Merge branch 'master' into parse-logical-keyword

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.06.30.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.09.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "f9e55dd550cfbf77f46507adf7cb8fd2" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "3b3882627964bd02e5c3b02065daac3c" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 

cmake/Modules/Packages/GPU.cmake

@@ -71,6 +71,11 @@ if(GPU_API STREQUAL "CUDA")
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
   # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
   set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
+
+  # apply the following to build "fat" CUDA binaries only for known CUDA toolkits
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+    message(WARNING "Untested CUDA Toolkit version. Use at your own risk")
+  else()
     # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
     if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
       string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
@@ -107,8 +112,6 @@ if(GPU_API STREQUAL "CUDA")
     if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
       string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
     endif()
-  if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-    message(WARNING "Unsupported CUDA version. Use at your own risk.")
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}

cmake/Modules/Packages/ML-QUIP.cmake

@@ -38,7 +38,7 @@ if(DOWNLOAD_QUIP)
   set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
   set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
   set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
-  set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\n")
+  set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\nHAVE_SCALAPACK=0\n")
   file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
 
   message(STATUS "QUIP download via git requested - we will build our own")

cmake/iwyu/iwyu-extra-map.imp

@@ -1,7 +1,28 @@
 [
-  { include: [ "<bits/types/struct_rusage.h>", private, "<sys/resource.h>", public ] },
-  { include: [ "<bits/exception.h>", public, "<exception>", public ] },
   { include: [ "@<Eigen/.*>", private, "<Eigen/Eigen>", public ] },
   { include: [ "@<gtest/.*>", private, "\"gtest/gtest.h\"", public ] },
   { include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
+  { include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
+  { include: [ "@<(cell|c_loops|container).hh>", private, "<voro++.hh>", public ] },
+  { include: [ "@\"atom_vec_.*.h\"", public, "\"style_atom.h\"", public ] },
+  { include: [ "@\"body_.*.h\"", public, "\"style_body.h\"", public ] },
+  { include: [ "@\"compute_.*.h\"", public, "\"style_compute.h\"", public ] },
+  { include: [ "@\"fix_.*.h\"", public, "\"style_fix.h\"", public ] },
+  { include: [ "@\"dump_.*.h\"", public, "\"style_dump.h\"", public ] },
+  { include: [ "@\"min_.*.h\"", public, "\"style_minimize.h\"", public ] },
+  { include: [ "@\"reader_.*.h\"", public, "\"style_reader.h\"", public ] },
+  { include: [ "@\"region_.*.h\"", public, "\"style_region.h\"", public ] },
+  { include: [ "@\"pair_.*.h\"", public, "\"style_pair.h\"", public ] },
+  { include: [ "@\"angle_.*.h\"", public, "\"style_angle.h\"", public ] },
+  { include: [ "@\"bond_.*.h\"", public, "\"style_bond.h\"", public ] },
+  { include: [ "@\"dihedral_.*.h\"", public, "\"style_dihedral.h\"", public ] },
+  { include: [ "@\"improper_.*.h\"", public, "\"style_improper.h\"", public ] },
+  { include: [ "@\"kspace_.*.h\"", public, "\"style_kspace.h\"", public ] },
+  { include: [ "@\"nbin_.*.h\"", public, "\"style_nbin.h\"", public ] },
+  { include: [ "@\"npair_.*.h\"", public, "\"style_npair.h\"", public ] },
+  { include: [ "@\"nstenci_.*.h\"", public, "\"style_nstencil.h\"", public ] },
+  { include: [ "@\"ntopo_.*.h\"", public, "\"style_ntopo.h\"", public ] },
+  { include: [ "<float.h>",   public, "<cfloat>", public ] },
+  { include: [ "<limits.h>",  public, "<climits>", public ] },
+  { include: [ "<bits/types/struct_tm.h>", private, "<ctime>", public ] },
 ]

cmake/presets/most.cmake

@@ -24,6 +24,7 @@ set(ALL_PACKAGES
   DRUDE
   EFF
   EXTRA-COMPUTE
+  EXTRA-DUMP
   EXTRA-FIX
   EXTRA-MOLECULE
   EXTRA-PAIR

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "31 August 2021" "2021-08-31"
+.TH LAMMPS "20 September 2021" "2021-09-20"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_development.rst

@@ -58,13 +58,16 @@ Report missing and unneeded '#include' statements (CMake only)
 The conventions for how and when to use and order include statements in
 LAMMPS are documented in :doc:`Modify_style`.  To assist with following
 these conventions one can use the `Include What You Use tool <https://include-what-you-use.org/>`_.
-This is still under development and for large and complex projects like LAMMPS
+This tool is still under development and for large and complex projects like LAMMPS
 there are some false positives, so suggested changes need to be verified manually.
-It is recommended to use at least version 0.14, which has much fewer incorrect
+It is recommended to use at least version 0.16, which has much fewer incorrect
-reports than earlier versions.
+reports than earlier versions.  To install the IWYU toolkit, you need to have
+the clang compiler **and** its development package installed.  Download the IWYU
+version that matches the version of the clang compiler, configure, build, and
+install it.
 
-The necessary steps to generate the report can be enabled via a
+The necessary steps to generate the report can be enabled via a CMake variable
-CMake variable:
+during CMake configuration.
 
 .. code-block:: bash
 

doc/src/Developer_utils.rst

@@ -209,6 +209,9 @@ Convenience functions
 .. doxygenfunction:: date2num
    :project: progguide
 
+.. doxygenfunction:: current_date
+   :project: progguide
+
 Customized standard functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Errors_debug.rst

@@ -40,11 +40,10 @@ We use it to show how to identify the origin of a segmentation fault.
 
 After recompiling LAMMPS and running the input you should get something like this:
 
-.. code-block:
+.. code-block::
 
    $ ./lmp -in in.melt
    LAMMPS (19 Mar 2020)
-   OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
      using 1 OpenMP thread(s) per MPI task
    Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
    Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)

doc/src/Intro_website.rst

@@ -26,7 +26,7 @@ available online are listed below.
 * `Tutorials <https://www.lammps.org/tutorials.html>`_
 
 * `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/prepost.html>`_
-* `Other software usable with LAMMPS <https://www.lammps.org/offsite.html>`_
+* `Other software usable with LAMMPS <https://www.lammps.org/external.html>`_
 * `Viz tools usable with LAMMPS <https://www.lammps.org/viz.html>`_
 
 * `Benchmark performance <https://www.lammps.org/bench.html>`_

doc/src/Modify_contribute.rst

@@ -115,8 +115,8 @@ External contributions
 
 If you prefer to do so, you can also develop and support your add-on
 feature **without** having it included in the LAMMPS distribution, for
-example as a download from a website of your own.  See the `Offsite
+example as a download from a website of your own.  See the `External
-LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page
+LAMMPS packages and tools <https://www.lammps.org/external.html>`_ page
 of the LAMMPS website for examples of groups that do this.  We are happy
 to advertise your package and website from that page.  Simply email the
 `developers <https://www.lammps.org/authors.html>`_ with info about your

doc/src/Modify_style.rst

@@ -305,19 +305,22 @@ you are uncertain, please ask.
   FILE pointers and only be done on MPI rank 0.  Use the :cpp:func:`utils::logmesg`
   convenience function where possible.
 
-- header files should only include the absolute minimum number of
+- Header files, especially those defining a "style", should only use
-  include files and **must not** contain any ``using`` statements;
+  the absolute minimum number of include files and **must not** contain
-  rather the include statements should be put into the corresponding
+  any ``using`` statements. Typically that would be only the header for
-  implementation files. For implementation files, the
+  the base class. Instead any include statements should be put into the
-  "include-what-you-use" principle should be employed.  However, when
+  corresponding implementation files and forward declarations be used.
-  including the ``pointers.h`` header (or one of the base classes
+  For implementation files, the "include what you use" principle should
-  derived from it) certain headers will be included and thus need to be
+  be employed.  However, there is the notable exception that when the
-  specified. These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`,
+  ``pointers.h`` header is included (or one of the base classes derived
-  `string`, `utils.h`, `fmt/format.h`, `climits`, `cinttypes`. This also
+  from it) certain headers will always be included and thus do not need
-  means any header can assume that `FILE`, `NULL`, and `INT_MAX` are
+  to be explicitly specified.
-  defined.
+  These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`, `string`, `utils.h`,
+  `vector`, `fmt/format.h`, `climits`, `cinttypes`.
+  This also means any such file can assume that `FILE`, `NULL`, and
+  `INT_MAX` are defined.
 
-- header files that define a new LAMMPS style (i.e. that have a
+- Header files that define a new LAMMPS style (i.e. that have a
   ``SomeStyle(some/name,SomeName);`` macro in them) should only use the
   include file for the base class and otherwise use forward declarations
   and pointers; when interfacing to a library use the PIMPL (pointer
@@ -325,7 +328,7 @@ you are uncertain, please ask.
   that contains all library specific data (and thus requires the library
   header) but use a forward declaration and define the struct only in
   the implementation file. This is a **strict** requirement since this
-  is where type clashes between packages and hard to fine bugs have
+  is where type clashes between packages and hard to find bugs have
   regularly manifested in the past.
 
 - Please use clang-format only to reformat files that you have

doc/src/Tools.rst

@@ -7,7 +7,7 @@ steps are often necessary to setup and analyze a simulation.  A list
 of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
 
 * `Pre/Post processing <https://www.lammps.org/prepost.html>`_
-* `Offsite LAMMPS packages & tools <https://www.lammps.org/offsite.html>`_
+* `External LAMMPS packages & tools <https://www.lammps.org/external.html>`_
 * `Pizza.py toolkit <pizza_>`_
 
 The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at

doc/src/fix_brownian.rst

@@ -8,9 +8,8 @@ fix brownian command
 fix brownian/sphere command
 ===========================
 
-fix brownian/sphere command
+fix brownian/asphere command
-===========================
+============================
-
 
 Syntax
 """"""

doc/src/package.rst

@@ -27,7 +27,7 @@ Syntax
              on = set Newton pairwise flag on (currently not allowed)
            *pair/only* = *off* or *on*
              off = apply "gpu" suffix to all available styles in the GPU package (default)
-             on  - apply "gpu" suffix only pair styles
+             on  = apply "gpu" suffix only pair styles
            *binsize* value = size
              size = bin size for neighbor list construction (distance units)
            *split* = fraction

doc/src/pair_hybrid.rst

@@ -198,8 +198,8 @@ same:
 
 Coefficients must be defined for each pair of atoms types via the
 :doc:`pair_coeff <pair_coeff>` command as described above, or in the
-data file read by the :doc:`read_data <read_data>` commands, or by
+"Pair Coeffs" or "PairIJ Coeffs" section of the data file read by the
-mixing as described below.
+:doc:`read_data <read_data>` command, or by mixing as described below.
 
 For all of the *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles,
 every atom type pair I,J (where I <= J) must be assigned to at least one
@@ -208,14 +208,21 @@ examples above, or in the data file read by the :doc:`read_data
 <read_data>`, or by mixing as described below.  Also all sub-styles
 must be used at least once in a :doc:`pair_coeff <pair_coeff>` command.
 
+.. note::
+
+   LAMMPS never performs mixing of parameters from different sub-styles,
+   **even** if they use the same type of coefficients, e.g. contain
+   a Lennard-Jones potential variant.  Those parameters must be provided
+   explicitly.
+
 If you want there to be no interactions between a particular pair of
-atom types, you have 3 choices.  You can assign the type pair to some
+atom types, you have 3 choices.  You can assign the pair of atom types
-sub-style and use the :doc:`neigh_modify exclude type <neigh_modify>`
+to some sub-style and use the :doc:`neigh_modify exclude type <neigh_modify>`
 command.  You can assign it to some sub-style and set the coefficients
 so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ
 potential).  Or, for *hybrid*, *hybrid/overlay*, or *hybrid/scaled*
 simulations, you can use this form of the pair_coeff command in your
-input script:
+input script or the "PairIJ Coeffs" section of your data file:
 
 .. code-block:: LAMMPS
 
@@ -238,19 +245,20 @@ styles with different requirements.
 
 ----------
 
-Different force fields (e.g. CHARMM vs AMBER) may have different rules
+Different force fields (e.g. CHARMM vs. AMBER) may have different rules
-for applying weightings that change the strength of pairwise
+for applying exclusions or weights that change the strength of pairwise
-interactions between pairs of atoms that are also 1-2, 1-3, and 1-4
+non-bonded interactions between pairs of atoms that are also 1-2, 1-3,
-neighbors in the molecular bond topology, as normally set by the
+and 1-4 neighbors in the molecular bond topology. This is normally a
-:doc:`special_bonds <special_bonds>` command.  Different weights can be
+global setting defined the :doc:`special_bonds <special_bonds>` command.
-assigned to different pair hybrid sub-styles via the :doc:`pair_modify
+However, different weights can be assigned to different hybrid
-special <pair_modify>` command. This allows multiple force fields to be
+sub-styles via the :doc:`pair_modify special <pair_modify>` command.
-used in a model of a hybrid system, however, there is no consistent
+This allows multiple force fields to be used in a model of a hybrid
-approach to determine parameters automatically for the interactions
+system, however, there is no consistent approach to determine parameters
-between the two force fields, this is only recommended when particles
+automatically for the interactions **between** atoms of the two force
+fields, thus this approach this is only recommended when particles
 described by the different force fields do not mix.
 
-Here is an example for mixing CHARMM and AMBER: The global *amber*
+Here is an example for combining CHARMM and AMBER: The global *amber*
 setting sets the 1-4 interactions to non-zero scaling factors and
 then overrides them with 0.0 only for CHARMM:
 
@@ -260,7 +268,7 @@ then overrides them with 0.0 only for CHARMM:
    pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
    pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
 
-The this input achieves the same effect:
+This input achieves the same effect:
 
 .. code-block:: LAMMPS
 
@@ -270,9 +278,9 @@ The this input achieves the same effect:
    pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
    pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
 
-Here is an example for mixing Tersoff with OPLS/AA based on
+Here is an example for combining Tersoff with OPLS/AA based on
-a data file that defines bonds for all atoms where for the
+a data file that defines bonds for all atoms where - for the
-Tersoff part of the system the force constants for the bonded
+Tersoff part of the system - the force constants for the bonded
 interactions have been set to 0. Note the global settings are
 effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA:
 

doc/src/read_data.rst

@@ -619,7 +619,7 @@ of analysis.
    * - bond
      - atom-ID molecule-ID atom-type x y z
    * - charge
-     - atom-type q x y z
+     - atom-ID atom-type q x y z
    * - dipole
      - atom-ID atom-type q x y z mux muy muz
    * - dpd

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

@@ -418,6 +418,7 @@ html_context['current_version'] = os.environ.get('LAMMPS_WEBSITE_BUILD_VERSION',
 html_context['git_commit'] = git_commit
 html_context['versions'] = [
   ('latest', 'https://docs.lammps.org/latest/'),
+  ('stable', 'https://docs.lammps.org/stable/'),
   (version, 'https://docs.lammps.org/')
 ]
 html_context['downloads'] = [('PDF', 'Manual.pdf')]

doc/utils/sphinx-config/false_positives.txt

@@ -2441,6 +2441,7 @@ packings
 padua
 Padua
 pafi
+PairIJ
 palegoldenrod
 palegreen
 paleturquoise

examples/COUPLE/lammps_quest/README

@@ -1,3 +1,9 @@
+IMPORTANT NOTE: This example has not been updated since 2014,
+so it is not likely to work anymore out of the box.  There have
+been changes to LAMMPS and its library interface that would need
+to be applied. Please see the manual for the documentation of
+the library interface.
+
 This directory has an application that runs classical MD via LAMMPS,
 but uses quantum forces calculated by the Quest DFT (density
 functional) code in place of the usual classical MD forces calculated

examples/COUPLE/lammps_spparks/README

@@ -1,3 +1,9 @@
+IMPORTANT NOTE: This example has not been updated since 2013,
+so it is not likely to work anymore out of the box.  There have
+been changes to LAMMPS and its library interface that would need
+to be applied. Please see the manual for the documentation of
+the library interface.
+
 This directory has an application that models grain growth in the
 presence of strain.
 

examples/COUPLE/multiple/multiple.cpp

@@ -28,13 +28,9 @@
 #include <cstdlib>
 #include <cstring>
 
-#include "lammps.h"         // these are LAMMPS include files
+#define LAMMPS_LIB_MPI  // to make lammps_open() visible
-#include "input.h"
-#include "atom.h"
 #include "library.h"
 
-using namespace LAMMPS_NS;
-
 int main(int narg, char **arg)
 {
   // setup MPI and various communicators
@@ -74,7 +70,7 @@ int main(int narg, char **arg)
   char str1[32],str2[32],str3[32];
 
   char **lmparg = new char*[8];
-  lmparg[0] = NULL;                 // required placeholder for program name
+  lmparg[0] = (char *) "LAMMPS";              // required placeholder for program name
   lmparg[1] = (char *) "-screen";
   sprintf(str1,"screen.%d",instance);
   lmparg[2] = str1;
@@ -86,13 +82,9 @@ int main(int narg, char **arg)
   sprintf(str3,"%g",temperature + instance*tdelta);
   lmparg[7] = str3;
 
-  // open N instances of LAMMPS
+  // create N instances of LAMMPS
-  // either of these methods will work
 
-  LAMMPS *lmp = new LAMMPS(8,lmparg,comm_lammps);
+  void *lmp = lammps_open(8,lmparg,comm_lammps,NULL);
-
-  //LAMMPS *lmp;
-  //lammps_open(8,lmparg,comm_lammps,(void **) &lmp);
 
   delete [] lmparg;
 
@@ -103,7 +95,7 @@ int main(int narg, char **arg)
   // query final temperature and print result for each instance
 
   double *ptr = (double *)
-    lammps_extract_compute(lmp,(char *) "thermo_temp",0,0);
+    lammps_extract_compute(lmp,"thermo_temp",LMP_STYLE_GLOBAL,LMP_TYPE_SCALAR);
   double finaltemp = *ptr;
 
   double *temps = new double[ninstance];
@@ -125,7 +117,7 @@ int main(int narg, char **arg)
 
   // delete LAMMPS instances
 
-  delete lmp;
+  lammps_close(lmp);
 
   // close down MPI
 

examples/COUPLE/plugin/README

@@ -13,7 +13,7 @@ like below.
 
 mpicc -c -O -Wall -g -I$HOME/lammps/src liblammpsplugin.c
 mpicc -c -O -Wall -g simple.c
-mpicc simple.o liblammsplugin.o -ldl -o simpleC
+mpicc simple.o liblammpsplugin.o -ldl -o simpleC
 
 You also need to build LAMMPS as a shared library
 (see examples/COUPLE/README), e.g. 

examples/COUPLE/plugin/liblammpsplugin.c

@@ -38,44 +38,98 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
 #define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)
   ADDSYM(open);
   ADDSYM(open_no_mpi);
+  ADDSYM(open_fortran);
   ADDSYM(close);
-  ADDSYM(version);
+
+  ADDSYM(mpi_init);
+  ADDSYM(mpi_finalize);
+  ADDSYM(kokkos_finalize);
+  ADDSYM(python_finalize);
+
   ADDSYM(file);
   ADDSYM(command);
   ADDSYM(commands_list);
   ADDSYM(commands_string);
-  ADDSYM(free);
+
-  ADDSYM(extract_setting);
+  ADDSYM(get_natoms);
-  ADDSYM(extract_global);
+  ADDSYM(get_thermo);
+
   ADDSYM(extract_box);
+  ADDSYM(reset_box);
+
+  ADDSYM(memory_usage);
+  ADDSYM(get_mpi_comm);
+
+  ADDSYM(extract_setting);
+  ADDSYM(extract_global_datatype);
+  ADDSYM(extract_global);
+
+  ADDSYM(extract_atom_datatype);
   ADDSYM(extract_atom);
+
   ADDSYM(extract_compute);
   ADDSYM(extract_fix);
   ADDSYM(extract_variable);
-
-  ADDSYM(get_thermo);
-  ADDSYM(get_natoms);
-
   ADDSYM(set_variable);
-  ADDSYM(reset_box);
 
   ADDSYM(gather_atoms);
   ADDSYM(gather_atoms_concat);
   ADDSYM(gather_atoms_subset);
   ADDSYM(scatter_atoms);
   ADDSYM(scatter_atoms_subset);
+  ADDSYM(gather_bonds);
 
-  ADDSYM(set_fix_external_callback);
+  ADDSYM(create_atoms);
 
-  ADDSYM(config_has_package);
+  ADDSYM(find_pair_neighlist);
-  ADDSYM(config_package_count);
+  ADDSYM(find_fix_neighlist);
-  ADDSYM(config_package_name);
+  ADDSYM(find_compute_neighlist);
+  ADDSYM(neighlist_num_elements);
+  ADDSYM(neighlist_element_neighbors);
+
+  ADDSYM(version);
+  ADDSYM(get_os_info);
+
+  ADDSYM(config_has_mpi_support);
   ADDSYM(config_has_gzip_support);
   ADDSYM(config_has_png_support);
   ADDSYM(config_has_jpeg_support);
   ADDSYM(config_has_ffmpeg_support);
   ADDSYM(config_has_exceptions);
-  ADDSYM(create_atoms);
+
+  ADDSYM(config_has_package);
+  ADDSYM(config_package_count);
+  ADDSYM(config_package_name);
+
+  ADDSYM(config_accelerator);
+  ADDSYM(has_gpu_device);
+  ADDSYM(get_gpu_device_info);
+
+  ADDSYM(has_style);
+  ADDSYM(style_count);
+  ADDSYM(style_name);
+
+  ADDSYM(has_id);
+  ADDSYM(id_count);
+  ADDSYM(id_name);
+
+  ADDSYM(plugin_count);
+  ADDSYM(plugin_name);
+
+  ADDSYM(set_fix_external_callback);
+  ADDSYM(fix_external_get_force);
+  ADDSYM(fix_external_set_energy_global);
+  ADDSYM(fix_external_set_energy_peratom);
+  ADDSYM(fix_external_set_virial_global);
+  ADDSYM(fix_external_set_virial_peratom);
+  ADDSYM(fix_external_set_vector_length);
+  ADDSYM(fix_external_set_vector);
+
+  ADDSYM(free);
+
+  ADDSYM(is_running);
+  ADDSYM(force_timeout);
+
 #ifdef LAMMPS_EXCEPTIONS
   lmp->has_exceptions = 1;
   ADDSYM(has_error);

examples/COUPLE/plugin/liblammpsplugin.h

@@ -39,75 +39,121 @@ extern "C" {
 
 #if defined(LAMMPS_BIGBIG)
 typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
-#elif defined(LAMMPS_SMALLBIG)
+#elif defined(LAMMPS_SMALLSMALL)
-typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
-#else
 typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
+#else
+typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
 #endif
 
-  
 struct _liblammpsplugin {
   int abiversion;
   int has_exceptions;
   void *handle;
-  void (*open)(int, char **, MPI_Comm, void **);
+  void *(*open)(int, char **, MPI_Comm, void **);
-  void (*open_no_mpi)(int, char **, void **);
+  void *(*open_no_mpi)(int, char **, void **);
+  void *(*open_fortran)(int, char **, void **, int);
   void (*close)(void *);
-  int  (*version)(void *);
+
+  void (*mpi_init)();
+  void (*mpi_finalize)();
+  void (*kokkos_finalize)();
+  void (*python_finalize)();
+
   void (*file)(void *, char *);
-  char *(*command)(void *, char *);
+  char *(*command)(void *, const char *);
-  void (*commands_list)(void *, int, char **);
+  void (*commands_list)(void *, int, const char **);
-  void (*commands_string)(void *, char *);
+  void (*commands_string)(void *, const char *);
-  void (*free)(void *);
+
-  int (*extract_setting)(void *, char *);
+  double (*get_natoms)(void *);
-  void *(*extract_global)(void *, char *);
+  double (*get_thermo)(void *, char *);
+
   void (*extract_box)(void *, double *, double *,
                       double *, double *, double *, int *, int *);
-  void *(*extract_atom)(void *, char *);
-  void *(*extract_compute)(void *, char *, int, int);
-  void *(*extract_fix)(void *, char *, int, int, int, int);
-  void *(*extract_variable)(void *, char *, char *);
-
-  double (*get_thermo)(void *, char *);
-  int (*get_natoms)(void *);
-
-  int (*set_variable)(void *, char *, char *);
   void (*reset_box)(void *, double *, double *, double, double, double);
 
+  void (*memory_usage)(void *, double *);
+  int (*get_mpi_comm)(void *);
+
+  int (*extract_setting)(void *, const char *);
+  int *(*extract_global_datatype)(void *, const char *);
+  void *(*extract_global)(void *, const char *);
+
+  void *(*extract_atom_datatype)(void *, const char *);
+  void *(*extract_atom)(void *, const char *);
+
+  void *(*extract_compute)(void *, const char *, int, int);
+  void *(*extract_fix)(void *, const char *, int, int, int, int);
+  void *(*extract_variable)(void *, const char *, char *);
+  int (*set_variable)(void *, char *, char *);
+
   void (*gather_atoms)(void *, char *, int, int, void *);
   void (*gather_atoms_concat)(void *, char *, int, int, void *);
   void (*gather_atoms_subset)(void *, char *, int, int, int, int *, void *);
   void (*scatter_atoms)(void *, char *, int, int, void *);
   void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *);
 
-  void (*set_fix_external_callback)(void *, char *, FixExternalFnPtr, void*);
+  void (*gather_bonds)(void *, void *);
   
-  int (*config_has_package)(char * package_name);
+// lammps_create_atoms() takes tagint and imageint as args
-  int (*config_package_count)();
+// ifdef insures they are compatible with rest of LAMMPS
-  int (*config_package_name)(int index, char * buffer, int max_size);
+// caller must match to how LAMMPS library is built
+
+#ifndef LAMMPS_BIGBIG
+ void (*create_atoms)(void *, int, int *, int *, double *,
+                      double *, int *, int);
+#else
+  void (*create_atoms)(void *, int, int64_t *, int *, double *,
+                       double *, int64_t *, int);
+#endif
+
+  int (*find_pair_neighlist)(void *, const char *, int, int, int);
+  int (*find_fix_neighlist)(void *, const char *, int);
+  int (*find_compute_neighlist)(void *, char *, int);
+  int (*neighlist_num_elements)(void *, int);
+  void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
+
+  int (*version)(void *);
+  void (*get_os_info)(char *, int);
+
+  int (*config_has_mpi_support)();
   int (*config_has_gzip_support)();
   int (*config_has_png_support)();
   int (*config_has_jpeg_support)();
   int (*config_has_ffmpeg_support)();
   int (*config_has_exceptions)();
 
-  int (*find_pair_neighlist)(void* ptr, char * style, int exact, int nsub, int request);
+  int (*config_has_package)(const char *);
-  int (*find_fix_neighlist)(void* ptr, char * id, int request);
+  int (*config_package_count)();
-  int (*find_compute_neighlist)(void* ptr, char * id, int request);
+  int (*config_package_name)(int, char *, int);
-  int (*neighlist_num_elements)(void* ptr, int idx);
-  void (*neighlist_element_neighbors)(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);
 
-// lammps_create_atoms() takes tagint and imageint as args
+  int (*config_accelerator)(const char *, const char *, const char *);
-// ifdef insures they are compatible with rest of LAMMPS
+  int (*has_gpu_device)();
-// caller must match to how LAMMPS library is built
+  void (*get_gpu_device_info)(char *, int);
 
-#ifdef LAMMPS_BIGBIG
+  int (*has_style)(void *, const char *, const char *);
-  void (*create_atoms)(void *, int, int64_t *, int *,
+  int (*style_count)(void *, const char *);
-                         double *, double *, int64_t *, int);
+  int (*style_name)(void *, const char *, int, char *, int);
-#else
+
-  void (*create_atoms)(void *, int, int *, int *,
+  int (*has_id)(void *, const char *, const char *);
-                         double *, double *, int *, int);
+  int (*id_count)(void *, const char *);
-#endif
+  int (*id_name)(void *, const char *, int, char *, int);
+
+  int (*plugin_count)();
+  int (*plugin_name)(int, char *, char *, int);
+
+  void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void*);
+  void (*fix_external_get_force)(void *, const char *);
+  void (*fix_external_set_energy_global)(void *, const char *, double);
+  void (*fix_external_set_energy_peratom)(void *, const char *, double *);
+  void (*fix_external_set_virial_global)(void *, const char *, double *);
+  void (*fix_external_set_virial_peratom)(void *, const char *, double **);
+  void (*fix_external_set_vector_length)(void *, const char *, int);
+  void (*fix_external_set_vector)(void *, const char *, int, double);
+
+  void (*free)(void *);
+
+  void (*is_running)(void *);
+  void (*force_timeout)(void *);
 
   int (*has_error)(void *);
   int (*get_last_error_message)(void *, char *, int);

examples/COUPLE/plugin/log.simple.plugin.1

@@ -1,9 +1,12 @@
-LAMMPS (18 Feb 2020)
+LAMMPS (31 Aug 2021)
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
-Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
+  using 1 OpenMP thread(s) per MPI task
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
   1 by 1 by 1 MPI processor grid
 Created 256 atoms
-  create_atoms CPU = 0.000297844 secs
+  using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
+  create_atoms CPU = 0.001 seconds
 Neighbor list info ...
   update every 20 steps, delay 0 steps, check no
   max neighbors/atom: 2000, page size: 100000
@@ -14,108 +17,108 @@ Neighbor list info ...
   (1) pair lj/cut, perpetual
       attributes: half, newton on
       pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
+      stencil: half/bin/3d
       bin: standard
 Setting up Verlet run ...
   Unit style    : lj
   Current step  : 0
   Time step     : 0.005
-Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0         1.44   -6.7733681            0   -4.6218056   -5.0244179 
       10    1.1298532   -6.3095502            0   -4.6213906   -2.6058175 
-Loop time of 0.00164276 on 1 procs for 10 steps with 256 atoms
+Loop time of 0.00239712 on 1 procs for 10 steps with 256 atoms
 
-Performance: 2629719.113 tau/day, 6087.313 timesteps/s
+Performance: 1802163.347 tau/day, 4171.674 timesteps/s
-93.7% CPU use with 1 MPI tasks x no OpenMP threads
+97.2% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0014956  | 0.0014956  | 0.0014956  |   0.0 | 91.04
+Pair    | 0.0020572  | 0.0020572  | 0.0020572  |   0.0 | 85.82
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 8.045e-05  | 8.045e-05  | 8.045e-05  |   0.0 |  4.90
+Comm    | 0.00018731 | 0.00018731 | 0.00018731 |   0.0 |  7.81
-Output  | 1.1399e-05 | 1.1399e-05 | 1.1399e-05 |   0.0 |  0.69
+Output  | 4.478e-05  | 4.478e-05  | 4.478e-05  |   0.0 |  1.87
-Modify  | 3.7431e-05 | 3.7431e-05 | 3.7431e-05 |   0.0 |  2.28
+Modify  | 6.3637e-05 | 6.3637e-05 | 6.3637e-05 |   0.0 |  2.65
-Other   |            | 1.789e-05  |            |       |  1.09
+Other   |            | 4.419e-05  |            |       |  1.84
 
-Nlocal:    256 ave 256 max 256 min
+Nlocal:        256.000 ave         256 max         256 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1431 ave 1431 max 1431 min
+Nghost:        1431.00 ave        1431 max        1431 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9984 ave 9984 max 9984 min
+Neighs:        9984.00 ave        9984 max        9984 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9984
-Ave neighs/atom = 39
+Ave neighs/atom = 39.000000
 Neighbor list builds = 0
 Dangerous builds not checked
 Setting up Verlet run ...
   Unit style    : lj
   Current step  : 10
   Time step     : 0.005
-Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       10    1.1298532   -6.3095502            0   -4.6213906   -2.6058175 
       20    0.6239063    -5.557644            0   -4.6254403   0.97451173 
-Loop time of 0.00199768 on 1 procs for 10 steps with 256 atoms
+Loop time of 0.00329271 on 1 procs for 10 steps with 256 atoms
 
-Performance: 2162504.180 tau/day, 5005.797 timesteps/s
+Performance: 1311987.619 tau/day, 3037.008 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+96.4% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0018518  | 0.0018518  | 0.0018518  |   0.0 | 92.70
+Pair    | 0.0029015  | 0.0029015  | 0.0029015  |   0.0 | 88.12
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 7.9768e-05 | 7.9768e-05 | 7.9768e-05 |   0.0 |  3.99
+Comm    | 0.00021807 | 0.00021807 | 0.00021807 |   0.0 |  6.62
-Output  | 1.1433e-05 | 1.1433e-05 | 1.1433e-05 |   0.0 |  0.57
+Output  | 4.9163e-05 | 4.9163e-05 | 4.9163e-05 |   0.0 |  1.49
-Modify  | 3.6904e-05 | 3.6904e-05 | 3.6904e-05 |   0.0 |  1.85
+Modify  | 7.0573e-05 | 7.0573e-05 | 7.0573e-05 |   0.0 |  2.14
-Other   |            | 1.773e-05  |            |       |  0.89
+Other   |            | 5.339e-05  |            |       |  1.62
 
-Nlocal:    256 ave 256 max 256 min
+Nlocal:        256.000 ave         256 max         256 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1431 ave 1431 max 1431 min
+Nghost:        1431.00 ave        1431 max        1431 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9952 ave 9952 max 9952 min
+Neighs:        9952.00 ave        9952 max        9952 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9952
-Ave neighs/atom = 38.875
+Ave neighs/atom = 38.875000
 Neighbor list builds = 0
 Dangerous builds not checked
 Setting up Verlet run ...
   Unit style    : lj
   Current step  : 20
   Time step     : 0.005
-Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       20    0.6239063   -5.5404291            0   -4.6082254    1.0394285 
       21   0.63845863   -5.5628733            0   -4.6089263   0.99398278 
-Loop time of 0.000304321 on 1 procs for 1 steps with 256 atoms
+Loop time of 0.000638039 on 1 procs for 1 steps with 256 atoms
 
-Performance: 1419553.695 tau/day, 3286.004 timesteps/s
+Performance: 677074.599 tau/day, 1567.302 timesteps/s
-98.9% CPU use with 1 MPI tasks x no OpenMP threads
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.00027815 | 0.00027815 | 0.00027815 |   0.0 | 91.40
+Pair    | 0.00042876 | 0.00042876 | 0.00042876 |   0.0 | 67.20
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 8.321e-06  | 8.321e-06  | 8.321e-06  |   0.0 |  2.73
+Comm    | 5.2872e-05 | 5.2872e-05 | 5.2872e-05 |   0.0 |  8.29
-Output  | 1.0513e-05 | 1.0513e-05 | 1.0513e-05 |   0.0 |  3.45
+Output  | 0.00012218 | 0.00012218 | 0.00012218 |   0.0 | 19.15
-Modify  | 3.968e-06  | 3.968e-06  | 3.968e-06  |   0.0 |  1.30
+Modify  | 1.3762e-05 | 1.3762e-05 | 1.3762e-05 |   0.0 |  2.16
-Other   |            | 3.365e-06  |            |       |  1.11
+Other   |            | 2.047e-05  |            |       |  3.21
 
-Nlocal:    256 ave 256 max 256 min
+Nlocal:        256.000 ave         256 max         256 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1431 ave 1431 max 1431 min
+Nghost:        1431.00 ave        1431 max        1431 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9705 ave 9705 max 9705 min
+Neighs:        9705.00 ave        9705 max        9705 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9705
-Ave neighs/atom = 37.9102
+Ave neighs/atom = 37.910156
 Neighbor list builds = 0
 Dangerous builds not checked
 Force on 1 atom via extract_atom: 26.9581
@@ -124,136 +127,136 @@ Setting up Verlet run ...
   Unit style    : lj
   Current step  : 21
   Time step     : 0.005
-Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       21   0.63845863   -5.5628733            0   -4.6089263   0.99398278 
       31    0.7494946   -5.7306417            0   -4.6107913   0.41043597 
-Loop time of 0.00196027 on 1 procs for 10 steps with 256 atoms
+Loop time of 0.00281277 on 1 procs for 10 steps with 256 atoms
 
-Performance: 2203779.175 tau/day, 5101.341 timesteps/s
+Performance: 1535852.558 tau/day, 3555.214 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+92.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0018146  | 0.0018146  | 0.0018146  |   0.0 | 92.57
+Pair    | 0.0024599  | 0.0024599  | 0.0024599  |   0.0 | 87.45
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 8.0268e-05 | 8.0268e-05 | 8.0268e-05 |   0.0 |  4.09
+Comm    | 0.00020234 | 0.00020234 | 0.00020234 |   0.0 |  7.19
-Output  | 1.0973e-05 | 1.0973e-05 | 1.0973e-05 |   0.0 |  0.56
+Output  | 3.6436e-05 | 3.6436e-05 | 3.6436e-05 |   0.0 |  1.30
-Modify  | 3.6913e-05 | 3.6913e-05 | 3.6913e-05 |   0.0 |  1.88
+Modify  | 6.7542e-05 | 6.7542e-05 | 6.7542e-05 |   0.0 |  2.40
-Other   |            | 1.756e-05  |            |       |  0.90
+Other   |            | 4.655e-05  |            |       |  1.65
 
-Nlocal:    256 ave 256 max 256 min
+Nlocal:        256.000 ave         256 max         256 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1431 ave 1431 max 1431 min
+Nghost:        1431.00 ave        1431 max        1431 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9688 ave 9688 max 9688 min
+Neighs:        9688.00 ave        9688 max        9688 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9688
-Ave neighs/atom = 37.8438
+Ave neighs/atom = 37.843750
 Neighbor list builds = 0
 Dangerous builds not checked
 Setting up Verlet run ...
   Unit style    : lj
   Current step  : 31
   Time step     : 0.005
-Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       31    0.7494946   -5.7306417            0   -4.6107913   0.41043597 
       51   0.71349216   -5.6772387            0   -4.6111811   0.52117681 
-Loop time of 0.00433063 on 1 procs for 20 steps with 256 atoms
+Loop time of 0.00560916 on 1 procs for 20 steps with 256 atoms
 
-Performance: 1995088.941 tau/day, 4618.261 timesteps/s
+Performance: 1540338.414 tau/day, 3565.598 timesteps/s
-99.3% CPU use with 1 MPI tasks x no OpenMP threads
+99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0035121  | 0.0035121  | 0.0035121  |   0.0 | 81.10
+Pair    | 0.0044403  | 0.0044403  | 0.0044403  |   0.0 | 79.16
-Neigh   | 0.00050258 | 0.00050258 | 0.00050258 |   0.0 | 11.61
+Neigh   | 0.00056186 | 0.00056186 | 0.00056186 |   0.0 | 10.02
-Comm    | 0.00019444 | 0.00019444 | 0.00019444 |   0.0 |  4.49
+Comm    | 0.00036797 | 0.00036797 | 0.00036797 |   0.0 |  6.56
-Output  | 1.2092e-05 | 1.2092e-05 | 1.2092e-05 |   0.0 |  0.28
+Output  | 3.676e-05  | 3.676e-05  | 3.676e-05  |   0.0 |  0.66
-Modify  | 7.2917e-05 | 7.2917e-05 | 7.2917e-05 |   0.0 |  1.68
+Modify  | 0.00011282 | 0.00011282 | 0.00011282 |   0.0 |  2.01
-Other   |            | 3.647e-05  |            |       |  0.84
+Other   |            | 8.943e-05  |            |       |  1.59
 
-Nlocal:    256 ave 256 max 256 min
+Nlocal:        256.000 ave         256 max         256 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1421 ave 1421 max 1421 min
+Nghost:        1421.00 ave        1421 max        1421 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9700 ave 9700 max 9700 min
+Neighs:        9700.00 ave        9700 max        9700 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9700
-Ave neighs/atom = 37.8906
+Ave neighs/atom = 37.890625
 Neighbor list builds = 1
 Dangerous builds not checked
 Setting up Verlet run ...
   Unit style    : lj
   Current step  : 51
   Time step     : 0.005
-Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       51   0.71349216   -5.6772387            0   -4.6111811   0.52117681 
       61   0.78045421   -5.7781094            0   -4.6120011  0.093808941 
-Loop time of 0.00196567 on 1 procs for 10 steps with 256 atoms
+Loop time of 0.00373815 on 1 procs for 10 steps with 256 atoms
 
-Performance: 2197727.285 tau/day, 5087.332 timesteps/s
+Performance: 1155650.623 tau/day, 2675.117 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+98.0% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0018222  | 0.0018222  | 0.0018222  |   0.0 | 92.70
+Pair    | 0.0030908  | 0.0030908  | 0.0030908  |   0.0 | 82.68
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 7.8285e-05 | 7.8285e-05 | 7.8285e-05 |   0.0 |  3.98
+Comm    | 0.00038189 | 0.00038189 | 0.00038189 |   0.0 | 10.22
-Output  | 1.0862e-05 | 1.0862e-05 | 1.0862e-05 |   0.0 |  0.55
+Output  | 4.1615e-05 | 4.1615e-05 | 4.1615e-05 |   0.0 |  1.11
-Modify  | 3.6719e-05 | 3.6719e-05 | 3.6719e-05 |   0.0 |  1.87
+Modify  | 0.00013851 | 0.00013851 | 0.00013851 |   0.0 |  3.71
-Other   |            | 1.764e-05  |            |       |  0.90
+Other   |            | 8.533e-05  |            |       |  2.28
 
-Nlocal:    256 ave 256 max 256 min
+Nlocal:        256.000 ave         256 max         256 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1421 ave 1421 max 1421 min
+Nghost:        1421.00 ave        1421 max        1421 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9700 ave 9700 max 9700 min
+Neighs:        9700.00 ave        9700 max        9700 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9700
-Ave neighs/atom = 37.8906
+Ave neighs/atom = 37.890625
 Neighbor list builds = 0
 Dangerous builds not checked
 Setting up Verlet run ...
   Unit style    : lj
   Current step  : 61
   Time step     : 0.005
-Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       61   0.78045421   -5.7781094            0   -4.6120011  0.093808941 
       81   0.77743907   -5.7735004            0   -4.6118971  0.090822641 
-Loop time of 0.00430528 on 1 procs for 20 steps with 256 atoms
+Loop time of 0.00612177 on 1 procs for 20 steps with 256 atoms
 
-Performance: 2006838.581 tau/day, 4645.460 timesteps/s
+Performance: 1411356.519 tau/day, 3267.029 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0034931  | 0.0034931  | 0.0034931  |   0.0 | 81.13
+Pair    | 0.0047211  | 0.0047211  | 0.0047211  |   0.0 | 77.12
-Neigh   | 0.00050437 | 0.00050437 | 0.00050437 |   0.0 | 11.72
+Neigh   | 0.00083088 | 0.00083088 | 0.00083088 |   0.0 | 13.57
-Comm    | 0.0001868  | 0.0001868  | 0.0001868  |   0.0 |  4.34
+Comm    | 0.00032716 | 0.00032716 | 0.00032716 |   0.0 |  5.34
-Output  | 1.1699e-05 | 1.1699e-05 | 1.1699e-05 |   0.0 |  0.27
+Output  | 3.9891e-05 | 3.9891e-05 | 3.9891e-05 |   0.0 |  0.65
-Modify  | 7.3308e-05 | 7.3308e-05 | 7.3308e-05 |   0.0 |  1.70
+Modify  | 0.00010926 | 0.00010926 | 0.00010926 |   0.0 |  1.78
-Other   |            | 3.604e-05  |            |       |  0.84
+Other   |            | 9.346e-05  |            |       |  1.53
 
-Nlocal:    256 ave 256 max 256 min
+Nlocal:        256.000 ave         256 max         256 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1405 ave 1405 max 1405 min
+Nghost:        1405.00 ave        1405 max        1405 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9701 ave 9701 max 9701 min
+Neighs:        9701.00 ave        9701 max        9701 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9701
-Ave neighs/atom = 37.8945
+Ave neighs/atom = 37.894531
 Neighbor list builds = 1
 Dangerous builds not checked
 Deleted 256 atoms, new total = 0
@@ -261,34 +264,34 @@ Setting up Verlet run ...
   Unit style    : lj
   Current step  : 81
   Time step     : 0.005
-Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       81    0.6239063   -5.5404291            0   -4.6082254    1.0394285 
       91   0.75393007   -5.7375259            0   -4.6110484   0.39357367 
-Loop time of 0.00195843 on 1 procs for 10 steps with 256 atoms
+Loop time of 0.00319065 on 1 procs for 10 steps with 256 atoms
 
-Performance: 2205851.941 tau/day, 5106.139 timesteps/s
+Performance: 1353954.393 tau/day, 3134.154 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0018143  | 0.0018143  | 0.0018143  |   0.0 | 92.64
+Pair    | 0.0027828  | 0.0027828  | 0.0027828  |   0.0 | 87.22
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 7.8608e-05 | 7.8608e-05 | 7.8608e-05 |   0.0 |  4.01
+Comm    | 0.00023286 | 0.00023286 | 0.00023286 |   0.0 |  7.30
-Output  | 1.0786e-05 | 1.0786e-05 | 1.0786e-05 |   0.0 |  0.55
+Output  | 4.0459e-05 | 4.0459e-05 | 4.0459e-05 |   0.0 |  1.27
-Modify  | 3.7106e-05 | 3.7106e-05 | 3.7106e-05 |   0.0 |  1.89
+Modify  | 7.3576e-05 | 7.3576e-05 | 7.3576e-05 |   0.0 |  2.31
-Other   |            | 1.762e-05  |            |       |  0.90
+Other   |            | 6.094e-05  |            |       |  1.91
 
-Nlocal:    256 ave 256 max 256 min
+Nlocal:        256.000 ave         256 max         256 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1431 ave 1431 max 1431 min
+Nghost:        1431.00 ave        1431 max        1431 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9705 ave 9705 max 9705 min
+Neighs:        9705.00 ave        9705 max        9705 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9705
-Ave neighs/atom = 37.9102
+Ave neighs/atom = 37.910156
 Neighbor list builds = 0
 Dangerous builds not checked
 Total wall time: 0:00:00

examples/COUPLE/plugin/log.simple.plugin.4

@@ -1,9 +1,12 @@
-LAMMPS (18 Feb 2020)
+LAMMPS (31 Aug 2021)
-Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
-Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
+  using 1 OpenMP thread(s) per MPI task
+Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
   1 by 1 by 2 MPI processor grid
 Created 256 atoms
-  create_atoms CPU = 0.000265157 secs
+  using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
+  create_atoms CPU = 0.003 seconds
 Neighbor list info ...
   update every 20 steps, delay 0 steps, check no
   max neighbors/atom: 2000, page size: 100000
@@ -14,7 +17,7 @@ Neighbor list info ...
   (1) pair lj/cut, perpetual
       attributes: half, newton on
       pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
+      stencil: half/bin/3d
       bin: standard
 Setting up Verlet run ...
   Unit style    : lj
@@ -24,30 +27,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0         1.44   -6.7733681            0   -4.6218056   -5.0244179 
       10    1.1298532   -6.3095502            0   -4.6213906   -2.6058175 
-Loop time of 0.00115264 on 2 procs for 10 steps with 256 atoms
+Loop time of 0.00330899 on 2 procs for 10 steps with 256 atoms
 
-Performance: 3747912.946 tau/day, 8675.724 timesteps/s
+Performance: 1305535.501 tau/day, 3022.073 timesteps/s
-94.5% CPU use with 2 MPI tasks x no OpenMP threads
+75.7% CPU use with 2 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.00074885 | 0.00075021 | 0.00075156 |   0.0 | 65.09
+Pair    | 0.0013522  | 0.0013813  | 0.0014104  |   0.1 | 41.74
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00031829 | 0.00031943 | 0.00032056 |   0.0 | 27.71
+Comm    | 0.00049139 | 0.00054241 | 0.00059342 |   0.0 | 16.39
-Output  | 9.306e-06  | 2.6673e-05 | 4.4041e-05 |   0.0 |  2.31
+Output  | 3.6986e-05 | 0.00056588 | 0.0010948  |   0.0 | 17.10
-Modify  | 2.0684e-05 | 2.0891e-05 | 2.1098e-05 |   0.0 |  1.81
+Modify  | 4.3909e-05 | 4.3924e-05 | 4.3939e-05 |   0.0 |  1.33
-Other   |            | 3.544e-05  |            |       |  3.07
+Other   |            | 0.0007755  |            |       | 23.44
 
-Nlocal:    128 ave 128 max 128 min
+Nlocal:        128.000 ave         128 max         128 min
 Histogram: 2 0 0 0 0 0 0 0 0 0
-Nghost:    1109 ave 1109 max 1109 min
+Nghost:        1109.00 ave        1109 max        1109 min
 Histogram: 2 0 0 0 0 0 0 0 0 0
-Neighs:    4992 ave 4992 max 4992 min
+Neighs:        4992.00 ave        4992 max        4992 min
 Histogram: 2 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 9984
-Ave neighs/atom = 39
+Ave neighs/atom = 39.000000
 Neighbor list builds = 0
 Dangerous builds not checked
 Setting up Verlet run ...
@@ -58,30 +61,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       10    1.1298532   -6.3095502            0   -4.6213906   -2.6058175 
       20    0.6239063    -5.557644            0   -4.6254403   0.97451173 
-Loop time of 0.00120443 on 2 procs for 10 steps with 256 atoms
+Loop time of 0.00648485 on 2 procs for 10 steps with 256 atoms
 
-Performance: 3586761.860 tau/day, 8302.689 timesteps/s
+Performance: 666168.017 tau/day, 1542.056 timesteps/s
-95.5% CPU use with 2 MPI tasks x no OpenMP threads
+44.3% CPU use with 2 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.00087798 | 0.00091359 | 0.0009492  |   0.0 | 75.85
+Pair    | 0.0022373  | 0.0024405  | 0.0026437  |   0.4 | 37.63
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00016739 | 0.00020368 | 0.00023997 |   0.0 | 16.91
+Comm    | 0.0024446  | 0.0026464  | 0.0028481  |   0.4 | 40.81
-Output  | 1.0124e-05 | 3.0513e-05 | 5.0901e-05 |   0.0 |  2.53
+Output  | 3.9069e-05 | 0.00059734 | 0.0011556  |   0.0 |  9.21
-Modify  | 1.89e-05   | 1.9812e-05 | 2.0725e-05 |   0.0 |  1.64
+Modify  | 4.869e-05  | 4.912e-05  | 4.9551e-05 |   0.0 |  0.76
-Other   |            | 3.683e-05  |            |       |  3.06
+Other   |            | 0.0007515  |            |       | 11.59
 
-Nlocal:    128 ave 134 max 122 min
+Nlocal:        128.000 ave         134 max         122 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    1109 ave 1115 max 1103 min
+Nghost:        1109.00 ave        1115 max        1103 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    4976 ave 5205 max 4747 min
+Neighs:        4976.00 ave        5205 max        4747 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
 
 Total # of neighbors = 9952
-Ave neighs/atom = 38.875
+Ave neighs/atom = 38.875000
 Neighbor list builds = 0
 Dangerous builds not checked
 Setting up Verlet run ...
@@ -92,34 +95,34 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       20    0.6239063   -5.5404291            0   -4.6082254    1.0394285 
       21   0.63845863   -5.5628733            0   -4.6089263   0.99398278 
-Loop time of 0.000206062 on 2 procs for 1 steps with 256 atoms
+Loop time of 0.00128072 on 2 procs for 1 steps with 256 atoms
 
-Performance: 2096456.406 tau/day, 4852.908 timesteps/s
+Performance: 337310.921 tau/day, 780.812 timesteps/s
-94.1% CPU use with 2 MPI tasks x no OpenMP threads
+60.2% CPU use with 2 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.00012947 | 0.00013524 | 0.00014101 |   0.0 | 65.63
+Pair    | 0.00047351 | 0.00049064 | 0.00050777 |   0.0 | 38.31
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.858e-05  | 2.4113e-05 | 2.9647e-05 |   0.0 | 11.70
+Comm    | 7.6767e-05 | 9.3655e-05 | 0.00011054 |   0.0 |  7.31
-Output  | 8.699e-06  | 2.4204e-05 | 3.9708e-05 |   0.0 | 11.75
+Output  | 5.4217e-05 | 0.00026297 | 0.00047172 |   0.0 | 20.53
-Modify  | 2.34e-06   | 2.3705e-06 | 2.401e-06  |   0.0 |  1.15
+Modify  | 1.1554e-05 | 1.2026e-05 | 1.2498e-05 |   0.0 |  0.94
-Other   |            | 2.013e-05  |            |       |  9.77
+Other   |            | 0.0004214  |            |       | 32.91
 
-Nlocal:    128 ave 135 max 121 min
+Nlocal:        128.000 ave         135 max         121 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    1109 ave 1116 max 1102 min
+Nghost:        1109.00 ave        1116 max        1102 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    4852.5 ave 5106 max 4599 min
+Neighs:        4852.50 ave        5106 max        4599 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
 
 Total # of neighbors = 9705
-Ave neighs/atom = 37.9102
+Ave neighs/atom = 37.910156
-Force on 1 atom via extract_atom: -18.109
-Force on 1 atom via extract_variable: -18.109
 Neighbor list builds = 0
 Dangerous builds not checked
+Force on 1 atom via extract_atom: -18.109
+Force on 1 atom via extract_variable: -18.109
 Force on 1 atom via extract_atom: 26.9581
 Force on 1 atom via extract_variable: 26.9581
 Setting up Verlet run ...
@@ -130,30 +133,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       21   0.63845863   -5.5628733            0   -4.6089263   0.99398278 
       31    0.7494946   -5.7306417            0   -4.6107913   0.41043597 
-Loop time of 0.00119048 on 2 procs for 10 steps with 256 atoms
+Loop time of 0.00784933 on 2 procs for 10 steps with 256 atoms
 
-Performance: 3628802.105 tau/day, 8400.005 timesteps/s
+Performance: 550365.761 tau/day, 1273.995 timesteps/s
-98.0% CPU use with 2 MPI tasks x no OpenMP threads
+59.6% CPU use with 2 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.00085276 | 0.00089699 | 0.00094123 |   0.0 | 75.35
+Pair    | 0.0019235  | 0.0033403  | 0.0047572  |   2.5 | 42.56
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00016896 | 0.00021444 | 0.00025992 |   0.0 | 18.01
+Comm    | 0.0016948  | 0.003118   | 0.0045411  |   2.5 | 39.72
-Output  | 9.413e-06  | 2.5939e-05 | 4.2465e-05 |   0.0 |  2.18
+Output  | 3.6445e-05 | 0.00064636 | 0.0012563  |   0.0 |  8.23
-Modify  | 1.8977e-05 | 2.0009e-05 | 2.1042e-05 |   0.0 |  1.68
+Modify  | 6.2842e-05 | 6.3209e-05 | 6.3577e-05 |   0.0 |  0.81
-Other   |            | 3.31e-05   |            |       |  2.78
+Other   |            | 0.0006814  |            |       |  8.68
 
-Nlocal:    128 ave 135 max 121 min
+Nlocal:        128.000 ave         135 max         121 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    1109 ave 1116 max 1102 min
+Nghost:        1109.00 ave        1116 max        1102 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    4844 ave 5096 max 4592 min
+Neighs:        4844.00 ave        5096 max        4592 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
 
 Total # of neighbors = 9688
-Ave neighs/atom = 37.8438
+Ave neighs/atom = 37.843750
 Neighbor list builds = 0
 Dangerous builds not checked
 Setting up Verlet run ...
@@ -164,30 +167,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       31    0.7494946   -5.7306417            0   -4.6107913   0.41043597 
       51   0.71349216   -5.6772387            0   -4.6111811   0.52117681 
-Loop time of 0.00252603 on 2 procs for 20 steps with 256 atoms
+Loop time of 0.00696051 on 2 procs for 20 steps with 256 atoms
 
-Performance: 3420382.192 tau/day, 7917.551 timesteps/s
+Performance: 1241287.730 tau/day, 2873.351 timesteps/s
-99.2% CPU use with 2 MPI tasks x no OpenMP threads
+79.2% CPU use with 2 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0016245  | 0.0017014  | 0.0017784  |   0.2 | 67.36
+Pair    | 0.0028267  | 0.0036088  | 0.004391   |   1.3 | 51.85
-Neigh   | 0.00025359 | 0.0002563  | 0.00025901 |   0.0 | 10.15
+Neigh   | 0.00040272 | 0.00040989 | 0.00041707 |   0.0 |  5.89
-Comm    | 0.00036863 | 0.00045124 | 0.00053385 |   0.0 | 17.86
+Comm    | 0.00081061 | 0.0015825  | 0.0023544  |   1.9 | 22.74
-Output  | 9.839e-06  | 2.8031e-05 | 4.6223e-05 |   0.0 |  1.11
+Output  | 3.6006e-05 | 0.00062106 | 0.0012061  |   0.0 |  8.92
-Modify  | 3.7027e-05 | 3.9545e-05 | 4.2063e-05 |   0.0 |  1.57
+Modify  | 6.8937e-05 | 7.1149e-05 | 7.336e-05  |   0.0 |  1.02
-Other   |            | 4.948e-05  |            |       |  1.96
+Other   |            | 0.0006671  |            |       |  9.58
 
-Nlocal:    128 ave 132 max 124 min
+Nlocal:        128.000 ave         132 max         124 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    1100 ave 1101 max 1099 min
+Nghost:        1100.00 ave        1101 max        1099 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    4850 ave 4953 max 4747 min
+Neighs:        4850.00 ave        4953 max        4747 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
 
 Total # of neighbors = 9700
-Ave neighs/atom = 37.8906
+Ave neighs/atom = 37.890625
 Neighbor list builds = 1
 Dangerous builds not checked
 Setting up Verlet run ...
@@ -198,30 +201,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       51   0.71349216   -5.6772387            0   -4.6111811   0.52117681 
       61   0.78045421   -5.7781094            0   -4.6120011  0.093808941 
-Loop time of 0.00115444 on 2 procs for 10 steps with 256 atoms
+Loop time of 0.00155862 on 2 procs for 10 steps with 256 atoms
 
-Performance: 3742065.976 tau/day, 8662.190 timesteps/s
+Performance: 2771678.197 tau/day, 6415.922 timesteps/s
-96.5% CPU use with 2 MPI tasks x no OpenMP threads
+95.0% CPU use with 2 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.00087346 | 0.00089311 | 0.00091275 |   0.0 | 77.36
+Pair    | 0.0012369  | 0.001266   | 0.001295   |   0.1 | 81.22
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00016192 | 0.0001823  | 0.00020269 |   0.0 | 15.79
+Comm    | 0.00019462 | 0.00022315 | 0.00025169 |   0.0 | 14.32
-Output  | 9.49e-06   | 2.6234e-05 | 4.2978e-05 |   0.0 |  2.27
+Output  | 2.0217e-05 | 2.1945e-05 | 2.3673e-05 |   0.0 |  1.41
-Modify  | 1.9095e-05 | 1.9843e-05 | 2.0591e-05 |   0.0 |  1.72
+Modify  | 2.562e-05  | 2.5759e-05 | 2.5898e-05 |   0.0 |  1.65
-Other   |            | 3.296e-05  |            |       |  2.85
+Other   |            | 2.181e-05  |            |       |  1.40
 
-Nlocal:    128 ave 132 max 124 min
+Nlocal:        128.000 ave         132 max         124 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    1100 ave 1101 max 1099 min
+Nghost:        1100.00 ave        1101 max        1099 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    4850 ave 4953 max 4747 min
+Neighs:        4850.00 ave        4953 max        4747 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
 
 Total # of neighbors = 9700
-Ave neighs/atom = 37.8906
+Ave neighs/atom = 37.890625
 Neighbor list builds = 0
 Dangerous builds not checked
 Setting up Verlet run ...
@@ -232,30 +235,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       61   0.78045421   -5.7781094            0   -4.6120011  0.093808941 
       81   0.77743907   -5.7735004            0   -4.6118971  0.090822641 
-Loop time of 0.00244325 on 2 procs for 20 steps with 256 atoms
+Loop time of 0.00351607 on 2 procs for 20 steps with 256 atoms
 
-Performance: 3536279.919 tau/day, 8185.833 timesteps/s
+Performance: 2457288.612 tau/day, 5688.168 timesteps/s
-99.0% CPU use with 2 MPI tasks x no OpenMP threads
+97.9% CPU use with 2 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0016916  | 0.0017038  | 0.001716   |   0.0 | 69.73
+Pair    | 0.0023896  | 0.0024147  | 0.0024397  |   0.1 | 68.67
-Neigh   | 0.00025229 | 0.00025512 | 0.00025795 |   0.0 | 10.44
+Neigh   | 0.00037331 | 0.00040456 | 0.0004358  |   0.0 | 11.51
-Comm    | 0.00035772 | 0.00036918 | 0.00038064 |   0.0 | 15.11
+Comm    | 0.00050571 | 0.00051343 | 0.00052116 |   0.0 | 14.60
-Output  | 1.0858e-05 | 2.7875e-05 | 4.4891e-05 |   0.0 |  1.14
+Output  | 2.6424e-05 | 5.6547e-05 | 8.667e-05  |   0.0 |  1.61
-Modify  | 3.817e-05  | 3.9325e-05 | 4.048e-05  |   0.0 |  1.61
+Modify  | 5.0287e-05 | 5.1071e-05 | 5.1856e-05 |   0.0 |  1.45
-Other   |            | 4.796e-05  |            |       |  1.96
+Other   |            | 7.58e-05   |            |       |  2.16
 
-Nlocal:    128 ave 128 max 128 min
+Nlocal:        128.000 ave         128 max         128 min
 Histogram: 2 0 0 0 0 0 0 0 0 0
-Nghost:    1088.5 ave 1092 max 1085 min
+Nghost:        1088.50 ave        1092 max        1085 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    4850.5 ave 4851 max 4850 min
+Neighs:        4850.50 ave        4851 max        4850 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
 
 Total # of neighbors = 9701
-Ave neighs/atom = 37.8945
+Ave neighs/atom = 37.894531
 Neighbor list builds = 1
 Dangerous builds not checked
 Deleted 256 atoms, new total = 0
@@ -267,30 +270,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
 Step Temp E_pair E_mol TotEng Press 
       81    0.6239063   -5.5404291            0   -4.6082254    1.0394285 
       91   0.75393007   -5.7375259            0   -4.6110484   0.39357367 
-Loop time of 0.00118092 on 2 procs for 10 steps with 256 atoms
+Loop time of 0.0109747 on 2 procs for 10 steps with 256 atoms
 
-Performance: 3658158.625 tau/day, 8467.960 timesteps/s
+Performance: 393631.731 tau/day, 911.185 timesteps/s
-98.6% CPU use with 2 MPI tasks x no OpenMP threads
+53.5% CPU use with 2 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0008476  | 0.00089265 | 0.00093771 |   0.0 | 75.59
+Pair    | 0.0012057  | 0.0012732  | 0.0013407  |   0.2 | 11.60
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00016335 | 0.00020946 | 0.00025557 |   0.0 | 17.74
+Comm    | 0.00018882 | 0.00025686 | 0.00032489 |   0.0 |  2.34
-Output  | 8.87e-06   | 2.5733e-05 | 4.2595e-05 |   0.0 |  2.18
+Output  | 2.1943e-05 | 0.0047067  | 0.0093915  |   6.8 | 42.89
-Modify  | 1.8755e-05 | 1.9814e-05 | 2.0872e-05 |   0.0 |  1.68
+Modify  | 2.4614e-05 | 2.5439e-05 | 2.6264e-05 |   0.0 |  0.23
-Other   |            | 3.326e-05  |            |       |  2.82
+Other   |            | 0.004712   |            |       | 42.94
 
-Nlocal:    128 ave 135 max 121 min
+Nlocal:        128.000 ave         135 max         121 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    1109 ave 1116 max 1102 min
+Nghost:        1109.00 ave        1116 max        1102 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    4852.5 ave 5106 max 4599 min
+Neighs:        4852.50 ave        5106 max        4599 min
 Histogram: 1 0 0 0 0 0 0 0 0 1
 
 Total # of neighbors = 9705
-Ave neighs/atom = 37.9102
+Ave neighs/atom = 37.910156
 Neighbor list builds = 0
 Dangerous builds not checked
 Total wall time: 0:00:00

examples/COUPLE/plugin/simple.c

@@ -87,7 +87,7 @@ int main(int narg, char **arg)
       MPI_Abort(MPI_COMM_WORLD,1);
     }
   }
-  if (lammps == 1) plugin->open(0,NULL,comm_lammps,&lmp);
+  if (lammps == 1) lmp = plugin->open(0,NULL,comm_lammps,NULL);
 
   while (1) {
     if (me == 0) {
@@ -139,7 +139,7 @@ int main(int narg, char **arg)
 
   cmds[0] = (char *)"run 10";
   cmds[1] = (char *)"run 20";
-  if (lammps == 1) plugin->commands_list(lmp,2,cmds);
+  if (lammps == 1) plugin->commands_list(lmp,2,(const char **)cmds);
 
   /* delete all atoms
      create_atoms() to create new ones with old coords, vels
@@ -164,12 +164,13 @@ int main(int narg, char **arg)
 
   if (lammps == 1) {
     plugin->close(lmp);
+    MPI_Barrier(comm_lammps);
+    MPI_Comm_free(&comm_lammps);
     liblammpsplugin_release(plugin);
   }
 
   /* close down MPI */
 
-  if (lammps == 1) MPI_Comm_free(&comm_lammps);
   MPI_Barrier(MPI_COMM_WORLD);
   MPI_Finalize();
 }

lib/gpu/geryon/ocl_device.h

@@ -462,7 +462,6 @@ int UCL_Device::set_platform(int pid) {
   _num_devices = 0;
   for (int i=0; i<num_unpart; i++) {
     cl_uint num_subdevices = 1;
-    cl_device_id *subdevice_list = device_list + i;
 
     #ifdef CL_VERSION_1_2
     cl_device_affinity_domain adomain;
@@ -479,19 +478,21 @@ int UCL_Device::set_platform(int pid) {
       CL_SAFE_CALL(clCreateSubDevices(device_list[i], props, 0, NULL,
                                       &num_subdevices));
     if (num_subdevices > 1) {
-      subdevice_list = new cl_device_id[num_subdevices];
+      cl_device_id *subdevice_list = new cl_device_id[num_subdevices];
       CL_SAFE_CALL(clCreateSubDevices(device_list[i], props, num_subdevices,
                                       subdevice_list, &num_subdevices));
+      for (int j=0; j<num_subdevices; j++) {
+        _cl_devices.push_back(device_list[i]);
+        add_properties(device_list[i]);
+        _num_devices++;
+      }
+      delete[] subdevice_list;
+    } else {
+      _cl_devices.push_back(device_list[i]);
+      add_properties(device_list[i]);
+      _num_devices++;
     }
     #endif
-
-    for (int j=0; j<num_subdevices; j++) {
-      _num_devices++;
-      _cl_devices.push_back(subdevice_list[j]);
-      add_properties(subdevice_list[j]);
-    }
-
-    if (num_subdevices > 1) delete[] subdevice_list;
   } // for i
   #endif
 

lib/gpu/geryon/ocl_timer.h

@@ -38,8 +38,10 @@ namespace ucl_opencl {
 /// Class for timing OpenCL events
 class UCL_Timer {
  public:
-  inline UCL_Timer() : _total_time(0.0f), _initialized(false), has_measured_time(false) { }
+  inline UCL_Timer() : start_event(nullptr), stop_event(nullptr), _total_time(0.0f),
-  inline UCL_Timer(UCL_Device &dev) : _total_time(0.0f), _initialized(false), has_measured_time(false)
+                       _initialized(false), has_measured_time(false) { }
+  inline UCL_Timer(UCL_Device &dev) : start_event(nullptr), stop_event(nullptr), _total_time(0.0f),
+                                      _initialized(false), has_measured_time(false)
     { init(dev); }
 
   inline ~UCL_Timer() { clear(); }

lib/gpu/lal_answer.h

@@ -127,9 +127,8 @@ class Answer {
   /// Add forces and torques from the GPU into a LAMMPS pointer
   void get_answers(double **f, double **tor);
 
-  inline double get_answers(double **f, double **tor, double *eatom,
+  inline double get_answers(double **f, double **tor, double *eatom, double **vatom,
-                            double **vatom, double *virial, double &ecoul,
+                            double *virial, double &ecoul, int &error_flag_in) {
-                            int &error_flag_in) {
     double ta=MPI_Wtime();
     time_answer.sync_stop();
     _time_cpu_idle+=MPI_Wtime()-ta;

lib/gpu/lal_device.cpp

@@ -348,7 +348,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int ngpu,
 }
 
 template <class numtyp, class acctyp>
-int DeviceT::set_ocl_params(std::string s_config, std::string extra_args) {
+int DeviceT::set_ocl_params(std::string s_config, const std::string &extra_args) {
   #ifdef USE_OPENCL
 
   #include "lal_pre_ocl_config.h"
@@ -368,7 +368,7 @@ int DeviceT::set_ocl_params(std::string s_config, std::string extra_args) {
   int token_count=0;
   std::string params[18];
   char ocl_config[2048];
-  strcpy(ocl_config,s_config.c_str());
+  strncpy(ocl_config,s_config.c_str(),2047);
   char *pch = strtok(ocl_config,",");
   _ocl_config_name=pch;
   pch = strtok(nullptr,",");
@@ -992,10 +992,8 @@ int DeviceT::compile_kernels() {
       static_cast<size_t>(_block_cell_2d) > gpu->group_size_dim(0) ||
       static_cast<size_t>(_block_cell_2d) > gpu->group_size_dim(1) ||
       static_cast<size_t>(_block_cell_id) > gpu->group_size_dim(0) ||
-      static_cast<size_t>(_max_shared_types*_max_shared_types*
+      static_cast<size_t>(_max_shared_types*_max_shared_types*sizeof(numtyp)*17 > gpu->slm_size()) ||
-                          sizeof(numtyp)*17 > gpu->slm_size()) ||
+      static_cast<size_t>(_max_bio_shared_types*2*sizeof(numtyp) > gpu->slm_size()))
-      static_cast<size_t>(_max_bio_shared_types*2*sizeof(numtyp) >
-                          gpu->slm_size()))
     return -13;
 
   if (_block_pair % _simd_size != 0 || _block_bio_pair % _simd_size != 0 ||
@@ -1071,9 +1069,8 @@ void lmp_clear_device() {
   global_device.clear_device();
 }
 
-double lmp_gpu_forces(double **f, double **tor, double *eatom,
+double lmp_gpu_forces(double **f, double **tor, double *eatom, double **vatom,
-                      double **vatom, double *virial, double &ecoul,
+                      double *virial, double &ecoul, int &error_flag) {
-                      int &error_flag) {
   return global_device.fix_gpu(f,tor,eatom,vatom,virial,ecoul,error_flag);
 }
 

lib/gpu/lal_device.h

@@ -163,17 +163,15 @@ class Device {
     { ans_queue.push(ans); }
 
   /// Add "answers" (force,energies,etc.) into LAMMPS structures
-  inline double fix_gpu(double **f, double **tor, double *eatom,
+  inline double fix_gpu(double **f, double **tor, double *eatom, double **vatom,
-                        double **vatom, double *virial, double &ecoul,
+                        double *virial, double &ecoul, int &error_flag) {
-                        int &error_flag) {
     error_flag=0;
     atom.data_unavail();
     if (ans_queue.empty()==false) {
       stop_host_timer();
       double evdw=0.0;
       while (ans_queue.empty()==false) {
-        evdw+=ans_queue.front()->get_answers(f,tor,eatom,vatom,virial,ecoul,
+        evdw += ans_queue.front()->get_answers(f,tor,eatom,vatom,virial,ecoul,error_flag);
-                                             error_flag);
         ans_queue.pop();
       }
       return evdw;
@@ -350,7 +348,7 @@ class Device {
   int _data_in_estimate, _data_out_estimate;
 
   std::string _ocl_config_name, _ocl_config_string, _ocl_compile_string;
-  int set_ocl_params(std::string, std::string);
+  int set_ocl_params(std::string, const std::string &);
 };
 
 }

lib/gpu/lal_neighbor.cpp

@@ -39,7 +39,7 @@ bool Neighbor::init(NeighborShared *shared, const int inum,
                     const int block_cell_2d, const int block_cell_id,
                     const int block_nbor_build, const int threads_per_atom,
                     const int simd_size, const bool time_device,
-                    const std::string compile_flags, const bool ilist_map) {
+                    const std::string &compile_flags, const bool ilist_map) {
   clear();
   _ilist_map = ilist_map;
 
@@ -743,7 +743,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
     mn = _max_nbors;
     const numtyp i_cell_size=static_cast<numtyp>(1.0/_cell_size);
     const int neigh_block=_block_cell_id;
-    const int GX=(int)ceil((float)nall/neigh_block);
+    const int GX=(int)ceil((double)nall/neigh_block);
     const numtyp sublo0=static_cast<numtyp>(sublo[0]);
     const numtyp sublo1=static_cast<numtyp>(sublo[1]);
     const numtyp sublo2=static_cast<numtyp>(sublo[2]);

lib/gpu/lal_neighbor.h

@@ -71,7 +71,7 @@ class Neighbor {
             const int block_cell_2d, const int block_cell_id,
             const int block_nbor_build, const int threads_per_atom,
             const int simd_size, const bool time_device,
-            const std::string compile_flags, const bool ilist_map);
+            const std::string &compile_flags, const bool ilist_map);
 
   /// Set the cutoff+skin
   inline void set_cutoff(const double cutoff) {

lib/gpu/lal_neighbor_shared.cpp

@@ -89,7 +89,7 @@ double NeighborShared::best_cell_size(const double subx, const double suby,
 }
 
 void NeighborShared::compile_kernels(UCL_Device &dev, const int gpu_nbor,
-                                     const std::string flags) {
+                                     const std::string &flags) {
   if (_compiled)
           return;
 

lib/gpu/lal_neighbor_shared.h

@@ -87,7 +87,7 @@ class NeighborShared {
 
   /// Compile kernels for neighbor lists
   void compile_kernels(UCL_Device &dev, const int gpu_nbor,
-                       const std::string flags);
+                       const std::string &flags);
 
   // ----------------------------- Kernels
   UCL_Program *nbor_program, *build_program;

lib/gpu/lal_pppm.cpp

@@ -69,14 +69,14 @@ grdtyp * PPPMT::init(const int nlocal, const int nall, FILE *_screen,
 
   flag=device->init(*ans,nlocal,nall);
   if (flag!=0)
-    return 0;
+    return nullptr;
   if (sizeof(grdtyp)==sizeof(double) && device->double_precision()==false) {
     flag=-15;
-    return 0;
+    return nullptr;
   }
   if (device->ptx_arch()>0.0 && device->ptx_arch()<1.1) {
     flag=-4;
-    return 0;
+    return nullptr;
   }
 
   ucl_device=device->gpu;
@@ -168,7 +168,7 @@ grdtyp * PPPMT::init(const int nlocal, const int nall, FILE *_screen,
                                        UCL_READ_WRITE)==UCL_SUCCESS);
   if (!success) {
     flag=-3;
-    return 0;
+    return nullptr;
   }
 
   error_flag.device.zero();
@@ -342,13 +342,15 @@ void PPPMT::interp(const grdtyp qqrd2e_scale) {
   vd_brick.update_device(true);
   time_in.stop();
 
+  int ainum=this->ans->inum();
+  if (ainum==0)
+    return;
+
   time_interp.start();
   // Compute the block size and grid size to keep all cores busy
   int BX=this->block_size();
   int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
 
-  int ainum=this->ans->inum();
-
   k_interp.set_size(GX,BX);
   k_interp.run(&atom->x, &atom->q, &ainum, &vd_brick, &d_rho_coeff,
                &_npts_x, &_npts_yx, &_brick_x, &_brick_y, &_brick_z, &_delxinv,

python/lammps/numpy_wrapper.py

@@ -92,8 +92,12 @@ class numpy_wrapper:
     if dim == LAMMPS_AUTODETECT:
       if dtype in (LAMMPS_INT_2D, LAMMPS_DOUBLE_2D, LAMMPS_INT64_2D):
         # TODO add other fields
-        if name in ("x", "v", "f", "angmom", "torque", "csforce", "vforce"):
+        if name in ("x", "v", "f", "x0", "omega", "angmom", "torque", "vforce", "vest"):
           dim = 3
+        elif name == "smd_data_9":
+          dim = 9
+        elif name == "smd_stress":
+          dim = 6
         else:
           dim = 2
       else:
@@ -386,6 +390,9 @@ class numpy_wrapper:
   # -------------------------------------------------------------------------
 
   def iarray(self, c_int_type, raw_ptr, nelem, dim=1):
+    if raw_ptr is None:
+      return None
+
     import numpy as np
     np_int_type = self._ctype_to_numpy_int(c_int_type)
 
@@ -405,7 +412,11 @@ class numpy_wrapper:
   # -------------------------------------------------------------------------
 
   def darray(self, raw_ptr, nelem, dim=1):
+    if raw_ptr is None:
+      return None
+
     import numpy as np
+
     if dim == 1:
       ptr = cast(raw_ptr, POINTER(c_double * nelem))
     else:

src/ASPHERE/pair_line_lj.cpp

@@ -301,8 +301,7 @@ void PairLineLJ::compute(int eflag, int vflag)
         }
       }
 
-      if (evflag) ev_tally(i,j,nlocal,newton_pair,
+      if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
-                           evdwl,0.0,fpair,delx,dely,delz);
     }
   }
 

src/ASPHERE/pair_tri_lj.cpp

@@ -375,8 +375,7 @@ void PairTriLJ::compute(int eflag, int vflag)
         }
       }
 
-      if (evflag) ev_tally(i,j,nlocal,newton_pair,
+      if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
-                           evdwl,0.0,fpair,delx,dely,delz);
     }
   }
 

src/AWPMD/pair_awpmd_cut.cpp

@@ -39,7 +39,6 @@
 #include <cstring>
 #include <map>
 #include <utility>
-#include <vector>
 
 using namespace LAMMPS_NS;
 

src/BOCS/fix_bocs.cpp

@@ -37,7 +37,6 @@
 
 #include <cmath>
 #include <cstring>
-#include <vector>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/BODY/fix_wall_body_polygon.cpp

@@ -337,8 +337,7 @@ void FixWallBodyPolygon::post_force(int /*vflag*/)
 
       num_contacts = 0;
       facc[0] = facc[1] = facc[2] = 0;
-      vertex_against_wall(i, wall_pos, x, f, torque, side,
+      vertex_against_wall(i, wall_pos, x, f, torque, side, contact_list, num_contacts, facc);
-                          contact_list, num_contacts, facc);
 
       if (num_contacts >= 2) {
 

src/BODY/pair_body_nparticle.cpp

@@ -324,8 +324,7 @@ void PairBodyNparticle::compute(int eflag, int vflag)
         }
       }
 
-      if (evflag) ev_tally(i,j,nlocal,newton_pair,
+      if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
-                           evdwl,0.0,fpair,delx,dely,delz);
     }
   }
 

src/BODY/pair_body_rounded_polygon.cpp

@@ -207,8 +207,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
       if (r > radi + radj + cut_inner) continue;
 
       if (npi == 1 && npj == 1) {
-        sphere_against_sphere(i, j, delx, dely, delz, rsq,
+        sphere_against_sphere(i, j, delx, dely, delz, rsq, k_nij, k_naij, x, v, f, evflag);
-                            k_nij, k_naij, x, v, f, evflag);
         continue;
       }
 

src/BROWNIAN/fix_brownian.cpp

@@ -20,17 +20,11 @@
 #include "fix_brownian.h"
 
 #include "atom.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
-#include "math_extra.h"
-#include "memory.h"
 #include "random_mars.h"
-#include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/BROWNIAN/fix_brownian_asphere.cpp

@@ -21,17 +21,10 @@
 
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
 #include "math_extra.h"
-#include "memory.h"
 #include "random_mars.h"
-#include "update.h"
-
-#include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/BROWNIAN/fix_brownian_base.cpp

@@ -17,15 +17,12 @@
    Contributing author: Sam Cameron (University of Bristol)
 ------------------------------------------------------------------------- */
 
-#include "fix_brownian.h"
+#include "fix_brownian_base.h"
 
-#include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
-#include "math_extra.h"
-#include "memory.h"
 #include "random_mars.h"
 #include "update.h"
 

src/BROWNIAN/fix_brownian_sphere.cpp

@@ -20,17 +20,12 @@
 #include "fix_brownian_sphere.h"
 
 #include "atom.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
 #include "math_extra.h"
-#include "memory.h"
 #include "random_mars.h"
-#include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/BROWNIAN/fix_propel_self.cpp

@@ -23,14 +23,11 @@
 
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
 #include "math_extra.h"
-#include "memory.h"
-#include "update.h"
 
+#include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;

src/CG-DNA/atom_vec_oxdna.cpp

@@ -14,7 +14,6 @@
 #include "atom_vec_oxdna.h"
 
 #include "atom.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 

src/CG-DNA/pair_oxdna_stk.cpp

@@ -19,7 +19,6 @@
 
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "atom_vec_oxdna.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -30,7 +29,6 @@
 
 #include <cmath>
 #include <cstring>
-#include <utility>
 
 using namespace LAMMPS_NS;
 using namespace MFOxdna;

src/CG-DNA/pair_oxrna2_excv.cpp

@@ -17,8 +17,6 @@
 
 #include "pair_oxrna2_excv.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 /* ----------------------------------------------------------------------

src/CG-DNA/pair_oxrna2_stk.cpp

@@ -19,7 +19,6 @@
 
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "atom_vec_oxdna.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -31,7 +30,6 @@
 
 #include <cmath>
 #include <cstring>
-#include <utility>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CG-SDK/pair_lj_sdk_coul_msm.cpp

@@ -18,13 +18,15 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_sdk_coul_msm.h"
-#include <cmath>
+
-#include <cstring>
 #include "atom.h"
+#include "error.h"
 #include "force.h"
 #include "kspace.h"
 #include "neigh_list.h"
-#include "error.h"
+
+#include <cmath>
+#include <cstring>
 
 #include "lj_sdk_common.h"
 

src/CLASS2/dihedral_class2.cpp

@@ -25,7 +25,6 @@
 #include "math_const.h"
 #include "memory.h"
 #include "neighbor.h"
-#include "update.h"
 
 #include <cmath>
 #include <cstring>

src/CLASS2/improper_class2.cpp

@@ -25,7 +25,6 @@
 #include "math_const.h"
 #include "memory.h"
 #include "neighbor.h"
-#include "update.h"
 
 #include <cmath>
 #include <cstring>

src/CLASS2/pair_lj_class2.cpp

@@ -397,8 +397,7 @@ void PairLJClass2::compute_outer(int eflag, int vflag)
             fpair = factor_lj*forcelj*r2inv;
         }
 
-        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
-                             evdwl,0.0,fpair,delx,dely,delz);
       }
     }
   }

src/COLLOID/fix_wall_colloid.cpp

@@ -18,10 +18,11 @@
 
 #include "fix_wall_colloid.h"
 
-#include <cmath>
 #include "atom.h"
 #include "error.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/COLVARS/colvarproxy_lammps.cpp

@@ -10,13 +10,6 @@
 
 
 #include "colvarproxy_lammps.h"
-#include <mpi.h>
-#include <sys/stat.h>
-#include <cerrno>
-#include <cstring>
-#include <iostream>
-#include <memory>
-#include <string>
 
 #include "lammps.h"
 #include "error.h"
@@ -26,6 +19,12 @@
 #include "colvarmodule.h"
 #include "colvarproxy.h"
 
+#include <sys/stat.h>
+#include <cerrno>
+#include <cstring>
+#include <iostream>
+#include <memory>
+
 #define HASH_FAIL  -1
 
 ////////////////////////////////////////////////////////////////////////

src/COLVARS/colvarproxy_lammps.h

@@ -12,11 +12,6 @@
 
 #include "colvarproxy_lammps_version.h"    // IWYU pragma: export
 
-#include <cstddef>
-#include <mpi.h>
-#include <string>
-#include <vector>
-
 #include "colvarmodule.h"
 #include "colvarproxy.h"
 #include "colvartypes.h"

src/COLVARS/fix_colvars.cpp

@@ -44,7 +44,6 @@
 #include <cstring>
 #include <iostream>
 #include <memory>
-#include <vector>
 
 static const char colvars_pub[] =
   "fix colvars command:\n\n"
@@ -1000,7 +999,7 @@ double FixColvars::compute_scalar()
 
 /* ---------------------------------------------------------------------- */
 /* local memory usage. approximately. */
-double FixColvars::memory_usage(void)
+double FixColvars::memory_usage()
 {
   double bytes = (double) (num_coords * (2*sizeof(int)+3*sizeof(double)));
   bytes += (double)(double) (nmax*size_one) + sizeof(this);

src/COMPRESS/dump_atom_gz.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -12,27 +11,25 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "domain.h"
 #include "dump_atom_gz.h"
+
+#include "domain.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) :
+DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg)
-  DumpAtom(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump atom/gz only writes compressed files");
-    error->all(FLERR,"Dump atom/gz only writes compressed files");
 }
 
 /* ---------------------------------------------------------------------- */
 
-DumpAtomGZ::~DumpAtomGZ()
+DumpAtomGZ::~DumpAtomGZ() {}
-{
-}
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -58,8 +55,7 @@ void DumpAtomGZ::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -109,9 +105,7 @@ void DumpAtomGZ::write_header(bigint ndump)
       header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
     }
 
-    if (time_flag) {
+    if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
-      header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
-    }
 
     header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
     header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
@@ -145,14 +139,14 @@ void DumpAtomGZ::write_data(int n, double *mybuf)
     for (int i = 0; i < n; i++) {
       int written = 0;
       if (image_flag == 1) {
-        written = snprintf(vbuffer, VBUFFER_SIZE, format,
+        written = snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
-              static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+                           static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4],
-              mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
+                           static_cast<int>(mybuf[m + 5]), static_cast<int>(mybuf[m + 6]),
-              static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
+                           static_cast<int>(mybuf[m + 7]));
       } else {
-        written = snprintf(vbuffer, VBUFFER_SIZE, format,
+        written =
-              static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+            snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
-              mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+                     static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
       }
       if (written > 0) {
         writer.write(vbuffer, written);
@@ -174,9 +168,7 @@ void DumpAtomGZ::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }

src/COMPRESS/dump_atom_zstd.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,6 +18,7 @@
 #ifdef LAMMPS_ZSTD
 
 #include "domain.h"
+
 #include "dump_atom_zstd.h"
 #include "error.h"
 #include "file_writer.h"
@@ -26,21 +26,16 @@
 
 #include <cstring>
 
-
 using namespace LAMMPS_NS;
 
-DumpAtomZstd::DumpAtomZstd(LAMMPS *lmp, int narg, char **arg) :
+DumpAtomZstd::DumpAtomZstd(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg)
-  DumpAtom(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump atom/zstd only writes compressed files");
-    error->all(FLERR,"Dump atom/zstd only writes compressed files");
 }
 
 /* ---------------------------------------------------------------------- */
 
-DumpAtomZstd::~DumpAtomZstd()
+DumpAtomZstd::~DumpAtomZstd() {}
-{
-}
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -66,8 +61,7 @@ void DumpAtomZstd::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -117,9 +111,7 @@ void DumpAtomZstd::write_header(bigint ndump)
       header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
     }
 
-    if (time_flag) {
+    if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
-      header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
-    }
 
     header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
     header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
@@ -153,14 +145,14 @@ void DumpAtomZstd::write_data(int n, double *mybuf)
     for (int i = 0; i < n; i++) {
       int written = 0;
       if (image_flag == 1) {
-        written = snprintf(vbuffer, VBUFFER_SIZE, format,
+        written = snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
-              static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+                           static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4],
-              mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
+                           static_cast<int>(mybuf[m + 5]), static_cast<int>(mybuf[m + 6]),
-              static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
+                           static_cast<int>(mybuf[m + 7]));
       } else {
-        written = snprintf(vbuffer, VBUFFER_SIZE, format,
+        written =
-              static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+            snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
-              mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+                     static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
       }
       if (written > 0) {
         writer.write(vbuffer, written);
@@ -182,9 +174,7 @@ void DumpAtomZstd::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }
@@ -198,9 +188,12 @@ int DumpAtomZstd::modify_param(int narg, char **arg)
     try {
       if (strcmp(arg[0], "checksum") == 0) {
         if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
-        if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
+        if (strcmp(arg[1], "yes") == 0)
-        else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
+          writer.setChecksum(true);
-        else error->all(FLERR,"Illegal dump_modify command");
+        else if (strcmp(arg[1], "no") == 0)
+          writer.setChecksum(false);
+        else
+          error->all(FLERR, "Illegal dump_modify command");
         return 2;
       } else if (strcmp(arg[0], "compression_level") == 0) {
         if (narg < 2) error->all(FLERR, "Illegal dump_modify command");

src/COMPRESS/dump_cfg_gz.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -12,10 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "dump_cfg_gz.h"
+
 #include "atom.h"
 #include "domain.h"
-#include "dump_cfg_gz.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
@@ -23,18 +24,14 @@
 using namespace LAMMPS_NS;
 #define UNWRAPEXPAND 10.0
 
-DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) :
+DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) : DumpCFG(lmp, narg, arg)
-  DumpCFG(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump cfg/gz only writes compressed files");
-    error->all(FLERR,"Dump cfg/gz only writes compressed files");
 }
 
 /* ---------------------------------------------------------------------- */
 
-DumpCFGGZ::~DumpCFGGZ()
+DumpCFGGZ::~DumpCFGGZ() {}
-{
-}
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -60,8 +57,7 @@ void DumpCFGGZ::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -111,8 +107,10 @@ void DumpCFGGZ::write_header(bigint n)
   //   so molecules are not split across periodic box boundaries
 
   double scale = 1.0;
-  if (atom->peri_flag) scale = atom->pdscale;
+  if (atom->peri_flag)
-  else if (unwrapflag == 1) scale = UNWRAPEXPAND;
+    scale = atom->pdscale;
+  else if (unwrapflag == 1)
+    scale = UNWRAPEXPAND;
 
   std::string header = fmt::format("Number of particles = {}\n", n);
   header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale);
@@ -127,8 +125,7 @@ void DumpCFGGZ::write_header(bigint n)
   header += fmt::format("H0(3,3) = {0:g} A\n", domain->zprd);
   header += fmt::format(".NO_VELOCITY.\n");
   header += fmt::format("entry_count = {}\n", nfield - 2);
-  for (int i = 0; i < nfield-5; i++)
+  for (int i = 0; i < nfield - 5; i++) header += fmt::format("auxiliary[{}] = {}\n", i, auxname[i]);
-    header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]);
 
   writer.write(header.c_str(), header.length());
 }
@@ -214,9 +211,7 @@ void DumpCFGGZ::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }

src/COMPRESS/dump_cfg_zstd.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -18,10 +17,12 @@
 
 #ifdef LAMMPS_ZSTD
 
+#include "dump_cfg_zstd.h"
+
 #include "atom.h"
 #include "domain.h"
-#include "dump_cfg_zstd.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
@@ -29,20 +30,14 @@
 using namespace LAMMPS_NS;
 #define UNWRAPEXPAND 10.0
 
-DumpCFGZstd::DumpCFGZstd(LAMMPS *lmp, int narg, char **arg) :
+DumpCFGZstd::DumpCFGZstd(LAMMPS *lmp, int narg, char **arg) : DumpCFG(lmp, narg, arg)
-  DumpCFG(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump cfg/zstd only writes compressed files");
-    error->all(FLERR,"Dump cfg/zstd only writes compressed files");
 }
 
-
 /* ---------------------------------------------------------------------- */
 
-DumpCFGZstd::~DumpCFGZstd()
+DumpCFGZstd::~DumpCFGZstd() {}
-{
-}
-
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -68,8 +63,7 @@ void DumpCFGZstd::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -95,9 +89,7 @@ void DumpCFGZstd::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    if (append_flag) {
+    if (append_flag) { error->one(FLERR, "dump cfg/zstd currently doesn't support append"); }
-      error->one(FLERR, "dump cfg/zstd currently doesn't support append");
-    }
 
     try {
       writer.open(filecurrent);
@@ -123,8 +115,10 @@ void DumpCFGZstd::write_header(bigint n)
   //   so molecules are not split across periodic box boundaries
 
   double scale = 1.0;
-  if (atom->peri_flag) scale = atom->pdscale;
+  if (atom->peri_flag)
-  else if (unwrapflag == 1) scale = UNWRAPEXPAND;
+    scale = atom->pdscale;
+  else if (unwrapflag == 1)
+    scale = UNWRAPEXPAND;
 
   std::string header = fmt::format("Number of particles = {}\n", n);
   header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale);
@@ -139,8 +133,7 @@ void DumpCFGZstd::write_header(bigint n)
   header += fmt::format("H0(3,3) = {0:g} A\n", domain->zprd);
   header += fmt::format(".NO_VELOCITY.\n");
   header += fmt::format("entry_count = {}\n", nfield - 2);
-  for (int i = 0; i < nfield-5; i++)
+  for (int i = 0; i < nfield - 5; i++) header += fmt::format("auxiliary[{}] = {}\n", i, auxname[i]);
-    header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]);
 
   writer.write(header.c_str(), header.length());
 }
@@ -226,9 +219,7 @@ void DumpCFGZstd::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }
@@ -242,9 +233,12 @@ int DumpCFGZstd::modify_param(int narg, char **arg)
     try {
       if (strcmp(arg[0], "checksum") == 0) {
         if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
-        if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
+        if (strcmp(arg[1], "yes") == 0)
-        else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
+          writer.setChecksum(true);
-        else error->all(FLERR,"Illegal dump_modify command");
+        else if (strcmp(arg[1], "no") == 0)
+          writer.setChecksum(false);
+        else
+          error->all(FLERR, "Illegal dump_modify command");
         return 2;
       } else if (strcmp(arg[0], "compression_level") == 0) {
         if (narg < 2) error->all(FLERR, "Illegal dump_modify command");

src/COMPRESS/dump_custom_gz.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -12,27 +11,25 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "domain.h"
 #include "dump_custom_gz.h"
+
+#include "domain.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) :
+DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) : DumpCustom(lmp, narg, arg)
-  DumpCustom(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump custom/gz only writes compressed files");
-    error->all(FLERR,"Dump custom/gz only writes compressed files");
 }
 
 /* ---------------------------------------------------------------------- */
 
-DumpCustomGZ::~DumpCustomGZ()
+DumpCustomGZ::~DumpCustomGZ() {}
-{
-}
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -58,8 +55,7 @@ void DumpCustomGZ::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -107,9 +103,7 @@ void DumpCustomGZ::write_header(bigint ndump)
       header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
     }
 
-    if (time_flag) {
+    if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
-      header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
-    }
 
     header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
     header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
@@ -174,9 +168,7 @@ void DumpCustomGZ::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }

src/COMPRESS/dump_custom_zstd.cpp

@@ -18,8 +18,10 @@
 
 #ifdef LAMMPS_ZSTD
 
-#include "domain.h"
 #include "dump_custom_zstd.h"
+
+#include "file_writer.h"
+#include "domain.h"
 #include "error.h"
 #include "update.h"
 

src/COMPRESS/dump_custom_zstd.h

@@ -28,7 +28,6 @@ DumpStyle(custom/zstd,DumpCustomZstd);
 
 #include "dump_custom.h"
 #include "zstd_file_writer.h"
-#include <stdio.h>
 
 namespace LAMMPS_NS {
 

src/COMPRESS/dump_local_gz.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -12,27 +11,25 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "domain.h"
 #include "dump_local_gz.h"
+
+#include "domain.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
+DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : DumpLocal(lmp, narg, arg)
-  DumpLocal(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump local/gz only writes compressed files");
-    error->all(FLERR,"Dump local/gz only writes compressed files");
 }
 
 /* ---------------------------------------------------------------------- */
 
-DumpLocalGZ::~DumpLocalGZ()
+DumpLocalGZ::~DumpLocalGZ() {}
-{
-}
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -58,8 +55,7 @@ void DumpLocalGZ::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -107,9 +103,7 @@ void DumpLocalGZ::write_header(bigint ndump)
       header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
     }
 
-    if (time_flag) {
+    if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
-      header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
-    }
 
     header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
     header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump);
@@ -174,9 +168,7 @@ void DumpLocalGZ::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }

src/COMPRESS/dump_local_zstd.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -18,28 +17,25 @@
 
 #ifdef LAMMPS_ZSTD
 
-#include "domain.h"
 #include "dump_local_zstd.h"
+
+#include "domain.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) :
+DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) : DumpLocal(lmp, narg, arg)
-  DumpLocal(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump local/zstd only writes compressed files");
-    error->all(FLERR,"Dump local/zstd only writes compressed files");
 }
 
-
 /* ---------------------------------------------------------------------- */
 
-DumpLocalZstd::~DumpLocalZstd()
+DumpLocalZstd::~DumpLocalZstd() {}
-{
-}
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -65,8 +61,7 @@ void DumpLocalZstd::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -92,9 +87,7 @@ void DumpLocalZstd::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    if (append_flag) {
+    if (append_flag) { error->one(FLERR, "dump cfg/zstd currently doesn't support append"); }
-      error->one(FLERR, "dump cfg/zstd currently doesn't support append");
-    }
 
     try {
       writer.open(filecurrent);
@@ -118,9 +111,7 @@ void DumpLocalZstd::write_header(bigint ndump)
       header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
     }
 
-    if (time_flag) {
+    if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
-      header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
-    }
 
     header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
     header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump);
@@ -185,9 +176,7 @@ void DumpLocalZstd::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }
@@ -201,9 +190,12 @@ int DumpLocalZstd::modify_param(int narg, char **arg)
     try {
       if (strcmp(arg[0], "checksum") == 0) {
         if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
-        if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
+        if (strcmp(arg[1], "yes") == 0)
-        else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
+          writer.setChecksum(true);
-        else error->all(FLERR,"Illegal dump_modify command");
+        else if (strcmp(arg[1], "no") == 0)
+          writer.setChecksum(false);
+        else
+          error->all(FLERR, "Illegal dump_modify command");
         return 2;
       } else if (strcmp(arg[0], "compression_level") == 0) {
         if (narg < 2) error->all(FLERR, "Illegal dump_modify command");

src/COMPRESS/dump_xyz_gz.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -13,26 +12,23 @@
 ------------------------------------------------------------------------- */
 
 #include "dump_xyz_gz.h"
+
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) :
+DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) : DumpXYZ(lmp, narg, arg)
-  DumpXYZ(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump xyz/gz only writes compressed files");
-    error->all(FLERR,"Dump xyz/gz only writes compressed files");
 }
 
-
 /* ---------------------------------------------------------------------- */
 
-DumpXYZGZ::~DumpXYZGZ()
+DumpXYZGZ::~DumpXYZGZ() {}
-{
-}
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -58,8 +54,7 @@ void DumpXYZGZ::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -117,8 +112,8 @@ void DumpXYZGZ::write_data(int n, double *mybuf)
     char vbuffer[VBUFFER_SIZE];
     int m = 0;
     for (int i = 0; i < n; i++) {
-      int written = snprintf(vbuffer, VBUFFER_SIZE, format,
+      int written =
-              typenames[static_cast<int> (mybuf[m+1])],
+          snprintf(vbuffer, VBUFFER_SIZE, format, typenames[static_cast<int>(mybuf[m + 1])],
                    mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
       if (written > 0) {
         writer.write(vbuffer, written);
@@ -139,9 +134,7 @@ void DumpXYZGZ::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }

src/COMPRESS/dump_xyz_zstd.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,27 +18,23 @@
 #ifdef LAMMPS_ZSTD
 
 #include "dump_xyz_zstd.h"
+
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-DumpXYZZstd::DumpXYZZstd(LAMMPS *lmp, int narg, char **arg) :
+DumpXYZZstd::DumpXYZZstd(LAMMPS *lmp, int narg, char **arg) : DumpXYZ(lmp, narg, arg)
-  DumpXYZ(lmp, narg, arg)
 {
-  if (!compressed)
+  if (!compressed) error->all(FLERR, "Dump xyz/zstd only writes compressed files");
-    error->all(FLERR,"Dump xyz/zstd only writes compressed files");
 }
 
-
 /* ---------------------------------------------------------------------- */
 
-DumpXYZZstd::~DumpXYZZstd()
+DumpXYZZstd::~DumpXYZZstd() {}
-{
-}
-
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
@@ -65,8 +60,7 @@ void DumpXYZZstd::openfile()
     char *ptr = strchr(filestar, '*');
     *ptr = '\0';
     if (padflag == 0)
-      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
+      sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
-              filestar,update->ntimestep,ptr+1);
     else {
       char bif[8], pad[16];
       strcpy(bif, BIGINT_FORMAT);
@@ -92,9 +86,7 @@ void DumpXYZZstd::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    if (append_flag) {
+    if (append_flag) { error->one(FLERR, "dump cfg/zstd currently doesn't support append"); }
-      error->one(FLERR, "dump cfg/zstd currently doesn't support append");
-    }
 
     try {
       writer.open(filecurrent);
@@ -128,8 +120,8 @@ void DumpXYZZstd::write_data(int n, double *mybuf)
     char vbuffer[VBUFFER_SIZE];
     int m = 0;
     for (int i = 0; i < n; i++) {
-      int written = snprintf(vbuffer, VBUFFER_SIZE, format,
+      int written =
-              typenames[static_cast<int> (mybuf[m+1])],
+          snprintf(vbuffer, VBUFFER_SIZE, format, typenames[static_cast<int>(mybuf[m + 1])],
                    mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
       if (written > 0) {
         writer.write(vbuffer, written);
@@ -150,9 +142,7 @@ void DumpXYZZstd::write()
     if (multifile) {
       writer.close();
     } else {
-      if (flush_flag && writer.isopen()) {
+      if (flush_flag && writer.isopen()) { writer.flush(); }
-        writer.flush();
-      }
     }
   }
 }
@@ -166,9 +156,12 @@ int DumpXYZZstd::modify_param(int narg, char **arg)
     try {
       if (strcmp(arg[0], "checksum") == 0) {
         if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
-        if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
+        if (strcmp(arg[1], "yes") == 0)
-        else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
+          writer.setChecksum(true);
-        else error->all(FLERR,"Illegal dump_modify command");
+        else if (strcmp(arg[1], "no") == 0)
+          writer.setChecksum(false);
+        else
+          error->all(FLERR, "Illegal dump_modify command");
         return 2;
       } else if (strcmp(arg[0], "compression_level") == 0) {
         if (narg < 2) error->all(FLERR, "Illegal dump_modify command");

src/COMPRESS/gz_file_writer.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -17,22 +16,18 @@
 ------------------------------------------------------------------------- */
 
 #include "gz_file_writer.h"
-#include <stdio.h>
 #include "fmt/format.h"
+#include <cstdio>
 
 using namespace LAMMPS_NS;
 
-GzFileWriter::GzFileWriter() : FileWriter(),
+GzFileWriter::GzFileWriter() : FileWriter(), compression_level(Z_BEST_COMPRESSION), gzFp(nullptr) {}
-    compression_level(Z_BEST_COMPRESSION),
-    gzFp(nullptr)
-{
-}
 
 /* ---------------------------------------------------------------------- */
 
 GzFileWriter::~GzFileWriter()
 {
-  close();
+  GzFileWriter::close();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -50,8 +45,7 @@ void GzFileWriter::open(const std::string &path, bool append)
 
   gzFp = gzopen(path.c_str(), mode.c_str());
 
-    if (gzFp == nullptr)
+  if (gzFp == nullptr) throw FileWriterException(fmt::format("Could not open file '{}'", path));
-      throw FileWriterException(fmt::format("Could not open file '{}'", path));
 }
 
 /* ---------------------------------------------------------------------- */
@@ -76,7 +70,7 @@ void GzFileWriter::flush()
 
 void GzFileWriter::close()
 {
-  if (!isopen()) return;
+  if (!GzFileWriter::isopen()) return;
 
   gzclose(gzFp);
   gzFp = nullptr;
@@ -100,7 +94,8 @@ void GzFileWriter::setCompressionLevel(int level)
   const int max_level = Z_BEST_COMPRESSION;
 
   if (level < min_level || level > max_level)
-    throw FileWriterException(fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
+    throw FileWriterException(
+        fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
 
   compression_level = level;
 }

src/COMPRESS/gz_file_writer.h

@@ -20,7 +20,6 @@
 
 #include "file_writer.h"
 
-#include <exception>
 #include <string>
 #include <zlib.h>
 

src/COMPRESS/zstd_file_writer.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,16 +18,13 @@
 #ifdef LAMMPS_ZSTD
 
 #include "zstd_file_writer.h"
-#include <stdio.h>
 #include "fmt/format.h"
+#include <cstdio>
 
 using namespace LAMMPS_NS;
 
-ZstdFileWriter::ZstdFileWriter() : FileWriter(),
+ZstdFileWriter::ZstdFileWriter() :
-    compression_level(0),
+    FileWriter(), compression_level(0), checksum_flag(1), cctx(nullptr), fp(nullptr)
-    checksum_flag(1),
-    cctx(nullptr),
-    fp(nullptr)
 {
   out_buffer_size = ZSTD_CStreamOutSize();
   out_buffer = new char[out_buffer_size];
@@ -38,7 +34,7 @@ ZstdFileWriter::ZstdFileWriter() : FileWriter(),
 
 ZstdFileWriter::~ZstdFileWriter()
 {
-  close();
+  ZstdFileWriter::close();
 
   delete[] out_buffer;
   out_buffer = nullptr;
@@ -57,9 +53,7 @@ void ZstdFileWriter::open(const std::string &path, bool append)
     fp = fopen(path.c_str(), "wb");
   }
 
-    if (!fp) {
+  if (!fp) { throw FileWriterException(fmt::format("Could not open file '{}'", path)); }
-        throw FileWriterException(fmt::format("Could not open file '{}'", path));
-    }
 
   cctx = ZSTD_createCCtx();
 
@@ -114,7 +108,7 @@ void ZstdFileWriter::flush()
 
 void ZstdFileWriter::close()
 {
-  if (!isopen()) return;
+  if (!ZstdFileWriter::isopen()) return;
 
   size_t remaining;
   ZSTD_inBuffer input = {nullptr, 0, 0};
@@ -150,7 +144,8 @@ void ZstdFileWriter::setCompressionLevel(int level)
   const int max_level = ZSTD_maxCLevel();
 
   if (level < min_level || level > max_level)
-    throw FileWriterException(fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
+    throw FileWriterException(
+        fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
 
   compression_level = level;
 }
@@ -159,8 +154,7 @@ void ZstdFileWriter::setCompressionLevel(int level)
 
 void ZstdFileWriter::setChecksum(bool enabled)
 {
-  if (isopen())
+  if (isopen()) throw FileWriterException("Checksum flag can not be changed while file is open");
-    throw FileWriterException("Checksum flag can not be changed while file is open");
   checksum_flag = enabled ? 1 : 0;
 }
 

src/CORESHELL/pair_born_coul_dsf_cs.cpp

@@ -18,13 +18,14 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_dsf_cs.h"
-#include <cmath>
+
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
-#include "neigh_list.h"
 #include "math_const.h"
 #include "math_special.h"
+#include "neigh_list.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CORESHELL/pair_born_coul_wolf_cs.cpp

@@ -14,12 +14,13 @@
 
 
 #include "pair_born_coul_wolf_cs.h"
-#include <cmath>
+
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
-#include "neigh_list.h"
 #include "math_const.h"
+#include "neigh_list.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CORESHELL/pair_coul_wolf_cs.cpp

@@ -13,13 +13,14 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_wolf_cs.h"
-#include <cmath>
+
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "neigh_list.h"
 #include "math_const.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/DIELECTRIC/atom_vec_dielectric.cpp

@@ -17,6 +17,9 @@
 #include "atom.h"
 #include "citeme.h"
 
+#include <cmath>
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 static const char cite_user_dielectric_package[] =

src/DIELECTRIC/compute_efield_atom.cpp

@@ -33,12 +33,14 @@
 #include "pppm_dielectric.h"
 #include "update.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputeEfieldAtom::ComputeEfieldAtom(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg), efield(NULL)
+  Compute(lmp, narg, arg), efield(nullptr)
 {
   if (narg < 3) error->all(FLERR,"Illegal compute efield/atom command");
 

src/DIELECTRIC/fix_polarize_bem_gmres.cpp

@@ -41,11 +41,9 @@
 #include "comm.h"
 #include "error.h"
 #include "force.h"
-#include "group.h"
 #include "kspace.h"
 #include "math_const.h"
 #include "memory.h"
-#include "modify.h"
 #include "msm_dielectric.h"
 #include "pair_coul_cut_dielectric.h"
 #include "pair_coul_long_dielectric.h"
@@ -54,7 +52,6 @@
 #include "pair_lj_cut_coul_msm_dielectric.h"
 #include "pppm_dielectric.h"
 #include "random_park.h"
-#include "timer.h"
 #include "update.h"
 
 #include <cmath>
@@ -69,8 +66,8 @@ using namespace MathConst;
 /* ---------------------------------------------------------------------- */
 
 FixPolarizeBEMGMRES::FixPolarizeBEMGMRES(LAMMPS *lmp, int narg, char **arg) :
-    Fix(lmp, narg, arg), q_backup(NULL), c(NULL), g(NULL), h(NULL), r(NULL), s(NULL), v(NULL),
+    Fix(lmp, narg, arg), q_backup(nullptr), c(nullptr), g(nullptr), h(nullptr), r(nullptr), s(nullptr), v(nullptr),
-    y(NULL)
+    y(nullptr)
 {
   if (narg < 5) error->all(FLERR, "Illegal fix polarize/bem/gmres command");
 
@@ -110,7 +107,7 @@ FixPolarizeBEMGMRES::FixPolarizeBEMGMRES(LAMMPS *lmp, int narg, char **arg) :
   if (atom->torque_flag) torqueflag = 1;
   if (atom->avec->forceclearflag) extraflag = 1;
 
-  grow_arrays(atom->nmax);
+  FixPolarizeBEMGMRES::grow_arrays(atom->nmax);
   atom->add_callback(0);    // to ensure to work with atom->sort()
 
   // output the residual and actual number of iterations
@@ -133,7 +130,7 @@ FixPolarizeBEMGMRES::~FixPolarizeBEMGMRES()
   memory->destroy(mat2tag);
   memory->destroy(tag2mat);
 
-  if (allocated) deallocate();
+  if (allocated) FixPolarizeBEMGMRES::deallocate();
   atom->delete_callback(id, 0);
 }
 

src/DIELECTRIC/fix_polarize_bem_icc.cpp

@@ -33,7 +33,6 @@
 #include "group.h"
 #include "kspace.h"
 #include "math_const.h"
-#include "memory.h"
 #include "msm_dielectric.h"
 #include "pair_coul_cut_dielectric.h"
 #include "pair_coul_long_dielectric.h"

src/DIELECTRIC/fix_polarize_functional.cpp

@@ -33,13 +33,11 @@
 #include "domain.h"
 #include "error.h"
 #include "force.h"
-#include "group.h"
 #include "kspace.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "math_special.h"
 #include "memory.h"
-#include "modify.h"
 #include "msm_dielectric.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
@@ -50,8 +48,6 @@
 #include "pair_lj_cut_coul_long_dielectric.h"
 #include "pair_lj_cut_coul_msm_dielectric.h"
 #include "pppm_dielectric.h"
-#include "random_park.h"
-#include "timer.h"
 #include "update.h"
 
 #include <cmath>
@@ -131,7 +127,7 @@ FixPolarizeFunctional::FixPolarizeFunctional(LAMMPS *lmp, int narg, char **arg)
   cg_r = cg_p = cg_Ap = nullptr;
   cg_A = nullptr;
 
-  grow_arrays(atom->nmax);
+  FixPolarizeFunctional::grow_arrays(atom->nmax);
   atom->add_callback(0);    // to ensure to work with atom->sort()
 }
 

src/DIELECTRIC/msm_dielectric.cpp

@@ -23,15 +23,9 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
 #include "gridcomm.h"
 #include "math_const.h"
 #include "memory.h"
-#include "neighbor.h"
-#include "pair.h"
-
-#include <cstring>
-#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/DIELECTRIC/pair_coul_cut_dielectric.cpp

@@ -19,7 +19,6 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "math_const.h"
@@ -29,7 +28,6 @@
 #include "neighbor.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/DIELECTRIC/pair_coul_long_dielectric.cpp

@@ -19,7 +19,6 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "kspace.h"
@@ -30,7 +29,6 @@
 #include "neighbor.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -221,10 +219,10 @@ void PairCoulLongDielectric::init_style()
 
   // insure use of KSpace long-range solver, set g_ewald
 
-  if (force->kspace == NULL) error->all(FLERR, "Pair style requires a KSpace style");
+  if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
   g_ewald = force->kspace->g_ewald;
 
   // setup force tables
 
-  if (ncoultablebits) init_tables(cut_coul, NULL);
+  if (ncoultablebits) init_tables(cut_coul, nullptr);
 }

src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp

@@ -19,7 +19,6 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "math_const.h"

src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp

@@ -19,7 +19,6 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "math_const.h"
@@ -29,7 +28,6 @@
 #include "neighbor.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -40,8 +38,8 @@ using namespace MathConst;
 
 PairLJCutCoulDebyeDielectric::PairLJCutCoulDebyeDielectric(LAMMPS *lmp) : PairLJCutCoulDebye(lmp)
 {
-  efield = NULL;
+  efield = nullptr;
-  epot = NULL;
+  epot = nullptr;
   nmax = 0;
 }
 

src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp

@@ -19,7 +19,6 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "kspace.h"
@@ -257,7 +256,7 @@ void PairLJCutCoulLongDielectric::init_style()
 
   // insure use of KSpace long-range solver, set g_ewald
 
-  if (force->kspace == NULL) error->all(FLERR, "Pair style requires a KSpace style");
+  if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
   g_ewald = force->kspace->g_ewald;
 
   // setup force tables

src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp

@@ -19,10 +19,8 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
-#include "integrate.h"
 #include "kspace.h"
 #include "math_const.h"
 #include "memory.h"
@@ -31,6 +29,7 @@
 #include "neighbor.h"
 
 #include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -365,7 +364,7 @@ void PairLJCutCoulMSMDielectric::init_style()
 
   // insure use of KSpace long-range solver, set g_ewald
 
-  if (force->kspace == NULL) error->all(FLERR, "Pair style requires a KSpace style");
+  if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
   g_ewald = force->kspace->g_ewald;
 
   // setup force tables
@@ -382,5 +381,5 @@ void *PairLJCutCoulMSMDielectric::extract(const char *str, int &dim)
   dim = 2;
   if (strcmp(str, "epsilon") == 0) return (void *) epsilon;
   if (strcmp(str, "sigma") == 0) return (void *) sigma;
-  return NULL;
+  return nullptr;
 }

src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp

@@ -19,19 +19,14 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
-#include "integrate.h"
-#include "kspace.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "neighbor.h"
-#include "respa.h"
-#include "update.h"
 
 #include <cmath>
 #include <cstring>

src/DIELECTRIC/pppm_dielectric.cpp

@@ -23,15 +23,11 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fft3d_wrap.h"
 #include "force.h"
 #include "gridcomm.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
-#include "neighbor.h"
-#include "pair.h"
-#include "remap_wrap.h"
 
 #include <cmath>
 

src/DIELECTRIC/pppm_disp_dielectric.cpp

@@ -21,21 +21,14 @@
 #include "angle.h"
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "bond.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fft3d_wrap.h"
 #include "force.h"
 #include "gridcomm.h"
 #include "math_const.h"
 #include "memory.h"
-#include "neighbor.h"
-#include "pair.h"
-#include "remap_wrap.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/DPD-MESO/pair_edpd.cpp

@@ -31,7 +31,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <ctime>
 #include <cstring>
 
 using namespace LAMMPS_NS;

src/DPD-REACT/fix_rx.cpp

@@ -34,7 +34,6 @@
 #include <cfloat> // DBL_EPSILON
 #include <cmath>
 #include <cstring>
-#include <vector> // std::vector<>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -59,7 +58,7 @@ namespace /* anonymous */
 {
 
 typedef double TimerType;
-TimerType getTimeStamp(void) { return MPI_Wtime(); }
+TimerType getTimeStamp() { return MPI_Wtime(); }
 double getElapsedTime( const TimerType &t0, const TimerType &t1) { return t1-t0; }
 
 } // end namespace
@@ -1246,7 +1245,7 @@ int FixRX::rkf45_h0 (const int neq, const double t, const double /*t_stop*/,
    return (iter + 1);
 }
 
-void FixRX::odeDiagnostics(void)
+void FixRX::odeDiagnostics()
 {
   TimerType timer_start = getTimeStamp();
 

src/DPD-SMOOTH/fix_meso_move.cpp

@@ -224,7 +224,7 @@ FixMesoMove::FixMesoMove (LAMMPS *lmp, int narg, char **arg) :
   // perform initial allocation of atom-based array
   // register with Atom class
 
-  grow_arrays(atom->nmax);
+  FixMesoMove::grow_arrays(atom->nmax);
   atom->add_callback(Atom::GROW);
   atom->add_callback(Atom::RESTART);
 

src/DRUDE/fix_drude.cpp

@@ -25,7 +25,6 @@
 #include <cstring>
 #include <map>
 #include <set>
-#include <vector>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -55,7 +54,7 @@ FixDrude::FixDrude(LAMMPS *lmp, int narg, char **arg) :
   }
 
   drudeid = nullptr;
-  grow_arrays(atom->nmax);
+  FixDrude::grow_arrays(atom->nmax);
   atom->add_callback(Atom::GROW);
   atom->add_callback(Atom::RESTART);
   atom->add_callback(Atom::BORDER);
@@ -516,7 +515,8 @@ void FixDrude::ring_copy_drude(int size, char *cbuf, void *ptr) {
  * ----------------------------------------------------------------------*/
 void FixDrude::set_arrays(int i) {
     if (drudetype[atom->type[i]] != NOPOL_TYPE) {
-        if (atom->nspecial[i] ==0) error->all(FLERR, "Polarizable atoms cannot be inserted with special lists info from the molecule template");
+        if (atom->nspecial[i] == nullptr)
+          error->all(FLERR, "Polarizable atoms cannot be inserted with special lists info from the molecule template");
         drudeid[i] = atom->special[i][0]; // Drude partner should be at first place in the special list
     } else {
         drudeid[i] = 0;

src/DRUDE/fix_tgnh_drude.cpp

@@ -24,6 +24,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix_deform.h"
+#include "fix_drude.h"
 #include "force.h"
 #include "irregular.h"
 #include "kspace.h"