update include handling for commands

src/neighbor.cpp

@@ -16,38 +16,37 @@
 ------------------------------------------------------------------------- */
 
 #include "neighbor.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "nbin.h"
-#include "nstencil.h"
-#include "npair.h"
-#include "ntopo.h"
-#include "style_nbin.h"
-#include "style_nstencil.h"
-#include "style_npair.h"
-#include "style_ntopo.h"
+
 #include "atom.h"
 #include "atom_vec.h"
+#include "citeme.h"
 #include "comm.h"
+#include "compute.h"
+#include "domain.h"
+#include "error.h"
+#include "fix.h"
 #include "force.h"
+#include "group.h"
+#include "memory.h"
+#include "modify.h"
+#include "nbin.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "npair.h"
+#include "nstencil.h"
+#include "ntopo.h"
+#include "output.h"
 #include "pair.h"
 #include "pair_hybrid.h"
-#include "domain.h"
-#include "group.h"
-#include "modify.h"
-#include "fix.h"
-#include "compute.h"
-#include "update.h"
 #include "respa.h"
-#include "output.h"
-#include "citeme.h"
-#include "memory.h"
-#include "error.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "style_nbin.h"
+#include "style_npair.h"
+#include "style_nstencil.h"
+#include "style_ntopo.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace NeighConst;

src/read_data.cpp

@@ -40,7 +40,6 @@
 #include "special.h"
 #include "update.h"
 
-#include <string>
 #include <cctype>
 #include <cstring>
 

src/reader_native.cpp

@@ -17,10 +17,8 @@
 #include "error.h"
 #include "memory.h"
 #include "tokenizer.h"
-#include "utils.h"
 
 #include <cstring>
-#include <cstdlib>
 #include <utility>
 #include <vector>
 

src/reader_xyz.cpp

@@ -16,10 +16,11 @@
 ------------------------------------------------------------------------- */
 
 #include "reader_xyz.h"
-#include <cstdlib>
+
 #include "memory.h"
 #include "error.h"
-#include "force.h"
+
+#include <cstdlib>
 
 using namespace LAMMPS_NS;
 

src/region.cpp

@@ -12,16 +12,17 @@
 ------------------------------------------------------------------------- */
 
 #include "region.h"
+
+#include "domain.h"
+#include "error.h"
+#include "input.h"
+#include "lattice.h"
+#include "math_extra.h"
+#include "update.h"
+#include "variable.h"
+
 #include <cmath>
 #include <cstring>
-#include "update.h"
-#include "domain.h"
-#include "lattice.h"
-#include "input.h"
-#include "variable.h"
-#include "math_extra.h"
-#include "error.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 

src/region_block.cpp

@@ -12,11 +12,12 @@
 ------------------------------------------------------------------------- */
 
 #include "region_block.h"
-#include <cstring>
-#include "force.h"
+
 #include "domain.h"
-#include "math_extra.h"
 #include "error.h"
+#include "math_extra.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/region_cone.cpp

@@ -16,11 +16,12 @@
 ------------------------------------------------------------------------- */
 
 #include "region_cone.h"
-#include <cmath>
-#include <cstring>
+
 #include "domain.h"
 #include "error.h"
-#include "force.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/region_cylinder.cpp

@@ -12,14 +12,15 @@
 ------------------------------------------------------------------------- */
 
 #include "region_cylinder.h"
+
+#include "domain.h"
+#include "error.h"
+#include "input.h"
+#include "update.h"
+#include "variable.h"
+
 #include <cmath>
 #include <cstring>
-#include "update.h"
-#include "domain.h"
-#include "input.h"
-#include "variable.h"
-#include "error.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 

src/region_intersect.cpp

@@ -12,10 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "region_intersect.h"
-#include <cstring>
+
 #include "domain.h"
 #include "error.h"
-#include "force.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/region_plane.cpp

@@ -12,9 +12,10 @@
 ------------------------------------------------------------------------- */
 
 #include "region_plane.h"
-#include <cmath>
+
 #include "error.h"
-#include "force.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/region_prism.cpp

@@ -16,11 +16,12 @@
 ------------------------------------------------------------------------- */
 
 #include "region_prism.h"
-#include <cstring>
+
 #include "domain.h"
-#include "force.h"
-#include "math_extra.h"
 #include "error.h"
+#include "math_extra.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/region_sphere.cpp

@@ -12,13 +12,14 @@
 ------------------------------------------------------------------------- */
 
 #include "region_sphere.h"
+
+#include "error.h"
+#include "input.h"
+#include "update.h"
+#include "variable.h"
+
 #include <cmath>
 #include <cstring>
-#include "update.h"
-#include "input.h"
-#include "variable.h"
-#include "error.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 

src/region_union.cpp

@@ -12,10 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "region_union.h"
-#include <cstring>
+
 #include "domain.h"
 #include "error.h"
-#include "force.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/replicate.cpp

@@ -12,19 +12,17 @@
 ------------------------------------------------------------------------- */
 
 #include "replicate.h"
-#include <mpi.h>
-#include <cstring>
+
+#include "accelerator_kokkos.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "force.h"
-#include "domain.h"
 #include "comm.h"
-#include "special.h"
-#include "accelerator_kokkos.h"
-#include "memory.h"
+#include "domain.h"
 #include "error.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "memory.h"
+#include "special.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/rerun.cpp

@@ -12,17 +12,18 @@
 ------------------------------------------------------------------------- */
 
 #include "rerun.h"
-#include <cstring>
-#include "read_dump.h"
+
 #include "domain.h"
-#include "update.h"
+#include "error.h"
+#include "finish.h"
 #include "integrate.h"
 #include "modify.h"
 #include "output.h"
-#include "finish.h"
+#include "read_dump.h"
 #include "timer.h"
-#include "error.h"
-#include "force.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/reset_atom_ids.cpp

@@ -12,19 +12,19 @@
 ------------------------------------------------------------------------- */
 
 #include "reset_atom_ids.h"
-#include <mpi.h>
-#include <cstring>
+
 #include "atom.h"
 #include "atom_vec.h"
-#include "domain.h"
 #include "comm.h"
-#include "modify.h"
-#include "fix.h"
-#include "special.h"
-#include "memory.h"
+#include "domain.h"
 #include "error.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "fix.h"
+#include "memory.h"
+#include "modify.h"
+#include "special.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/reset_mol_ids.cpp

@@ -16,17 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "reset_mol_ids.h"
-#include <mpi.h>
+
 #include "atom.h"
-#include "domain.h"
 #include "comm.h"
+#include "compute_chunk_atom.h"
+#include "compute_fragment_atom.h"
+#include "domain.h"
+#include "error.h"
 #include "group.h"
 #include "modify.h"
-#include "compute_fragment_atom.h"
-#include "compute_chunk_atom.h"
-#include "utils.h"
-#include "error.h"
-#include "fmt/format.h"
 
 using namespace LAMMPS_NS;
 

src/respa.cpp

@@ -16,30 +16,29 @@
 ------------------------------------------------------------------------- */
 
 #include "respa.h"
-#include <cstring>
-#include <string>
-#include "neighbor.h"
+
+#include "angle.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "domain.h"
-#include "comm.h"
-#include "fix.h"
-#include "force.h"
-#include "pair.h"
 #include "bond.h"
-#include "angle.h"
+#include "comm.h"
 #include "dihedral.h"
+#include "domain.h"
+#include "error.h"
+#include "fix.h"
+#include "fix_respa.h"
+#include "force.h"
 #include "improper.h"
 #include "kspace.h"
-#include "output.h"
-#include "update.h"
 #include "modify.h"
-#include "fix_respa.h"
-#include "timer.h"
-#include "error.h"
-#include "utils.h"
+#include "neighbor.h"
+#include "output.h"
+#include "pair.h"
 #include "pair_hybrid.h"
-#include "fmt/format.h"
+#include "timer.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/run.cpp

@@ -12,17 +12,18 @@
 ------------------------------------------------------------------------- */
 
 #include "run.h"
-#include <cstring>
+
 #include "domain.h"
-#include "update.h"
-#include "force.h"
+#include "error.h"
+#include "finish.h"
+#include "input.h"
 #include "integrate.h"
 #include "modify.h"
 #include "output.h"
-#include "finish.h"
-#include "input.h"
 #include "timer.h"
-#include "error.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/set.cpp

@@ -12,32 +12,30 @@
 ------------------------------------------------------------------------- */
 
 #include "set.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
-#include <climits>
+
 #include "atom.h"
 #include "atom_vec.h"
+#include "atom_vec_body.h"
 #include "atom_vec_ellipsoid.h"
 #include "atom_vec_line.h"
 #include "atom_vec_tri.h"
-#include "atom_vec_body.h"
-#include "domain.h"
-#include "region.h"
-#include "group.h"
 #include "comm.h"
-#include "force.h"
-#include "input.h"
-#include "variable.h"
-#include "random_park.h"
-#include "random_mars.h"
-#include "math_extra.h"
-#include "math_const.h"
-#include "memory.h"
+#include "domain.h"
 #include "error.h"
+#include "force.h"
+#include "group.h"
+#include "input.h"
+#include "math_const.h"
+#include "math_extra.h"
+#include "memory.h"
 #include "modify.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "random_mars.h"
+#include "random_park.h"
+#include "region.h"
+#include "variable.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/special.cpp

@@ -12,18 +12,16 @@
 ------------------------------------------------------------------------- */
 
 #include "special.h"
-#include <mpi.h>
-#include "atom.h"
-#include "atom_vec.h"
-#include "force.h"
-#include "comm.h"
-#include "modify.h"
-#include "fix.h"
+
 #include "accelerator_kokkos.h"  // IWYU pragma: export
+#include "atom.h"
 #include "atom_masks.h"
+#include "atom_vec.h"
+#include "comm.h"
+#include "fix.h"
+#include "force.h"
 #include "memory.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "modify.h"
 
 using namespace LAMMPS_NS;
 

src/table_file_reader.cpp

@@ -17,7 +17,6 @@
 
 #include "table_file_reader.h"
 
-#include "error.h"
 #include "text_file_reader.h"
 #include "tokenizer.h"
 

src/text_file_reader.cpp

@@ -15,14 +15,11 @@
    Contributing authors: Richard Berger (Temple U)
 ------------------------------------------------------------------------- */
 
-#include "lammps.h"
-#include "force.h"
-#include "error.h"
-#include "comm.h"
-#include "utils.h"
 #include "text_file_reader.h"
-#include "tokenizer.h"
+
 #include "fmt/format.h"
+#include "tokenizer.h"
+#include "utils.h"
 
 #include <cstring>
 

src/text_file_reader.h

@@ -19,8 +19,8 @@
 #define LMP_TEXT_FILE_READER_H
 
 #include <cstdio>
-#include <string>
 #include <exception>
+
 #include "tokenizer.h"
 
 namespace LAMMPS_NS

src/thermo.cpp

@@ -16,37 +16,36 @@
 //   before lmptype.h can set flags to insure it is done correctly
 
 #include "thermo.h"
-#include <mpi.h>
+
+#include "angle.h"
+#include "atom.h"
+#include "bond.h"
+#include "comm.h"
+#include "compute.h"
+#include "dihedral.h"
+#include "domain.h"
+#include "error.h"
+#include "fix.h"
+#include "force.h"
+#include "group.h"
+#include "improper.h"
+#include "input.h"
+#include "kspace.h"
+#include "lattice.h"
+#include "math_const.h"
+#include "memory.h"
+#include "modify.h"
+#include "neighbor.h"
+#include "output.h"
+#include "pair.h"
+#include "timer.h"
+#include "tokenizer.h"
+#include "universe.h"
+#include "update.h"
+#include "variable.h"
+
 #include <cmath>
 #include <cstring>
-#include "atom.h"
-#include "update.h"
-#include "comm.h"
-#include "domain.h"
-#include "universe.h"
-#include "lattice.h"
-#include "group.h"
-#include "modify.h"
-#include "fix.h"
-#include "compute.h"
-#include "input.h"
-#include "variable.h"
-#include "neighbor.h"
-#include "force.h"
-#include "pair.h"
-#include "bond.h"
-#include "angle.h"
-#include "dihedral.h"
-#include "improper.h"
-#include "kspace.h"
-#include "output.h"
-#include "timer.h"
-#include "memory.h"
-#include "error.h"
-#include "math_const.h"
-#include "utils.h"
-#include "fmt/format.h"
-#include "tokenizer.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/write_data.cpp

@@ -12,29 +12,27 @@
 ------------------------------------------------------------------------- */
 
 #include "write_data.h"
-#include <mpi.h>
-#include <cstring>
-#include <string>
+
+#include "angle.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "force.h"
-#include "pair.h"
 #include "bond.h"
-#include "angle.h"
-#include "dihedral.h"
-#include "improper.h"
-#include "update.h"
-#include "modify.h"
-#include "fix.h"
-#include "domain.h"
-#include "universe.h"
 #include "comm.h"
-#include "output.h"
-#include "thermo.h"
-#include "memory.h"
+#include "dihedral.h"
+#include "domain.h"
 #include "error.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "fix.h"
+#include "force.h"
+#include "improper.h"
+#include "memory.h"
+#include "modify.h"
+#include "output.h"
+#include "pair.h"
+#include "thermo.h"
+#include "universe.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;