Merge pull request #2338 from akohlmey/include-cleanup

Update list of included headers for latest updates of the convention

cmake/CMakeLists.txt

@@ -249,6 +249,26 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
   endif()
 endif()
 
+#######################################
+# add custom target for IWYU analysis
+#######################################
+set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
+mark_as_advanced(ENABLE_IWYU)
+if(ENABLE_IWYU)
+  find_program(IWYU_EXE NAMES include-what-you-use iwyu)
+  find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
+  if (IWYU_EXE AND IWYU_TOOL)
+    add_custom_target(
+      iwyu
+      ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
+      COMMENT "Running IWYU")
+    add_dependencies(iwyu lammps)
+  else()
+    message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
+      "and the iwyu-tool/iwyu_tool script installed in your PATH")
+  endif()
+endif()
+
 set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
 mark_as_advanced(ENABLE_SANITIZER)
 set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
@@ -293,7 +313,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   endif()
 endif()
 
-
 find_package(JPEG QUIET)
 option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)

cmake/iwyu/iwyu-extra-map.imp

@@ -0,0 +1,7 @@
+[
+  { 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 ] },
+]

doc/include-file-conventions.md

@@ -91,32 +91,31 @@ statements should follow the "include what you use" principle.
 
 Include files should be included in this order:
 * the header matching the implementation (`some_class.h` for file `some_class.cpp`)
-* mpi.h
+* mpi.h  (only if needed)
-* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
 * LAMMPS local headers (preferably in alphabetical order)
+* system and library headers (anything that is using angular brackets; preferably in alphabetical order)
+* conditional include statements (i.e. anything bracketed with ifdefs)
 
 ### Special Cases and Exceptions
 
 #### pointers.h
 
-The `pointer.h` header file also includes `cstdio`, `cstddef`,
+The `pointer.h` header file also includes (in this order) `lmptype.h`,
-`string`, `lmptype.h`, and `utils.h` (and through those indirectly
+`mpi.h`, `cstddef`, `cstdio`, `string`, `utils.h`, and `fmt/format.h`
- `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
+and through `lmptype.h` indirectly also `climits`, `cstdlib`, `cinttypes`.
 This means any header including `pointers.h` can assume that `FILE`,
-`NULL`, `INT_MAX` are defined, they may freely use std::string
+`NULL`, `INT_MAX` are defined, and the may freely use the std::string
-and functions from the utils namespace without including the
+for arguments. Corresponding implementation files do not need to include
-corresponding header files.
+those headers.
 
 ## Tools
 
 The [Include What You Use tool](https://include-what-you-use.org/)
 can be used to provide supporting information about compliance with
-the rules listed here.  There are some limitations and the IWYU tool
+the rules listed here.  Through setting `-DENABLE_IWYU=on` when running
-may give incorrect advice.  The tools is activated by setting the
+CMake, a custom build target is added that will enable recording
-CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
+the compilation commands and then run the `iwyu_tool` using the
-path of the `include-what-you-use` command.  When activated, the
+recorded compilation commands information when typing `make iwyu`.
-tool will be run after each compilation and provide suggestions for
-which include files should be added or removed.
 
 ## Legacy Code
 

doc/src/Build_development.rst

@@ -28,6 +28,40 @@ variable VERBOSE set to 1:
 
 ----------
 
+.. _iwyu_processing:
+
+Report missing and unneeded '#include' statements
+-------------------------------------------------
+
+The conventions for how and when to use and order include statements in
+LAMMPS are `documented in a separate file <https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md>`_
+(also included in the source code distribution).  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
+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
+reports than earlier versions.
+
+The necessary steps to generate the report can be enabled via a
+CMake variable:
+
+.. code-block:: bash
+
+   -D ENABLE_IWYU=value    # value = no (default) or yes
+
+This will check if the required binary (include-what-you-use or iwyu)
+and python script script (iwyu-tool or iwyu_tool or iwyu_tool.py) can
+be found in the path.  The analysis can then be started with:
+
+.. code-block:: bash
+
+   make iwyu
+
+This may first run some compilation, as the analysis is dependent
+on recording all commands required to do the compilation.
+
+----------
+
 .. _sanitizer:
 
 Address, Undefined Behavior, and Thread Sanitizer Support

doc/utils/sphinx-config/false_positives.txt

@@ -1355,6 +1355,7 @@ iva
 Ivanov
 Ivector
 Iw
+iwyu
 ixcm
 ixx
 Ixx

lib/awpmd/ivutils/include/logexc.h

@@ -273,7 +273,7 @@ public:
 };
 
 /// format a string 
-const char *fmt(const char *format,...);
+const char *logfmt(const char *format,...);
 
 /// macros with common usage
 #define LOGFATAL(code,text,lineinfo) ((lineinfo) ? ::message(vblFATAL,(code)," %s at %s:%d",(text),__FILE__,__LINE__) : \

lib/awpmd/ivutils/src/logexc.cpp

@@ -16,7 +16,7 @@ message_logger &message_logger::global(){
 message_logger *message_logger::glogp=NULL;
 stdfile_logger default_log("",0,stdout,stderr,vblALLBAD|vblMESS1,vblFATAL,1);
 
-const char *fmt(const char *format,...){
+const char *logfmt(const char *format,...){
   va_list args;
   va_start(args,format);
   static char buff[1024];

lib/awpmd/systems/interact/TCP/wpmd.cpp

@@ -170,7 +170,7 @@ int AWPMD::set_pbc(const Vector_3P pcell, int pbc_){
 int AWPMD::set_electrons(int s, int n, Vector_3P x, Vector_3P v, double* w, double* pw, double mass, double *q)
 {
   if(s < 0 || s > 1)
-    return LOGERR(-1,fmt("AWPMD.set_electrons: invaid s setting (%d)!",s),LINFO);
+    return LOGERR(-1,logfmt("AWPMD.set_electrons: invaid s setting (%d)!",s),LINFO);
 
   norm_matrix_state[s] = NORM_UNDEFINED;
   nwp[s]=ne[s]=n;
@@ -363,20 +363,20 @@ int AWPMD::interaction(int flag, Vector_3P fi, Vector_3P fe_x,
     //3. inverting the overlap matrix
     int info=0;
     if(nes){
-      /*FILE *f1=fopen(fmt("matrO_%d.d",s),"wt");
+      /*FILE *f1=fopen(logfmt("matrO_%d.d",s),"wt");
       fileout(f1,Y[s],"%15g");
       fclose(f1);8*/
-      
+
       ZPPTRF("L",&nes,Y[s].arr,&info);
       // analyze return code here
       if(info<0)
-        return LOGERR(info,fmt("AWPMD.interacton: call to ZPTRF failed (exitcode %d)!",info),LINFO); 
+        return LOGERR(info,logfmt("AWPMD.interacton: call to ZPTRF failed (exitcode %d)!",info),LINFO); 
       ZPPTRI("L",&nes,Y[s].arr,&info);
       if(info<0)
-        return LOGERR(info,fmt("AWPMD.interacton: call to ZPTRI failed (exitcode %d)!",info),LINFO); 
+        return LOGERR(info,logfmt("AWPMD.interacton: call to ZPTRI failed (exitcode %d)!",info),LINFO); 
 
-      
+
-      /*f1=fopen(fmt("matrY_%d.d",s),"wt");
+      /*f1=fopen(logfmt("matrY_%d.d",s),"wt");
       fileout(f1,Y[s],"%15g");
       fclose(f1);*/
     }
@@ -758,7 +758,7 @@ void AWPMD::norm_factorize(int s) {
   int nes8 = ne[s]*8, info;
   DGETRF(&nes8, &nes8, Norm[s].arr, &nes8, &ipiv[0], &info);
   if(info < 0)
-    LOGERR(info,fmt("AWPMD.norm_factorize: call to DGETRF failed (exitcode %d)!",info),LINFO); 
+    LOGERR(info,logfmt("AWPMD.norm_factorize: call to DGETRF failed (exitcode %d)!",info),LINFO); 
 
   norm_matrix_state[s] = NORM_FACTORIZED;
 }
@@ -773,7 +773,7 @@ void AWPMD::norm_invert(int s) {
 
   DGETRI(&nes8, Norm[s].arr, &nes8, &ipiv[0], (double*)IDD.arr, &IDD_size, &info); // use IDD for work storage
   if(info < 0)
-    LOGERR(info,fmt("AWPMD.norm_invert: call to DGETRI failed (exitcode %d)!",info),LINFO); 
+    LOGERR(info,logfmt("AWPMD.norm_invert: call to DGETRI failed (exitcode %d)!",info),LINFO); 
 
   norm_matrix_state[s] = NORM_INVERTED;
 }
@@ -829,7 +829,7 @@ int AWPMD::step(double dt){
 //e gets current electronic coordinates
 int AWPMD::get_electrons(int spin, Vector_3P x, Vector_3P v, double* w, double* pw, double mass){
   if(spin<0 || spin >1)
-    return -1; // invalid spin: return LOGERR(-1,fmt("AWPMD.get_electrons: invaid spin setting (%d)!",spin),LINFO);
+    return -1; // invalid spin: return LOGERR(-1,logfmt("AWPMD.get_electrons: invaid spin setting (%d)!",spin),LINFO);
   if(mass<0)
     mass=me;
   for(int i=0;i<ni;i++){
@@ -887,4 +887,4 @@ int AWPMD::interaction_ii(int flag,Vector_3P fi){
     }
   }
   return 1;
-}
+}

lib/awpmd/systems/interact/TCP/wpmd_split.h

@@ -119,11 +119,11 @@ public:
   ///    Electronic charges q are -1 by default (when q=NULL), otherwise the charges are assigned for each split
   int set_electrons(int s, int nel, Vector_3P x, Vector_3P v, double* w, double* pw, Vector_2 *c, int *splits, double mass=-1, double *q=NULL);
 
-  
+
   ///\en Starts adding new electron: continue with \ref add_split functions.
   int add_electron(int s){
     if(s < 0 || s > 1)
-      return LOGERR(-1,fmt("AWPMD_split.add_electron: invaid spin setting (%d)!",s),LINFO);
+      return LOGERR(-1,logfmt("AWPMD_split.add_electron: invaid spin setting (%d)!",s),LINFO);
     s_add=s;
     spl_add=0;
     return ne[s_add];

src/ASPHERE/compute_erotate_asphere.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_erotate_asphere.h"
-#include <mpi.h>
+
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"

src/ASPHERE/compute_temp_asphere.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_temp_asphere.h"
-#include <mpi.h>
+
 #include <cstring>
 #include "math_extra.h"
 #include "atom.h"

src/ASPHERE/fix_nph_asphere.cpp

@@ -13,7 +13,7 @@
 
 #include "fix_nph_asphere.h"
 #include <cstring>
-#include <string>
+
 #include "modify.h"
 #include "error.h"
 

src/ASPHERE/fix_npt_asphere.cpp

@@ -13,7 +13,7 @@
 
 #include "fix_npt_asphere.h"
 #include <cstring>
-#include <string>
+
 #include "modify.h"
 #include "error.h"
 

src/ASPHERE/fix_nvt_asphere.cpp

@@ -13,11 +13,11 @@
 
 #include "fix_nvt_asphere.h"
 #include <cstring>
-#include <string>
+
 #include "group.h"
 #include "modify.h"
 #include "error.h"
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/ASPHERE/pair_gayberne.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_gayberne.h"
-#include <mpi.h>
+
 #include <cmath>
 #include "math_extra.h"
 #include "atom.h"
@@ -28,7 +28,7 @@
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 

src/ASPHERE/pair_line_lj.cpp

@@ -20,7 +20,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 

src/ASPHERE/pair_resquared.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_resquared.h"
-#include <mpi.h>
+
 #include <cmath>
 #include "math_extra.h"
 #include "atom.h"
@@ -27,7 +27,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 

src/ASPHERE/pair_tri_lj.cpp

@@ -21,7 +21,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 

src/BODY/body_nparticle.cpp

@@ -12,16 +12,15 @@
 ------------------------------------------------------------------------- */
 
 #include "body_nparticle.h"
-#include <cstring>
+
-#include <cstdlib>
-#include "my_pool_chunk.h"
-#include "math_extra.h"
-#include "atom_vec_body.h"
 #include "atom.h"
-#include "force.h"
+#include "atom_vec_body.h"
-#include "memory.h"
 #include "error.h"
-#include "fmt/format.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "my_pool_chunk.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/BODY/body_rounded_polygon.cpp

@@ -16,17 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "body_rounded_polygon.h"
-#include <cmath>
+
-#include <cstring>
-#include "my_pool_chunk.h"
-#include "atom_vec_body.h"
 #include "atom.h"
-#include "force.h"
+#include "atom_vec_body.h"
 #include "domain.h"
+#include "error.h"
 #include "math_extra.h"
 #include "memory.h"
-#include "error.h"
+#include "my_pool_chunk.h"
-#include "fmt/format.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/BODY/body_rounded_polyhedron.cpp

@@ -16,17 +16,16 @@
 ------------------------------------------------------------------------- */
 
 #include "body_rounded_polyhedron.h"
-#include <cmath>
+
-#include <cstring>
-#include <cstdlib>
-#include "my_pool_chunk.h"
-#include "atom_vec_body.h"
 #include "atom.h"
-#include "force.h"
+#include "atom_vec_body.h"
+#include "error.h"
 #include "math_extra.h"
 #include "memory.h"
-#include "error.h"
+#include "my_pool_chunk.h"
-#include "fmt/format.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/BODY/compute_body_local.cpp

@@ -12,15 +12,15 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_body_local.h"
-#include <mpi.h>
+
-#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body.h"
-#include "update.h"
-#include "force.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/BODY/compute_temp_body.cpp

@@ -17,7 +17,7 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_temp_body.h"
-#include <mpi.h>
+
 #include <cstring>
 #include "math_extra.h"
 #include "atom.h"

src/BODY/fix_nph_body.cpp

@@ -17,11 +17,11 @@
 
 #include "fix_nph_body.h"
 #include <cstring>
-#include <string>
+
 #include "group.h"
 #include "modify.h"
 #include "error.h"
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/BODY/fix_npt_body.cpp

@@ -17,11 +17,11 @@
 
 #include "fix_npt_body.h"
 #include <cstring>
-#include <string>
+
 #include "group.h"
 #include "modify.h"
 #include "error.h"
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/BODY/fix_nvt_body.cpp

@@ -17,11 +17,11 @@
 
 #include "fix_nvt_body.h"
 #include <cstring>
-#include <string>
+
 #include "group.h"
 #include "modify.h"
 #include "error.h"
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/BODY/pair_body_nparticle.cpp

@@ -23,7 +23,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 

src/BODY/pair_body_rounded_polygon.cpp

@@ -19,7 +19,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_body_rounded_polygon.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "math_extra.h"
@@ -34,7 +34,7 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 

src/BODY/pair_body_rounded_polyhedron.cpp

@@ -21,7 +21,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_body_rounded_polyhedron.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -37,7 +37,7 @@
 #include "error.h"
 #include "math_extra.h"
 #include "math_const.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CLASS2/angle_class2.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_class2.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -27,7 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CLASS2/bond_class2.cpp

@@ -17,7 +17,7 @@
 
 #include <cstring>
 #include "bond_class2.h"
-#include <mpi.h>
+
 #include <cmath>
 #include "atom.h"
 #include "neighbor.h"
@@ -25,7 +25,7 @@
 #include "force.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 

src/CLASS2/dihedral_class2.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "dihedral_class2.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -27,8 +27,8 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CLASS2/improper_class2.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "improper_class2.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -27,8 +27,8 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CLASS2/pair_lj_class2.cpp

@@ -10,7 +10,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_class2.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -24,7 +24,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CLASS2/pair_lj_class2_coul_cut.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_class2_coul_cut.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -23,7 +23,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/CLASS2/pair_lj_class2_coul_long.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_class2_coul_long.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -27,7 +27,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/COLLOID/fix_wall_colloid.cpp

@@ -16,10 +16,9 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_wall_colloid.h"
-#include <mpi.h>
+
 #include <cmath>
 #include "atom.h"
-#include "atom_vec.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/COLLOID/pair_brownian.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_brownian.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -36,7 +36,7 @@
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/COLLOID/pair_brownian_poly.cpp

@@ -17,7 +17,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_brownian_poly.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"

src/COLLOID/pair_colloid.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_colloid.h"
-#include <mpi.h>
+
 #include <cmath>
 #include "atom.h"
 #include "comm.h"
@@ -25,7 +25,7 @@
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;

src/COLLOID/pair_lubricate.cpp

@@ -17,7 +17,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lubricate.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -35,7 +35,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/COLLOID/pair_lubricateU.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lubricateU.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -34,7 +34,7 @@
 #include "variable.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/COLLOID/pair_lubricateU_poly.cpp

@@ -18,7 +18,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lubricateU_poly.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"

src/COLLOID/pair_lubricate_poly.cpp

@@ -18,7 +18,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lubricate_poly.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"

src/COMPRESS/dump_atom_gz.cpp

@@ -15,10 +15,10 @@
 #include "domain.h"
 #include "error.h"
 #include "update.h"
-#include "utils.h"
+
 
 #include <cstring>
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 

src/COMPRESS/dump_atom_zstd.cpp

@@ -17,14 +17,14 @@
 
 #ifdef LAMMPS_ZSTD
 
-#include "dump_atom_zstd.h"
 #include "domain.h"
+#include "dump_atom_zstd.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
-#include "utils.h"
 
 #include <cstring>
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 

src/COMPRESS/dump_cfg_gz.cpp

@@ -16,10 +16,10 @@
 #include "domain.h"
 #include "error.h"
 #include "update.h"
-#include "utils.h"
+
 
 #include <cstring>
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 #define UNWRAPEXPAND 10.0

src/COMPRESS/dump_cfg_zstd.cpp

@@ -16,15 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #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 "utils.h"
 
 #include <cstring>
-#include "fmt/format.h"
 
 using namespace LAMMPS_NS;
 #define UNWRAPEXPAND 10.0

src/COMPRESS/dump_custom_gz.cpp

@@ -15,10 +15,10 @@
 #include "domain.h"
 #include "error.h"
 #include "update.h"
-#include "utils.h"
+
 
 #include <cstring>
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 

src/COMPRESS/dump_custom_zstd.cpp

@@ -17,14 +17,14 @@
 
 #ifdef LAMMPS_ZSTD
 
-#include "dump_custom_zstd.h"
 #include "domain.h"
+#include "dump_custom_zstd.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
-#include "utils.h"
 
 #include <cstring>
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 

src/COMPRESS/dump_local_gz.cpp

@@ -15,10 +15,10 @@
 #include "domain.h"
 #include "error.h"
 #include "update.h"
-#include "utils.h"
+
 
 #include <cstring>
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 

src/COMPRESS/dump_local_zstd.cpp

@@ -21,10 +21,10 @@
 #include "domain.h"
 #include "error.h"
 #include "update.h"
-#include "utils.h"
+
 
 #include <cstring>
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 

src/COMPRESS/dump_xyz_gz.cpp

@@ -14,10 +14,10 @@
 #include "dump_xyz_gz.h"
 #include "error.h"
 #include "update.h"
-#include "utils.h"
+
 
 #include <cstring>
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 

src/COMPRESS/dump_xyz_zstd.cpp

@@ -19,11 +19,10 @@
 
 #include "dump_xyz_zstd.h"
 #include "error.h"
+#include "file_writer.h"
 #include "update.h"
-#include "utils.h"
 
 #include <cstring>
-#include "fmt/format.h"
 
 using namespace LAMMPS_NS;
 

src/CORESHELL/compute_temp_cs.cpp

@@ -17,9 +17,9 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_temp_cs.h"
-#include <mpi.h>
+
 #include <cstring>
-#include <string>
+
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
@@ -31,7 +31,7 @@
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
-#include "fmt/format.h"
+
 
 using namespace LAMMPS_NS;
 

src/DIPOLE/atom_vec_dipole.cpp

@@ -12,15 +12,10 @@
 ------------------------------------------------------------------------- */
 
 #include "atom_vec_dipole.h"
-#include <cmath>
+
 #include "atom.h"
-#include "comm.h"
+
-#include "domain.h"
+#include <cmath>
-#include "modify.h"
-#include "fix.h"
-#include "memory.h"
-#include "error.h"
-#include "utils.h"
 
 using namespace LAMMPS_NS;
 

src/DIPOLE/pair_lj_cut_dipole_cut.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_dipole_cut.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -23,7 +23,7 @@
 #include "memory.h"
 #include "error.h"
 #include "update.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 

src/DIPOLE/pair_lj_cut_dipole_long.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_dipole_long.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "atom.h"
@@ -25,7 +25,7 @@
 #include "memory.h"
 #include "error.h"
 #include "update.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/DIPOLE/pair_lj_long_dipole_long.cpp

@@ -16,7 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_long_dipole_long.h"
-#include <mpi.h>
+
 #include <cmath>
 #include <cstring>
 #include "math_const.h"
@@ -30,7 +30,7 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/GPU/fix_gpu.cpp

@@ -13,7 +13,7 @@
 
 #include "fix_gpu.h"
 #include <cstring>
-#include <cstdlib>
+
 #include "atom.h"
 #include "force.h"
 #include "pair.h"
@@ -30,7 +30,7 @@
 #include "neighbor.h"
 #include "citeme.h"
 #include "error.h"
-#include "utils.h"
+
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/GPU/pair_beck_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_beck_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_born_coul_long_cs_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_born_coul_long_cs_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_born_coul_long_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_born_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_born_coul_wolf_cs_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_born_coul_wolf_cs_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_born_coul_wolf_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_born_coul_wolf_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_born_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_born_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_buck_coul_cut_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_buck_coul_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_buck_coul_long_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_buck_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_buck_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_buck_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_colloid_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_colloid_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_coul_cut_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_coul_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_coul_debye_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_coul_debye_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_coul_dsf_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_coul_dsf_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_coul_long_cs_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_coul_long_cs_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_coul_long_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_dpd_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_dpd_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_dpd_tstat_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_dpd_tstat_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_eam_alloy_gpu.cpp

@@ -17,7 +17,7 @@
 
 #include "pair_eam_alloy_gpu.h"
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "force.h"
@@ -29,7 +29,7 @@
 #include "neigh_request.h"
 #include "gpu_extra.h"
 #include "domain.h"
-#include "utils.h"
+
 #include "suffix.h"
 #include "tokenizer.h"
 #include "potential_file_reader.h"

src/GPU/pair_eam_fs_gpu.cpp

@@ -17,7 +17,7 @@
 
 #include "pair_eam_fs_gpu.h"
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "force.h"
@@ -30,7 +30,7 @@
 #include "gpu_extra.h"
 #include "domain.h"
 #include "suffix.h"
-#include "utils.h"
+
 #include "tokenizer.h"
 #include "potential_file_reader.h"
 

src/GPU/pair_eam_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_eam_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "force.h"

src/GPU/pair_gauss_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_gauss_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_gayberne_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_gayberne_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "math_extra.h"
 #include "atom.h"

src/GPU/pair_lj96_cut_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj96_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_charmm_coul_long_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_charmm_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_class2_coul_long_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_class2_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_class2_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_class2_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cubic_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cubic_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_coul_cut_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cut_coul_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_coul_debye_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cut_coul_debye_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_coul_dsf_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cut_coul_dsf_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_coul_long_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cut_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_coul_msm_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cut_coul_msm_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_dipole_cut_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cut_dipole_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_dipole_long_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cut_dipole_long_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_cut_tip4p_long_gpu.cpp

@@ -17,7 +17,7 @@
 
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "pair_lj_cut_tip4p_long_gpu.h"
 #include "atom.h"

src/GPU/pair_lj_expand_coul_long_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_expand_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_expand_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_expand_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"

src/GPU/pair_lj_gromacs_gpu.cpp

@@ -18,7 +18,7 @@
 #include "pair_lj_gromacs_gpu.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
+
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"