Merge branch 'master' into pair-style-nnp

.github/CODEOWNERS

@@ -13,29 +13,37 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
-src/COMPRESS/*        @akohlmey
+src/COMPRESS/*        @rbberger
 src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
 src/MESSAGE/*         @sjplimp
+src/MLIAP/*           @athomps
+src/SNAP/*            @athomps
 src/SPIN/*            @julient31
+src/USER-BROWNIAN/*   @samueljmcameron
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
 src/USER-COLVARS/*    @giacomofiorin
+src/USER-FEP/*        @agiliopadua
+src/USER-HDNNP/*      @singraber
 src/USER-INTEL/*      @wmbrownintel
 src/USER-MANIFOLD/*   @Pakketeretet2
+src/USER-MDI/*        @taylor-a-barnes
 src/USER-MEAMC/*      @martok
 src/USER-MESONT/*     @iafoss
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
+src/USER-PACE/*       @yury-lysogorskiy
 src/USER-PLUMED/*     @gtribello
 src/USER-PHONON/*     @lingtikong
 src/USER-PTM/*        @pmla
 src/USER-OMP/*        @akohlmey
 src/USER-QMMM/*       @akohlmey
 src/USER-REAXC/*      @hasanmetin
+src/USER-REACTION/*   @jrgissing
 src/USER-SCAFACOS/*   @rhalver
 src/USER-TALLY/*      @akohlmey
 src/USER-UEF/*        @danicholson
@@ -47,7 +55,6 @@ src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
-src/USER-REACTION/fix_bond_react.*  @jrgissing
 src/USER-MISC/*_grem.*              @dstelter92
 src/USER-MISC/compute_stress_mop*.* @RomainVermorel
 
@@ -122,6 +129,8 @@ tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
 tools/code_standard/* @rbberger
 tools/valgrind/*      @akohlmey
+tools/swig/*          @akohlmey
+tools/offline/*       @rbberger
 
 # tests
 unittest/*            @akohlmey @rbberger
@@ -130,7 +139,7 @@ unittest/*            @akohlmey @rbberger
 cmake/*               @junghans @rbberger
 cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
 cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
-cmake/presets/*.cmake @junghans @rbberger @akohlmey
+cmake/presets/*.cmake @akohlmey
 
 # python
 python/*              @rbberger
@@ -142,6 +151,7 @@ fortran/*             @akohlmey
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+examples/plugin/*     @akohlmey
 
 # for releases
 src/version.h         @sjplimp

cmake/CMakeLists.txt

@@ -7,6 +7,11 @@ cmake_minimum_required(VERSION 3.10)
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
 endif()
+# set policy to silence warnings about missing executable permissions in
+# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
+if (POLICY CMP0109)
+  cmake_policy(SET CMP0109 OLD)
+endif()
 ########################################
 
 project(lammps CXX)
@@ -104,6 +109,12 @@ endif()
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
 
+# allow enabling clang-tidy for C++ files
+set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
+if(ENABLE_CLANG_TIDY)
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
+endif()
+
 include(GNUInstallDirs)
 file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)

cmake/Modules/YAML.cmake

@@ -6,15 +6,27 @@ set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of li
 mark_as_advanced(YAML_URL)
 mark_as_advanced(YAML_MD5)
 
+# support cross-compilation to windows
+if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
+    set(YAML_CROSS_HOST --host=i686-mingw64)
+  elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    set(YAML_CROSS_HOST --host=x86_64-mingw64)
+  else()
+    message(FATAL_ERROR "Unsupported cross-compilation "
+      " for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}"
+      " on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}")
+  endif()
+endif()
+
 ExternalProject_Add(libyaml
                     URL               ${YAML_URL}
                     URL_MD5           ${YAML_MD5}
                     SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
                     BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
                     CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
-                                      CXX=${CMAKE_CXX_COMPILER}
+                                      CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
-                                      CC=${CMAKE_C_COMPILER}
+                                      --prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
-                                      --prefix=<INSTALL_DIR> --disable-shared
                     BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
                     TEST_COMMAND      "")
 

cmake/presets/clang.cmake

@@ -4,10 +4,18 @@ set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "clang++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "clang" CACHE STRING "" FORCE)
 set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

cmake/presets/intel.cmake

@@ -3,10 +3,20 @@
 set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "icpc" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icc" CACHE STRING "" FORCE)
 set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

cmake/presets/oneapi.cmake

@@ -1,12 +1,22 @@
-# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
+# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP and Fortran (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "icpx" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
 set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

doc/src/Build_development.rst

@@ -28,6 +28,28 @@ variable VERBOSE set to 1:
 
 ----------
 
+.. _clang-tidy
+
+Enable static code analysis with clang-tidy
+-------------------------------------------
+
+The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
+static code analysis tool to diagnose (and potentially fix) typical
+programming errors or coding style violations.  It has a modular framework
+of tests that can be adjusted to help identifying problems before they
+become bugs and also assist in modernizing large code bases (like LAMMPS).
+It can be enabled for all C++ code with the following CMake flag
+
+.. code-block:: bash
+
+   -D ENABLE_CLANG_TIDY=value    # value = no (default) or yes
+
+With this flag enabled all source files will be processed twice, first to
+be compiled and then to be analyzed. Please note that the analysis can be
+significantly more time consuming than the compilation itself.
+
+----------
+
 .. _iwyu_processing:
 
 Report missing and unneeded '#include' statements

doc/src/Packages_details.rst

@@ -448,7 +448,7 @@ time via the "-sf kk" or "-suffix kk" :doc:`command-line switches <Run_options>`
 :ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
 have styles optimized for CPUs, KNLs, and GPUs.
 
-You must have a C++11 compatible compiler to use this package.
+You must have a C++14 compatible compiler to use this package.
 KOKKOS makes extensive use of advanced C++ features, which can
 expose compiler bugs, especially when compiling for maximum
 performance at high optimization levels. Please see the file

src/PYTHON/python_compat.h

@@ -18,15 +18,31 @@
 
 // Wrap API changes between Python 2 and 3 using macros
 #if PY_MAJOR_VERSION == 2
+#if defined(_MSC_VER) || defined(__MINGW32__)
+#define PY_INT_FROM_LONG(X) PyLong_FromLongLong(X)
+#else
 #define PY_INT_FROM_LONG(X) PyInt_FromLong(X)
+#endif
+#if defined(_MSC_VER) || defined(__MINGW32__)
+#define PY_INT_AS_LONG(X) PyLong_AsLongLong(X)
+#else
 #define PY_INT_AS_LONG(X) PyInt_AsLong(X)
+#endif
 #define PY_STRING_FROM_STRING(X) PyString_FromString(X)
 #define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, nullptr)
 #define PY_STRING_AS_STRING(X) PyString_AsString(X)
 
 #elif PY_MAJOR_VERSION == 3
+#if defined(_MSC_VER) || defined(__MINGW32__)
+#define PY_INT_FROM_LONG(X) PyLong_FromLongLong(X)
+#else
 #define PY_INT_FROM_LONG(X) PyLong_FromLong(X)
+#endif
+#if defined(_MSC_VER) || defined(__MINGW32__)
+#define PY_INT_AS_LONG(X) PyLong_AsLongLong(X)
+#else
 #define PY_INT_AS_LONG(X) PyLong_AsLong(X)
+#endif
 #define PY_STRING_FROM_STRING(X) PyUnicode_FromString(X)
 #define PY_VOID_POINTER(X) PyCapsule_New((void *) X, nullptr, nullptr)
 #define PY_STRING_AS_STRING(X) PyUnicode_AsUTF8(X)

src/SPIN/compute_spin.cpp

@@ -58,7 +58,7 @@ ComputeSpin::ComputeSpin(LAMMPS *lmp, int narg, char **arg) :
   long_spin_flag = 0;
   precession_spin_flag = 0;
 
-  init();
+  ComputeSpin::init();
 
   allocate();
 

src/USER-MISC/compute_gyration_shape.cpp

@@ -44,7 +44,7 @@ ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) :
   // ID of compute gyration
   id_gyration = utils::strdup(arg[3]);
 
-  init();
+  ComputeGyrationShape::init();
 
   vector = new double[6];
 }

src/USER-MISC/compute_gyration_shape_chunk.cpp

@@ -40,7 +40,7 @@ ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char
   // ID of compute gyration
   id_gyration_chunk = utils::strdup(arg[3]);
 
-  init();
+  ComputeGyrationShapeChunk::init();
 
   array_flag = 1;
   size_array_cols = 6;

src/arg_info.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://lammps.sandia.gov/, Sandia National Laboratories
@@ -14,8 +13,8 @@
 
 #include "arg_info.h"
 
-#include <stdexcept>
 #include <cstring>
+#include <stdexcept>
 
 using namespace LAMMPS_NS;
 
@@ -29,46 +28,51 @@ using namespace LAMMPS_NS;
  * \param arg      string with possible reference
  * \param allowed  integer with bitmap of allowed types of references */
 
-ArgInfo::ArgInfo(const std::string &arg, int allowed)
+ArgInfo::ArgInfo(const std::string &arg, int allowed) : type(NONE), dim(0), index1(-1), index2(-1)
-  : type(NONE), dim(0), index1(-1), index2(-1)
 {
   if ((arg.size() > 2) && (arg[1] == '_')) {
-    if ((arg[0] == 'c') && (allowed & COMPUTE))  type = COMPUTE;
+    if ((arg[0] == 'c') && (allowed & COMPUTE))
-    else if ((arg[0] == 'f') && (allowed & FIX)) type = FIX;
+      type = COMPUTE;
-    else if ((arg[0] == 'v') && (allowed & VARIABLE)) type = VARIABLE;
+    else if ((arg[0] == 'f') && (allowed & FIX))
-    else if ((arg[0] == 'd') && (allowed & DNAME)) type = DNAME;
+      type = FIX;
-    else if ((arg[0] == 'i') && (allowed & INAME)) type = INAME;
+    else if ((arg[0] == 'v') && (allowed & VARIABLE))
+      type = VARIABLE;
+    else if ((arg[0] == 'd') && (allowed & DNAME))
+      type = DNAME;
+    else if ((arg[0] == 'i') && (allowed & INAME))
+      type = INAME;
     else {
       index1 = 0;
       name = arg;
       return;
     }
 
-    std::size_t has_idx1 = arg.find('[',2);
+    std::size_t has_idx1 = arg.find('[', 2);
     if (has_idx1 != std::string::npos) {
-      name = arg.substr(2,has_idx1-2);
+      name = arg.substr(2, has_idx1 - 2);
       dim = 1;
 
-      std::size_t has_idx2 = arg.find('[',has_idx1+1);
+      std::size_t has_idx2 = arg.find('[', has_idx1 + 1);
       if (has_idx2 != std::string::npos) {
         dim = 2;
 
-        if (arg[arg.size()-1] != ']') {
+        if (arg[arg.size() - 1] != ']') {
           type = UNKNOWN;
         } else {
           try {
-            index2 = std::stoi(arg.substr(has_idx2+1,arg.size()-(has_idx2+2)));
+            index2 = std::stoi(arg.substr(has_idx2 + 1, arg.size() - (has_idx2 + 2)));
           } catch (std::invalid_argument &) {
             type = UNKNOWN;
           }
         }
-      } else has_idx2 = arg.size();
+      } else
+        has_idx2 = arg.size();
 
-      if (arg[has_idx2-1] != ']') {
+      if (arg[has_idx2 - 1] != ']') {
         type = UNKNOWN;
       } else {
         try {
-          index1 = std::stoi(arg.substr(has_idx1+1,arg.size()-(has_idx2+2)));
+          index1 = std::stoi(arg.substr(has_idx1 + 1, arg.size() - (has_idx2 + 2)));
         } catch (std::invalid_argument &) {
           type = UNKNOWN;
         }
@@ -97,8 +101,7 @@ ArgInfo::ArgInfo(const std::string &arg, int allowed)
 
 char *ArgInfo::copy_name()
 {
-  char *dest = new char[name.size()+1];
+  char *dest = new char[name.size() + 1];
-  strcpy(dest,name.c_str());
+  strcpy(dest, name.c_str());    // NOLINT
   return dest;
 }
-

src/compute_angmom_chunk.cpp

@@ -44,7 +44,7 @@ ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) :
 
   idchunk = utils::strdup(arg[3]);
 
-  init();
+  ComputeAngmomChunk::init();
 
   // chunk-based data
 

src/compute_com_chunk.cpp

@@ -46,7 +46,7 @@ ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) :
 
   idchunk = utils::strdup(arg[3]);
 
-  init();
+  ComputeCOMChunk::init();
 
   // chunk-based data
 

src/compute_dipole_chunk.cpp

@@ -62,7 +62,7 @@ ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
     else error->all(FLERR,"Illegal compute dipole/chunk command");
   }
 
-  init();
+  ComputeDipoleChunk::init();
 
   // chunk-based data
 

src/compute_gyration_chunk.cpp

@@ -39,7 +39,7 @@ ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
 
   idchunk = utils::strdup(arg[3]);
 
-  init();
+  ComputeGyrationChunk::init();
 
   // optional args
 

src/compute_inertia_chunk.cpp

@@ -44,7 +44,7 @@ ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
 
   idchunk = utils::strdup(arg[3]);
 
-  init();
+  ComputeInertiaChunk::init();
 
   // chunk-based data
 

src/compute_msd_chunk.cpp

@@ -48,7 +48,7 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
   idchunk = utils::strdup(arg[3]);
 
   firstflag = 1;
-  init();
+  ComputeMSDChunk::init();
 
   // create a new fix STORE style for reference positions
   // id = compute-ID + COMPUTE_STORE, fix group = compute group

src/compute_omega_chunk.cpp

@@ -48,7 +48,7 @@ ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
 
   idchunk = utils::strdup(arg[3]);
 
-  init();
+  ComputeOmegaChunk::init();
 
   // chunk-based data
 

src/compute_property_chunk.cpp

@@ -36,7 +36,7 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
 
   idchunk = utils::strdup(arg[3]);
 
-  init();
+  ComputePropertyChunk::init();
 
   // parse values
 

src/compute_temp_chunk.cpp

@@ -48,7 +48,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
   idchunk = utils::strdup(arg[3]);
 
   biasflag = 0;
-  init();
+  ComputeTempChunk::init();
 
   // optional per-chunk values
 

src/compute_torque_chunk.cpp

@@ -43,7 +43,7 @@ ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) :
 
   idchunk = utils::strdup(arg[3]);
 
-  init();
+  ComputeTorqueChunk::init();
 
   // chunk-based data
 

src/compute_vcm_chunk.cpp

@@ -44,7 +44,7 @@ ComputeVCMChunk::ComputeVCMChunk(LAMMPS *lmp, int narg, char **arg) :
 
   idchunk = utils::strdup(arg[3]);
 
-  init();
+  ComputeVCMChunk::init();
 
   // chunk-based data
 

src/force.cpp

@@ -449,7 +449,7 @@ Angle *Force::new_angle(const std::string &style, int trysuffix, int &sflag)
 
     if (lmp->suffix2) {
       sflag = 2;
-      std::string estyle = style + "/" + lmp->suffix;
+      std::string estyle = style + "/" + lmp->suffix2;
       if (angle_map->find(estyle) != angle_map->end()) {
         AngleCreator &angle_creator = (*angle_map)[estyle];
         return angle_creator(lmp);
@@ -679,7 +679,7 @@ KSpace *Force::new_kspace(const std::string &style, int trysuffix, int &sflag)
     }
 
     if (lmp->suffix2) {
-      sflag = 1;
+      sflag = 2;
       std::string estyle = style + "/" + lmp->suffix2;
       if (kspace_map->find(estyle) != kspace_map->end()) {
         KSpaceCreator &kspace_creator = (*kspace_map)[estyle];

src/lmptype.h

@@ -244,7 +244,7 @@ union ubuf {
 
 #if defined(__INTEL_LLVM_COMPILER) || defined(__INTEL_COMPILER)
 #define _alignvar(expr, val) __declspec(align(val)) expr
-#elif defined(__GNUC__)
+#elif defined(__GNUC__) || defined(__PGI)
 #define _alignvar(expr, val) expr __attribute((aligned(val)))
 #else
 #define _alignvar(expr, val) expr
@@ -252,9 +252,9 @@ union ubuf {
 
 // declaration to lift aliasing restrictions
 
-#if defined(__INTEL_LLVM_COMPILER) || defined(__INTEL_COMPILER)
+#if defined(__INTEL_COMPILER) || defined(__PGI)
 #define _noalias restrict
-#elif defined(__GNUC__)
+#elif defined(__GNUC__) || defined(__INTEL_LLVM_COMPILER)
 #define _noalias __restrict
 #else
 #define _noalias

src/utils.cpp

@@ -638,7 +638,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod
 char *utils::strdup(const std::string &text)
 {
   char *tmp = new char[text.size() + 1];
-  strcpy(tmp, text.c_str());
+  strcpy(tmp, text.c_str());    // NOLINT
   return tmp;
 }
 

unittest/cplusplus/test_lammps_class.cpp

@@ -362,7 +362,11 @@ TEST(LAMMPS_init, NoOpenMP)
     FILE *fp = fopen("in.lammps_class_noomp", "w");
     fputs("\n", fp);
     fclose(fp);
+#if defined(__WIN32)
+    _putenv("OMP_NUM_THREADS");
+#else
     unsetenv("OMP_NUM_THREADS");
+#endif
 
     const char *args[] = {"LAMMPS_init", "-in", "in.lammps_class_noomp", "-log", "none", "-nocite"};
     char **argv        = (char **)args;

unittest/force-styles/CMakeLists.txt

@@ -26,7 +26,7 @@ set(TEST_INPUT_FOLDER ${CMAKE_CURRENT_SOURCE_DIR}/tests)
 add_library(style_tests STATIC yaml_writer.cpp error_stats.cpp test_config_reader.cpp test_main.cpp)
 target_compile_definitions(style_tests PRIVATE -DTEST_INPUT_FOLDER=${TEST_INPUT_FOLDER})
 target_include_directories(style_tests PRIVATE ${LAMMPS_SOURCE_DIR})
-target_link_libraries(style_tests PUBLIC GTest::GTest GTest::GMock Yaml::Yaml)
+target_link_libraries(style_tests PUBLIC GTest::GTest GTest::GMock Yaml::Yaml lammps)
 if(BUILD_MPI)
   target_link_libraries(style_tests PUBLIC MPI::MPI_CXX)
 else()

unittest/fortran/CMakeLists.txt

@@ -7,6 +7,7 @@ endif()
 include(CheckLanguage)
 check_language(Fortran)
 if(CMAKE_Fortran_COMPILER)
+  enable_language(C)
   enable_language(Fortran)
   get_filename_component(LAMMPS_FORTRAN_MODULE ${LAMMPS_SOURCE_DIR}/../fortran/lammps.f90 ABSOLUTE)
   if(BUILD_MPI)