1 \le q, p, s \le N_{\rm e}`,
+where
+
+.. math::
+
+    \ell(p,q,s)  = \left\{
+    \begin{array}{ll}
+    s + (q-1) N_{\rm e} - q(q-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2 , & \mbox{if } s \ge q \\
+    q + (s-1) N_{\rm e} - s(s-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2, & \mbox{if } s < q .
+    \end{array}
+    \right.
+
+The number of three-body descriptors per atom is thus :math:`N_{\rm 3b} N_{\rm e}^2(N_{\rm e}+1)/2`.
+While the number of three-body PODs is cubic function of the number of elements,
+the computational complexity of the three-body PODs is independent of the number of elements.
+
+Four-Body SNAP Descriptors
+""""""""""""""""""""""""""
+
+In addition to the proper orthogonal descriptors described above, we also employ
+the spectral neighbor analysis potential (SNAP) descriptors. SNAP uses bispectrum components
+to characterize the local neighborhood of each atom in a very general way. The mathematical definition
+of the bispectrum calculation and its derivatives w.r.t. atom positions is described in
+:doc:`compute snap <compute_sna_atom>`. In SNAP, the
+total energy is decomposed into a sum over atom energies. The energy of
+atom *i* is expressed as a weighted sum over bispectrum components.
+
+.. math::
+
+   E_i^{\rm SNAP} = \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}
+
+
+where the SNAP descriptors are related to the bispectrum components by
+
+.. math::
+
+    D^{(4)}_{ikp}  = \left\{
+    \begin{array}{ll}
+    \displaystyle B_{ik}, & \mbox{if } Z_i = p \\
+    0, & \mbox{if } Z_i \neq p
+    \end{array}
+    \right.
+
+Here :math:`B_{ik}` is the *k*\ -th bispectrum component of atom *i*. The number of
+bispectrum components :math:`N_{\rm 4b}` depends on the value of *fourbody_snap_twojmax* :math:`= 2 J_{\rm max}`
+and *fourbody_snap_chemflag*. If *fourbody_snap_chemflag* = 0
+then :math:`N_{\rm 4b} = (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
+If *fourbody_snap_chemflag* = 1 then :math:`N_{\rm 4b} = N_{\rm e}^3 (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
+The bispectrum calculation is described in more detail in :doc:`compute sna/atom <compute_sna_atom>`.
+
+Linear Proper Orthogonal Descriptor Potentials
+""""""""""""""""""""""""""""""""""""""""""""""
+
+The proper orthogonal descriptors and SNAP descriptors are used to define the atomic energies
+in the following expansion
+
+.. math::
+
+    E_{i}(\boldsymbol \eta) = \sum_{p=1}^{N_{\rm e}} c^{(1)}_p D^{(1)}_{ip} + \sum_{m=1}^{N_{\rm 2b}}  \sum_{l=1}^{N_{\rm e}(N_{\rm e}+1)/2} c^{(2)}_{ml} D^{(2)}_{iml}(\boldsymbol \eta) + \sum_{m=1}^{N_{\rm r}} \sum_{n=1}^{N_{\rm a}}  \sum_{\ell=1}^{N_{\rm e}^2(N_{\rm e}+1)/2} c^{(3)}_{mn\ell} D^{(3)}_{imn\ell}(\boldsymbol \eta) + \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}(\boldsymbol \eta),
+
+where :math:`D^{(1)}_{ip}, D^{(2)}_{iml}, D^{(3)}_{imn\ell}, D^{(4)}_{ikp}` are the  one-body, two-body, three-body, four-body descriptors,
+respectively, and :math:`c^{(1)}_p, c^{(2)}_{ml}, c^{(3)}_{mn\ell}, c^{(4)}_{kp}` are their respective expansion
+coefficients. In a more compact notation that implies summation over descriptor indices
+the atomic energies can be written as
+
+.. math::
+
+    E_i(\boldsymbol \eta) =  \sum_{m=1}^{N_{\rm e}} c^{(1)}_m D^{(1)}_{im} +  \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_k D^{(2)}_{im} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m D^{(3)}_{im} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m D^{(4)}_{im}
+
+where :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2`,
+:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2`, and
+:math:`N_{\rm d}^{(4)} = N_{\rm 4b} N_{\rm e}` are
+the number of two-body, three-body, and four-body descriptors, respectively.
+
+The potential energy is then obtained by summing local atomic energies :math:`E_i`
+for all atoms :math:`i` in the system
+
+.. math::
+
+    E(\boldsymbol \eta) = \sum_{i}^N E_{i}(\boldsymbol \eta)
+
+Because the descriptors are one-body, two-body, and three-body terms,
+the resulting POD potential is a three-body PES. We can express the potential
+energy as a linear combination of the global descriptors as follows
+
+.. math::
+
+    E(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m d^{(1)}_{m} +  \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m d^{(2)}_{m} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m d^{(3)}_{m} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m d^{(4)}_{m}
+
+where  the global descriptors are given by
+
+.. math::
+
+    d_{m}^{(1)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(1)}(\boldsymbol \eta), \quad d_{m}^{(2)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(2)}(\boldsymbol \eta), \quad d_{m}^{(3)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(3)}(\boldsymbol \eta), \quad d_{m}^{(4)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(4)}(\boldsymbol \eta)
+
+Hence, we obtain the atomic forces as
+
+.. math::
+
+    \boldsymbol F = -\nabla E(\boldsymbol \eta) = - \sum_{m=1}^{N_{\rm d}^{(2)}}  c^{(2)}_m  \nabla d_m^{(2)} - \sum_{m=1}^{N_{\rm d}^{(3)}}  c^{(3)}_m \nabla d_m^{(3)} - \sum_{m=1}^{N_{\rm d}^{(4)}}  c^{(4)}_m \nabla d_m^{(4)}
+
+where :math:`\nabla d_m^{(2)}`, :math:`\nabla d_m^{(3)}` and :math:`\nabla d_m^{(4)}` are derivatives of the two-body
+three-body, and four-body global descriptors with respect to atom positions, respectively.
+Note that since the first-body global descriptors are constant, their derivatives are zero.
+
+Quadratic Proper Orthogonal Descriptor Potentials
+"""""""""""""""""""""""""""""""""""""""""""""""""
+
+We recall two-body PODs :math:`D^{(2)}_{ik}, 1 \le k \le N_{\rm d}^{(2)}`,
+and three-body PODs :math:`D^{(3)}_{im}, 1 \le m \le N_{\rm d}^{(3)}`,
+with :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2` and
+:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2` being
+the number of descriptors per atom for the two-body PODs and three-body PODs,
+respectively. We employ them to define a new set of atomic descriptors as follows
+
+.. math::
+
+    D^{(2*3)}_{ikm} = \frac{1}{2N}\left( D^{(2)}_{ik} \sum_{j=1}^N D^{(3)}_{jm} + D^{(3)}_{im} \sum_{j=1}^N D^{(2)}_{jk}  \right)
+
+for :math:`1 \le i \le N, 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`.
+The new descriptors are four-body because they involve central atom :math:`i` together
+with three neighbors :math:`j, k` and :math:`l`. The total number of new  descriptors per atom is equal to
+
+.. math::
+
+    N_{\rm d}^{(2*3)} = N_{\rm d}^{(2)} * N_{\rm d}^{(3)} = N_{\rm 2b} N_{\rm 3b} N_{\rm e}^3 (N_{\rm e}+1)^2/4 .
+
+The new global descriptors are calculated as
+
+.. math::
+
+    d^{(2*3)}_{km} = \sum_{i=1}^N D^{(2*3)}_{ikm} = \left( \sum_{i=1}^N D^{(2)}_{ik} \right) \left( \sum_{i=1}^N D^{(3)}_{im} \right) = d^{(2)}_{k} d^{(3)}_m,
+
+for :math:`1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. Hence, the gradient
+of the new global descriptors with respect to atom positions is calculated as
+
+.. math::
+
+    \nabla d^{(2*3)}_{km} = d^{(3)}_m \nabla d^{(2)}_{k}  +  d^{(2)}_{k} \nabla d^{(3)}_m, \quad 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)} .
+
+The quadratic  POD potential is defined as a linear combination of the
+original and new global descriptors as follows
+
+.. math::
+
+    E^{(2*3)} = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d^{(2*3)}_{km} .
+
+It thus follows that
+
+.. math::
+
+    E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \left( \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)} \right) d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} \left( \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)} \right) d_m^{(3)}  ,
+
+which is simplified to
+
+.. math::
+
+    E^{(2*3)} =  0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b_k^{(2)} d_k^{(2)} +  0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}}   b_m^{(3)} d_m^{(3)}
+
+where
+
+.. math::
+
+    b_k^{(2)} & = \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)}, \quad k = 1,\ldots, N_{\rm 2d}^{(2*3)}, \\
+    b_m^{(3)} & = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)}, \quad m = 1,\ldots, N_{\rm 3d}^{(2*3)} .
+
+The quadratic POD potential results in the following atomic forces
+
+.. math::
+
+    \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km}  \nabla d^{(2*3)}_{km} .
+
+It can be shown that
+
+.. math::
+
+    \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}}   b^{(2)}_k \nabla d_k^{(2)} - \sum_{m=1}^{N_{\rm 3d}^{(2*3)}}  b^{(3)}_m  \nabla d_m^{(3)} .
+
+The calculation of the atomic forces for the quadratic POD  potential
+only requires the extra calculation of :math:`b_k^{(2)}` and :math:`b_m^{(3)}` which can be negligible.
+As a result, the quadratic  POD potential does not increase the computational complexity.
+
+
+Training
+""""""""
+
+POD potentials are trained using the least-squares regression against
+density functional theory (DFT) data.  Let :math:`J` be the number of
+training configurations, with :math:`N_j` being the number of atoms in
+the j-th configuration. Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and
+:math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` be the DFT energies and
+forces for :math:`J` configurations. Next, we calculate the global
+descriptors and their derivatives for all training configurations. Let
+:math:`d_{jm}, 1 \le m \le M`, be the global descriptors associated with
+the j-th configuration, where :math:`M` is the number of global
+descriptors. We then form a matrix :math:`\boldsymbol A \in
+\mathbb{R}^{J \times M}` with entries :math:`A_{jm} = d_{jm}/ N_j` for
+:math:`j=1,\ldots,J` and :math:`m=1,\ldots,M`.  Moreover, we form a
+matrix :math:`\boldsymbol B \in \mathbb{R}^{\mathcal{N} \times M}` by
+stacking the derivatives of the global descriptors for all training
+configurations from top to bottom, where :math:`\mathcal{N} =
+3\sum_{j=1}^{J} N_j`.
+
+The coefficient vector :math:`\boldsymbol c` of the POD potential is
+found by solving the following least-squares problem
+
+.. math::
+
+    {\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A(\boldsymbol \eta) \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B(\boldsymbol \eta) \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,
+
+where :math:`w_E` and :math:`w_F` are weights for the energy
+(*fitting_weight_energy*) and force (*fitting_weight_force*),
+respectively; and :math:`w_R` is the regularization parameter (*fitting_regularization_parameter*).  Here :math:`\bar{\boldsymbol E}^{\star} \in
+\mathbb{R}^{J}` is a vector of with entries :math:`\bar{E}^{\star}_j =
+E^{\star}_j/N_j` and :math:`\boldsymbol F^{\star}` is a vector of
+:math:`\mathcal{N}` entries obtained by stacking :math:`\{\boldsymbol
+F^{\star}_j\}_{j=1}^{J}` from top to bottom.
+
+The training procedure is the same for both the linear and quadratic POD
+potentials.  However, since the quadratic POD potential has a
+significantly larger number of the global descriptors, it is more
+expensive to train the linear POD potential. This is because the
+training of the quadratic POD potential still requires us to calculate
+and store the quadratic global descriptors and their
+gradient. Furthermore, the quadratic POD potential may require more
+training data in order to prevent over-fitting. In order to reduce the
+computational cost of fitting the quadratic POD potential and avoid
+over-fitting, we can use subsets of two-body and three-body PODs for
+constructing the new descriptors.
+
+
+Restrictions
+""""""""""""
+
+This command is part of the ML-POD package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style pod <pair_pod>`
+
+Default
+"""""""
+
+The keyword defaults are also given in the description of the input files.
+
+----------
+
+.. _Grepl20072:
+
+**(Grepl)** Grepl, Maday, Nguyen, and Patera, ESAIM: Mathematical Modelling and Numerical Analysis 41(3), 575-605, (2007).
+
+.. _Nguyen20222:
+
+**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).

doc/src/fix.rst

@@ -216,9 +216,9 @@ accelerated styles exist.
 * :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
 * :doc:`efield <fix_efield>` - impose electric field on system
 * :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
-* :doc:`electrode/conp <fix_electrode_conp>` - impose electric potential
+* :doc:`electrode/conp <fix_electrode>` - impose electric potential
-* :doc:`electrode/conq <fix_electrode_conp>` - impose total electric charge
+* :doc:`electrode/conq <fix_electrode>` - impose total electric charge
-* :doc:`electrode/thermo <fix_electrode_conp>` - apply thermo-potentiostat
+* :doc:`electrode/thermo <fix_electrode>` - apply thermo-potentiostat
 * :doc:`electron/stopping <fix_electron_stopping>` - electronic stopping power as a friction force
 * :doc:`electron/stopping/fit <fix_electron_stopping>` - electronic stopping power as a friction force
 * :doc:`enforce2d <fix_enforce2d>` - zero out *z*-dimension velocity and force

doc/src/fix_bond_react.rst

@@ -177,12 +177,12 @@ due to the internal dynamic grouping performed by fix bond/react.
    If the group-ID is an existing static group, react-group-IDs
    should also be specified as this static group or a subset.
 
-The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids <reset_mol_ids>`
+The *reset_mol_ids* keyword invokes the :doc:`reset_atoms mol
-command after a reaction occurs, to ensure that molecule IDs are
+<reset_atoms>` command after a reaction occurs, to ensure that
-consistent with the new bond topology. The group-ID used for
+molecule IDs are consistent with the new bond topology. The group-ID
-:doc:`reset_mol_ids <reset_mol_ids>` is the group-ID for this fix.
+used for :doc:`reset_atoms mol <reset_atoms>` is the group-ID for this
-Resetting molecule IDs is necessarily a global operation, so it can
+fix.  Resetting molecule IDs is necessarily a global operation, so it
-be slow for very large systems.
+can be slow for very large systems.
 
 The following comments pertain to each *react* argument (in other
 words, they can be customized for each reaction, or reaction step):

doc/src/fix_electrode.rst

@@ -0,0 +1,421 @@
+.. index:: fix electrode/conp
+.. index:: fix electrode/conq
+.. index:: fix electrode/thermo
+.. index:: fix electrode/conp/intel
+.. index:: fix electrode/conq/intel
+.. index:: fix electrode/thermo/intel
+
+fix electrode/conp command
+==========================
+
+Accelerator Variant: *electrode/conp/intel*
+
+fix electrode/conq command
+==========================
+
+Accelerator Variant: *electrode/conq/intel*
+
+fix electrode/thermo command
+============================
+
+Accelerator Variant: *electrode/thermo/intel*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID style args keyword value ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style = *electrode/conp* or *electrode/conq* or *electrode/thermo*
+* args = arguments used by a particular style
+
+  .. parsed-literal::
+
+       *electrode/conp* args = potential eta
+       *electrode/conq* args = charge eta
+       *electrode/thermo* args = potential eta *temp* values
+            potential = electrode potential
+            charge = electrode charge
+            eta = reciprocal width of electrode charge smearing
+            *temp* values = T_v tau_v rng_v
+                T_v = temperature of thermo-potentiostat
+                tau_v = time constant of thermo-potentiostat
+                rng_v = integer used to initialize random number generator
+
+* zero or more keyword/value pairs may be appended
+* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
+
+.. parsed-literal::
+
+    *algo* values = *mat_inv* or *mat_cg* tol or *cg* tol
+        specify the algorithm used to compute the electrode charges
+    *symm* value = *on* or *off*
+        turn on/off charge neutrality constraint for the electrodes
+    *couple* values = group-ID val
+        group-ID = group of atoms treated as additional electrode
+        val = electric potential or charge on this electrode
+    *etypes* value = *on* or *off*
+        turn on/off type-based optimized neighbor lists (electrode and electrolyte types may not overlap)
+    *ffield* value = *on* or *off*
+        turn on/off finite-field implementation
+    *write_mat* value = filename
+        filename = file to which to write elastance matrix
+    *write_inv* value = filename
+        filename = file to which to write inverted matrix
+    *read_mat* value = filename
+        filename = file from which to read elastance matrix
+    *read_inv* value = filename
+        filename = file from which to read inverted matrix
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on
+   fix fxconp electrodes electrode/conq 0.0 1.805 algo cg 1e-5
+   fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0
+
+Description
+"""""""""""
+
+The *electrode* fixes implement the constant potential method (CPM)
+(:ref:`Siepmann <Siepmann>`, :ref:`Reed <Reed3>`), and modern variants,
+to accurately model electrified, conductive electrodes. This is
+primarily useful for studying electrode-electrolyte interfaces,
+especially at high potential differences or ionicities, with non-planar
+electrodes such as nanostructures or nanopores, and to study dynamic
+phenomena such as charging or discharging time scales or conductivity or
+ionic diffusivities.
+
+Each *electrode* fix allows users to set additional electrostatic
+relationships between the specified groups which model useful
+electrostatic configurations:
+
+* *electrode/conp* sets potentials or potential differences between electrodes
+
+  *  (resulting in changing electrode total charges)
+
+* *electrode/conq* sets the total charge on each electrode
+
+  *  (resulting in changing electrode potentials)
+
+* *electrode/thermo* sets a thermopotentiostat
+  :ref:`(Deissenbeck)<Deissenbeck>` between two electrodes
+
+  * (resulting in changing charges and potentials with appropriate
+     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
+additional group.  While *electrode/thermo* only accepts two groups,
+*electrode/conp* and *electrode/conq* accept any number of groups, up to
+LAMMPS's internal restrictions (see Restrictions below). Electrode
+groups must not overlap, i.e.  the fix will issue an error if any
+particle is detected to belong to at least two electrode groups.
+
+CPM involves updating charges on groups of electrode particles, per time
+step, so that the system's total energy is minimized with respect to
+those charges.  From basic electrostatics, this is equivalent to making
+each group conductive, or imposing an equal electrostatic potential on
+every particle in the same group (hence the name CPM).  The charges are
+usually modelled as a Gaussian distribution to make the charge-charge
+interaction matrix invertible (:ref:`Gingrich <Gingrich>`).  The keyword
+*eta* specifies the distribution's width in units of inverse length.
+
+.. versionadded:: TBD
+
+Three algorithms are available to minimize the energy, varying in how
+matrices are pre-calculated before a run to provide computational
+speedup. These algorithms can be selected using the keyword *algo*:
+
+* *algo mat_inv* pre-calculates the capacitance matrix and obtains the
+  charge configuration in one matrix-vector calculation per time step
+
+* *algo mat_cg* pre-calculates the elastance matrix (inverse of
+  capacitance matrix) and obtains the charge configuration using a
+  conjugate gradient solver in multiple matrix-vector calculations per
+  time step
+
+* *algo cg* does not perform any pre-calculation and obtains the charge
+  configuration using a conjugate gradient solver and multiple
+  calculations of the electric potential per time step.
+
+For both *cg* methods, the command must specify the conjugate gradient
+tolerance. *fix electrode/thermo* currently only supports the *mat_inv*
+algorithm.
+
+The keyword *symm* can be set *on* (or *off*) to turn on (or turn off)
+the capacitance matrix constraint that sets total electrode charge to be
+zero.  This has slightly different effects for each *fix electrode*
+variant.  For *fix electrode/conp*, with *symm off*, the potentials
+specified are absolute potentials, but the charge configurations
+satisfying them may add up to an overall non-zero, varying charge for
+the electrodes (and thus the simulation box). With *symm on*, the total
+charge over all electrode groups is constrained to zero, and potential
+differences rather than absolute potentials are the physically relevant
+quantities.
+
+For *fix electrode/conq*, with *symm off*, overall neutrality is
+explicitly obeyed or violated by the user input (which is not
+checked!). With *symm on*, overall neutrality is ensured by ignoring the
+user-input charge for the last listed electrode (instead, its charge
+will always be minus the total sum of all other electrode charges). For
+*fix electrode/thermo*, overall neutrality is always automatically
+imposed for any setting of *symm*, but *symm on* allows finite-field
+mode (*ffield on*, described below) for faster simulations.
+
+For all three fixes, any potential (or charge for *conq*) can be
+specified as an equal-style variable prefixed with "v\_". For example,
+the following code will ramp the potential difference between electrodes
+from 0.0V to 2.0V over the course of the simulation:
+
+.. code-block:: LAMMPS
+
+   fix fxconp bot electrode/conp 0.0 1.805 couple top v_v symm on
+   variable v equal ramp(0.0, 2.0)
+
+Note that these fixes only parse their supplied variable name when
+starting a run, and so these fixes will accept equal-style variables
+defined *after* the fix definition, including variables dependent on the
+fix's own output. This is useful, for example, in the fix's internal
+finite-field commands (see below).  For an advanced example of this see
+the in.conq2 input file in the directory
+``examples/PACKAGES/electrode/graph-il``.
+
+This fix necessitates the use of a long range solver that calculates and
+provides the matrix of electrode-electrode interactions and a vector of
+electrode-electrolyte interactions.  The Kspace styles
+*ewald/electrode*, *pppm/electrode* and *pppm/electrode/intel* are
+created specifically for this task :ref:`(Ahrens-Iwers) <Ahrens-Iwers>`.
+
+For systems with non-periodic boundaries in one or two directions dipole
+corrections are available with the :doc:`kspace_modify <kspace_modify>`.
+For ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) <Hu>`
+can be used by setting "slab ew2d":
+
+.. code-block:: LAMMPS
+
+   kspace_modify slab <slab_factor>
+   kspace_modify wire <wire_factor>
+   kspace_modify slab ew2d
+
+Two implementations for the calculation of the elastance matrix are
+available with pppm and can be selected using the *amat onestep/twostep*
+keyword.  *onestep* is the default; *twostep* can be faster for large
+electrodes and a moderate mesh size but requires more memory.
+
+.. code-block:: LAMMPS
+
+   kspace_modify amat onestep/twostep
+
+For all versions of the fix, the keyword-value *ffield on* enables the
+finite-field mode (:ref:`Dufils <Dufils>`, :ref:`Tee <Tee>`), which uses
+an electric field across a periodic cell instead of non-periodic
+boundary conditions to impose a potential difference between the two
+electrodes bounding the cell. The fix (with name *fix-ID*) detects which
+of the two electrodes is "on top" (has the larger maximum *z*-coordinate
+among all particles).  Assuming the first electrode group is on top, it
+then issues the following commands internally:
+
+.. code-block:: LAMMPS
+
+   variable fix-ID_ffield_zfield equal (f_fix-ID[2]-f_fix-ID[1])/lz
+   efield fix-ID_efield all efield 0.0 0.0 v_fix-ID_ffield_zfield
+
+which implements the required electric field as the potential difference
+divided by cell length.  The internal commands use variable so that the
+electric field will correctly vary with changing potentials in the
+correct way (for example with equal-style potential difference or with
+*fix electrode/conq*).  This keyword requires two electrodes and will
+issue an error with any other number of electrodes. This keyword
+requires electroneutrality to be imposed (*symm on*) and will issue an
+error otherwise.
+
+.. versionchanged:: TBD
+
+For all versions of the fix, the keyword-value *etypes on* enables
+type-based optimized neighbor lists. With this feature enabled, LAMMPS
+provides the fix with an occasional neighbor list restricted to
+electrode-electrode interactions for calculating the electrode matrix,
+and a perpetual neighbor list restricted to electrode-electrolyte
+interactions for calculating the electrode potentials, using particle
+types to list only desired interactions, and typically resulting in
+5--10\% less computational time.  Without this feature the fix will
+simply use the active pair style's neighbor list.  This feature cannot
+be enabled if any electrode particle has the same type as any
+electrolyte particle (which would be unusual in a typical simulation)
+and the fix will issue an error in that case.
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This fix currently does not write any information to restart files.
+
+The *fix_modify tf* option enables the Thomas-Fermi metallicity model
+(:ref:`Scalfi <Scalfi>`) and allows parameters to be set for each atom type.
+
+.. code-block:: LAMMPS
+
+   fix_modify ID tf type length voronoi
+
+
+If this option is used parameters must be set for all atom types of the
+electrode.
+
+The *fix_modify timer* option turns on (off) additional timer outputs in the log
+file, for code developers to track optimization.
+
+.. code-block:: LAMMPS
+
+   fix_modify ID timer on/off
+
+----------
+
+These fixes compute a global (extensive) scalar, a global (intensive)
+vector, and a global array, which can be accessed by various
+:doc:`output commands <Howto_output>`.
+
+The global scalar outputs the energy added to the system by this fix,
+which is the negative of the total charge on each electrode multiplied
+by that electrode's potential.
+
+The global vector outputs the potential on each electrode (and thus has
+*N* entries if the fix manages *N* electrode groups), in :doc:`units
+<units>` of electric field multiplied by distance (thus volts for *real*
+and *metal* units).  The electrode groups' ordering follows the order in
+which they were input in the fix command using *couple*. The global
+vector output is useful for *fix electrode/conq* and *fix
+electrode/thermo*, where potential is dynamically updated based on
+electrolyte configuration instead of being directly set.
+
+The global array has *N* rows and *2N+1* columns, where the fix manages
+*N* electrode groups managed by the fix. For the *I*-th row of the
+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
+  of the *I*-th row of the electrode capacitance matrix (definition
+  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)
+
+The :math:`N \times N` electrode capacitance matrix, denoted :math:`\mathbf{C}`
+in the following equation, summarizes how the total charge induced on each
+electrode (:math:`\mathbf{Q}` as an *N*-vector) is related to the potential on
+each electrode, :math:`\mathbf{V}`, and the charge-at-0V :math:`\mathbf{Q}_{0V}`
+(which is influenced by the local electrolyte structure):
+
+.. math::
+
+   \mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V}
+
+The charge-at-0V, electrode capacitance and elastance matrices are internally
+used to calculate the potentials required to induce the specified total
+electrode charges in *fix electrode/conq* and *fix electrode/thermo*. With the
+*symm on* option, the electrode capacitance matrix would be singular, and thus
+its last row is replaced with *N* copies of its top-left entry
+(:math:`\mathbf{C}_{11}`) for invertibility.
+
+The global array output is mainly useful for quickly determining the 'vacuum
+capacitance' of the system (capacitance with only electrodes, no electrolyte),
+and can also be used for advanced simulations setting the potential as some
+function of the charge-at-0V (such as the ``in.conq2`` example mentioned above).
+
+Please cite :ref:`(Ahrens-Iwers2022) <Ahrens-Iwers2>` in any publication that
+uses this implementation.  Please cite also the publication on the combination
+of the CPM with PPPM if you use *pppm/electrode* :ref:`(Ahrens-Iwers)
+<Ahrens-Iwers>`.
+
+----------
+
+Restrictions
+""""""""""""
+
+For algorithms that use a matrix for the electrode-electrode
+interactions, positions of electrode particles have to be immobilized at
+all times.
+
+With *ffield off* (i.e. the default), the box geometry is expected to be
+*z*-non-periodic (i.e. *boundary p p f*), and this fix will issue an
+error if the box is *z*-periodic. With *ffield on*, the box geometry is
+expected to be *z*-periodic, and this fix will issue an error if the box
+is *z*-non-periodic.
+
+The parallelization for the fix works best if electrode atoms are evenly
+distributed across processors. For a system with two electrodes at the bottom
+and top of the cell this can be achieved with *processors * * 2*, or with the
+line
+
+.. code-block:: LAMMPS
+
+   if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
+
+which avoids an error if the script is run on an odd number of
+processors (such as on just one processor for testing).
+
+The fix creates an additional group named *[fix-ID]_group* which is the
+union of all electrode groups supplied to LAMMPS. This additional group
+counts towards LAMMPS's limitation on the total number of groups
+(currently 32), which may not allow scripts that use that many groups to
+run with this fix.
+
+The matrix-based algorithms (*algo mat_inv* and *algo mat_cg*) currently
+store an interaction matrix (either elastance or capacitance) of *N* by
+*N* doubles for each MPI process. This memory requirement may be
+prohibitive for large electrode groups.  The fix will issue a warning if
+it expects to use more than 0.5 GiB of memory.
+
+Default
+"""""""
+
+The default keyword-option settings are *algo mat_inv*, *symm off*,
+*etypes off* and *ffield off*.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+.. _Siepmann:
+
+**(Siepmann)** Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
+
+.. _Reed3:
+
+**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007).
+
+.. _Deissenbeck:
+
+**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
+
+.. _Gingrich:
+
+**(Gingrich)** Gingrich, `MSc thesis` <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).
+
+.. _Ahrens-Iwers:
+
+**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
+
+.. _Hu:
+
+**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014).
+
+.. _Dufils:
+
+**(Dufils)** Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019).
+
+.. _Tee:
+
+**(Tee)** Tee and Searles, J. Chem. Phys. 156, 184101 (2022).
+
+.. _Scalfi:
+
+**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
+
+.. _Ahrens-Iwers2:
+
+**(Ahrens-Iwers2022)** Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).

doc/src/fix_electrode_conp.rst

@@ -1,230 +0,0 @@
-.. index:: fix electrode/conp
-.. index:: fix electrode/conq
-.. index:: fix electrode/thermo
-.. index:: fix electrode/conp/intel
-.. index:: fix electrode/conq/intel
-.. index:: fix electrode/thermo/intel
-
-fix electrode/conp command
-==========================
-
-Accelerator Variant: *electrode/conp/intel*
-
-fix electrode/conq command
-==========================
-
-Accelerator Variant: *electrode/conq/intel*
-
-fix electrode/thermo command
-============================
-
-Accelerator Variant: *electrode/thermo/intel*
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   fix ID group-ID style args keyword value ...
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* style = *electrode/conp* or *electrode/conq* or *electrode/thermo*
-* args = arguments used by a particular style
-
-  .. parsed-literal::
-
-       *electrode/conp* args = potential eta
-       *electrode/conq* args = charge eta
-       *electrode/thermo* args = potential eta *temp* values
-            potential = electrode potential
-            charge = electrode charge
-            eta = reciprocal width of electrode charge smearing
-            *temp* values = T_v tau_v rng_v
-                T_v = temperature of thermo-potentiostat
-                tau_v = time constant of thermo-potentiostat
-                rng_v = integer used to initialize random number generator
-
-* zero or more keyword/value pairs may be appended
-* keyword = *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
-
-.. parsed-literal::
-
-    *symm* value = *on* or *off*
-        turn on/off charge neutrality constraint for the electrodes
-    *couple* values = group-ID val
-        group-ID = group of atoms treated as additional electrode
-        val = electric potential or charge on this electrode
-    *etypes* values = type
-        type = atom type (can be a range) exclusive to the electrode for optimized neighbor lists
-    *ffield* value = *on* or *off*
-        turn on/off finite-field implementation
-    *write_mat* value = filename
-        filename = file to which to write elastance matrix
-    *write_inv* value = filename
-        filename = file to which to write inverted matrix
-    *read_mat* value = filename
-        filename = file from which to read elastance matrix
-    *read_inv* value = filename
-        filename = file from which to read inverted matrix
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on
-   fix fxconp electrodes electrode/conq 0.0 1.805
-   fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0
-
-Description
-"""""""""""
-
-fix electrode/conp mode implements a constant potential method (CPM)
-(:ref:`Siepmann <Siepmann>`, :ref:`Reed <Reed3>`). Charges of groups specified
-via group-ID and optionally with the `couple` keyword are adapted to meet their respective
-potential at every time step.  An arbitrary number of electrodes can be set but
-the respective groups may not overlap. Electrode charges have a Gaussian charge
-distribution with reciprocal width eta. The energy minimization is achieved via
-matrix inversion :ref:`(Wang) <Wang5>`.
-
-fix electrode/conq enforces a total charge specified in the input on each electrode. The energy is
-minimized w.r.t. the charge distribution within the electrode.
-
-fix electrode/thermo implements a thermo-potentiostat :ref:`(Deissenbeck)
-<Deissenbeck>`. Temperature and time constant of the thermo-potentiostat need
-to be specified using the temp keyword. Currently, only two electrodes are possible with
-this style.
-
-This fix necessitates the use of a long range solver that calculates and provides the matrix
-of electrode-electrode interactions and a vector of electrode-electrolyte
-interactions.  The Kspace styles *ewald/electrode*, *pppm/electrode* and
-*pppm/electrode/intel* are created specifically for this task
-:ref:`(Ahrens-Iwers) <Ahrens-Iwers>`.
-
-For systems with non-periodic boundaries in one or two directions dipole
-corrections are available with the :doc:`kspace_modify <kspace_modify>`.  For
-ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) <Hu>` can be used
-by setting "slab ew2d":
-
-.. code-block:: LAMMPS
-
-   kspace_modify slab <slab_factor>
-   kspace_modify wire <wire_factor>
-   kspace_modify slab ew2d
-
-Two implementations for the calculation of the elastance matrix are available
-with pppm and can be selected using the *amat onestep/twostep* keyword.
-*onestep* is the default; *twostep* can be faster for large electrodes and a
-moderate mesh size but requires more memory.
-
-.. code-block:: LAMMPS
-
-   kspace_modify amat onestep/twostep
-
-
-The *fix_modify tf* option enables the Thomas-Fermi metallicity model
-(:ref:`Scalfi <Scalfi>`) and allows parameters to be set for each atom type.
-
-.. code-block:: LAMMPS
-
-   fix_modify ID tf type length voronoi
-
-
-If this option is used parameters must be set for all atom types of the electrode.
-
-The *fix_modify timer* option turns on (off) additional timer outputs in the log
-file, for code developers to track optimization.
-
-.. code-block:: LAMMPS
-
-   fix_modify ID timer on/off
-
-The *fix_modify set* options allow calculated quantities to be accessed via
-internal variables. Currently four types of quantities can be accessed:
-
-.. code-block:: LAMMPS
-
-   fix-modify ID set v group-ID variablename
-   fix-modify ID set qsb group-ID variablename
-   fix-modify ID set mc group-ID1 group-ID2 variablename
-   fix-modify ID set me group-ID1 group-ID2 variablename
-
-One use case is to output the potential that is internally calculated and
-applied to each electrode group by *fix electrode/conq* or *fix electrode/thermo*.
-For that case the *v* option makes *fix electrode* update the variable
-*variablename* with the potential applied to group *group-ID*, where *group-ID*
-must be a group whose charges are updated by *fix electrode* and *variablename*
-must be an internal-style variable:
-
-.. code-block:: LAMMPS
-
-   fix conq bot electrode/conq -1.0 1.979 couple top 1.0
-   variable vbot internal 0.0
-   fix_modify conq set v bot vbot
-
-The *qsb* option similarly outputs the total updated charge of the group if its
-potential were 0.0V. The *mc* option requires two *group-IDs*, and outputs the
-entry \{*group-ID1*, *group-ID2*\} of the (symmetric) *macro-capacitance* matrix
-(MC) which relates the electrodes' applied potentials (V), total charges (Q), and
-total charges at 0.0 V (Qsb):
-
-.. math::
-
-   \mathbf{Q} = \mathbf{Q}_{SB} + \mathbf{MC} \cdot \mathbf{V}
-
-Lastly, the *me* option also requires two *group-IDs* and outputs the entry
-\{*group-ID1*, *group-ID2*\} of the *macro-elastance* matrix, which is the
-inverse of the macro-capacitance matrix. (As the names denote, the
-macro-capacitance matrix gives electrode charges from potentials, and the
-macro-elastance matrix gives electrode potentials from charges).
-
-.. warning::
-
-   Positions of electrode particles have to be immobilized at all times.
-
-The parallelization for the fix works best if electrode atoms are evenly
-distributed across processors. For a system with two electrodes at the bottom
-and top of the cell this can be achieved with *processors * * 2*, or with the
-line
-
-.. code-block:: LAMMPS
-
-   if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
-
-which avoids an error if the script is run on an odd number of processors (such
-as on just one processor for testing).
-
-----------
-
-.. include:: accel_styles.rst
-
-----------
-
-.. _Siepmann:
-
-**(Siepmann)** Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
-
-.. _Reed3:
-
-**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007).
-
-.. _Wang5:
-
-**(Wang)** Wang *et al.*, J. Chem. Phys. 141, 184102 (2014).
-
-.. _Deissenbeck:
-
-**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
-
-.. _Ahrens-Iwers:
-
-**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
-
-.. _Hu:
-
-**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014).
-
-.. _Scalfi:
-
-**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
-

doc/src/kspace_style.rst

@@ -283,7 +283,7 @@ parameters and how to choose them is described in
 ----------
 
 The *electrode* styles add methods that are required for the constant potential
-method implemented in :doc:`fix electrode/* <fix_electrode_conp>`.  The styles
+method implemented in :doc:`fix electrode/* <fix_electrode>`.  The styles
 *ewald/electrode*, *pppm/electrode* and *pppm/electrode/intel* are available.
 These styles do not support the `kspace_modify slab nozforce` command.
 

doc/src/pair_pod.rst

@@ -0,0 +1,97 @@
+.. index:: pair_style pod
+
+pair_style pod command
+========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style pod
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style pod
+   pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Pair style *pod* defines the proper orthogonal descriptor (POD)
+potential :ref:`(Nguyen) <Nguyen20221>`.  The mathematical definition of
+the POD potential is described from :doc:`fitpod <fitpod_command>`, which is
+used to fit the POD potential to *ab initio* energy and force data.
+
+Only a single pair_coeff command is used with the *pod* style which
+specifies a POD parameter file followed by a coefficient file.
+
+The coefficient file (``Ta_coefficients.pod``) contains coefficients for the
+POD potential. The top of the coefficient file can contain any number of
+blank and comment lines (start with #), but follows a strict format
+after that. The first non-blank non-comment line must contain:
+
+* POD_coefficients: *ncoeff*
+
+This is followed by *ncoeff* coefficients, one per line. The coefficient
+file is generated after training the POD potential using :doc:`fitpod
+<fitpod_command>`.
+
+The POD parameter file (``Ta_param.pod``) can contain blank and comment lines
+(start with #) anywhere. Each non-blank non-comment line must contain
+one keyword/value pair. See :doc:`fitpod <fitpod_command>` for the description
+of all the keywords that can be assigned in the parameter file.
+
+As an example, if a LAMMPS indium phosphide simulation has 4 atoms
+types, with the first two being indium and the third and fourth being
+phophorous, the pair_coeff command would look like this:
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * pod InP_param.pod InP_coefficients.pod In In P P
+
+The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
+The two filenames are for the parameter and coefficient files, respectively.
+The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
+POD 'In' element. The two trailing 'P' arguments map LAMMPS atom types
+3 and 4 to the POD 'P' element.
+
+If a POD mapping value is specified as NULL, the mapping is not
+performed.  This can be used when a *pod* potential is used as part of
+the *hybrid* pair style.  The NULL values are placeholders for atom
+types that will be used with other potentials.
+
+Examples about training and using POD potentials are found in the
+directory lammps/examples/PACKAGES/pod.
+
+----------
+
+Restrictions
+""""""""""""
+
+This style is part of the ML-POD package.  It is only enabled if LAMMPS
+was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style does not compute per-atom energies and per-atom stresses.
+
+Related commands
+""""""""""""""""
+
+:doc:`fitpod <fitpod_command>`,
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Nguyen20221:
+
+**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).

doc/src/pair_style.rst

@@ -314,6 +314,7 @@ accelerated styles exist.
 * :doc:`oxrna2/xstk <pair_oxrna2>` -
 * :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
 * :doc:`pace/extrapolation <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades
+* :doc:`pod <pair_pod>` - Proper orthogonal decomposition (POD) machine-learning potential
 * :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
 * :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
 * :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential

doc/src/pair_sw.rst

@@ -176,9 +176,13 @@ are placeholders for atom types that will be used with other potentials.
 
 .. note::
 
-   When the *threebody off* keyword is used, multiple pair_coeff commands may
+   When the *threebody off* keyword is used, multiple pair_coeff
-   be used to specific the pairs of atoms which don't require three-body term.
+   commands may be used to specific the pairs of atoms which don't
-   In these cases, the first 2 arguments are not required to be \* \*.
+   require three-body term.  In these cases, the first 2 arguments are
+   not required to be \* \*, the potential parameter file is only read
+   by the first :doc:`pair_coeff command <pair_coeff>` and the element
+   to atom type mappings must be consistent across all *pair_coeff*
+   statements.  If not LAMMPS will abort with an error.
 
 Stillinger-Weber files in the *potentials* directory of the LAMMPS
 distribution have a ".sw" suffix.  Lines that are not blank or

doc/src/reset_atom_ids.rst

@@ -1,94 +0,0 @@
-.. index:: reset_atom_ids
-
-reset_atom_ids command
-======================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   reset_atom_ids keyword values ...
-
-   * zero or more keyword/value pairs may be appended
-   * keyword = *sort*
-
-.. parsed-literal::
-
-   *sort* value = *yes* or *no*
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   reset_atom_ids
-   reset_atom_ids sort yes
-
-Description
-"""""""""""
-
-Reset atom IDs for the system, including all the global IDs stored
-for bond, angle, dihedral, improper topology data.  This will
-create a set of IDs that are numbered contiguously from 1 to N
-for a N atoms system.
-
-This can be useful to do after performing a "delete_atoms" command for
-a molecular system.  The delete_atoms compress yes option will not
-perform this operation due to the existence of bond topology.  It can
-also be useful to do after any simulation which has lost atoms,
-e.g. due to atoms moving outside a simulation box with fixed
-boundaries (see the "boundary command"), or due to evaporation (see
-the "fix evaporate" command).
-
-If the *sort* keyword is used with a setting of *yes*, then the
-assignment of new atom IDs will be the same no matter how many
-processors LAMMPS is running on.  This is done by first doing a
-spatial sort of all the atoms into bins and sorting them within each
-bin.  Because the set of bins is independent of the number of
-processors, this enables a consistent assignment of new IDs to each
-atom.
-
-This can be useful to do after using the "create_atoms" command and/or
-"replicate" command.  In general those commands do not guarantee
-assignment of the same atom ID to the same physical atom when LAMMPS
-is run on different numbers of processors.  Enforcing consistent IDs
-can be useful for debugging or comparing output from two different
-runs.
-
-Note that the spatial sort requires communication of atom IDs and
-coordinates between processors in an all-to-all manner.  This is done
-efficiently in LAMMPS, but it is more expensive than how atom IDs are
-reset without sorting.
-
-Note that whether sorting or not, the resetting of IDs is not a
-compression, where gaps in atom IDs are removed by decrementing atom
-IDs that are larger.  Instead the IDs for all atoms are erased, and
-new IDs are assigned so that the atoms owned by an individual
-processor have consecutive IDs, as the :doc:`create_atoms
-<create_atoms>` command explains.
-
-.. note::
-
-   If this command is used before a :doc:`pair style <pair_style>` is
-   defined, an error about bond topology atom IDs not being found may
-   result.  This is because the cutoff distance for ghost atom
-   communication was not sufficient to find atoms in bonds, angles, etc
-   that are owned by other processors.  The :doc:`comm_modify cutoff <comm_modify>` command can be used to correct this issue.
-   Or you can define a pair style before using this command.  If you do
-   the former, you should unset the comm_modify cutoff after using
-   reset_atom_ids so that subsequent communication is not inefficient.
-
-Restrictions
-""""""""""""
-none
-
-Related commands
-""""""""""""""""
-
-:doc:`delete_atoms <delete_atoms>`
-
-Default
-"""""""
-
-By default, *sort* is no.

doc/src/reset_atoms.rst

@@ -0,0 +1,283 @@
+.. index:: reset_atoms
+
+reset_atoms command
+===================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   reset_atoms property arguments ...
+
+* property = *id* or *image* or *mol*
+* additional arguments depend on the property
+
+  .. code-block:: LAMMPS
+
+     reset_atoms id keyword value ...
+
+  * zero or more keyword/value pairs can be appended
+  * keyword = *sort*
+
+    .. parsed-literal::
+
+       *sort* value = *yes* or *no*
+
+  .. code-block:: LAMMPS
+
+     reset_atoms image group-ID
+
+  * group-ID = ID of group of atoms whose image flags will be reset
+
+  .. code-block:: LAMMPS
+
+     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
+  * keyword = *compress* or *offset* or *single*
+
+    .. parsed-literal::
+
+       *compress* value = *yes* or *no*
+       *offset* value = *Noffset* >= -1
+       *single* value = *yes* or *no* to treat single atoms (no bonds) as molecules
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   reset_atoms id
+   reset_atoms id sort yes
+   reset_atoms image all
+   reset_atoms image mobile
+   reset_atoms mol all
+   reset_atoms mol all offset 10 single yes
+   reset_atoms mol solvent compress yes offset 100
+   reset_atoms mol solvent compress no
+
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+The *reset_atoms* command resets the values of a specified atom
+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
+has undergone significant modifications like adding or removing 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
+new values, but it treats each atom independently.
+
+The *property* setting can be *id* or *image* or *mol*.  For *id*, the
+IDs of all the atoms are reset to contiguous values.  For *image*, the
+image flags of atoms in the specified *group-ID* are reset so that at
+least one atom in each molecule is in the simulation box (image flag =
+0).  For *mol*, the molecule IDs of all atoms are reset to contiguous
+values.
+
+More details on these operations and their arguments or optional
+keyword/value settings are given below.
+
+----------
+
+*Property id*
+
+Reset atom IDs for the entire system, including all the global IDs
+stored for bond, angle, dihedral, improper topology data.  This will
+create a set of IDs that are numbered contiguously from 1 to N for a N
+atoms system.
+
+This can be useful to do after performing a "delete_atoms" command for
+a molecular system.  The delete_atoms compress yes option will not
+perform this operation due to the existence of bond topology.  It can
+also be useful to do after any simulation which has lost atoms,
+e.g. due to atoms moving outside a simulation box with fixed
+boundaries (see the "boundary command"), or due to evaporation (see
+the "fix evaporate" command).
+
+If the *sort* keyword is used with a setting of *yes*, then the
+assignment of new atom IDs will be the same no matter how many
+processors LAMMPS is running on.  This is done by first doing a
+spatial sort of all the atoms into bins and sorting them within each
+bin.  Because the set of bins is independent of the number of
+processors, this enables a consistent assignment of new IDs to each
+atom.
+
+This can be useful to do after using the "create_atoms" command and/or
+"replicate" command.  In general those commands do not guarantee
+assignment of the same atom ID to the same physical atom when LAMMPS
+is run on different numbers of processors.  Enforcing consistent IDs
+can be useful for debugging or comparing output from two different
+runs.
+
+Note that the spatial sort requires communication of atom IDs and
+coordinates between processors in an all-to-all manner.  This is done
+efficiently in LAMMPS, but it is more expensive than how atom IDs are
+reset without sorting.
+
+Note that whether sorting or not, the resetting of IDs is not a
+compression, where gaps in atom IDs are removed by decrementing atom
+IDs that are larger.  Instead the IDs for all atoms are erased, and
+new IDs are assigned so that the atoms owned by an individual
+processor have consecutive IDs, as the :doc:`create_atoms
+<create_atoms>` command explains.
+
+.. note::
+
+   If this command is used before a :doc:`pair style <pair_style>` is
+   defined, an error about bond topology atom IDs not being found may
+   result.  This is because the cutoff distance for ghost atom
+   communication was not sufficient to find atoms in bonds, angles, etc
+   that are owned by other processors.  The :doc:`comm_modify cutoff
+   <comm_modify>` command can be used to correct this issue.  Or you can
+   define a pair style before using this command.  If you do the former,
+   you should unset the *comm_modify cutoff* after using *reset
+   atoms id* so that subsequent communication is not inefficient.
+
+----------
+
+*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
+that if the molecule straddles a periodic simulation box boundary, the
+images flags of all atoms in the molecule will be consistent.  This
+avoids inconsistent image flags that could result from resetting all
+image flags to zero with the :doc:`set <set>` command.
+
+.. note::
+
+   If the system has no bonds, there is no reason to use this command,
+   since image flags for different atoms do not need to be
+   consistent.  Use the :doc:`set <set>` command with its *image*
+   keyword instead.
+
+Only image flags for atoms in the specified *group-ID* are reset; all
+others remain unchanged.  No check is made for whether the group
+covers complete molecule fragments and thus whether the command will
+result in inconsistent image flags.
+
+Molecular fragments are identified by the algorithm used by the
+:doc:`compute fragment/atom <compute_cluster_atom>` command.  For each
+fragment the average of the largest and the smallest image flag in
+each direction across all atoms in the fragment is computed and
+subtracted from the current image flag in the same direction.
+
+This can be a useful operation to perform after running longer
+equilibration runs of mobile systems where molecules would pass
+through the system multiple times and thus produce non-zero image
+flags.
+
+.. note::
+
+   Same as explained for the :doc:`compute fragment/atom
+   <compute_cluster_atom>` command, molecules are identified using the
+   current bond topology.  This will **not** account for bonds broken by
+   the :doc:`bond_style quartic <bond_quartic>` command, because this
+   bond style does not perform a full update of the bond topology data
+   structures within LAMMPS.  In that case, using the :doc:`delete_bonds
+   all bond 0 remove <delete_bonds>` will permanently delete such
+   broken bonds and should thus be used first.
+
+----------
+
+*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
+IDs for atoms in the group.  Only molecule IDs for atoms in the
+specified *group-ID* are reset; molecule IDs for atoms not in the
+group are not changed.
+
+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>`
+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
+atoms within molecules, one (physical) molecule may become two or more
+(logical) molecules.  For example if the group excludes atoms in the
+middle of a linear chain, then each end of the chain is considered an
+independent molecule and will be assigned a different molecule ID.
+
+This can be a useful operation to perform after running reactive
+molecular dynamics run with :doc:`fix bond/react <fix_bond_react>`,
+:doc:`fix bond/create <fix_bond_create>`, or :doc:`fix bond/break
+<fix_bond_break>`, all of which can change molecule topologies. It can
+also be useful after molecules have been deleted with the
+:doc:`delete_atoms <delete_atoms>` command or after a simulation which
+has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>`
+command.
+
+The *compress* keyword determines how new molecule IDs are computed.  If
+the setting is *yes* (the default) and there are N molecules in the
+group, the new molecule IDs will be a set of N contiguous values.  See
+the *offset* keyword for details on selecting the range of these values.
+If the setting is *no*, the molecule ID of every atom in the molecule
+will be set to the smallest atom ID of any atom in the molecule.
+
+The *single* keyword determines whether single atoms (not bonded to
+another atom) are treated as one-atom molecules or not, based on the
+*yes* or *no* setting.  If the setting is *no* (the default), their
+molecule IDs are set to 0.  This setting can be important if the new
+molecule IDs will be used as input to other commands such as
+:doc:`compute chunk/atom molecule <compute_chunk_atom>` or :doc:`fix
+rigid molecule <fix_rigid>`.
+
+The *offset* keyword is only used if the *compress* setting is *yes*.
+Its default value is *Noffset* = -1.  In that case, if the specified
+group is *all*, then the new compressed molecule IDs will range from 1
+to N.  If the specified group is not *all* and the largest molecule ID
+of atoms outside that group is M, then the new compressed molecule IDs will
+range from M+1 to M+N, to avoid collision with existing molecule
+IDs.  If an *Noffset* >= 0 is specified, then the new compressed
+molecule IDs will range from *Noffset*\ +1 to *Noffset*\ +N.  If the group
+is not *all* there may be collisions with the molecule IDs of other atoms.
+
+.. note::
+
+   Same as explained for the :doc:`compute fragment/atom
+   <compute_cluster_atom>` command, molecules are identified using the
+   current bond topology.  This will **not** account for bonds broken by
+   the :doc:`bond_style quartic <bond_quartic>` command, because this
+   bond style does not perform a full update of the bond topology data
+   structures within LAMMPS.  In that case, using the :doc:`delete_bonds
+   all bond 0 remove <delete_bonds>` will permanently delete such broken
+   bonds and should thus be used first.
+
+
+Restrictions
+""""""""""""
+
+The *image* property can only be used when the atom style supports bonds.
+
+Related commands
+""""""""""""""""
+
+: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:`fix evaporate <fix_evaporate>`,
+:doc:`delete_atoms <delete_atoms>`,
+:doc:`delete_bonds <delete_bonds>`
+
+Defaults
+""""""""
+
+For property *id*, the default keyword setting is sort = no.
+
+For property *mol*, the default keyword settings are compress = yes,
+single = no, and offset = -1.

doc/src/reset_mol_ids.rst

@@ -1,116 +0,0 @@
-.. index:: reset_mol_ids
-
-reset_mol_ids command
-=====================
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   reset_mol_ids group-ID keyword value ...
-
-* group-ID = ID of group of atoms whose molecule IDs will be reset
-* zero or more keyword/value pairs may be appended
-* keyword = *compress* or *offset* or *single*
-
-  .. parsed-literal::
-
-       *compress* value = *yes* or *no*
-       *offset* value = *Noffset* >= -1
-       *single* value = *yes* or *no* to treat single atoms (no bonds) as molecules
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   reset_mol_ids all
-   reset_mol_ids all offset 10 single yes
-   reset_mol_ids solvent compress yes offset 100
-   reset_mol_ids solvent compress no
-
-Description
-"""""""""""
-
-Reset molecule IDs for a group of atoms based on current bond
-connectivity.  This will typically create a new set of molecule IDs
-for atoms in the group.  Only molecule IDs for atoms in the specified
-group are reset; molecule IDs for atoms not in the group are not
-changed.
-
-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>`
-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
-atoms within molecules, one (physical) molecule may become two or more
-(logical) molecules.  For example if the group excludes atoms in the
-middle of a linear chain, then each end of the chain is considered an
-independent molecule and will be assigned a different molecule ID.
-
-This can be a useful operation to perform after running reactive
-molecular dynamics run with :doc:`fix bond/react <fix_bond_react>`,
-:doc:`fix bond/create <fix_bond_create>`, or :doc:`fix bond/break
-<fix_bond_break>`, all of which can change molecule topologies. It can
-also be useful after molecules have been deleted with the
-:doc:`delete_atoms <delete_atoms>` command or after a simulation which
-has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>`
-command.
-
-The *compress* keyword determines how new molecule IDs are computed.  If
-the setting is *yes* (the default) and there are N molecules in the
-group, the new molecule IDs will be a set of N contiguous values.  See
-the *offset* keyword for details on selecting the range of these values.
-If the setting is *no*, the molecule ID of every atom in the molecule
-will be set to the smallest atom ID of any atom in the molecule.
-
-The *single* keyword determines whether single atoms (not bonded to
-another atom) are treated as one-atom molecules or not, based on the
-*yes* or *no* setting.  If the setting is *no* (the default), their
-molecule IDs are set to 0.  This setting can be important if the new
-molecule IDs will be used as input to other commands such as
-:doc:`compute chunk/atom molecule <compute_chunk_atom>` or :doc:`fix
-rigid molecule <fix_rigid>`.
-
-The *offset* keyword is only used if the *compress* setting is *yes*.
-Its default value is *Noffset* = -1.  In that case, if the specified
-group is *all*, then the new compressed molecule IDs will range from 1
-to N.  If the specified group is not *all* and the largest molecule ID
-of atoms outside that group is M, then the new compressed molecule IDs will
-range from M+1 to M+N, to avoid collision with existing molecule
-IDs.  If an *Noffset* >= 0 is specified, then the new compressed
-molecule IDs will range from *Noffset*\ +1 to *Noffset*\ +N.  If the group
-is not *all* there may be collisions with the molecule IDs of other atoms.
-
-.. note::
-
-   The same as explained for the :doc:`compute fragment/atom
-   <compute_cluster_atom>` command, molecules are identified using the
-   current bond topology.  This will not account for bonds broken by
-   the :doc:`bond_style quartic <bond_quartic>` command because it
-   does not perform a full update of the bond topology data structures
-   within LAMMPS.
-
-Restrictions
-""""""""""""
-none
-
-Related commands
-""""""""""""""""
-
-:doc:`reset_atom_ids <reset_atom_ids>`, :doc:`fix bond/react <fix_bond_react>`,
-:doc:`fix bond/create <fix_bond_create>`,
-:doc:`fix bond/break <fix_bond_break>`,
-:doc:`fix evaporate <fix_evaporate>`,
-:doc:`delete_atoms <delete_atoms>`,
-:doc:`compute fragment/atom <compute_cluster_atom>`
-
-Default
-"""""""
-
-The default keyword settings are compress = yes, single = no, and
-offset = -1.

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -1,25 +1,33 @@
 from pygments.lexer import RegexLexer, words, include, default
 from pygments.token import *
 
-LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
+LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify",
-"balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box",
+                   "atom_style", "balance", "bond_coeff", "bond_style",
-"clear", "comm_modify", "comm_style",
+                   "bond_write", "boundary", "clear", "comm_modify",
-"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms",
+                   "comm_style", "compute_modify", "create_atoms",
-"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
+                   "create_bonds", "create_box", "delete_atoms",
-"displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else",
+                   "delete_bonds", "dielectric", "dihedral_coeff",
-"fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
+                   "dihedral_style", "dimension", "displace_atoms",
-"improper_style", "include", "info", "jump", "kim",
+                   "dump_modify", "dynamical_matrix", "echo", "elif",
-"kspace_modify", "kspace_style", "label", "labelmap", "lattice", "log",
+                   "else", "fix_modify", "group2ndx", "hyper", "if",
-"mass", "mdi", "message", "minimize", "min_modify", "min_style", "molecule",
+                   "improper_coeff", "improper_style", "include",
-"ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next",
+                   "info", "jump", "kim", "kspace_modify",
-"package", "pair_coeff", "pair_modify", "pair_style", "pair_write",
+                   "kspace_style", "label", "labelmap", "lattice",
-"partition", "prd", "print", "processors", "python", "quit", "read_data",
+                   "log", "mass", "mdi", "message", "minimize",
-"read_dump", "read_restart", "replicate", "rerun", "reset_ids",
+                   "min_modify", "min_style", "molecule", "ndx2group",
-"reset_timestep", "restart", "run", "run_style", "server", "set", "shell",
+                   "neb", "neb/spin", "neighbor", "neigh_modify",
-"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt", "then",
+                   "newton", "next", "package", "pair_coeff",
-"thermo", "thermo_modify", "thermo_style", "third_order", "timer", "timestep",
+                   "pair_modify", "pair_style", "pair_write",
-"units", "velocity", "write_coeff",
+                   "partition", "plugin", "prd", "print", "processors",
-"write_data", "write_restart")
+                   "python", "quit", "read_data", "read_dump",
+                   "read_restart", "replicate", "rerun", "reset_atoms",
+                   "reset_timestep", "restart", "run", "run_style",
+                   "server", "set", "shell", "special_bonds", "suffix",
+                   "tad", "temper", "temper/grem", "temper/npt", "then",
+                   "thermo", "thermo_modify", "thermo_style",
+                   "third_order", "timer", "timestep", "units",
+                   "velocity", "write_coeff", "write_data",
+                   "write_restart")
 
 #fix ID group-ID style args
 #compute ID group-ID style args

doc/utils/sphinx-config/false_positives.txt

@@ -228,6 +228,7 @@ Bartels
 Bartelt
 barycenter
 barye
+basename
 Bashford
 bashrc
 Baskes
@@ -256,6 +257,7 @@ berlin
 Berne
 Bertotti
 Bessarab
+bessel
 Beutler
 Bext
 Bfrac
@@ -447,6 +449,7 @@ checkbox
 checkmark
 checkqeq
 checksum
+chemflag
 chemistries
 Chemnitz
 Cheng
@@ -608,6 +611,7 @@ curv
 Cusentino
 customIDs
 cutbond
+cutghost
 cuthi
 cutinner
 cutlo
@@ -738,6 +742,7 @@ diel
 Dietz
 differentiable
 diffusively
+diffusivities
 diffusivity
 dihedral
 dihedrals
@@ -749,6 +754,7 @@ dimensionality
 dimensioned
 dimgray
 dipolar
+dipoleflag
 dir
 Direc
 dirname
@@ -757,6 +763,7 @@ discretization
 discretized
 discretizing
 disp
+dispersionflag
 dissipative
 Dissipative
 distharm
@@ -819,6 +826,7 @@ du
 dU
 Ducastelle
 Dudarev
+Dufils
 Duin
 Dullweber
 dumpfile
@@ -906,6 +914,7 @@ elastance
 Electroneg
 electronegative
 electronegativity
+electroneutrality
 Eleftheriou
 ElementN
 elementset
@@ -1022,12 +1031,14 @@ evirials
 ew
 ewald
 Ewald
+ewaldflag
 excitations
 excv
 exe
 executables
 extep
 extrema
+extxyz
 exy
 ey
 ez
@@ -1094,8 +1105,10 @@ Fincham
 Fint
 fingerprintconstants
 fingerprintsperelement
+finitecutflag
 Finnis
 Fiorin
+fitpod
 fixID
 fj
 Fji
@@ -1138,6 +1151,7 @@ Forschungszentrum
 fortran
 Fortran
 Fosado
+fourbody
 fourier
 fp
 fphi
@@ -1271,6 +1285,7 @@ greenyellow
 Greffet
 grem
 gREM
+Grepl
 Grest
 Grigera
 Grimme
@@ -1510,6 +1525,9 @@ inumeric
 inv
 invariants
 inversed
+invertible
+invertibility
+ionicities
 ionizable
 ionocovalent
 iostreams
@@ -1629,6 +1647,7 @@ Kalia
 Kamberaj
 Kantorovich
 Kapfer
+Karhunen
 Karls
 Karlsruhe
 Karniadakis
@@ -1883,6 +1902,7 @@ ln
 localhost
 localTemp
 localvectors
+Loeve
 Loewen
 logfile
 logfreq
@@ -1934,6 +1954,7 @@ Mackrodt
 MacOS
 Macromolecules
 macroparticle
+Maday
 Madura
 Magda
 Magdeburg
@@ -2198,6 +2219,7 @@ msd
 msi
 MSI
 msm
+msmflag
 msse
 msst
 Mtchell
@@ -2277,6 +2299,8 @@ nanometer
 nanometers
 nanoparticle
 nanoparticles
+nanopores
+nanostructures
 nanotube
 Nanotube
 nanotubes
@@ -2551,6 +2575,7 @@ Omelyan
 omp
 OMP
 oneAPI
+onebody
 onelevel
 oneway
 onlysalt
@@ -2632,6 +2657,7 @@ Pastewka
 pathangle
 pathname
 pathnames
+Patera
 Patomtrans
 Pattnaik
 Pavese
@@ -2773,6 +2799,7 @@ PowerShell
 ppme
 ppn
 pppm
+pppmflag
 Prakash
 Praprotnik
 prd
@@ -2927,6 +2954,7 @@ Rcmx
 Rcmy
 Rco
 Rcut
+rcut
 rcutfac
 rdc
 rdf
@@ -2952,6 +2980,7 @@ refactoring
 reflectionstyle
 Reinders
 reinit
+reinitflag
 relaxbox
 relink
 relres
@@ -3019,6 +3048,7 @@ Rij
 RIj
 Rik
 Rin
+rin
 Rinaldi
 Rino
 RiRj
@@ -3155,6 +3185,7 @@ sdpd
 SDPD
 se
 seagreen
+Searles
 Secor
 sectoring
 sed
@@ -3285,6 +3316,7 @@ SPH
 spica
 SPICA
 Spickermann
+spinflag
 splined
 spparks
 Sprik
@@ -3470,6 +3502,7 @@ thermo
 thermochemical
 thermochemistry
 thermodynamically
+thermopotentiostat
 Thermophysical
 thermostatted
 thermostatting
@@ -3837,6 +3870,7 @@ workflows
 Workum
 Worley
 Wriggers
+writedata
 Wuppertal
 Wurtzite
 www

examples/PACKAGES/electrode/README

@@ -1,14 +1,14 @@
 These examples demonstrate the use of the ELECTRODE package for constant potential molecular dynamics.
 
 planar/
-  au-vac.data   -- gold electrodes with vacuum
+  data.au-vac -- gold electrodes with vacuum
   in.planar* -- comparison of gold electrodes with vacuum to theoretical capacitance of planar capacitor
     -- 5x, further labeled by long-range solver (ewald / pppm) and boundary correction (ew2d / ew3dc / ffield)
     -- the pppm-ew2d combination would not give correct results and will throw an error if selected
   test.sh -- run all in.planar files and check charge at 1.2V and %difference from theoretical (last column)
 
 graph-il/
-  graph-il.data -- graphene electrodes with electrolyte (coarse-grained BMIm-PF6)
+  data.graph-il -- graphene electrodes with electrolyte (coarse-grained BMIm-PF6)
   in.conp    -- reference run at constant potential
   in.etypes  -- type-based smart neighborlists
   in.ffield  -- finite field method with fully periodic cell
@@ -18,10 +18,22 @@ graph-il/
   in.thermo  -- thermalize electrolyte with thermopotentiostat instead of NVT
 
 au-aq/
-  au-aq.data -- gold electrodes with electrolyte (SPC water + NaCl)
+  data.au-aq -- gold electrodes with electrolyte (SPC water + NaCl)
   in.ffield  -- finite field method with fully periodic cell
   in.tf      -- Thomas-Fermi metallicity model with more delocalized charges
 
+madelung/
+  data.au-elyt -- tiny electrodes with two electrolyte atoms in between
+  settings.mod -- common settings
+  in.*         -- setup KSpace and fix electrode/conp
+  plate_cap.py -- compute reference energy and charges from Madelung style sum
+  eval.py      -- compare output of reference and Lammps job (used by test.sh)
+  test.sh      -- run all in.* files and check charge at 1 V and %difference from theoretical (last column)
+
+piston/
+  data.piston -- two electrodes with water
+  in.piston   -- equilibrate distance between rigid electrodes
+
 # future work:
   # in.cylinder -- comparison of carbon nanotube to theoretical induced charge for charge near circular conductor
 

examples/PACKAGES/electrode/au-aq/in.ffield

@@ -4,7 +4,7 @@
 boundary p p p # ffield uses periodic z-boundary and no slab
 include settings.mod # styles, groups, computes and fixes
 
-fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
+fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot

examples/PACKAGES/electrode/au-aq/in.tf

@@ -6,7 +6,7 @@
 boundary p p p # ffield uses periodic z-boundary and no slab
 include settings.mod # styles, groups, computes and fixes
 
-fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
+fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
 fix_modify conp tf 6 1.0 18.1715745
 fix_modify conp tf 7 1.0 18.1715745
 

examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential using finite field
 # for z-periodic gold-saline electrochemical cell
 
@@ -37,8 +37,8 @@ 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 = 0.002 seconds
+  special bonds CPU = 0.006 seconds
-  read_data CPU = 0.051 seconds
+  read_data CPU = 0.097 seconds
 
 group bot type 6
 1620 atoms in group bot
@@ -52,11 +52,12 @@ group electrolyte type 1 2 3 4 5
 
 fix nvt electrolyte nvt temp 298.0 298.0 241
 fix shake SPC shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
     2160 = # of frozen angles
-  find clusters CPU = 0.002 seconds
+  find clusters CPU = 0.006 seconds
 
 variable q atom q
 variable qz atom q*(z-lz/2)
@@ -67,12 +68,41 @@ compute qzbot bot reduce sum v_qz
 compute ctemp electrolyte temp
 
 
-fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
+fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
 3240 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.24017705
@@ -82,9 +112,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.093542e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 472567 349920
-  generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
+Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 17
   ghost atom cutoff = 17
@@ -105,35 +135,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 194.8 | 194.8 | 194.8 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qtop         c_qbot        c_qztop        c_qzbot    
-         0   171.61215      298.06731     -39212.819     -35306.164      4.1391573     -4.1391573      78.718381      131.56372    
+         0   171.61215      298.06731     -39021.917     -35115.261      4.1391573     -4.1391573      78.718381      131.56372    
-        50   147.03139      255.37383     -39870.139     -36523.051      4.1312167     -4.1312167      78.563872      131.30255    
+        50   147.03139      255.37383     -39679.603     -36332.515      4.1312167     -4.1312167      78.563872      131.30255    
-       100   149.89027      260.33932     -39878.859     -36466.689      4.0217834     -4.0217834      76.482548      127.82573    
+       100   149.89027      260.33932     -39693.369     -36281.2        4.0217834     -4.0217834      76.482548      127.82573    
-       150   151.7382       263.54893     -39873.178     -36418.942      4.0469977     -4.0469977      76.967548      128.59855    
+       150   151.7382       263.54893     -39686.526     -36232.29       4.0469977     -4.0469977      76.967548      128.59855    
-       200   151.7508       263.57081     -39827.015     -36372.492      4.1830375     -4.1830375      79.554159      132.93925    
+       200   151.7508       263.57081     -39634.089     -36179.566      4.1830375     -4.1830375      79.554159      132.93925    
-       250   152.61146      265.06566     -39791.293     -36317.177      4.1835865     -4.1835865      79.56665       132.97185    
+       250   152.61146      265.06566     -39598.341     -36124.226      4.1835865     -4.1835865      79.56665       132.97185    
-       300   153.51486      266.63475     -39751.841     -36257.16       4.1571861     -4.1571861      79.061431      132.12905    
+       300   153.51486      266.63475     -39560.107     -36065.426      4.1571861     -4.1571861      79.06143       132.12905    
-       350   156.35115      271.561       -39754.955     -36195.708      4.3498059     -4.3498059      82.720202      138.28678    
+       350   156.35115      271.561       -39554.338     -35995.09       4.3498059     -4.3498059      82.720202      138.28678    
-       400   156.26118      271.40474     -39690.781     -36133.582      4.3444079     -4.3444079      82.619396      138.11873    
+       400   156.26118      271.40474     -39490.412     -35933.213      4.344408      -4.344408       82.619398      138.11874    
-       450   158.54164      275.36558     -39681.083     -36071.97       4.2020488     -4.2020488      79.912674      133.55185    
+       450   158.54163      275.36557     -39487.28      -35878.167      4.2020489     -4.2020489      79.912677      133.55186    
-       500   161.40138      280.33258     -39684.185     -36009.972      4.3021924     -4.3021924      81.807527      136.7464     
+       500   161.40137      280.33257     -39485.763     -35811.55       4.3021927     -4.3021927      81.807532      136.74641    
-Loop time of 246.197 on 1 procs for 500 steps with 9798 atoms
+Loop time of 146.959 on 1 procs for 500 steps with 9798 atoms
 
-Performance: 0.175 ns/day, 136.776 hours/ns, 2.031 timesteps/s
+Performance: 0.294 ns/day, 81.644 hours/ns, 3.402 timesteps/s, 33.336 katom-step/s
-356.3% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 105.64     | 105.64     | 105.64     |   0.0 | 42.91
+Pair    | 69.832     | 69.832     | 69.832     |   0.0 | 47.52
-Bond    | 0.0010592  | 0.0010592  | 0.0010592  |   0.0 |  0.00
+Bond    | 0.00091634 | 0.00091634 | 0.00091634 |   0.0 |  0.00
-Kspace  | 37.643     | 37.643     | 37.643     |   0.0 | 15.29
+Kspace  | 33.817     | 33.817     | 33.817     |   0.0 | 23.01
-Neigh   | 5.8827     | 5.8827     | 5.8827     |   0.0 |  2.39
+Neigh   | 4.2067     | 4.2067     | 4.2067     |   0.0 |  2.86
-Comm    | 0.18181    | 0.18181    | 0.18181    |   0.0 |  0.07
+Comm    | 0.12212    | 0.12212    | 0.12212    |   0.0 |  0.08
-Output  | 0.0055762  | 0.0055762  | 0.0055762  |   0.0 |  0.00
+Output  | 0.0031896  | 0.0031896  | 0.0031896  |   0.0 |  0.00
-Modify  | 96.78      | 96.78      | 96.78      |   0.0 | 39.31
+Modify  | 38.92      | 38.92      | 38.92      |   0.0 | 26.48
-Other   |            | 0.06346    |            |       |  0.03
+Other   |            | 0.05687    |            |       |  0.04
 
 Nlocal:           9798 ave        9798 max        9798 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -147,4 +177,4 @@ Ave neighs/atom = 842.63544
 Ave special neighs/atom = 1.3227189
 Neighbor list builds = 22
 Dangerous builds = 0
-Total wall time: 0:19:39
+Total wall time: 0:05:33

examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential using finite field
 # for z-periodic gold-saline electrochemical cell
 
@@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.002 seconds
-  read_data CPU = 0.149 seconds
+  read_data CPU = 0.118 seconds
 
 group bot type 6
 1620 atoms in group bot
@@ -53,11 +53,12 @@ group electrolyte type 1 2 3 4 5
 
 fix nvt electrolyte nvt temp 298.0 298.0 241
 fix shake SPC shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
     2160 = # of frozen angles
-  find clusters CPU = 0.003 seconds
+  find clusters CPU = 0.002 seconds
 
 variable q atom q
 variable qz atom q*(z-lz/2)
@@ -68,12 +69,41 @@ compute qzbot bot reduce sum v_qz
 compute ctemp electrolyte temp
 
 
-fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
+fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
 3240 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.24017705
@@ -83,9 +113,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.093542e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 138958 87480
-  generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
+Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 17
   ghost atom cutoff = 17
@@ -106,35 +136,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 118.2 | 120.7 | 123.2 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qtop         c_qbot        c_qztop        c_qzbot    
-         0   171.61215      298.06731     -39212.819     -35306.164      4.1391573     -4.1391573      78.718381      131.56372    
+         0   171.61215      298.06731     -39021.917     -35115.261      4.1391573     -4.1391573      78.718381      131.56372    
-        50   147.03139      255.37383     -39870.139     -36523.051      4.1312167     -4.1312167      78.563872      131.30255    
+        50   147.03139      255.37383     -39679.603     -36332.515      4.1312167     -4.1312167      78.563872      131.30255    
-       100   149.89027      260.33932     -39878.859     -36466.689      4.0217834     -4.0217834      76.482548      127.82573    
+       100   149.89027      260.33932     -39693.369     -36281.2        4.0217834     -4.0217834      76.482548      127.82573    
-       150   151.7382       263.54893     -39873.178     -36418.942      4.0469977     -4.0469977      76.967548      128.59855    
+       150   151.7382       263.54893     -39686.526     -36232.29       4.0469977     -4.0469977      76.967548      128.59855    
-       200   151.7508       263.57081     -39827.015     -36372.492      4.1830375     -4.1830375      79.554159      132.93925    
+       200   151.7508       263.57081     -39634.089     -36179.566      4.1830375     -4.1830375      79.554159      132.93925    
-       250   152.61146      265.06566     -39791.293     -36317.177      4.1835865     -4.1835865      79.56665       132.97185    
+       250   152.61146      265.06566     -39598.341     -36124.226      4.1835864     -4.1835864      79.56665       132.97185    
-       300   153.51486      266.63475     -39751.841     -36257.16       4.1571861     -4.1571861      79.061431      132.12905    
+       300   153.51486      266.63475     -39560.107     -36065.426      4.1571861     -4.1571861      79.06143       132.12905    
-       350   156.35115      271.561       -39754.955     -36195.708      4.3498059     -4.3498059      82.7202        138.28678    
+       350   156.35115      271.561       -39554.338     -35995.09       4.3498059     -4.3498059      82.720201      138.28678    
-       400   156.26118      271.40474     -39690.781     -36133.582      4.3444079     -4.3444079      82.619398      138.11873    
+       400   156.26118      271.40474     -39490.412     -35933.213      4.3444079     -4.3444079      82.619397      138.11873    
-       450   158.54163      275.36558     -39681.083     -36071.97       4.2020488     -4.2020488      79.912675      133.55185    
+       450   158.54163      275.36558     -39487.279     -35878.167      4.202049      -4.202049       79.912678      133.55186    
-       500   161.40138      280.33257     -39684.185     -36009.972      4.3021924     -4.3021924      81.807527      136.7464     
+       500   161.40137      280.33256     -39485.763     -35811.55       4.3021925     -4.3021925      81.807529      136.7464     
-Loop time of 111.902 on 4 procs for 500 steps with 9798 atoms
+Loop time of 97.2399 on 4 procs for 500 steps with 9798 atoms
 
-Performance: 0.386 ns/day, 62.168 hours/ns, 4.468 timesteps/s
+Performance: 0.444 ns/day, 54.022 hours/ns, 5.142 timesteps/s, 50.381 katom-step/s
-97.2% CPU use with 4 MPI tasks x no OpenMP threads
+87.0% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 21.816     | 31.136     | 40.866     | 166.5 | 27.82
+Pair    | 19.363     | 28.08      | 37.126     | 160.3 | 28.88
-Bond    | 0.00073413 | 0.00080346 | 0.00084203 |   0.0 |  0.00
+Bond    | 0.00094043 | 0.00096516 | 0.00098016 |   0.0 |  0.00
-Kspace  | 29.546     | 39.137     | 48.326     | 146.4 | 34.97
+Kspace  | 31.655     | 40.554     | 49.143     | 131.3 | 41.71
-Neigh   | 2.5867     | 2.5872     | 2.5877     |   0.0 |  2.31
+Neigh   | 2.2289     | 2.2294     | 2.2297     |   0.0 |  2.29
-Comm    | 0.33289    | 0.33603    | 0.33791    |   0.3 |  0.30
+Comm    | 0.5341     | 0.54079    | 0.5478     |   0.9 |  0.56
-Output  | 0.0022537  | 0.0030028  | 0.005192   |   2.3 |  0.00
+Output  | 0.0024141  | 0.0026943  | 0.0034176  |   0.8 |  0.00
-Modify  | 38.498     | 38.635     | 38.77      |   2.2 | 34.53
+Modify  | 25.6       | 25.755     | 25.908     |   2.8 | 26.49
-Other   |            | 0.06679    |            |       |  0.06
+Other   |            | 0.07733    |            |       |  0.08
 
 Nlocal:         2449.5 ave        2908 max        2012 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
@@ -148,4 +178,4 @@ Ave neighs/atom = 842.63544
 Ave special neighs/atom = 1.3227189
 Neighbor list builds = 22
 Dangerous builds = 0
-Total wall time: 0:07:48
+Total wall time: 0:03:03

examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential using finite field
 # for z-periodic gold-saline electrochemical cell
 # using Thomas-Fermi metallicity model: electrode q and qz will be
@@ -39,8 +39,8 @@ 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 = 0.010 seconds
+  special bonds CPU = 0.003 seconds
-  read_data CPU = 0.115 seconds
+  read_data CPU = 0.065 seconds
 
 group bot type 6
 1620 atoms in group bot
@@ -54,11 +54,12 @@ group electrolyte type 1 2 3 4 5
 
 fix nvt electrolyte nvt temp 298.0 298.0 241
 fix shake SPC shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
     2160 = # of frozen angles
-  find clusters CPU = 0.010 seconds
+  find clusters CPU = 0.002 seconds
 
 variable q atom q
 variable qz atom q*(z-lz/2)
@@ -69,7 +70,7 @@ compute qzbot bot reduce sum v_qz
 compute ctemp electrolyte temp
 
 
-fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
+fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
 3240 atoms in group conp_group
 fix_modify conp tf 6 1.0 18.1715745
 fix_modify conp tf 7 1.0 18.1715745
@@ -77,6 +78,35 @@ fix_modify conp tf 7 1.0 18.1715745
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.24017705
@@ -86,9 +116,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.093542e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 472567 349920
-  generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
+Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 17
   ghost atom cutoff = 17
@@ -109,35 +139,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 194.8 | 194.8 | 194.8 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qtop         c_qbot        c_qztop        c_qzbot    
-         0   171.61215      298.06731     -39190.106     -35283.45       4.0804484     -4.0804484      79.075127      131.20697    
+         0   171.61215      298.06731     -39001.911     -35095.255      4.0804484     -4.0804484      79.075127      131.20697    
-        50   147.14308      255.56782     -39849.964     -36500.334      3.9990346     -3.9990346      77.497181      128.57759    
+        50   147.14308      255.56782     -39665.525     -36315.894      3.9990346     -3.9990346      77.497181      128.57759    
-       100   149.94935      260.44194     -39857.533     -36444.019      3.8613914     -3.8613914      74.82985       124.15315    
+       100   149.94935      260.44194     -39679.441     -36265.927      3.8613914     -3.8613914      74.82985       124.15315    
-       150   151.95924      263.93285     -39855.567     -36396.299      3.8677064     -3.8677064      74.957279      124.33201    
+       150   151.95924      263.93285     -39677.184     -36217.916      3.8677064     -3.8677064      74.957279      124.33201    
-       200   151.66737      263.42591     -39802.585     -36349.961      3.99842       -3.99842        77.491015      128.54496    
+       200   151.66737      263.42591     -39618.173     -36165.549      3.99842       -3.99842        77.491015      128.54496    
-       250   152.36874      264.64408     -39763.306     -36294.716      3.9925863     -3.9925863      77.379445      128.37226    
+       250   152.36874      264.64408     -39579.164     -36110.574      3.9925863     -3.9925863      77.379445      128.37226    
-       300   153.83916      267.19802     -39737.075     -36235.012      3.94995       -3.94995        76.553896      127.00395    
+       300   153.83916      267.19802     -39554.899     -36052.836      3.94995       -3.94995        76.553896      127.00395    
-       350   155.88897      270.75827     -39722.265     -36173.539      4.0598524     -4.0598524      78.679643      130.5394     
+       350   155.88897      270.75827     -39535.02      -35986.294      4.0598524     -4.0598524      78.679643      130.5394     
-       400   156.51993      271.85415     -39674.759     -36111.669      4.1312899     -4.1312899      80.060369      132.83599    
+       400   156.51993      271.85415     -39484.219     -35921.13       4.1312898     -4.1312898      80.060368      132.83598    
-       450   160.21339      278.26919     -39697.962     -36050.793      3.9068098     -3.9068098      75.713484      125.59216    
+       450   160.21339      278.26919     -39517.776     -35870.607      3.9068098     -3.9068098      75.713484      125.59216    
-       500   161.63639      280.74075     -39669.412     -35989.849      3.9261656     -3.9261656      76.0806        126.22255    
+       500   161.63639      280.74075     -39488.333     -35808.771      3.9261656     -3.9261656      76.080599      126.22255    
-Loop time of 280.183 on 1 procs for 500 steps with 9798 atoms
+Loop time of 185.804 on 1 procs for 500 steps with 9798 atoms
 
-Performance: 0.154 ns/day, 155.657 hours/ns, 1.785 timesteps/s
+Performance: 0.233 ns/day, 103.225 hours/ns, 2.691 timesteps/s, 26.366 katom-step/s
-341.9% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 119.69     | 119.69     | 119.69     |   0.0 | 42.72
+Pair    | 91         | 91         | 91         |   0.0 | 48.98
-Bond    | 0.0010952  | 0.0010952  | 0.0010952  |   0.0 |  0.00
+Bond    | 0.0010315  | 0.0010315  | 0.0010315  |   0.0 |  0.00
-Kspace  | 42.137     | 42.137     | 42.137     |   0.0 | 15.04
+Kspace  | 40.32      | 40.32      | 40.32      |   0.0 | 21.70
-Neigh   | 6.5403     | 6.5403     | 6.5403     |   0.0 |  2.33
+Neigh   | 5.6505     | 5.6505     | 5.6505     |   0.0 |  3.04
-Comm    | 0.19411    | 0.19411    | 0.19411    |   0.0 |  0.07
+Comm    | 0.15304    | 0.15304    | 0.15304    |   0.0 |  0.08
-Output  | 0.0053644  | 0.0053644  | 0.0053644  |   0.0 |  0.00
+Output  | 0.0041829  | 0.0041829  | 0.0041829  |   0.0 |  0.00
-Modify  | 111.54     | 111.54     | 111.54     |   0.0 | 39.81
+Modify  | 48.607     | 48.607     | 48.607     |   0.0 | 26.16
-Other   |            | 0.07244    |            |       |  0.03
+Other   |            | 0.06807    |            |       |  0.04
 
 Nlocal:           9798 ave        9798 max        9798 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -151,4 +181,4 @@ Ave neighs/atom = 842.7079
 Ave special neighs/atom = 1.3227189
 Neighbor list builds = 23
 Dangerous builds = 0
-Total wall time: 0:21:11
+Total wall time: 0:06:18

examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential using finite field
 # for z-periodic gold-saline electrochemical cell
 # using Thomas-Fermi metallicity model: electrode q and qz will be
@@ -41,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.002 seconds
-  read_data CPU = 0.091 seconds
+  read_data CPU = 0.114 seconds
 
 group bot type 6
 1620 atoms in group bot
@@ -55,11 +55,12 @@ group electrolyte type 1 2 3 4 5
 
 fix nvt electrolyte nvt temp 298.0 298.0 241
 fix shake SPC shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
     2160 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.002 seconds
 
 variable q atom q
 variable qz atom q*(z-lz/2)
@@ -70,7 +71,7 @@ compute qzbot bot reduce sum v_qz
 compute ctemp electrolyte temp
 
 
-fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
+fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
 3240 atoms in group conp_group
 fix_modify conp tf 6 1.0 18.1715745
 fix_modify conp tf 7 1.0 18.1715745
@@ -78,6 +79,35 @@ fix_modify conp tf 7 1.0 18.1715745
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.24017705
@@ -87,9 +117,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.093542e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 138958 87480
-  generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
+Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 17
   ghost atom cutoff = 17
@@ -110,35 +140,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 118.2 | 120.7 | 123.2 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qtop         c_qbot        c_qztop        c_qzbot    
-         0   171.61215      298.06731     -39190.106     -35283.45       4.0804484     -4.0804484      79.075127      131.20697    
+         0   171.61215      298.06731     -39001.911     -35095.255      4.0804484     -4.0804484      79.075127      131.20697    
-        50   147.14308      255.56782     -39849.964     -36500.334      3.9990346     -3.9990346      77.497181      128.57759    
+        50   147.14308      255.56782     -39665.525     -36315.894      3.9990346     -3.9990346      77.497181      128.57759    
-       100   149.94935      260.44194     -39857.533     -36444.019      3.8613914     -3.8613914      74.82985       124.15315    
+       100   149.94935      260.44194     -39679.441     -36265.927      3.8613914     -3.8613914      74.82985       124.15315    
-       150   151.95924      263.93285     -39855.567     -36396.299      3.8677064     -3.8677064      74.957279      124.33201    
+       150   151.95924      263.93285     -39677.184     -36217.916      3.8677064     -3.8677064      74.957279      124.33201    
-       200   151.66737      263.42591     -39802.585     -36349.961      3.99842       -3.99842        77.491015      128.54496    
+       200   151.66737      263.42591     -39618.173     -36165.549      3.99842       -3.99842        77.491015      128.54496    
-       250   152.36874      264.64408     -39763.306     -36294.716      3.9925863     -3.9925863      77.379445      128.37226    
+       250   152.36874      264.64408     -39579.163     -36110.574      3.9925863     -3.9925863      77.379445      128.37226    
-       300   153.83916      267.19802     -39737.075     -36235.012      3.94995       -3.94995        76.553896      127.00395    
+       300   153.83916      267.19802     -39554.899     -36052.835      3.94995       -3.94995        76.553896      127.00395    
-       350   155.88897      270.75827     -39722.265     -36173.539      4.0598524     -4.0598524      78.679643      130.5394     
+       350   155.88897      270.75826     -39535.02      -35986.294      4.0598523     -4.0598523      78.679642      130.5394     
-       400   156.51993      271.85415     -39674.759     -36111.669      4.1312899     -4.1312899      80.060369      132.83599    
+       400   156.51993      271.85415     -39484.219     -35921.13       4.1312897     -4.1312897      80.060366      132.83598    
-       450   160.21339      278.26919     -39697.962     -36050.793      3.9068098     -3.9068098      75.713485      125.59216    
+       450   160.21339      278.26919     -39517.776     -35870.607      3.9068099     -3.9068099      75.713486      125.59216    
-       500   161.63639      280.74075     -39669.412     -35989.849      3.9261654     -3.9261654      76.080597      126.22255    
+       500   161.63639      280.74075     -39488.333     -35808.771      3.9261657     -3.9261657      76.080602      126.22256    
-Loop time of 110.716 on 4 procs for 500 steps with 9798 atoms
+Loop time of 104.099 on 4 procs for 500 steps with 9798 atoms
 
-Performance: 0.390 ns/day, 61.509 hours/ns, 4.516 timesteps/s
+Performance: 0.415 ns/day, 57.833 hours/ns, 4.803 timesteps/s, 47.061 katom-step/s
-97.2% CPU use with 4 MPI tasks x no OpenMP threads
+87.7% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 21.17      | 30.449     | 39.65      | 164.9 | 27.50
+Pair    | 20.951     | 30.326     | 40.07      | 166.7 | 29.13
-Bond    | 0.0007313  | 0.00077537 | 0.00081477 |   0.0 |  0.00
+Bond    | 0.00098259 | 0.0010706  | 0.0011926  |   0.3 |  0.00
-Kspace  | 29.854     | 38.911     | 48.058     | 143.8 | 35.14
+Kspace  | 33.465     | 43.037     | 52.268     | 137.5 | 41.34
-Neigh   | 2.7206     | 2.7213     | 2.722      |   0.0 |  2.46
+Neigh   | 2.6007     | 2.6014     | 2.6021     |   0.0 |  2.50
-Comm    | 0.33023    | 0.33225    | 0.33384    |   0.2 |  0.30
+Comm    | 0.57766    | 0.58318    | 0.58875    |   0.7 |  0.56
-Output  | 0.0024528  | 0.0027565  | 0.0035754  |   0.9 |  0.00
+Output  | 0.0022277  | 0.0024765  | 0.0031841  |   0.8 |  0.00
-Modify  | 38.091     | 38.233     | 38.365     |   2.1 | 34.53
+Modify  | 27.292     | 27.47      | 27.647     |   3.1 | 26.39
-Other   |            | 0.06636    |            |       |  0.06
+Other   |            | 0.0787     |            |       |  0.08
 
 Nlocal:         2449.5 ave        2908 max        2017 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
@@ -147,9 +177,9 @@ Histogram: 2 0 0 0 0 0 0 0 0 2
 Neighs:    2.06421e+06 ave  2.7551e+06 max 1.40237e+06 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
 
-Total # of neighbors = 8256853
+Total # of neighbors = 8256852
-Ave neighs/atom = 842.708
+Ave neighs/atom = 842.7079
 Ave special neighs/atom = 1.3227189
 Neighbor list builds = 23
 Dangerous builds = 0
-Total wall time: 0:08:22
+Total wall time: 0:03:12

examples/PACKAGES/electrode/graph-il/.gitignore

@@ -1 +1,2 @@
 log.lammps*
+in.temp

examples/PACKAGES/electrode/graph-il/algo_test.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+LMP_BIN="$1"
+NP="${2:-1}"
+echo "MPI over $NP procs:"
+for feat in conp etypes tf
+do
+  echo "Using base input file in.$feat:"
+  echo "mat_inv, log excerpts:"
+  logfile="log.algo_test.$NP.$feat"
+  mpirun -np $NP $LMP_BIN -i in.$feat -l $logfile > /dev/null 2>&1
+  grep -A2 'Per MPI rank' $logfile
+  grep -B1 'Loop time' $logfile
+  rm $logfile
+  for cgtype in mat_cg cg
+  do
+    for tol in 1e-4 1e-5 1e-6
+    do
+      echo "$cgtype, tol = $tol, log excerpts:"
+      logfile="log.algo_test.$NP.$feat.$cgtype.$tol"
+      sed '/electrode/ s/$/ algo '"$cgtype"' '"$tol"'/' in.$feat > in.temp
+      mpirun -np $NP $LMP_BIN -i in.temp -l $logfile > /dev/null 2>&1
+      grep -A2 'Per MPI rank' $logfile
+      grep -B1 'Loop time' $logfile
+      rm $logfile
+    done
+  done
+done

examples/PACKAGES/electrode/graph-il/in.conp

@@ -3,9 +3,9 @@
 
 boundary p p f # slab calculation
 include settings.mod # styles, groups, computes and fixes
-kspace_modify slab 3.0
+kspace_modify slab 3.0 # amat twostep
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop

examples/PACKAGES/electrode/graph-il/in.conq

@@ -5,14 +5,10 @@ boundary p p f # slab calculation
 include settings.mod # styles, groups, computes and fixes
 kspace_modify slab 3.0
 
-fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
+fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on
-
+variable dv equal f_conq[2]-f_conq[1] 
-# ask fix conq to output electrode potentials to internal variables
+# symm on and off give different electrode potentials, but identical potential difference
-variable vbot internal 0.0
-variable vtop internal 0.0
-fix_modify conq set v bot vbot
-fix_modify conq set v top vtop
 
 thermo 50
-thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
+thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv
 run 500

examples/PACKAGES/electrode/graph-il/in.conq2

@@ -5,30 +5,16 @@ boundary p p f # slab calculation
 include settings.mod # styles, groups, computes and fixes
 kspace_modify slab 3.0
 
-fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
+fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on
 
-# get the four entries of electrode elastance matrix
+variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge
-variable me00 internal 0.0
+variable qex_top equal  1.0-f_conp[2][1] # difference between desired and 0V charge
-variable me01 internal 0.0
-variable me10 internal 0.0
-variable me11 internal 0.0
-fix_modify conp set me bot bot me00
-fix_modify conp set me bot top me01
-fix_modify conp set me top bot me10
-fix_modify conp set me top top me11
-
-# get the 0V charges (qsb), and excess charge required to reach preset total charges
-variable qsb_bot internal 0.0
-variable qsb_top internal 0.0
-fix_modify conp set qsb bot qsb_bot
-fix_modify conp set qsb top qsb_top
-variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
-variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
 
 # calculate imposed potential as elastance * excess charge
 # note: fix will wait until the run setup to look for its potential variables
-variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
+# which is why we can define variable names *after* fix conp without error
-variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
+variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top
+variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop

examples/PACKAGES/electrode/graph-il/in.etypes

@@ -5,7 +5,7 @@ boundary p p f # slab calculation
 include settings.mod # styles, groups, computes and fixes
 kspace_modify slab 3.0
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop

examples/PACKAGES/electrode/graph-il/in.ffield

@@ -4,7 +4,7 @@
 boundary p p p # ffield uses periodic z-boundary and no slab
 include settings.mod # styles, groups, computes and fixes
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop

examples/PACKAGES/electrode/graph-il/in.ramp

@@ -6,7 +6,7 @@ include settings.mod # styles, groups, computes and fixes
 kspace_modify slab 3.0
 
 variable v equal ramp(2,4)
-fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5
+fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v

examples/PACKAGES/electrode/graph-il/in.thermo

@@ -6,9 +6,9 @@ include settings.mod # styles, groups, computes and fixes
 kspace_modify slab 3.0
 
 unfix nvt # remove NVT thermostat included from "settings.mod"
-fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng
+fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng
 # to compare to regular constant potential, switch previous line to this:
-#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on
+#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on
 fix nve electrolyte nve
 
 # note ionic liquid does not reach 500K immediately

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential
 # for graphene-ionic liquid supercapacitor
 
@@ -37,13 +37,20 @@ 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 = 0.004 seconds
-  read_data CPU = 0.036 seconds
+  read_data CPU = 0.027 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -52,24 +59,54 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
      320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.005 seconds
 
 variable q atom q
 compute qtop top reduce sum v_q
 compute qbot bot reduce sum v_q
 compute ctemp electrolyte temp
-kspace_modify slab 3.0
+kspace_modify slab 3.0 # amat twostep
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv
 832 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20904498
@@ -79,9 +116,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.1149519e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 307242 204800
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -97,35 +134,35 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 57.15 | 57.15 | 57.15 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 57.19 | 57.19 | 57.19 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
-         0   0              0              25137191       25137191       0.0085142912  -0.0085142912 
+         0   0              0              25137190       25137190       0.0085142912  -0.0085142912 
         50   17.83755       64.26354       25137031       25137214       0.0045923944  -0.0045923944 
-       100   48.393682      174.34846      25136774       25137273      -0.009514517    0.009514517  
+       100   48.393682      174.34846      25136775       25137273      -0.009514517    0.009514517  
-       150   70.421272      253.7075       25136655       25137380      -0.033017005    0.033017005  
+       150   70.421272      253.7075       25136657       25137382      -0.033017005    0.033017005  
-       200   82.204844      296.16031      25136667       25137514      -0.063668175    0.063668175  
+       200   82.204844      296.16031      25136670       25137517      -0.063668175    0.063668175  
-       250   87.54223       315.38937      25136757       25137659      -0.096776257    0.096776257  
+       250   87.54223       315.38937      25136762       25137663      -0.096776257    0.096776257  
-       300   91.704746      330.38571      25136865       25137810      -0.1283784      0.1283784    
+       300   91.704746      330.38571      25136871       25137816      -0.1283784      0.1283784    
-       350   100.36017      361.56871      25136934       25137968      -0.15649799     0.15649799   
+       350   100.36017      361.56871      25136941       25137975      -0.15649799     0.15649799   
-       400   111.37575      401.25467      25136986       25138133      -0.18065435     0.18065435   
+       400   111.37575      401.25467      25136994       25138141      -0.18065435     0.18065435   
-       450   121.79848      438.80476      25137043       25138298      -0.19979365     0.19979365   
+       450   121.79848      438.80476      25137052       25138307      -0.19979365     0.19979365   
-       500   126.95916      457.39718      25137145       25138453      -0.21037535     0.21037535   
+       500   126.95916      457.39718      25137155       25138463      -0.21037535     0.21037535   
-Loop time of 103.439 on 1 procs for 500 steps with 3776 atoms
+Loop time of 91.5523 on 1 procs for 500 steps with 3776 atoms
 
-Performance: 0.418 ns/day, 57.466 hours/ns, 4.834 timesteps/s
+Performance: 0.472 ns/day, 50.862 hours/ns, 5.461 timesteps/s, 20.622 katom-step/s
-393.6% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 19.309     | 19.309     | 19.309     |   0.0 | 18.67
+Pair    | 18.906     | 18.906     | 18.906     |   0.0 | 20.65
-Bond    | 0.0018867  | 0.0018867  | 0.0018867  |   0.0 |  0.00
+Bond    | 0.0012922  | 0.0012922  | 0.0012922  |   0.0 |  0.00
-Kspace  | 23.047     | 23.047     | 23.047     |   0.0 | 22.28
+Kspace  | 34.476     | 34.476     | 34.476     |   0.0 | 37.66
-Neigh   | 0.25707    | 0.25707    | 0.25707    |   0.0 |  0.25
+Neigh   | 0.26641    | 0.26641    | 0.26641    |   0.0 |  0.29
-Comm    | 0.070734   | 0.070734   | 0.070734   |   0.0 |  0.07
+Comm    | 0.069067   | 0.069067   | 0.069067   |   0.0 |  0.08
-Output  | 0.0023085  | 0.0023085  | 0.0023085  |   0.0 |  0.00
+Output  | 0.0021466  | 0.0021466  | 0.0021466  |   0.0 |  0.00
-Modify  | 60.73      | 60.73      | 60.73      |   0.0 | 58.71
+Modify  | 37.805     | 37.805     | 37.805     |   0.0 | 41.29
-Other   |            | 0.01994    |            |       |  0.02
+Other   |            | 0.0271     |            |       |  0.03
 
 Nlocal:           3776 ave        3776 max        3776 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -139,4 +176,4 @@ Ave neighs/atom = 457.18432
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 7
 Dangerous builds = 0
-Total wall time: 0:03:10
+Total wall time: 0:01:48

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential
 # for graphene-ionic liquid supercapacitor
 
@@ -38,13 +38,20 @@ 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 = 0.003 seconds
-  read_data CPU = 0.014 seconds
+  read_data CPU = 0.038 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -53,24 +60,54 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
      320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.003 seconds
 
 variable q atom q
 compute qtop top reduce sum v_q
 compute qbot bot reduce sum v_q
 compute ctemp electrolyte temp
-kspace_modify slab 3.0
+kspace_modify slab 3.0 # amat twostep
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv
 832 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20904498
@@ -80,9 +117,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.1149519e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 151593 85504
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -98,35 +135,35 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 23.13 | 26.96 | 30.79 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 23.16 | 26.99 | 30.82 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
-         0   0              0              25137191       25137191       0.0085142912  -0.0085142912 
+         0   0              0              25137190       25137190       0.0085142912  -0.0085142912 
         50   17.83755       64.26354       25137031       25137214       0.0045923944  -0.0045923944 
-       100   48.393682      174.34846      25136774       25137273      -0.009514517    0.009514517  
+       100   48.393682      174.34846      25136775       25137273      -0.009514517    0.009514517  
-       150   70.421272      253.7075       25136655       25137380      -0.033017005    0.033017005  
+       150   70.421272      253.7075       25136657       25137382      -0.033017005    0.033017005  
-       200   82.204844      296.16031      25136667       25137514      -0.063668175    0.063668175  
+       200   82.204844      296.16031      25136670       25137517      -0.063668175    0.063668175  
-       250   87.54223       315.38937      25136757       25137659      -0.096776257    0.096776257  
+       250   87.54223       315.38937      25136762       25137663      -0.096776257    0.096776257  
-       300   91.704746      330.38571      25136865       25137810      -0.1283784      0.1283784    
+       300   91.704746      330.38571      25136871       25137816      -0.1283784      0.1283784    
-       350   100.36017      361.56871      25136934       25137968      -0.15649799     0.15649799   
+       350   100.36017      361.56871      25136941       25137975      -0.15649799     0.15649799   
-       400   111.37575      401.25467      25136986       25138133      -0.18065435     0.18065435   
+       400   111.37575      401.25467      25136994       25138141      -0.18065435     0.18065435   
-       450   121.79848      438.80476      25137043       25138298      -0.19979365     0.19979365   
+       450   121.79848      438.80476      25137052       25138307      -0.19979365     0.19979365   
-       500   126.95916      457.39718      25137145       25138453      -0.21037535     0.21037535   
+       500   126.95916      457.39718      25137155       25138463      -0.21037535     0.21037535   
-Loop time of 49.6656 on 4 procs for 500 steps with 3776 atoms
+Loop time of 49.6413 on 4 procs for 500 steps with 3776 atoms
 
-Performance: 0.870 ns/day, 27.592 hours/ns, 10.067 timesteps/s
+Performance: 0.870 ns/day, 27.578 hours/ns, 10.072 timesteps/s, 38.033 katom-step/s
-95.1% CPU use with 4 MPI tasks x no OpenMP threads
+76.3% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.968      | 6.1677     | 6.382      |   6.5 | 12.42
+Pair    | 5.3666     | 5.4998     | 5.6946     |   5.4 | 11.08
-Bond    | 0.00071151 | 0.00078617 | 0.00090387 |   0.0 |  0.00
+Bond    | 0.0011638  | 0.0012711  | 0.0014555  |   0.3 |  0.00
-Kspace  | 17.345     | 17.558     | 17.755     |   3.8 | 35.35
+Kspace  | 24.047     | 24.241     | 24.374     |   2.6 | 48.83
-Neigh   | 0.10939    | 0.10945    | 0.10948    |   0.0 |  0.22
+Neigh   | 0.088235   | 0.088328   | 0.088432   |   0.0 |  0.18
-Comm    | 0.15295    | 0.15474    | 0.15699    |   0.4 |  0.31
+Comm    | 0.30907    | 0.31913    | 0.32916    |   1.7 |  0.64
-Output  | 0.00074458 | 0.0010336  | 0.0018799  |   1.5 |  0.00
+Output  | 0.0010669  | 0.0014463  | 0.0024232  |   1.5 |  0.00
-Modify  | 25.634     | 25.641     | 25.645     |   0.1 | 51.63
+Modify  | 19.435     | 19.445     | 19.454     |   0.2 | 39.17
-Other   |            | 0.03276    |            |       |  0.07
+Other   |            | 0.04549    |            |       |  0.09
 
 Nlocal:            944 ave         951 max         941 min
 Histogram: 1 2 0 0 0 0 0 0 0 1
@@ -140,4 +177,4 @@ Ave neighs/atom = 457.18432
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 7
 Dangerous builds = 0
-Total wall time: 0:01:11
+Total wall time: 0:00:55

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.1

@@ -0,0 +1,186 @@
+LAMMPS (3 Nov 2022)
+# electrodes with constrained total charges
+# for graphene-ionic liquid supercapacitor
+
+boundary p p f # slab calculation
+include settings.mod # styles, groups, computes and fixes
+# set boundary in main script because ffield is periodic
+units real
+# distribute electrode atoms among all processors:
+if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
+
+atom_style full
+pair_style lj/cut/coul/long 16
+bond_style harmonic
+angle_style harmonic
+kspace_style pppm/electrode 1e-7
+# kspace_modify in main script because ffield is periodic
+
+read_data "data.graph-il"
+Reading data file ...
+  orthogonal box = (0 0 -68) to (32.2 34.4 68)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  3776 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  640 bonds
+  reading angles ...
+  320 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.002 seconds
+  read_data CPU = 0.023 seconds
+
+# replicate 4 4 1 # test different sys sizes
+
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
+416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
+
+group bmi type 1 2 3
+960 atoms in group bmi
+group electrolyte type 1 2 3 4
+1280 atoms in group electrolyte
+
+fix nvt electrolyte nvt temp 500.0 500.0 100
+fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+     320 = # of frozen angles
+  find clusters CPU = 0.002 seconds
+
+variable q atom q
+compute qtop top reduce sum v_q
+compute qbot bot reduce sum v_q
+compute ctemp electrolyte temp
+kspace_modify slab 3.0
+
+fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on
+832 atoms in group conp_group
+variable dv equal f_conq[2]-f_conq[1]
+# symm on and off give different electrode potentials, but identical potential difference
+
+thermo 50
+thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv
+run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM/electrode initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.20904498
+  grid = 32 32 200
+  stencil order = 5
+  estimated absolute RMS force accuracy = 3.7023506e-05
+  estimated relative force accuracy = 1.1149519e-07
+  using double precision MKL FFT
+  3d grid and FFT values/proc = 307242 204800
+Generated 15 of 15 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 = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 4 4 16
+  3 neighbor lists, perpetual/occasional/extra = 2 1 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) fix electrode/conq, occasional, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) fix electrode/conq, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
+   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop       f_conq[1]      f_conq[2]         v_dv     
+         0   0              0              25137446       25137446      -1              1             -9.931852       10.097344      20.029196    
+        50   20.206425      72.797911      25137263       25137472      -1              1             -9.4359366      9.5964514      19.032388    
+       100   55.931663      201.50563      25136961       25137537      -1              1             -8.0440112      8.1861787      16.23019     
+       150   81.389273      293.22204      25136818       25137656      -1              1             -6.1113109      6.2267114      12.338022    
+       200   92.867946      334.57639      25136841       25137798      -1              1             -4.1857807      4.2740694      8.4598501    
+       250   97.518304      351.33028      25136942       25137946      -1              1             -2.8383703      2.9101475      5.7485179    
+       300   102.36577      368.79431      25137045       25138099      -1              1             -2.3831643      2.4461115      4.8292759    
+       350   113.66597      409.50566      25137086       25138256      -1              1             -2.7083563      2.7457811      5.4541374    
+       400   122.8443       442.57252      25137148       25138413      -1              1             -3.4311003      3.3941657      6.825266     
+       450   128.63713      463.44243      25137235       25138560      -1              1             -4.132871       3.9852959      8.1181669    
+       500   131.18361      472.61665      25137344       25138695      -1              1             -4.5104095      4.2567261      8.7671355    
+Loop time of 89.4461 on 1 procs for 500 steps with 3776 atoms
+
+Performance: 0.483 ns/day, 49.692 hours/ns, 5.590 timesteps/s, 21.108 katom-step/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 19.404     | 19.404     | 19.404     |   0.0 | 21.69
+Bond    | 0.0014902  | 0.0014902  | 0.0014902  |   0.0 |  0.00
+Kspace  | 35.449     | 35.449     | 35.449     |   0.0 | 39.63
+Neigh   | 0.26499    | 0.26499    | 0.26499    |   0.0 |  0.30
+Comm    | 0.068497   | 0.068497   | 0.068497   |   0.0 |  0.08
+Output  | 0.0023974  | 0.0023974  | 0.0023974  |   0.0 |  0.00
+Modify  | 34.225     | 34.225     | 34.225     |   0.0 | 38.26
+Other   |            | 0.03044    |            |       |  0.03
+
+Nlocal:           3776 ave        3776 max        3776 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          12510 ave       12510 max       12510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1725588
+Ave neighs/atom = 456.98835
+Ave special neighs/atom = 0.50847458
+Neighbor list builds = 6
+Dangerous builds = 0
+Total wall time: 0:01:48

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.4

@@ -0,0 +1,187 @@
+LAMMPS (3 Nov 2022)
+# electrodes with constrained total charges
+# for graphene-ionic liquid supercapacitor
+
+boundary p p f # slab calculation
+include settings.mod # styles, groups, computes and fixes
+# set boundary in main script because ffield is periodic
+units real
+# distribute electrode atoms among all processors:
+if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
+processors * * 2
+
+atom_style full
+pair_style lj/cut/coul/long 16
+bond_style harmonic
+angle_style harmonic
+kspace_style pppm/electrode 1e-7
+# kspace_modify in main script because ffield is periodic
+
+read_data "data.graph-il"
+Reading data file ...
+  orthogonal box = (0 0 -68) to (32.2 34.4 68)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  3776 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  640 bonds
+  reading angles ...
+  320 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.002 seconds
+  read_data CPU = 0.034 seconds
+
+# replicate 4 4 1 # test different sys sizes
+
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
+416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
+
+group bmi type 1 2 3
+960 atoms in group bmi
+group electrolyte type 1 2 3 4
+1280 atoms in group electrolyte
+
+fix nvt electrolyte nvt temp 500.0 500.0 100
+fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+     320 = # of frozen angles
+  find clusters CPU = 0.002 seconds
+
+variable q atom q
+compute qtop top reduce sum v_q
+compute qbot bot reduce sum v_q
+compute ctemp electrolyte temp
+kspace_modify slab 3.0
+
+fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on
+832 atoms in group conp_group
+variable dv equal f_conq[2]-f_conq[1]
+# symm on and off give different electrode potentials, but identical potential difference
+
+thermo 50
+thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv
+run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM/electrode initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.20904498
+  grid = 32 32 200
+  stencil order = 5
+  estimated absolute RMS force accuracy = 3.7023506e-05
+  estimated relative force accuracy = 1.1149519e-07
+  using double precision MKL FFT
+  3d grid and FFT values/proc = 151593 85504
+Generated 15 of 15 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 = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 4 4 16
+  3 neighbor lists, perpetual/occasional/extra = 2 1 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) fix electrode/conq, occasional, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) fix electrode/conq, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
+   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop       f_conq[1]      f_conq[2]         v_dv     
+         0   0              0              25137446       25137446      -1              1             -9.931852       10.097344      20.029196    
+        50   20.206425      72.797911      25137263       25137472      -1              1             -9.4359366      9.5964514      19.032388    
+       100   55.931663      201.50563      25136961       25137537      -1              1             -8.0440112      8.1861787      16.23019     
+       150   81.389273      293.22204      25136818       25137656      -1              1             -6.1113109      6.2267114      12.338022    
+       200   92.867946      334.57639      25136841       25137798      -1              1             -4.1857807      4.2740694      8.4598501    
+       250   97.518304      351.33028      25136942       25137946      -1              1             -2.8383703      2.9101475      5.7485179    
+       300   102.36577      368.79431      25137045       25138099      -1              1             -2.3831643      2.4461115      4.8292759    
+       350   113.66597      409.50566      25137086       25138256      -1              1             -2.7083563      2.7457811      5.4541374    
+       400   122.8443       442.57252      25137148       25138413      -1              1             -3.4311003      3.3941657      6.825266     
+       450   128.63713      463.44243      25137235       25138560      -1              1             -4.132871       3.9852959      8.1181669    
+       500   131.18361      472.61665      25137344       25138695      -1              1             -4.5104095      4.2567261      8.7671355    
+Loop time of 53.4299 on 4 procs for 500 steps with 3776 atoms
+
+Performance: 0.809 ns/day, 29.683 hours/ns, 9.358 timesteps/s, 35.336 katom-step/s
+74.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.5806     | 5.8872     | 6.1547     |   8.8 | 11.02
+Bond    | 0.0011404  | 0.0012245  | 0.0012898  |   0.2 |  0.00
+Kspace  | 26.55      | 26.822     | 27.129     |   4.1 | 50.20
+Neigh   | 0.098647   | 0.099673   | 0.10083    |   0.3 |  0.19
+Comm    | 0.35493    | 0.37282    | 0.3909     |   2.1 |  0.70
+Output  | 0.0012274  | 0.001617   | 0.0026374  |   1.5 |  0.00
+Modify  | 20.172     | 20.188     | 20.203     |   0.3 | 37.78
+Other   |            | 0.05647    |            |       |  0.11
+
+Nlocal:            944 ave         948 max         940 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:         5920.5 ave        5941 max        5899 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:         431397 ave      442329 max      421103 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 1725588
+Ave neighs/atom = 456.98835
+Ave special neighs/atom = 0.50847458
+Neighbor list builds = 6
+Dangerous builds = 0
+Total wall time: 0:00:59

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.1

@@ -0,0 +1,193 @@
+LAMMPS (3 Nov 2022)
+# electrodes with constrained total charges imposed from dynamically computed potentials
+# for graphene-ionic liquid supercapacitor
+
+boundary p p f # slab calculation
+include settings.mod # styles, groups, computes and fixes
+# set boundary in main script because ffield is periodic
+units real
+# distribute electrode atoms among all processors:
+if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
+
+atom_style full
+pair_style lj/cut/coul/long 16
+bond_style harmonic
+angle_style harmonic
+kspace_style pppm/electrode 1e-7
+# kspace_modify in main script because ffield is periodic
+
+read_data "data.graph-il"
+Reading data file ...
+  orthogonal box = (0 0 -68) to (32.2 34.4 68)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  3776 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  640 bonds
+  reading angles ...
+  320 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.002 seconds
+  read_data CPU = 0.022 seconds
+
+# replicate 4 4 1 # test different sys sizes
+
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
+416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
+
+group bmi type 1 2 3
+960 atoms in group bmi
+group electrolyte type 1 2 3 4
+1280 atoms in group electrolyte
+
+fix nvt electrolyte nvt temp 500.0 500.0 100
+fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+     320 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+
+variable q atom q
+compute qtop top reduce sum v_q
+compute qbot bot reduce sum v_q
+compute ctemp electrolyte temp
+kspace_modify slab 3.0
+
+fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on
+832 atoms in group conp_group
+
+variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge
+variable qex_top equal  1.0-f_conp[2][1] # difference between desired and 0V charge
+
+# calculate imposed potential as elastance * excess charge
+# note: fix will wait until the run setup to look for its potential variables
+# which is why we can define variable names *after* fix conp without error
+variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top
+variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top
+
+thermo 50
+thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
+run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM/electrode initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.20904498
+  grid = 32 32 200
+  stencil order = 5
+  estimated absolute RMS force accuracy = 3.7023506e-05
+  estimated relative force accuracy = 1.1149519e-07
+  using double precision MKL FFT
+  3d grid and FFT values/proc = 307242 204800
+Generated 15 of 15 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 = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 4 4 16
+  3 neighbor lists, perpetual/occasional/extra = 2 1 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) fix electrode/conp, occasional, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) fix electrode/conp, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
+   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop         v_vbot         v_vtop    
+         0   0              0              25137446       25137446      -1              1             -9.931852       10.097344    
+        50   20.206425      72.797911      25137263       25137472      -1              1             -9.4359366      9.5964514    
+       100   55.931663      201.50563      25136961       25137537      -1              1             -8.0440112      8.1861787    
+       150   81.389273      293.22204      25136818       25137656      -1              1             -6.1113109      6.2267114    
+       200   92.867946      334.57639      25136841       25137798      -1              1             -4.1857807      4.2740694    
+       250   97.518304      351.33028      25136942       25137946      -1              1             -2.8383703      2.9101475    
+       300   102.36577      368.79431      25137045       25138099      -1              1             -2.3831643      2.4461115    
+       350   113.66597      409.50566      25137086       25138256      -1              1             -2.7083563      2.7457811    
+       400   122.8443       442.57252      25137148       25138413      -1              1             -3.4311003      3.3941657    
+       450   128.63713      463.44243      25137235       25138560      -1              1             -4.132871       3.9852959    
+       500   131.18361      472.61665      25137344       25138695      -1              1             -4.5104095      4.2567261    
+Loop time of 85.5691 on 1 procs for 500 steps with 3776 atoms
+
+Performance: 0.505 ns/day, 47.538 hours/ns, 5.843 timesteps/s, 22.064 katom-step/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 18.558     | 18.558     | 18.558     |   0.0 | 21.69
+Bond    | 0.001404   | 0.001404   | 0.001404   |   0.0 |  0.00
+Kspace  | 33.78      | 33.78      | 33.78      |   0.0 | 39.48
+Neigh   | 0.27017    | 0.27017    | 0.27017    |   0.0 |  0.32
+Comm    | 0.067438   | 0.067438   | 0.067438   |   0.0 |  0.08
+Output  | 0.0026656  | 0.0026656  | 0.0026656  |   0.0 |  0.00
+Modify  | 32.86      | 32.86      | 32.86      |   0.0 | 38.40
+Other   |            | 0.02916    |            |       |  0.03
+
+Nlocal:           3776 ave        3776 max        3776 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          12510 ave       12510 max       12510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1725588
+Ave neighs/atom = 456.98835
+Ave special neighs/atom = 0.50847458
+Neighbor list builds = 6
+Dangerous builds = 0
+Total wall time: 0:01:42

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.4

@@ -0,0 +1,194 @@
+LAMMPS (3 Nov 2022)
+# electrodes with constrained total charges imposed from dynamically computed potentials
+# for graphene-ionic liquid supercapacitor
+
+boundary p p f # slab calculation
+include settings.mod # styles, groups, computes and fixes
+# set boundary in main script because ffield is periodic
+units real
+# distribute electrode atoms among all processors:
+if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
+processors * * 2
+
+atom_style full
+pair_style lj/cut/coul/long 16
+bond_style harmonic
+angle_style harmonic
+kspace_style pppm/electrode 1e-7
+# kspace_modify in main script because ffield is periodic
+
+read_data "data.graph-il"
+Reading data file ...
+  orthogonal box = (0 0 -68) to (32.2 34.4 68)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  3776 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  640 bonds
+  reading angles ...
+  320 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.005 seconds
+  read_data CPU = 0.044 seconds
+
+# replicate 4 4 1 # test different sys sizes
+
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
+416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
+
+group bmi type 1 2 3
+960 atoms in group bmi
+group electrolyte type 1 2 3 4
+1280 atoms in group electrolyte
+
+fix nvt electrolyte nvt temp 500.0 500.0 100
+fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+     320 = # of frozen angles
+  find clusters CPU = 0.002 seconds
+
+variable q atom q
+compute qtop top reduce sum v_q
+compute qbot bot reduce sum v_q
+compute ctemp electrolyte temp
+kspace_modify slab 3.0
+
+fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on
+832 atoms in group conp_group
+
+variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge
+variable qex_top equal  1.0-f_conp[2][1] # difference between desired and 0V charge
+
+# calculate imposed potential as elastance * excess charge
+# note: fix will wait until the run setup to look for its potential variables
+# which is why we can define variable names *after* fix conp without error
+variable vbot equal f_conp[1][4]*v_qex_bot+f_conp[1][5]*v_qex_top
+variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top
+
+thermo 50
+thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
+run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM/electrode initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.20904498
+  grid = 32 32 200
+  stencil order = 5
+  estimated absolute RMS force accuracy = 3.7023506e-05
+  estimated relative force accuracy = 1.1149519e-07
+  using double precision MKL FFT
+  3d grid and FFT values/proc = 151593 85504
+Generated 15 of 15 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 = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 4 4 16
+  3 neighbor lists, perpetual/occasional/extra = 2 1 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) fix electrode/conp, occasional, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) fix electrode/conp, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
+   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop         v_vbot         v_vtop    
+         0   0              0              25137446       25137446      -1              1             -9.931852       10.097344    
+        50   20.206425      72.797911      25137263       25137472      -1              1             -9.4359366      9.5964514    
+       100   55.931663      201.50563      25136961       25137537      -1              1             -8.0440112      8.1861787    
+       150   81.389273      293.22204      25136818       25137656      -1              1             -6.1113109      6.2267114    
+       200   92.867946      334.57639      25136841       25137798      -1              1             -4.1857807      4.2740694    
+       250   97.518304      351.33028      25136942       25137946      -1              1             -2.8383703      2.9101475    
+       300   102.36577      368.79431      25137045       25138099      -1              1             -2.3831643      2.4461115    
+       350   113.66597      409.50566      25137086       25138256      -1              1             -2.7083563      2.7457811    
+       400   122.8443       442.57252      25137148       25138413      -1              1             -3.4311003      3.3941657    
+       450   128.63713      463.44243      25137235       25138560      -1              1             -4.132871       3.9852959    
+       500   131.18361      472.61665      25137344       25138695      -1              1             -4.5104095      4.2567261    
+Loop time of 54.0351 on 4 procs for 500 steps with 3776 atoms
+
+Performance: 0.799 ns/day, 30.019 hours/ns, 9.253 timesteps/s, 34.940 katom-step/s
+75.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.5878     | 6.8799     | 7.1455     |   8.0 | 12.73
+Bond    | 0.0011081  | 0.0014187  | 0.0018792  |   0.8 |  0.00
+Kspace  | 25.907     | 26.173     | 26.464     |   4.1 | 48.44
+Neigh   | 0.16417    | 0.16425    | 0.16438    |   0.0 |  0.30
+Comm    | 0.34948    | 0.36296    | 0.37524    |   1.9 |  0.67
+Output  | 0.0017398  | 0.0021707  | 0.0033966  |   1.5 |  0.00
+Modify  | 20.392     | 20.403     | 20.416     |   0.2 | 37.76
+Other   |            | 0.04783    |            |       |  0.09
+
+Nlocal:            944 ave         948 max         940 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:         5920.5 ave        5941 max        5899 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:         431397 ave      442329 max      421103 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 1725588
+Ave neighs/atom = 456.98835
+Ave special neighs/atom = 0.50847458
+Neighbor list builds = 6
+Dangerous builds = 0
+Total wall time: 0:01:00

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential and smart neighborlists
 # for graphene-ionic liquid supercapacitor
 
@@ -37,13 +37,20 @@ 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 = 0.002 seconds
-  read_data CPU = 0.024 seconds
+  read_data CPU = 0.021 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
@@ -64,12 +72,41 @@ compute qbot bot reduce sum v_q
 compute ctemp electrolyte temp
 kspace_modify slab 3.0
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on
 832 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20904498
@@ -79,9 +116,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.1149519e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 307242 204800
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -102,35 +139,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
-         0   0              0              25137191       25137191       0.0085142912  -0.0085142912 
+         0   0              0              25137190       25137190       0.0085142912  -0.0085142912 
         50   17.83755       64.26354       25137031       25137214       0.0045923944  -0.0045923944 
-       100   48.393682      174.34846      25136774       25137273      -0.009514517    0.009514517  
+       100   48.393682      174.34846      25136775       25137273      -0.009514517    0.009514517  
-       150   70.421272      253.7075       25136655       25137380      -0.033017005    0.033017005  
+       150   70.421272      253.7075       25136657       25137382      -0.033017005    0.033017005  
-       200   82.204844      296.16031      25136667       25137514      -0.063668175    0.063668175  
+       200   82.204844      296.16031      25136670       25137517      -0.063668175    0.063668175  
-       250   87.54223       315.38937      25136757       25137659      -0.096776257    0.096776257  
+       250   87.54223       315.38937      25136762       25137663      -0.096776257    0.096776257  
-       300   91.704746      330.38571      25136865       25137810      -0.1283784      0.1283784    
+       300   91.704746      330.38571      25136871       25137816      -0.1283784      0.1283784    
-       350   100.36017      361.56871      25136934       25137968      -0.15649799     0.15649799   
+       350   100.36017      361.56871      25136942       25137975      -0.15649799     0.15649799   
-       400   111.37575      401.25467      25136986       25138133      -0.18065435     0.18065435   
+       400   111.37575      401.25467      25136994       25138141      -0.18065435     0.18065435   
-       450   121.79848      438.80476      25137043       25138298      -0.19979365     0.19979365   
+       450   121.79848      438.80476      25137052       25138307      -0.19979365     0.19979365   
-       500   126.95916      457.39718      25137145       25138453      -0.21037535     0.21037535   
+       500   126.95916      457.39718      25137155       25138463      -0.21037535     0.21037535   
-Loop time of 63.497 on 1 procs for 500 steps with 3776 atoms
+Loop time of 87.0709 on 1 procs for 500 steps with 3776 atoms
 
-Performance: 0.680 ns/day, 35.276 hours/ns, 7.874 timesteps/s
+Performance: 0.496 ns/day, 48.373 hours/ns, 5.742 timesteps/s, 21.683 katom-step/s
-393.9% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 20.628     | 20.628     | 20.628     |   0.0 | 32.49
+Pair    | 18.617     | 18.617     | 18.617     |   0.0 | 21.38
-Bond    | 0.0019309  | 0.0019309  | 0.0019309  |   0.0 |  0.00
+Bond    | 0.0014056  | 0.0014056  | 0.0014056  |   0.0 |  0.00
-Kspace  | 23.61      | 23.61      | 23.61      |   0.0 | 37.18
+Kspace  | 34.856     | 34.856     | 34.856     |   0.0 | 40.03
-Neigh   | 0.28156    | 0.28156    | 0.28156    |   0.0 |  0.44
+Neigh   | 0.30015    | 0.30015    | 0.30015    |   0.0 |  0.34
-Comm    | 0.061191   | 0.061191   | 0.061191   |   0.0 |  0.10
+Comm    | 0.065303   | 0.065303   | 0.065303   |   0.0 |  0.08
-Output  | 0.0022666  | 0.0022666  | 0.0022666  |   0.0 |  0.00
+Output  | 0.0021663  | 0.0021663  | 0.0021663  |   0.0 |  0.00
-Modify  | 18.891     | 18.891     | 18.891     |   0.0 | 29.75
+Modify  | 33.201     | 33.201     | 33.201     |   0.0 | 38.13
-Other   |            | 0.02047    |            |       |  0.03
+Other   |            | 0.0282     |            |       |  0.03
 
 Nlocal:           3776 ave        3776 max        3776 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -144,4 +181,4 @@ Ave neighs/atom = 457.18432
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 7
 Dangerous builds = 0
-Total wall time: 0:02:24
+Total wall time: 0:01:43

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential and smart neighborlists
 # for graphene-ionic liquid supercapacitor
 
@@ -38,13 +38,20 @@ 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 = 0.004 seconds
-  read_data CPU = 0.016 seconds
+  read_data CPU = 0.047 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
      320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.005 seconds
 
 variable q atom q
 compute qtop top reduce sum v_q
@@ -65,12 +73,41 @@ compute qbot bot reduce sum v_q
 compute ctemp electrolyte temp
 kspace_modify slab 3.0
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on
 832 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20904498
@@ -80,9 +117,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.1149519e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 151593 85504
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -103,35 +140,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
-         0   0              0              25137191       25137191       0.0085142912  -0.0085142912 
+         0   0              0              25137190       25137190       0.0085142912  -0.0085142912 
         50   17.83755       64.26354       25137031       25137214       0.0045923944  -0.0045923944 
-       100   48.393682      174.34846      25136774       25137273      -0.009514517    0.009514517  
+       100   48.393682      174.34846      25136775       25137273      -0.009514517    0.009514517  
-       150   70.421272      253.7075       25136655       25137380      -0.033017005    0.033017005  
+       150   70.421272      253.7075       25136657       25137382      -0.033017005    0.033017005  
-       200   82.204844      296.16031      25136667       25137514      -0.063668175    0.063668175  
+       200   82.204844      296.16031      25136670       25137517      -0.063668175    0.063668175  
-       250   87.54223       315.38937      25136757       25137659      -0.096776257    0.096776257  
+       250   87.54223       315.38937      25136762       25137663      -0.096776257    0.096776257  
-       300   91.704746      330.38571      25136865       25137810      -0.1283784      0.1283784    
+       300   91.704746      330.38571      25136871       25137816      -0.1283784      0.1283784    
-       350   100.36017      361.56871      25136934       25137968      -0.15649799     0.15649799   
+       350   100.36017      361.56871      25136942       25137975      -0.15649799     0.15649799   
-       400   111.37575      401.25467      25136986       25138133      -0.18065435     0.18065435   
+       400   111.37575      401.25467      25136994       25138141      -0.18065435     0.18065435   
-       450   121.79848      438.80476      25137043       25138298      -0.19979365     0.19979365   
+       450   121.79848      438.80476      25137052       25138307      -0.19979365     0.19979365   
-       500   126.95916      457.39718      25137145       25138453      -0.21037535     0.21037535   
+       500   126.95916      457.39718      25137155       25138463      -0.21037535     0.21037535   
-Loop time of 30.7883 on 4 procs for 500 steps with 3776 atoms
+Loop time of 48.4075 on 4 procs for 500 steps with 3776 atoms
 
-Performance: 1.403 ns/day, 17.105 hours/ns, 16.240 timesteps/s
+Performance: 0.892 ns/day, 26.893 hours/ns, 10.329 timesteps/s, 39.002 katom-step/s
-94.1% CPU use with 4 MPI tasks x no OpenMP threads
+75.3% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 6.5102     | 6.7303     | 6.9362     |   7.6 | 21.86
+Pair    | 5.3095     | 5.5504     | 5.7923     |   8.2 | 11.47
-Bond    | 0.00064504 | 0.00071061 | 0.000779   |   0.0 |  0.00
+Bond    | 0.0011128  | 0.0012414  | 0.0014028  |   0.3 |  0.00
-Kspace  | 14.081     | 14.287     | 14.507     |   5.2 | 46.40
+Kspace  | 24.084     | 24.322     | 24.559     |   3.9 | 50.24
-Neigh   | 0.11831    | 0.11841    | 0.11851    |   0.0 |  0.38
+Neigh   | 0.093557   | 0.09408    | 0.094377   |   0.1 |  0.19
-Comm    | 0.12216    | 0.12434    | 0.12651    |   0.6 |  0.40
+Comm    | 0.30394    | 0.31319    | 0.3225     |   1.6 |  0.65
-Output  | 0.00083347 | 0.0010533  | 0.0017069  |   1.2 |  0.00
+Output  | 0.0012719  | 0.0015908  | 0.0024592  |   1.3 |  0.00
-Modify  | 9.5052     | 9.5071     | 9.5093     |   0.1 | 30.88
+Modify  | 18.066     | 18.079     | 18.091     |   0.2 | 37.35
-Other   |            | 0.01927    |            |       |  0.06
+Other   |            | 0.04692    |            |       |  0.10
 
 Nlocal:            944 ave         951 max         941 min
 Histogram: 1 2 0 0 0 0 0 0 0 1
@@ -145,4 +182,4 @@ Ave neighs/atom = 457.18432
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 7
 Dangerous builds = 0
-Total wall time: 0:00:56
+Total wall time: 0:00:54

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential using finite field
 # for z-periodic graphene-ionic liquid supercapacitor
 
@@ -37,13 +37,20 @@ 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 = 0.002 seconds
-  read_data CPU = 0.022 seconds
+  read_data CPU = 0.021 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
@@ -63,12 +71,41 @@ compute qtop top reduce sum v_q
 compute qbot bot reduce sum v_q
 compute ctemp electrolyte temp
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes
 832 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20949995
@@ -78,9 +115,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.0544465e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 147537 92160
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -101,35 +138,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 49.5 | 49.5 | 49.5 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 46.1 | 46.1 | 46.1 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
-         0   0              0              25137187       25137187       0.0085209384  -0.0085209384 
+         0   0              0              25137186       25137186       0.0085209384  -0.0085209384 
-        50   17.837642      64.263873      25137027       25137211       0.0045513522  -0.0045513522 
+        50   17.837642      64.263873      25137027       25137210       0.0045513522  -0.0045513522 
-       100   48.393984      174.34955      25136771       25137269      -0.0097291786   0.0097291786 
+       100   48.393984      174.34955      25136771       25137270      -0.0097291786   0.0097291786 
-       150   70.421823      253.70949      25136651       25137377      -0.033522793    0.033522793  
+       150   70.421823      253.70949      25136653       25137378      -0.033522793    0.033522793  
-       200   82.205535      296.1628       25136664       25137510      -0.064555648    0.064555648  
+       200   82.205535      296.1628       25136667       25137513      -0.064555648    0.064555648  
-       250   87.542843      315.39158      25136754       25137655      -0.098075546    0.098075546  
+       250   87.542843      315.39158      25136758       25137660      -0.098075546    0.098075546  
-       300   91.705733      330.38927      25136862       25137806      -0.13006751     0.13006751   
+       300   91.705733      330.38927      25136868       25137812      -0.13006751     0.13006751   
-       350   100.36128      361.5727       25136930       25137964      -0.15852814     0.15852814   
+       350   100.36128      361.5727       25136938       25137971      -0.15852814     0.15852814   
-       400   111.37586      401.25505      25136982       25138129      -0.18297207     0.18297207   
+       400   111.37586      401.25505      25136990       25138137      -0.18297207     0.18297207   
-       450   121.79814      438.80351      25137039       25138294      -0.2023394      0.2023394    
+       450   121.79814      438.80351      25137049       25138303      -0.2023394      0.2023394    
-       500   126.95882      457.39597      25137142       25138449      -0.21305221     0.21305221   
+       500   126.95882      457.39597      25137151       25138459      -0.21305221     0.21305221   
-Loop time of 36.7618 on 1 procs for 500 steps with 3776 atoms
+Loop time of 53.8411 on 1 procs for 500 steps with 3776 atoms
 
-Performance: 1.175 ns/day, 20.423 hours/ns, 13.601 timesteps/s
+Performance: 0.802 ns/day, 29.912 hours/ns, 9.287 timesteps/s, 35.066 katom-step/s
-393.9% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 19.737     | 19.737     | 19.737     |   0.0 | 53.69
+Pair    | 19.843     | 19.843     | 19.843     |   0.0 | 36.85
-Bond    | 0.00092668 | 0.00092668 | 0.00092668 |   0.0 |  0.00
+Bond    | 0.0016963  | 0.0016963  | 0.0016963  |   0.0 |  0.00
-Kspace  | 6.5854     | 6.5854     | 6.5854     |   0.0 | 17.91
+Kspace  | 11.232     | 11.232     | 11.232     |   0.0 | 20.86
-Neigh   | 0.33914    | 0.33914    | 0.33914    |   0.0 |  0.92
+Neigh   | 0.39189    | 0.39189    | 0.39189    |   0.0 |  0.73
-Comm    | 0.090124   | 0.090124   | 0.090124   |   0.0 |  0.25
+Comm    | 0.12348    | 0.12348    | 0.12348    |   0.0 |  0.23
-Output  | 0.0013975  | 0.0013975  | 0.0013975  |   0.0 |  0.00
+Output  | 0.0017904  | 0.0017904  | 0.0017904  |   0.0 |  0.00
-Modify  | 9.9834     | 9.9834     | 9.9834     |   0.0 | 27.16
+Modify  | 22.207     | 22.207     | 22.207     |   0.0 | 41.25
-Other   |            | 0.02455    |            |       |  0.07
+Other   |            | 0.04008    |            |       |  0.07
 
 Nlocal:           3776 ave        3776 max        3776 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -143,4 +180,4 @@ Ave neighs/atom = 493.56224
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 7
 Dangerous builds = 0
-Total wall time: 0:01:39
+Total wall time: 0:01:10

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with constant potential using finite field
 # for z-periodic graphene-ionic liquid supercapacitor
 
@@ -38,13 +38,20 @@ 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 = 0.002 seconds
-  read_data CPU = 0.016 seconds
+  read_data CPU = 0.033 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -53,23 +60,53 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
      320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.002 seconds
 
 variable q atom q
 compute qtop top reduce sum v_q
 compute qbot bot reduce sum v_q
 compute ctemp electrolyte temp
 
-fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes
+fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes
 832 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20949995
@@ -79,9 +116,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.0544465e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 46644 23552
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -102,35 +139,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 21.96 | 22.27 | 22.77 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 21.23 | 21.34 | 21.65 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
-         0   0              0              25137187       25137187       0.0085209384  -0.0085209384 
+         0   0              0              25137186       25137186       0.0085209384  -0.0085209384 
-        50   17.837642      64.263873      25137027       25137211       0.0045513522  -0.0045513522 
+        50   17.837642      64.263873      25137027       25137210       0.0045513522  -0.0045513522 
-       100   48.393984      174.34955      25136771       25137269      -0.0097291786   0.0097291786 
+       100   48.393984      174.34955      25136771       25137270      -0.0097291786   0.0097291786 
-       150   70.421823      253.70949      25136651       25137377      -0.033522793    0.033522793  
+       150   70.421823      253.70949      25136653       25137378      -0.033522793    0.033522793  
-       200   82.205535      296.1628       25136664       25137510      -0.064555648    0.064555648  
+       200   82.205535      296.1628       25136667       25137513      -0.064555648    0.064555648  
-       250   87.542843      315.39158      25136754       25137655      -0.098075546    0.098075546  
+       250   87.542843      315.39158      25136758       25137660      -0.098075546    0.098075546  
-       300   91.705733      330.38927      25136862       25137806      -0.13006751     0.13006751   
+       300   91.705733      330.38927      25136868       25137812      -0.13006751     0.13006751   
-       350   100.36128      361.5727       25136930       25137964      -0.15852814     0.15852814   
+       350   100.36128      361.5727       25136938       25137971      -0.15852814     0.15852814   
-       400   111.37586      401.25505      25136982       25138129      -0.18297207     0.18297207   
+       400   111.37586      401.25505      25136990       25138137      -0.18297207     0.18297207   
-       450   121.79814      438.80351      25137039       25138294      -0.2023394      0.2023394    
+       450   121.79814      438.80351      25137049       25138303      -0.2023394      0.2023394    
-       500   126.95882      457.39597      25137142       25138449      -0.21305221     0.21305221   
+       500   126.95882      457.39597      25137151       25138459      -0.21305221     0.21305221   
-Loop time of 19.3932 on 4 procs for 500 steps with 3776 atoms
+Loop time of 26.2807 on 4 procs for 500 steps with 3776 atoms
 
-Performance: 2.228 ns/day, 10.774 hours/ns, 25.782 timesteps/s
+Performance: 1.644 ns/day, 14.600 hours/ns, 19.025 timesteps/s, 71.840 katom-step/s
-96.3% CPU use with 4 MPI tasks x no OpenMP threads
+83.1% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 7.1247     | 7.6399     | 8.1323     |  13.3 | 39.39
+Pair    | 5.8233     | 6.1941     | 6.6294     |  12.1 | 23.57
-Bond    | 0.00072445 | 0.00077581 | 0.00085933 |   0.0 |  0.00
+Bond    | 0.0010807  | 0.0011705  | 0.0013494  |   0.3 |  0.00
-Kspace  | 5.098      | 5.5905     | 6.1036     |  15.6 | 28.83
+Kspace  | 8.0325     | 8.4703     | 8.8457     |  10.4 | 32.23
-Neigh   | 0.145      | 0.14517    | 0.14532    |   0.0 |  0.75
+Neigh   | 0.14184    | 0.1421     | 0.14238    |   0.1 |  0.54
-Comm    | 0.24683    | 0.25127    | 0.25907    |   1.0 |  1.30
+Comm    | 0.52248    | 0.54323    | 0.56352    |   2.7 |  2.07
-Output  | 0.00084146 | 0.0011298  | 0.0019741  |   1.5 |  0.01
+Output  | 0.00079782 | 0.0011547  | 0.0021987  |   1.8 |  0.00
-Modify  | 5.6957     | 5.7129     | 5.729      |   0.6 | 29.46
+Modify  | 10.831     | 10.856     | 10.881     |   0.7 | 41.31
-Other   |            | 0.05153    |            |       |  0.27
+Other   |            | 0.07293    |            |       |  0.28
 
 Nlocal:            944 ave         951 max         941 min
 Histogram: 1 2 0 0 0 0 0 0 0 1
@@ -144,4 +181,4 @@ Ave neighs/atom = 493.56224
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 7
 Dangerous builds = 0
-Total wall time: 0:00:44
+Total wall time: 0:00:32

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with equal-style ramped (electrode-)constant potential
 # for graphene-ionic liquid supercapacitor
 
@@ -37,13 +37,20 @@ 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 = 0.002 seconds
-  read_data CPU = 0.014 seconds
+  read_data CPU = 0.021 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
@@ -65,12 +73,41 @@ compute ctemp electrolyte temp
 kspace_modify slab 3.0
 
 variable v equal ramp(2,4)
-fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5
+fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on
 832 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20904498
@@ -80,9 +117,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.1149519e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 307242 204800
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -103,35 +140,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop          v_v      
-         0   0              0              25137191       25137191       0.0085142912  -0.0085142912   2            
+         0   0              0              25137190       25137190       0.0085142912  -0.0085142912   2            
-        50   17.839699      64.271283      25137031       25137214      -0.0067894391   0.0067894391   2.2          
+        50   17.839699      64.271283      25137031       25137215      -0.0067894391   0.0067894391   2.2          
-       100   48.411618      174.41308      25136774       25137273      -0.033422174    0.033422174    2.4          
+       100   48.411618      174.41308      25136776       25137275      -0.033422174    0.033422174    2.4          
-       150   70.478909      253.91515      25136654       25137380      -0.071583953    0.071583953    2.6          
+       150   70.478909      253.91515      25136658       25137384      -0.071583953    0.071583953    2.6          
-       200   82.322716      296.58497      25136666       25137513      -0.11962095     0.11962095     2.8          
+       200   82.322716      296.58497      25136673       25137521      -0.11962095     0.11962095     2.8          
-       250   87.739905      316.10153      25136754       25137658      -0.17281469     0.17281469     3            
+       250   87.739905      316.10153      25136766       25137670      -0.17281469     0.17281469     3            
-       300   91.974584      331.35786      25136861       25137808      -0.22657123     0.22657123     3.2          
+       300   91.974584      331.35786      25136877       25137825      -0.22657123     0.22657123     3.2          
-       350   100.73048      362.90284      25136928       25137965      -0.27817429     0.27817429     3.4          
+       350   100.73048      362.90284      25136949       25137987      -0.27817429     0.27817429     3.4          
-       400   111.78597      402.73256      25136977       25138129      -0.32659395     0.32659395     3.6          
+       400   111.78597      402.73256      25137004       25138156      -0.32659395     0.32659395     3.6          
-       450   122.14181      440.04167      25137033       25138291      -0.37054363     0.37054363     3.8          
+       450   122.14181      440.04167      25137066       25138324      -0.37054363     0.37054363     3.8          
-       500   127.32331      458.70912      25137133       25138444      -0.40653009     0.40653009     4            
+       500   127.32331      458.70912      25137171       25138482      -0.40653009     0.40653009     4            
-Loop time of 50.8569 on 1 procs for 500 steps with 3776 atoms
+Loop time of 87.6405 on 1 procs for 500 steps with 3776 atoms
 
-Performance: 0.849 ns/day, 28.254 hours/ns, 9.831 timesteps/s
+Performance: 0.493 ns/day, 48.689 hours/ns, 5.705 timesteps/s, 21.543 katom-step/s
-393.5% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 18.166     | 18.166     | 18.166     |   0.0 | 35.72
+Pair    | 18.484     | 18.484     | 18.484     |   0.0 | 21.09
-Bond    | 0.00091918 | 0.00091918 | 0.00091918 |   0.0 |  0.00
+Bond    | 0.0016824  | 0.0016824  | 0.0016824  |   0.0 |  0.00
-Kspace  | 17.267     | 17.267     | 17.267     |   0.0 | 33.95
+Kspace  | 35.426     | 35.426     | 35.426     |   0.0 | 40.42
-Neigh   | 0.27635    | 0.27635    | 0.27635    |   0.0 |  0.54
+Neigh   | 0.30201    | 0.30201    | 0.30201    |   0.0 |  0.34
-Comm    | 0.044714   | 0.044714   | 0.044714   |   0.0 |  0.09
+Comm    | 0.066546   | 0.066546   | 0.066546   |   0.0 |  0.08
-Output  | 0.0018345  | 0.0018345  | 0.0018345  |   0.0 |  0.00
+Output  | 0.0022768  | 0.0022768  | 0.0022768  |   0.0 |  0.00
-Modify  | 15.086     | 15.086     | 15.086     |   0.0 | 29.66
+Modify  | 33.33      | 33.33      | 33.33      |   0.0 | 38.03
-Other   |            | 0.01409    |            |       |  0.03
+Other   |            | 0.0286     |            |       |  0.03
 
 Nlocal:           3776 ave        3776 max        3776 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -145,4 +182,4 @@ Ave neighs/atom = 457.17161
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 7
 Dangerous builds = 0
-Total wall time: 0:01:50
+Total wall time: 0:01:44

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with equal-style ramped (electrode-)constant potential
 # for graphene-ionic liquid supercapacitor
 
@@ -38,13 +38,20 @@ 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 = 0.003 seconds
-  read_data CPU = 0.024 seconds
+  read_data CPU = 0.034 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
      320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.002 seconds
 
 variable q atom q
 compute qtop top reduce sum v_q
@@ -66,12 +74,41 @@ compute ctemp electrolyte temp
 kspace_modify slab 3.0
 
 variable v equal ramp(2,4)
-fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5
+fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on
 832 atoms in group conp_group
 
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20904498
@@ -81,9 +118,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.1149519e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 151593 85504
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -104,35 +141,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop          v_v      
-         0   0              0              25137191       25137191       0.0085142912  -0.0085142912   2            
+         0   0              0              25137190       25137190       0.0085142912  -0.0085142912   2            
-        50   17.839699      64.271283      25137031       25137214      -0.0067894391   0.0067894391   2.2          
+        50   17.839699      64.271283      25137031       25137215      -0.0067894391   0.0067894391   2.2          
-       100   48.411618      174.41308      25136774       25137273      -0.033422174    0.033422174    2.4          
+       100   48.411618      174.41308      25136776       25137275      -0.033422174    0.033422174    2.4          
-       150   70.478909      253.91515      25136654       25137380      -0.071583953    0.071583953    2.6          
+       150   70.478909      253.91515      25136658       25137384      -0.071583953    0.071583953    2.6          
-       200   82.322716      296.58497      25136666       25137513      -0.11962095     0.11962095     2.8          
+       200   82.322716      296.58497      25136673       25137521      -0.11962095     0.11962095     2.8          
-       250   87.739905      316.10153      25136754       25137658      -0.17281469     0.17281469     3            
+       250   87.739905      316.10153      25136766       25137670      -0.17281469     0.17281469     3            
-       300   91.974584      331.35786      25136861       25137808      -0.22657123     0.22657123     3.2          
+       300   91.974584      331.35786      25136877       25137825      -0.22657123     0.22657123     3.2          
-       350   100.73048      362.90284      25136928       25137965      -0.27817429     0.27817429     3.4          
+       350   100.73048      362.90284      25136949       25137987      -0.27817429     0.27817429     3.4          
-       400   111.78597      402.73256      25136977       25138129      -0.32659395     0.32659395     3.6          
+       400   111.78597      402.73256      25137004       25138156      -0.32659395     0.32659395     3.6          
-       450   122.14181      440.04167      25137033       25138291      -0.37054363     0.37054363     3.8          
+       450   122.14181      440.04167      25137066       25138324      -0.37054363     0.37054363     3.8          
-       500   127.32331      458.70912      25137133       25138444      -0.40653009     0.40653009     4            
+       500   127.32331      458.70912      25137171       25138482      -0.40653009     0.40653009     4            
-Loop time of 31.7642 on 4 procs for 500 steps with 3776 atoms
+Loop time of 49.2075 on 4 procs for 500 steps with 3776 atoms
 
-Performance: 1.360 ns/day, 17.647 hours/ns, 15.741 timesteps/s
+Performance: 0.878 ns/day, 27.337 hours/ns, 10.161 timesteps/s, 38.368 katom-step/s
-94.1% CPU use with 4 MPI tasks x no OpenMP threads
+75.7% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 6.7949     | 7.0359     | 7.3092     |   7.9 | 22.15
+Pair    | 5.7517     | 5.9151     | 6.0961     |   6.6 | 12.02
-Bond    | 0.00069874 | 0.00073747 | 0.00077928 |   0.0 |  0.00
+Bond    | 0.0011959  | 0.0013362  | 0.0014512  |   0.2 |  0.00
-Kspace  | 14.375     | 14.648     | 14.89      |   5.5 | 46.12
+Kspace  | 24.223     | 24.404     | 24.566     |   3.2 | 49.59
-Neigh   | 0.12057    | 0.1206     | 0.12062    |   0.0 |  0.38
+Neigh   | 0.10283    | 0.10288    | 0.10301    |   0.0 |  0.21
-Comm    | 0.13412    | 0.13439    | 0.13483    |   0.1 |  0.42
+Comm    | 0.30801    | 0.31944    | 0.33141    |   2.0 |  0.65
-Output  | 0.0010019  | 0.0013088  | 0.0020937  |   1.3 |  0.00
+Output  | 0.0010416  | 0.0014127  | 0.0024086  |   1.5 |  0.00
-Modify  | 9.8017     | 9.8025     | 9.8031     |   0.0 | 30.86
+Modify  | 18.405     | 18.418     | 18.432     |   0.3 | 37.43
-Other   |            | 0.02036    |            |       |  0.06
+Other   |            | 0.04459    |            |       |  0.09
 
 Nlocal:            944 ave         951 max         941 min
 Histogram: 1 2 0 0 0 0 0 0 0 1
@@ -146,4 +183,4 @@ Ave neighs/atom = 457.17161
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 7
 Dangerous builds = 0
-Total wall time: 0:00:58
+Total wall time: 0:00:55

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with thermopotentiostat
 # for graphene-ionic liquid supercapacitor
 
@@ -38,12 +38,19 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.002 seconds
-  read_data CPU = 0.024 seconds
+  read_data CPU = 0.021 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -52,11 +59,12 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
      320 = # of frozen angles
-  find clusters CPU = 0.000 seconds
+  find clusters CPU = 0.001 seconds
 
 variable q atom q
 compute qtop top reduce sum v_q
@@ -65,10 +73,10 @@ compute ctemp electrolyte temp
 kspace_modify slab 3.0
 
 unfix nvt # remove NVT thermostat included from "settings.mod"
-fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng
+fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng
 832 atoms in group conp_group
 # to compare to regular constant potential, switch previous line to this:
-#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on
+#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on
 fix nve electrolyte nve
 
 # note ionic liquid does not reach 500K immediately
@@ -77,6 +85,35 @@ fix nve electrolyte nve
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20904498
@@ -86,9 +123,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.1149519e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 307242 204800
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -109,35 +146,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
-         0   0              0              25137187       25137187       0.12767613    -0.12767613   
+         0   0              0              25137188       25137188       0.12767608    -0.12767608   
-        50   16.63971       59.94807       25137031       25137203       0.11714714    -0.11714714   
+        50   16.63971       59.94807       25137031       25137202       0.11714711    -0.11714711   
-       100   40.785523      146.93846      25136782       25137202       0.1278358     -0.1278358    
+       100   40.785523      146.93846      25136782       25137202       0.12783578    -0.12783578   
-       150   53.394067      192.3634       25136654       25137204       0.080257143   -0.080257143  
+       150   53.394067      192.3634       25136653       25137203       0.080257127   -0.080257127  
-       200   56.419019      203.26143      25136624       25137205       0.024756489   -0.024756489  
+       200   56.419019      203.26143      25136623       25137204       0.024756474   -0.024756474  
-       250   54.922935      197.87147      25136640       25137205      -0.024533719    0.024533719  
+       250   54.922935      197.87147      25136641       25137206      -0.024533734    0.024533734  
-       300   52.884861      190.52888      25136660       25137205      -0.066341094    0.066341094  
+       300   52.884861      190.52888      25136664       25137209      -0.066341109    0.066341109  
-       350   52.41676       188.84244      25136666       25137206      -0.089546252    0.089546252  
+       350   52.41676       188.84244      25136670       25137210      -0.089546266    0.089546266  
-       400   54.366979      195.86852      25136646       25137206      -0.10239753     0.10239753   
+       400   54.366979      195.86852      25136651       25137211      -0.10239755     0.10239755   
-       450   54.906542      197.81241      25136642       25137208      -0.099987401    0.099987401  
+       450   54.906542      197.81241      25136645       25137210      -0.099987411    0.099987411  
-       500   54.33841       195.7656       25136642       25137201      -0.21295942     0.21295942   
+       500   54.33841       195.7656       25136656       25137216      -0.21295943     0.21295943   
-Loop time of 49.9831 on 1 procs for 500 steps with 3776 atoms
+Loop time of 87.5281 on 1 procs for 500 steps with 3776 atoms
 
-Performance: 0.864 ns/day, 27.768 hours/ns, 10.003 timesteps/s
+Performance: 0.494 ns/day, 48.627 hours/ns, 5.712 timesteps/s, 21.570 katom-step/s
-393.3% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 17.01      | 17.01      | 17.01      |   0.0 | 34.03
+Pair    | 18.819     | 18.819     | 18.819     |   0.0 | 21.50
-Bond    | 0.0010374  | 0.0010374  | 0.0010374  |   0.0 |  0.00
+Bond    | 0.0014336  | 0.0014336  | 0.0014336  |   0.0 |  0.00
-Kspace  | 18.096     | 18.096     | 18.096     |   0.0 | 36.20
+Kspace  | 34.891     | 34.891     | 34.891     |   0.0 | 39.86
-Neigh   | 0.1828     | 0.1828     | 0.1828     |   0.0 |  0.37
+Neigh   | 0.21542    | 0.21542    | 0.21542    |   0.0 |  0.25
-Comm    | 0.043856   | 0.043856   | 0.043856   |   0.0 |  0.09
+Comm    | 0.063383   | 0.063383   | 0.063383   |   0.0 |  0.07
-Output  | 0.0018373  | 0.0018373  | 0.0018373  |   0.0 |  0.00
+Output  | 0.0020476  | 0.0020476  | 0.0020476  |   0.0 |  0.00
-Modify  | 14.632     | 14.632     | 14.632     |   0.0 | 29.27
+Modify  | 33.507     | 33.507     | 33.507     |   0.0 | 38.28
-Other   |            | 0.01548    |            |       |  0.03
+Other   |            | 0.0281     |            |       |  0.03
 
 Nlocal:           3776 ave        3776 max        3776 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -151,4 +188,4 @@ Ave neighs/atom = 457.08845
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 5
 Dangerous builds = 0
-Total wall time: 0:01:50
+Total wall time: 0:01:44

examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (3 Nov 2022)
 # electrodes with thermopotentiostat
 # for graphene-ionic liquid supercapacitor
 
@@ -39,12 +39,19 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.002 seconds
-  read_data CPU = 0.025 seconds
+  read_data CPU = 0.036 seconds
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-416 atoms in group bot
+
-group top molecule 642
+variable zpos atom "z > 0"
+group zpos variable zpos
+1891 atoms in group zpos
+group ele type 5
+832 atoms in group ele
+group top intersect ele zpos
 416 atoms in group top
+group bot subtract ele top
+416 atoms in group bot
 
 group bmi type 1 2 3
 960 atoms in group bmi
@@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
 
 fix nvt electrolyte nvt temp 500.0 500.0 100
 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
+Finding SHAKE clusters ...
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
      320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.005 seconds
 
 variable q atom q
 compute qtop top reduce sum v_q
@@ -66,10 +74,10 @@ compute ctemp electrolyte temp
 kspace_modify slab 3.0
 
 unfix nvt # remove NVT thermostat included from "settings.mod"
-fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng
+fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng
 832 atoms in group conp_group
 # to compare to regular constant potential, switch previous line to this:
-#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on
+#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on
 fix nve electrolyte nve
 
 # note ionic liquid does not reach 500K immediately
@@ -78,6 +86,35 @@ fix nve electrolyte nve
 thermo 50
 thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
 run 500
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- kspace_style pppm/electrode command:
+
+@article{Ahrens2021,
+author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0063381},
+title = {{Constant potential simulations on a mesh}},
+journal = {Journal of Chemical Physics},
+year = {2021}
+volume = {155},
+pages = {104104},
+}
+- fix electrode command:
+
+@article{Ahrens2022
+author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
+doi = {10.1063/5.0099239},
+title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
+journal = {The Journal of Chemical Physics},
+year = {2022}
+volume = {157},
+pages = {084801},
+}
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
 PPPM/electrode initialization ...
   using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
   G vector (1/distance) = 0.20904498
@@ -87,9 +124,9 @@ PPPM/electrode initialization ...
   estimated relative force accuracy = 1.1149519e-07
   using double precision MKL FFT
   3d grid and FFT values/proc = 151593 85504
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
+Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 18
   ghost atom cutoff = 18
@@ -110,35 +147,35 @@ Neighbor list info ...
       pair build: skip
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
    Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
-         0   0              0              25137187       25137187       0.12767613    -0.12767613   
+         0   0              0              25137188       25137188       0.12767608    -0.12767608   
-        50   16.63971       59.94807       25137031       25137203       0.11714714    -0.11714714   
+        50   16.63971       59.94807       25137031       25137202       0.11714711    -0.11714711   
-       100   40.785523      146.93846      25136782       25137202       0.1278358     -0.1278358    
+       100   40.785523      146.93846      25136782       25137202       0.12783578    -0.12783578   
-       150   53.394067      192.3634       25136654       25137204       0.080257143   -0.080257143  
+       150   53.394067      192.3634       25136653       25137203       0.080257127   -0.080257127  
-       200   56.419019      203.26143      25136624       25137205       0.024756489   -0.024756489  
+       200   56.419019      203.26143      25136623       25137204       0.024756474   -0.024756474  
-       250   54.922935      197.87147      25136640       25137205      -0.024533719    0.024533719  
+       250   54.922935      197.87147      25136641       25137206      -0.024533734    0.024533734  
-       300   52.884861      190.52888      25136660       25137205      -0.066341094    0.066341094  
+       300   52.884861      190.52888      25136664       25137209      -0.066341109    0.066341109  
-       350   52.41676       188.84244      25136666       25137206      -0.089546252    0.089546252  
+       350   52.41676       188.84244      25136670       25137210      -0.089546266    0.089546266  
-       400   54.366979      195.86852      25136646       25137206      -0.10239753     0.10239753   
+       400   54.366979      195.86852      25136651       25137211      -0.10239755     0.10239755   
-       450   54.906542      197.81241      25136642       25137208      -0.099987401    0.099987401  
+       450   54.906542      197.81241      25136645       25137210      -0.099987411    0.099987411  
-       500   54.33841       195.7656       25136642       25137201      -0.21295942     0.21295942   
+       500   54.33841       195.7656       25136656       25137216      -0.21295943     0.21295943   
-Loop time of 27.6772 on 4 procs for 500 steps with 3776 atoms
+Loop time of 49.2564 on 4 procs for 500 steps with 3776 atoms
 
-Performance: 1.561 ns/day, 15.376 hours/ns, 18.065 timesteps/s
+Performance: 0.877 ns/day, 27.365 hours/ns, 10.151 timesteps/s, 38.330 katom-step/s
-91.7% CPU use with 4 MPI tasks x no OpenMP threads
+76.1% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 4.6214     | 4.8032     | 4.9546     |   6.5 | 17.35
+Pair    | 5.6984     | 5.9083     | 6.1177     |   6.4 | 12.00
-Bond    | 0.0005324  | 0.00060509 | 0.00069468 |   0.0 |  0.00
+Bond    | 0.0011785  | 0.0012201  | 0.0013055  |   0.1 |  0.00
-Kspace  | 13.883     | 14.034     | 14.216     |   3.8 | 50.71
+Kspace  | 24.311     | 24.519     | 24.729     |   3.1 | 49.78
-Neigh   | 0.061704   | 0.061727   | 0.06176    |   0.0 |  0.22
+Neigh   | 0.075406   | 0.075487   | 0.07556    |   0.0 |  0.15
-Comm    | 0.10101    | 0.10374    | 0.10645    |   0.8 |  0.37
+Comm    | 0.29972    | 0.30943    | 0.31881    |   1.7 |  0.63
-Output  | 0.00086818 | 0.0010909  | 0.001715   |   1.1 |  0.00
+Output  | 0.0012474  | 0.001684   | 0.0027062  |   1.5 |  0.00
-Modify  | 8.65       | 8.6524     | 8.6545     |   0.1 | 31.26
+Modify  | 18.377     | 18.384     | 18.391     |   0.2 | 37.32
-Other   |            | 0.02055    |            |       |  0.07
+Other   |            | 0.05679    |            |       |  0.12
 
 Nlocal:            944 ave         951 max         940 min
 Histogram: 1 1 1 0 0 0 0 0 0 1
@@ -152,4 +189,4 @@ Ave neighs/atom = 457.08845
 Ave special neighs/atom = 0.50847458
 Neighbor list builds = 5
 Dangerous builds = 0
-Total wall time: 0:00:50
+Total wall time: 0:00:55

examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.1

@@ -1,153 +0,0 @@
-LAMMPS (24 Mar 2022)
-# electrodes with constrained total charges
-# for graphene-ionic liquid supercapacitor
-
-boundary p p f # slab calculation
-include settings.mod # styles, groups, computes and fixes
-# set boundary in main script because ffield is periodic
-units real
-# distribute electrode atoms among all processors:
-if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
-
-atom_style full
-pair_style lj/cut/coul/long 16
-bond_style harmonic
-angle_style harmonic
-kspace_style pppm/electrode 1e-7
-# kspace_modify in main script because ffield is periodic
-
-read_data "data.graph-il"
-Reading data file ...
-  orthogonal box = (0 0 -68) to (32.2 34.4 68)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  3776 atoms
-  scanning bonds ...
-  2 = max bonds/atom
-  scanning angles ...
-  1 = max angles/atom
-  reading bonds ...
-  640 bonds
-  reading angles ...
-  320 angles
-Finding 1-2 1-3 1-4 neighbors ...
-  special bond factors lj:    0        0        0       
-  special bond factors coul:  0        0        0       
-     2 = max # of 1-2 neighbors
-     1 = max # of 1-3 neighbors
-     1 = max # of 1-4 neighbors
-     2 = max # of special neighbors
-  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.012 seconds
-
-group bot molecule 641
-416 atoms in group bot
-group top molecule 642
-416 atoms in group top
-
-group bmi type 1 2 3
-960 atoms in group bmi
-group electrolyte type 1 2 3 4
-1280 atoms in group electrolyte
-
-fix nvt electrolyte nvt temp 500.0 500.0 100
-fix shake bmi shake 1e-4 20 0 b 1 2 a 1
-       0 = # of size 2 clusters
-       0 = # of size 3 clusters
-       0 = # of size 4 clusters
-     320 = # of frozen angles
-  find clusters CPU = 0.000 seconds
-
-variable q atom q
-compute qtop top reduce sum v_q
-compute qbot bot reduce sum v_q
-compute ctemp electrolyte temp
-kspace_modify slab 3.0
-
-fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
-832 atoms in group conp_group
-
-# ask fix conq to output electrode potentials to internal variables
-variable vbot internal 0.0
-variable vtop internal 0.0
-fix_modify conq set v bot vbot
-fix_modify conq set v top vtop
-
-thermo 50
-thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
-run 500
-PPPM/electrode initialization ...
-  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
-  G vector (1/distance) = 0.20904498
-  grid = 32 32 200
-  stencil order = 5
-  estimated absolute RMS force accuracy = 3.7023506e-05
-  estimated relative force accuracy = 1.1149519e-07
-  using double precision MKL FFT
-  3d grid and FFT values/proc = 307242 204800
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 4 4 16
-  3 neighbor lists, perpetual/occasional/extra = 2 1 0
-  (1) pair lj/cut/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d
-      bin: standard
-  (2) fix electrode/conq, occasional, skip from (1)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) fix electrode/conq, perpetual, skip from (1)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
-   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop         v_vbot         v_vtop    
-         0   0              0              25136984       25136984      -1              1             -9.931852       10.097344    
-        50   20.206425      72.797911      25136825       25137033      -1              1             -9.4359366      9.5964514    
-       100   55.931663      201.50563      25136587       25137163      -1              1             -8.0440112      8.1861787    
-       150   81.389273      293.22204      25136533       25137371      -1              1             -6.1113109      6.2267114    
-       200   92.867946      334.57639      25136646       25137603      -1              1             -4.1857807      4.2740694    
-       250   97.518304      351.33028      25136809       25137814      -1              1             -2.8383703      2.9101475    
-       300   102.36577      368.79431      25136933       25137987      -1              1             -2.3831643      2.4461115    
-       350   113.66597      409.50566      25136960       25138131      -1              1             -2.7083563      2.7457811    
-       400   122.8443       442.57252      25136991       25138256      -1              1             -3.4311003      3.3941657    
-       450   128.63713      463.44243      25137048       25138373      -1              1             -4.132871       3.9852959    
-       500   131.18361      472.61665      25137142       25138493      -1              1             -4.5104095      4.2567261    
-Loop time of 48.9361 on 1 procs for 500 steps with 3776 atoms
-
-Performance: 0.883 ns/day, 27.187 hours/ns, 10.217 timesteps/s
-393.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 17.652     | 17.652     | 17.652     |   0.0 | 36.07
-Bond    | 0.0010418  | 0.0010418  | 0.0010418  |   0.0 |  0.00
-Kspace  | 16.566     | 16.566     | 16.566     |   0.0 | 33.85
-Neigh   | 0.21584    | 0.21584    | 0.21584    |   0.0 |  0.44
-Comm    | 0.04167    | 0.04167    | 0.04167    |   0.0 |  0.09
-Output  | 0.0014585  | 0.0014585  | 0.0014585  |   0.0 |  0.00
-Modify  | 14.445     | 14.445     | 14.445     |   0.0 | 29.52
-Other   |            | 0.0134     |            |       |  0.03
-
-Nlocal:           3776 ave        3776 max        3776 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:          12510 ave       12510 max       12510 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1725588
-Ave neighs/atom = 456.98835
-Ave special neighs/atom = 0.50847458
-Neighbor list builds = 6
-Dangerous builds = 0
-Total wall time: 0:01:43

examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq.g++.4

@@ -1,154 +0,0 @@
-LAMMPS (24 Mar 2022)
-# electrodes with constrained total charges
-# for graphene-ionic liquid supercapacitor
-
-boundary p p f # slab calculation
-include settings.mod # styles, groups, computes and fixes
-# set boundary in main script because ffield is periodic
-units real
-# distribute electrode atoms among all processors:
-if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
-processors * * 2
-
-atom_style full
-pair_style lj/cut/coul/long 16
-bond_style harmonic
-angle_style harmonic
-kspace_style pppm/electrode 1e-7
-# kspace_modify in main script because ffield is periodic
-
-read_data "data.graph-il"
-Reading data file ...
-  orthogonal box = (0 0 -68) to (32.2 34.4 68)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  3776 atoms
-  scanning bonds ...
-  2 = max bonds/atom
-  scanning angles ...
-  1 = max angles/atom
-  reading bonds ...
-  640 bonds
-  reading angles ...
-  320 angles
-Finding 1-2 1-3 1-4 neighbors ...
-  special bond factors lj:    0        0        0       
-  special bond factors coul:  0        0        0       
-     2 = max # of 1-2 neighbors
-     1 = max # of 1-3 neighbors
-     1 = max # of 1-4 neighbors
-     2 = max # of special neighbors
-  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.020 seconds
-
-group bot molecule 641
-416 atoms in group bot
-group top molecule 642
-416 atoms in group top
-
-group bmi type 1 2 3
-960 atoms in group bmi
-group electrolyte type 1 2 3 4
-1280 atoms in group electrolyte
-
-fix nvt electrolyte nvt temp 500.0 500.0 100
-fix shake bmi shake 1e-4 20 0 b 1 2 a 1
-       0 = # of size 2 clusters
-       0 = # of size 3 clusters
-       0 = # of size 4 clusters
-     320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
-
-variable q atom q
-compute qtop top reduce sum v_q
-compute qbot bot reduce sum v_q
-compute ctemp electrolyte temp
-kspace_modify slab 3.0
-
-fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
-832 atoms in group conp_group
-
-# ask fix conq to output electrode potentials to internal variables
-variable vbot internal 0.0
-variable vtop internal 0.0
-fix_modify conq set v bot vbot
-fix_modify conq set v top vtop
-
-thermo 50
-thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
-run 500
-PPPM/electrode initialization ...
-  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
-  G vector (1/distance) = 0.20904498
-  grid = 32 32 200
-  stencil order = 5
-  estimated absolute RMS force accuracy = 3.7023506e-05
-  estimated relative force accuracy = 1.1149519e-07
-  using double precision MKL FFT
-  3d grid and FFT values/proc = 151593 85504
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 4 4 16
-  3 neighbor lists, perpetual/occasional/extra = 2 1 0
-  (1) pair lj/cut/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d
-      bin: standard
-  (2) fix electrode/conq, occasional, skip from (1)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) fix electrode/conq, perpetual, skip from (1)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
-   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop         v_vbot         v_vtop    
-         0   0              0              25136984       25136984      -1              1             -9.931852       10.097344    
-        50   20.206425      72.797911      25136825       25137033      -1              1             -9.4359366      9.5964514    
-       100   55.931663      201.50563      25136587       25137163      -1              1             -8.0440112      8.1861787    
-       150   81.389273      293.22204      25136533       25137371      -1              1             -6.1113109      6.2267114    
-       200   92.867946      334.57639      25136646       25137603      -1              1             -4.1857807      4.2740694    
-       250   97.518304      351.33028      25136809       25137814      -1              1             -2.8383703      2.9101475    
-       300   102.36577      368.79431      25136933       25137987      -1              1             -2.3831643      2.4461115    
-       350   113.66597      409.50566      25136960       25138131      -1              1             -2.7083563      2.7457811    
-       400   122.8443       442.57252      25136991       25138256      -1              1             -3.4311003      3.3941657    
-       450   128.63713      463.44243      25137048       25138373      -1              1             -4.132871       3.9852959    
-       500   131.18361      472.61665      25137142       25138493      -1              1             -4.5104095      4.2567261    
-Loop time of 28.8336 on 4 procs for 500 steps with 3776 atoms
-
-Performance: 1.498 ns/day, 16.019 hours/ns, 17.341 timesteps/s
-94.1% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 5.7721     | 5.9353     | 6.144      |   6.0 | 20.58
-Bond    | 0.00057855 | 0.00067043 | 0.00074793 |   0.0 |  0.00
-Kspace  | 13.485     | 13.694     | 13.857     |   4.0 | 47.49
-Neigh   | 0.092021   | 0.092044   | 0.092068   |   0.0 |  0.32
-Comm    | 0.11486    | 0.11638    | 0.11801    |   0.4 |  0.40
-Output  | 0.00090452 | 0.001109   | 0.0017097  |   1.0 |  0.00
-Modify  | 8.974      | 8.9761     | 8.978      |   0.1 | 31.13
-Other   |            | 0.01837    |            |       |  0.06
-
-Nlocal:            944 ave         948 max         940 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Nghost:         5920.5 ave        5941 max        5899 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Neighs:         431397 ave      442329 max      421103 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 1725588
-Ave neighs/atom = 456.98835
-Ave special neighs/atom = 0.50847458
-Neighbor list builds = 6
-Dangerous builds = 0
-Total wall time: 0:00:51

examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.1

@@ -1,170 +0,0 @@
-LAMMPS (24 Mar 2022)
-# electrodes with constrained total charges imposed from dynamically computed potentials
-# for graphene-ionic liquid supercapacitor
-
-boundary p p f # slab calculation
-include settings.mod # styles, groups, computes and fixes
-# set boundary in main script because ffield is periodic
-units real
-# distribute electrode atoms among all processors:
-if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
-
-atom_style full
-pair_style lj/cut/coul/long 16
-bond_style harmonic
-angle_style harmonic
-kspace_style pppm/electrode 1e-7
-# kspace_modify in main script because ffield is periodic
-
-read_data "data.graph-il"
-Reading data file ...
-  orthogonal box = (0 0 -68) to (32.2 34.4 68)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  3776 atoms
-  scanning bonds ...
-  2 = max bonds/atom
-  scanning angles ...
-  1 = max angles/atom
-  reading bonds ...
-  640 bonds
-  reading angles ...
-  320 angles
-Finding 1-2 1-3 1-4 neighbors ...
-  special bond factors lj:    0        0        0       
-  special bond factors coul:  0        0        0       
-     2 = max # of 1-2 neighbors
-     1 = max # of 1-3 neighbors
-     1 = max # of 1-4 neighbors
-     2 = max # of special neighbors
-  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.031 seconds
-
-group bot molecule 641
-416 atoms in group bot
-group top molecule 642
-416 atoms in group top
-
-group bmi type 1 2 3
-960 atoms in group bmi
-group electrolyte type 1 2 3 4
-1280 atoms in group electrolyte
-
-fix nvt electrolyte nvt temp 500.0 500.0 100
-fix shake bmi shake 1e-4 20 0 b 1 2 a 1
-       0 = # of size 2 clusters
-       0 = # of size 3 clusters
-       0 = # of size 4 clusters
-     320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
-
-variable q atom q
-compute qtop top reduce sum v_q
-compute qbot bot reduce sum v_q
-compute ctemp electrolyte temp
-kspace_modify slab 3.0
-
-fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
-832 atoms in group conp_group
-
-# get the four entries of electrode elastance matrix
-variable me00 internal 0.0
-variable me01 internal 0.0
-variable me10 internal 0.0
-variable me11 internal 0.0
-fix_modify conp set me bot bot me00
-fix_modify conp set me bot top me01
-fix_modify conp set me top bot me10
-fix_modify conp set me top top me11
-
-# get the 0V charges (qsb), and excess charge required to reach preset total charges
-variable qsb_bot internal 0.0
-variable qsb_top internal 0.0
-fix_modify conp set qsb bot qsb_bot
-fix_modify conp set qsb top qsb_top
-variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
-variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
-
-# calculate imposed potential as elastance * excess charge
-# note: fix will wait until the run setup to look for its potential variables
-variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
-variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
-
-thermo 50
-thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
-run 500
-PPPM/electrode initialization ...
-  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
-  G vector (1/distance) = 0.20904498
-  grid = 32 32 200
-  stencil order = 5
-  estimated absolute RMS force accuracy = 3.7023506e-05
-  estimated relative force accuracy = 1.1149519e-07
-  using double precision MKL FFT
-  3d grid and FFT values/proc = 307242 204800
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 4 4 16
-  3 neighbor lists, perpetual/occasional/extra = 2 1 0
-  (1) pair lj/cut/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d
-      bin: standard
-  (2) fix electrode/conp, occasional, skip from (1)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) fix electrode/conp, perpetual, skip from (1)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
-   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop         v_vbot         v_vtop    
-         0   0              0              25136984       25136984      -1              1             -9.931852       10.097344    
-        50   20.206425      72.797911      25136825       25137033      -1              1             -9.4359366      9.5964514    
-       100   55.931663      201.50563      25136587       25137163      -1              1             -8.0440112      8.1861787    
-       150   81.389273      293.22204      25136533       25137371      -1              1             -6.1113109      6.2267114    
-       200   92.867946      334.57639      25136646       25137603      -1              1             -4.1857807      4.2740694    
-       250   97.518304      351.33028      25136809       25137814      -1              1             -2.8383703      2.9101475    
-       300   102.36577      368.79431      25136933       25137987      -1              1             -2.3831643      2.4461115    
-       350   113.66597      409.50566      25136960       25138131      -1              1             -2.7083563      2.7457811    
-       400   122.8443       442.57252      25136991       25138256      -1              1             -3.4311003      3.3941657    
-       450   128.63713      463.44243      25137048       25138373      -1              1             -4.132871       3.9852959    
-       500   131.18361      472.61665      25137142       25138493      -1              1             -4.5104095      4.2567261    
-Loop time of 62.9692 on 1 procs for 500 steps with 3776 atoms
-
-Performance: 0.686 ns/day, 34.983 hours/ns, 7.940 timesteps/s
-393.7% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 20.307     | 20.307     | 20.307     |   0.0 | 32.25
-Bond    | 0.0020074  | 0.0020074  | 0.0020074  |   0.0 |  0.00
-Kspace  | 23.562     | 23.562     | 23.562     |   0.0 | 37.42
-Neigh   | 0.26149    | 0.26149    | 0.26149    |   0.0 |  0.42
-Comm    | 0.059436   | 0.059436   | 0.059436   |   0.0 |  0.09
-Output  | 0.0023888  | 0.0023888  | 0.0023888  |   0.0 |  0.00
-Modify  | 18.756     | 18.756     | 18.756     |   0.0 | 29.79
-Other   |            | 0.01897    |            |       |  0.03
-
-Nlocal:           3776 ave        3776 max        3776 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:          12510 ave       12510 max       12510 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1725588
-Ave neighs/atom = 456.98835
-Ave special neighs/atom = 0.50847458
-Neighbor list builds = 6
-Dangerous builds = 0
-Total wall time: 0:02:26

examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conq2.g++.4

@@ -1,171 +0,0 @@
-LAMMPS (24 Mar 2022)
-# electrodes with constrained total charges imposed from dynamically computed potentials
-# for graphene-ionic liquid supercapacitor
-
-boundary p p f # slab calculation
-include settings.mod # styles, groups, computes and fixes
-# set boundary in main script because ffield is periodic
-units real
-# distribute electrode atoms among all processors:
-if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
-processors * * 2
-
-atom_style full
-pair_style lj/cut/coul/long 16
-bond_style harmonic
-angle_style harmonic
-kspace_style pppm/electrode 1e-7
-# kspace_modify in main script because ffield is periodic
-
-read_data "data.graph-il"
-Reading data file ...
-  orthogonal box = (0 0 -68) to (32.2 34.4 68)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  3776 atoms
-  scanning bonds ...
-  2 = max bonds/atom
-  scanning angles ...
-  1 = max angles/atom
-  reading bonds ...
-  640 bonds
-  reading angles ...
-  320 angles
-Finding 1-2 1-3 1-4 neighbors ...
-  special bond factors lj:    0        0        0       
-  special bond factors coul:  0        0        0       
-     2 = max # of 1-2 neighbors
-     1 = max # of 1-3 neighbors
-     1 = max # of 1-4 neighbors
-     2 = max # of special neighbors
-  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.019 seconds
-
-group bot molecule 641
-416 atoms in group bot
-group top molecule 642
-416 atoms in group top
-
-group bmi type 1 2 3
-960 atoms in group bmi
-group electrolyte type 1 2 3 4
-1280 atoms in group electrolyte
-
-fix nvt electrolyte nvt temp 500.0 500.0 100
-fix shake bmi shake 1e-4 20 0 b 1 2 a 1
-       0 = # of size 2 clusters
-       0 = # of size 3 clusters
-       0 = # of size 4 clusters
-     320 = # of frozen angles
-  find clusters CPU = 0.001 seconds
-
-variable q atom q
-compute qtop top reduce sum v_q
-compute qbot bot reduce sum v_q
-compute ctemp electrolyte temp
-kspace_modify slab 3.0
-
-fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
-832 atoms in group conp_group
-
-# get the four entries of electrode elastance matrix
-variable me00 internal 0.0
-variable me01 internal 0.0
-variable me10 internal 0.0
-variable me11 internal 0.0
-fix_modify conp set me bot bot me00
-fix_modify conp set me bot top me01
-fix_modify conp set me top bot me10
-fix_modify conp set me top top me11
-
-# get the 0V charges (qsb), and excess charge required to reach preset total charges
-variable qsb_bot internal 0.0
-variable qsb_top internal 0.0
-fix_modify conp set qsb bot qsb_bot
-fix_modify conp set qsb top qsb_top
-variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
-variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
-
-# calculate imposed potential as elastance * excess charge
-# note: fix will wait until the run setup to look for its potential variables
-variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
-variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
-
-thermo 50
-thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
-run 500
-PPPM/electrode initialization ...
-  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
-  G vector (1/distance) = 0.20904498
-  grid = 32 32 200
-  stencil order = 5
-  estimated absolute RMS force accuracy = 3.7023506e-05
-  estimated relative force accuracy = 1.1149519e-07
-  using double precision MKL FFT
-  3d grid and FFT values/proc = 151593 85504
-  generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 4 4 16
-  3 neighbor lists, perpetual/occasional/extra = 2 1 0
-  (1) pair lj/cut/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d
-      bin: standard
-  (2) fix electrode/conp, occasional, skip from (1)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) fix electrode/conp, perpetual, skip from (1)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
-   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop         v_vbot         v_vtop    
-         0   0              0              25136984       25136984      -1              1             -9.931852       10.097344    
-        50   20.206425      72.797911      25136825       25137033      -1              1             -9.4359366      9.5964514    
-       100   55.931663      201.50563      25136587       25137163      -1              1             -8.0440112      8.1861787    
-       150   81.389273      293.22204      25136533       25137371      -1              1             -6.1113109      6.2267114    
-       200   92.867946      334.57639      25136646       25137603      -1              1             -4.1857807      4.2740694    
-       250   97.518304      351.33028      25136809       25137814      -1              1             -2.8383703      2.9101475    
-       300   102.36577      368.79431      25136933       25137987      -1              1             -2.3831643      2.4461115    
-       350   113.66597      409.50566      25136960       25138131      -1              1             -2.7083563      2.7457811    
-       400   122.8443       442.57252      25136991       25138256      -1              1             -3.4311003      3.3941657    
-       450   128.63713      463.44243      25137048       25138373      -1              1             -4.132871       3.9852959    
-       500   131.18361      472.61665      25137142       25138493      -1              1             -4.5104095      4.2567261    
-Loop time of 33.4031 on 4 procs for 500 steps with 3776 atoms
-
-Performance: 1.293 ns/day, 18.557 hours/ns, 14.969 timesteps/s
-94.3% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 7.1262     | 7.3913     | 7.611      |   6.8 | 22.13
-Bond    | 0.0007191  | 0.00079089 | 0.00087005 |   0.0 |  0.00
-Kspace  | 15.139     | 15.358     | 15.623     |   4.7 | 45.98
-Neigh   | 0.10374    | 0.10377    | 0.10383    |   0.0 |  0.31
-Comm    | 0.14245    | 0.14353    | 0.14563    |   0.3 |  0.43
-Output  | 0.0012987  | 0.0015671  | 0.0022434  |   1.0 |  0.00
-Modify  | 10.381     | 10.383     | 10.384     |   0.0 | 31.08
-Other   |            | 0.02134    |            |       |  0.06
-
-Nlocal:            944 ave         948 max         940 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Nghost:         5920.5 ave        5941 max        5899 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Neighs:         431397 ave      442329 max      421103 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 1725588
-Ave neighs/atom = 456.98835
-Ave special neighs/atom = 0.50847458
-Neighbor list builds = 6
-Dangerous builds = 0
-Total wall time: 0:01:01

examples/PACKAGES/electrode/graph-il/settings.mod

@@ -12,8 +12,13 @@ kspace_style pppm/electrode 1e-7
 
 read_data "data.graph-il"
 
-group bot molecule 641
+# replicate 4 4 1 # test different sys sizes
-group top molecule 642
+
+variable zpos atom "z > 0"
+group zpos variable zpos
+group ele type 5
+group top intersect ele zpos
+group bot subtract ele top
 
 group bmi type 1 2 3
 group electrolyte type 1 2 3 4

examples/PACKAGES/electrode/madelung/.gitignore

@@ -0,0 +1,2 @@
+*.csv
+*.txt

examples/PACKAGES/electrode/madelung/data.au-elyt

@@ -0,0 +1,27 @@
+LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0
+
+4 atoms
+3 atom types
+
+0 1 xlo xhi
+0 1 ylo yhi
+-10 10 zlo zhi
+
+Masses
+
+1 196.966553
+2 196.966553
+3 1.0
+
+Pair Coeffs # lj/cut/coul/long
+
+1 0 0
+2 0 0
+3 0 0
+
+Atoms # full
+
+1 1 1  0.00 0.00 0.00 -2.00 # bottom electrode
+2 2 2  0.00 0.00 0.00  2.00 # top electrode
+3 3 3  0.50 0.00 0.00 -1.00 # bottom electrolyte
+4 3 3 -0.50 0.00 0.00  1.00 # top electrolyte