update/trim list of include files according to the IWYU principle

src/BODY/fix_nph_body.cpp

@@ -18,11 +18,8 @@
 #include "fix_nph_body.h"
 
 #include "error.h"
-#include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/BODY/fix_npt_body.cpp

@@ -18,11 +18,8 @@
 #include "fix_npt_body.h"
 
 #include "error.h"
-#include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/BODY/fix_nvt_body.cpp

@@ -21,8 +21,6 @@
 #include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/BODY/fix_wall_body_polygon.cpp

@@ -16,18 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_wall_body_polygon.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polygon.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
-#include "error.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/BODY/pair_body_nparticle.cpp

@@ -12,18 +12,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_body_nparticle.h"
-#include <cmath>
-#include <cstring>
-#include "math_extra.h"
+
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_nparticle.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
+#include "force.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/COLLOID/pair_yukawa_colloid.cpp

@@ -16,13 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_yukawa_colloid.h"
-#include <cmath>
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "error.h"
+#include "force.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/COMPRESS/gz_file_writer.h

@@ -19,9 +19,10 @@
 #define LMP_GZ_FILE_WRITER_H
 
 #include "file_writer.h"
+
+#include <exception>
 #include <string>
 #include <zlib.h>
-#include <exception>
 
 namespace LAMMPS_NS {
 
@@ -40,8 +41,6 @@ public:
 
     void setCompressionLevel(int level);
 };
-
-
 }
 
 #endif

src/COMPRESS/zstd_file_writer.h

@@ -21,9 +21,9 @@
 #define LMP_ZSTD_FILE_WRITER_H
 
 #include "file_writer.h"
+
 #include <string>
 #include <zstd.h>
-#include <exception>
 
 namespace LAMMPS_NS {
 
@@ -47,8 +47,6 @@ public:
     void setCompressionLevel(int level);
     void setChecksum(bool enabled);
 };
-
-
 }
 
 #endif

src/GPU/pair_born_coul_long_cs_gpu.cpp

@@ -16,28 +16,21 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_long_cs_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/GPU/pair_born_coul_long_gpu.cpp

@@ -16,28 +16,21 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_born_coul_wolf_cs_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_wolf_cs_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/GPU/pair_born_coul_wolf_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_wolf_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/GPU/pair_born_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_buck_coul_cut_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_buck_coul_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_buck_coul_long_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_buck_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_buck_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_buck_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_colloid_gpu.cpp

@@ -16,26 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_colloid_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_coul_cut_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_coul_debye_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_debye_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_coul_dsf_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_dsf_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911

src/GPU/pair_coul_long_cs_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_long_cs_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 #define EWALD_F   1.12837917

src/GPU/pair_coul_long_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_dpd_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_dpd_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "random_mars.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/GPU/pair_dpd_tstat_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_dpd_tstat_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "random_mars.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/GPU/pair_eam_alloy_gpu.cpp

@@ -16,23 +16,23 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_eam_alloy_gpu.h"
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "gpu_extra.h"
 #include "domain.h"
-
+#include "error.h"
+#include "force.h"
+#include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "potential_file_reader.h"
 #include "suffix.h"
 #include "tokenizer.h"
-#include "potential_file_reader.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -389,7 +389,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
       ValueTokenizer values = reader.next_values(1);
       file->nelements = values.next_int();
 
-      if (values.count() != file->nelements + 1)
+      if ((int)values.count() != file->nelements + 1)
         error->one(FLERR,"Incorrect element names in EAM potential file");
 
       file->elements = new char*[file->nelements];

src/GPU/pair_eam_fs_gpu.cpp

@@ -16,23 +16,23 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_eam_fs_gpu.h"
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "gpu_extra.h"
 #include "domain.h"
-#include "suffix.h"
-
-#include "tokenizer.h"
+#include "error.h"
+#include "force.h"
+#include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "potential_file_reader.h"
+#include "suffix.h"
+#include "tokenizer.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -388,7 +388,7 @@ void PairEAMFSGPU::read_file(char *filename)
       ValueTokenizer values = reader.next_values(1);
       file->nelements = values.next_int();
 
-      if (values.count() != file->nelements + 1)
+      if ((int)values.count() != file->nelements + 1)
         error->one(FLERR,"Incorrect element names in EAM potential file");
 
       file->elements = new char*[file->nelements];

src/GPU/pair_eam_gpu.cpp

@@ -16,22 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_eam_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
 #include "domain.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
-#include "neigh_request.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define MAXLINE 1024
 
 using namespace LAMMPS_NS;

src/GPU/pair_gauss_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_gauss_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_gayberne_gpu.cpp

@@ -16,28 +16,22 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_gayberne_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj96_cut_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj96_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp

@@ -15,23 +15,18 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_charmm_gpu.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 
@@ -205,8 +200,8 @@ double PairLJCharmmCoulCharmmGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairLJCharmmCoulCharmmGPU::cpu_compute(int start, int inum, int eflag,
-                                          int vflag, int *ilist,
-                                          int *numneigh, int **firstneigh)
+                                            int /* vflag */, int *ilist,
+                                            int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;

src/GPU/pair_lj_charmm_coul_long_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_charmm_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_lj_class2_coul_long_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_class2_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_lj_class2_gpu.cpp

@@ -18,20 +18,14 @@
 #include "pair_lj_class2_gpu.h"
 
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "gpu_extra.h"
-#include "integrate.h"
-#include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "neighbor.h"
 #include "suffix.h"
-#include "universe.h"
-#include "update.h"
 
 #include <cmath>
 

src/GPU/pair_lj_cubic_gpu.cpp

@@ -18,23 +18,16 @@
 #include "pair_lj_cubic_gpu.h"
 
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "gpu_extra.h"
-#include "integrate.h"
-#include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "neighbor.h"
 #include "suffix.h"
-#include "universe.h"
-#include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 #include "pair_lj_cubic_const.h"
 

src/GPU/pair_lj_cut_coul_cut_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj_cut_coul_debye_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_debye_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj_cut_coul_dsf_gpu.cpp

@@ -17,25 +17,19 @@
 
 #include "pair_lj_cut_coul_dsf_gpu.h"
 #include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911

src/GPU/pair_lj_cut_coul_long_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_lj_cut_coul_msm_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_msm_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj_cut_dipole_cut_gpu.cpp

@@ -16,25 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_dipole_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/GPU/pair_lj_cut_dipole_long_gpu.cpp

@@ -16,27 +16,22 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_dipole_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "kspace.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911

src/GPU/pair_lj_cut_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj_cut_tip4p_long_gpu.cpp

@@ -15,30 +15,24 @@
    Contributing author: Vsevolod Nikolskiy (HSE)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-
-#include <cstring>
 #include "pair_lj_cut_tip4p_long_gpu.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
-#include "domain.h"
-#include "kspace.h"
+
 #include "angle.h"
+#include "atom.h"
 #include "bond.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_lj_expand_coul_long_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_expand_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_lj_expand_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_expand_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj_gromacs_gpu.cpp

@@ -16,27 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_gromacs_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj_sdk_coul_long_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_sdk_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592

src/GPU/pair_lj_sdk_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_sdk_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_lj_sf_dipole_sf_gpu.cpp

@@ -16,25 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_sf_dipole_sf_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/GPU/pair_mie_cut_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_mie_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_morse_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_morse_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_resquared_gpu.cpp

@@ -16,28 +16,22 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_resquared_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_soft_gpu.cpp

@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_soft_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
 #include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_sw_gpu.cpp

@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_sw_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;

src/GPU/pair_table_gpu.cpp

@@ -16,30 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_table_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
-#define LOOKUP 0
-#define LINEAR 1
-#define SPLINE 2
-#define BITMAP 3
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/GPU/pair_tersoff_gpu.cpp

@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tersoff_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "gpu_extra.h"
 #include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "domain.h"
-#include "gpu_extra.h"
+#include "neigh_request.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;

src/GPU/pair_tersoff_mod_gpu.cpp

@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tersoff_mod_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;

src/GPU/pair_tersoff_zbl_gpu.cpp

@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tersoff_zbl_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;

src/GPU/pair_ufm_gpu.cpp

@@ -18,26 +18,19 @@
  ------------------------------------------------------------------------- */
 
 #include "pair_ufm_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_vashishta_gpu.cpp

@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_vashishta_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;

src/GPU/pair_yukawa_colloid_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_yukawa_colloid_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_yukawa_gpu.cpp

@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_yukawa_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/GPU/pair_zbl_gpu.cpp

@@ -16,27 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_zbl_gpu.h"
-#include "lmptype.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition

src/KSPACE/fft3d.cpp

@@ -20,11 +20,12 @@
 ------------------------------------------------------------------------- */
 
 #include "fft3d.h"
-#include <mpi.h>
-#include <cstdio>
+
+#include "remap.h"
+
 #include <cstdlib>
 #include <cmath>
-#include "remap.h"
+
 #if defined(_OPENMP)
 #include <omp.h>
 #endif

src/KSPACE/msm_cg.cpp

@@ -16,9 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "msm_cg.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "gridcomm.h"
 #include "domain.h"
@@ -26,7 +24,9 @@
 #include "force.h"
 #include "neighbor.h"
 #include "memory.h"
-#include "fmt/format.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/KSPACE/remap.cpp

@@ -12,8 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "remap.h"
-#include <mpi.h>
-#include <cstdio>
+
 #include <cstdlib>
 
 #define PACK_DATA FFT_SCALAR

src/MANYBODY/pair_eam_he.cpp

@@ -19,13 +19,13 @@
 
 #include "atom.h"
 #include "comm.h"
-#include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "update.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */

src/MANYBODY/pair_eim.h

@@ -23,6 +23,7 @@ PairStyle(eim,PairEIM)
 #include "pair.h"
 
 #include <map>
+#include <utility>
 
 namespace LAMMPS_NS {
 

src/MANYBODY/pair_vashishta_table.cpp

@@ -16,11 +16,10 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_vashishta_table.h"
-#include <cstdio>
+
 #include "atom.h"
 #include "error.h"
 #include "force.h"
-#include "comm.h"
 #include "memory.h"
 #include "neigh_list.h"
 

src/MC/fix_charge_regulation.cpp

@@ -32,15 +32,12 @@
 #include "improper.h"
 #include "kspace.h"
 #include "math_const.h"
-#include "math_extra.h"
 #include "math_special.h"
 #include "memory.h"
 #include "modify.h"
-#include "molecule.h"
 #include "neighbor.h"
 #include "pair.h"
 #include "random_park.h"
-#include "region.h"
 #include "update.h"
 
 #include <cmath>

src/MC/fix_tfmc.cpp

@@ -17,18 +17,19 @@
 
 #include "fix_tfmc.h"
 
-#include <cstring>
-#include <cmath>
-#include <cfloat>
 #include "atom.h"
-#include "force.h"
-#include "group.h"
-#include "random_mars.h"
 #include "comm.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "group.h"
 #include "memory.h"
 #include "modify.h"
-#include "error.h"
+#include "random_mars.h"
+
+#include <cfloat>
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/MISC/fix_orient_bcc.cpp

@@ -33,7 +33,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/MISC/fix_orient_fcc.cpp

@@ -30,7 +30,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/MLIAP/pair_mliap.cpp

@@ -35,7 +35,6 @@
 
 #include <cmath>
 #include <cstring>
-#include "error.h"
 
 using namespace LAMMPS_NS;
 

src/MOLECULE/dihedral_charmm.cpp

@@ -17,19 +17,18 @@
 
 #include "dihedral_charmm.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
 #include "force.h"
-#include "pair.h"
-#include "update.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
 
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/MOLECULE/dihedral_charmmfsw.cpp

@@ -20,19 +20,18 @@
 
 #include "dihedral_charmmfsw.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
 #include "force.h"
-#include "pair.h"
-#include "update.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
 
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/QEQ/fix_qeq_point.cpp

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

src/QEQ/fix_qeq_shielded.cpp

@@ -32,7 +32,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/RIGID/fix_rigid_nh_small.cpp

@@ -31,7 +31,6 @@
 #include "math_extra.h"
 #include "memory.h"
 #include "modify.h"
-#include "molecule.h"
 #include "rigid_const.h"
 #include "update.h"
 

src/SNAP/pair_snap.cpp

@@ -25,7 +25,6 @@
 #include "tokenizer.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/SPIN/fix_langevin_spin.cpp

@@ -22,21 +22,20 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_langevin_spin.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
-#include "group.h"
 #include "math_const.h"
-#include "memory.h"
 #include "modify.h"
-// #include "random_park.h"
 #include "random_mars.h"
 #include "respa.h"
 #include "update.h"
 
+#include <cmath>
+#include <cstring>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;

src/SPIN/fix_neb_spin.cpp

@@ -27,7 +27,6 @@
 #include "comm.h"
 #include "compute.h"
 #include "error.h"
-#include "force.h"
 #include "group.h"
 #include "memory.h"
 #include "modify.h"

src/SPIN/pair_spin.cpp

@@ -22,20 +22,21 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_spin.h"
-#include <cstring>
+
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
-#include "fix.h"
+#include "fix_nve_spin.h"
 #include "force.h"
 #include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "neighbor.h"
 #include "neigh_request.h"
+#include "neighbor.h"
 #include "pair.h"
 #include "update.h"
-#include "fix_nve_spin.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/USER-COLVARS/ndx_group.cpp

@@ -22,11 +22,8 @@
 #include "comm.h"
 #include "error.h"
 #include "group.h"
-#include "memory.h"
 #include "tokenizer.h"
 
-#include <cstdlib>
-
 using namespace LAMMPS_NS;
 #define BUFLEN 4096
 #define DELTA 16384

src/USER-DRUDE/fix_tgnh_drude.cpp

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

src/USER-DRUDE/fix_tgnvt_drude.cpp

@@ -17,8 +17,6 @@
 #include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/USER-EFF/compute_temp_region_eff.cpp

@@ -27,8 +27,6 @@
 #include "region.h"
 #include "update.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */

src/USER-EFF/fix_nve_eff.cpp

@@ -15,15 +15,14 @@
    Contributing author: Andres Jaramillo-Botero (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-
 #include "fix_nve_eff.h"
+
 #include "atom.h"
-#include "force.h"
-#include "update.h"
-#include "respa.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "respa.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-EFF/fix_nvt_eff.cpp

@@ -17,8 +17,6 @@
 #include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/USER-MEAMC/pair_meamc.cpp

@@ -17,20 +17,21 @@
 
 #include "pair_meamc.h"
 
-#include <memory>
-
-#include "meam.h"
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
+#include "force.h"
+#include "meam.h"
+#include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "memory.h"
-#include "error.h"
+#include "neighbor.h"
 #include "potential_file_reader.h"
 #include "tokenizer.h"
 
+#include <cstring>
+#include <memory>
+
 using namespace LAMMPS_NS;
 
 #define MAXLINE 1024

src/USER-MEAMC/pair_meamc.h

@@ -22,8 +22,8 @@ PairStyle(meam,PairMEAMC)
 #define LMP_PAIR_MEAMC_H
 
 #include "pair.h"
+
 #include <vector>
-#include <string>
 
 namespace LAMMPS_NS {
 

src/USER-MESODPD/atom_vec_edpd.cpp

@@ -15,7 +15,6 @@
 
 #include "atom.h"
 #include "error.h"
-#include "modify.h"
 #include "update.h"
 
 #include <cstring>

src/USER-MESODPD/pair_edpd.cpp

@@ -18,20 +18,20 @@
 
 #include "pair_edpd.h"
 
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "random_mars.h"
+#include "update.h"
+
 #include <cmath>
 #include <ctime>
 #include <cstring>
-#include "atom.h"
-#include "comm.h"
-#include "update.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "random_mars.h"
-#include "citeme.h"
-#include "memory.h"
-#include "error.h"
-
 
 using namespace LAMMPS_NS;
 
@@ -275,11 +275,9 @@ void PairEDPD::settings(int narg, char **arg)
 
   // initialize Marsaglia RNG with processor-unique seed
 
-  if (seed <= 0) {
-    struct timespec time;
-    clock_gettime( CLOCK_REALTIME, &time );
-    seed = time.tv_nsec;  // if seed is non-positive, get the current time as the seed
-  }
+  if (seed <= 0)
+    error->all(FLERR,"Invalid random number seed");
+
   delete random;
   random = new RanMars(lmp,(seed + comm->me) % 900000000);
   randomT = new RanMars(lmp,(2*seed + comm->me) % 900000000);

src/USER-MISC/angle_gaussian.cpp

@@ -13,16 +13,17 @@
 
 #include "angle_gaussian.h"
 
-#include <cmath>
 #include "atom.h"
-#include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
 #include "force.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/USER-MISC/compute_gyration_shape.cpp

@@ -19,7 +19,6 @@
 
 #include "error.h"
 #include "math_eigen.h"
-#include "math_extra.h"
 #include "math_special.h"
 #include "modify.h"
 #include "update.h"

src/USER-MISC/compute_gyration_shape_chunk.cpp

@@ -19,7 +19,6 @@
 
 #include "error.h"
 #include "math_eigen.h"
-#include "math_extra.h"
 #include "math_special.h"
 #include "memory.h"
 #include "modify.h"

src/USER-MISC/compute_pressure_grem.cpp

@@ -21,8 +21,6 @@
 #include "kspace.h"
 #include "error.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 /* ----------------------------------------------------------------------

src/USER-MISC/dihedral_table_cut.cpp

@@ -29,7 +29,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 #include <fstream>  // IWYU pragma: keep
 #include <sstream>  // IWYU pragma: keep
 

src/USER-MISC/fix_addtorque.cpp

@@ -28,8 +28,6 @@
 #include "update.h"
 #include "variable.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;