From c7c4297cfc45ececef10a927ad04c29f0e23c582 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 3 Sep 2020 00:51:58 -0400
Subject: [PATCH] update include handling for commands

---
 src/neighbor.cpp          | 49 +++++++++++++++++----------------
 src/read_data.cpp         |  1 -
 src/reader_native.cpp     |  2 --
 src/reader_xyz.cpp        |  5 ++--
 src/region.cpp            | 17 ++++++------
 src/region_block.cpp      |  7 ++---
 src/region_cone.cpp       |  7 ++---
 src/region_cylinder.cpp   | 13 ++++-----
 src/region_intersect.cpp  |  5 ++--
 src/region_plane.cpp      |  5 ++--
 src/region_prism.cpp      |  7 ++---
 src/region_sphere.cpp     | 11 ++++----
 src/region_union.cpp      |  5 ++--
 src/replicate.cpp         | 16 +++++------
 src/rerun.cpp             | 13 ++++-----
 src/reset_atom_ids.cpp    | 18 ++++++-------
 src/reset_mol_ids.cpp     | 12 ++++-----
 src/respa.cpp             | 31 +++++++++++----------
 src/run.cpp               | 13 ++++-----
 src/set.cpp               | 34 +++++++++++------------
 src/special.cpp           | 16 +++++------
 src/table_file_reader.cpp |  1 -
 src/text_file_reader.cpp  |  9 +++----
 src/text_file_reader.h    |  2 +-
 src/thermo.cpp            | 57 +++++++++++++++++++--------------------
 src/write_data.cpp        | 34 +++++++++++------------
 26 files changed, 191 insertions(+), 199 deletions(-)

diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index c9b16f67a0..66ab92496a 100644
--- a/src/neighbor.cpp
+++ b/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;
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 7cdb768dd2..2a6801b3a5 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -40,7 +40,6 @@
 #include "special.h"
 #include "update.h"
 
-#include <string>
 #include <cctype>
 #include <cstring>
 
diff --git a/src/reader_native.cpp b/src/reader_native.cpp
index 8ebab4b349..8931c569ff 100644
--- a/src/reader_native.cpp
+++ b/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>
 
diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp
index ad8cb0cc6e..5350e01117 100644
--- a/src/reader_xyz.cpp
+++ b/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;
 
diff --git a/src/region.cpp b/src/region.cpp
index 8a6ec3305a..15b6fee272 100644
--- a/src/region.cpp
+++ b/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;
 
diff --git a/src/region_block.cpp b/src/region_block.cpp
index e06c05d1a7..2204f2e6a4 100644
--- a/src/region_block.cpp
+++ b/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;
 
diff --git a/src/region_cone.cpp b/src/region_cone.cpp
index 400fb07229..d669008e93 100644
--- a/src/region_cone.cpp
+++ b/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;
 
diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp
index dc1584a96b..f7676a3d74 100644
--- a/src/region_cylinder.cpp
+++ b/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;
 
diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp
index 4096657d30..a61e2556b0 100644
--- a/src/region_intersect.cpp
+++ b/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;
 
diff --git a/src/region_plane.cpp b/src/region_plane.cpp
index bf12f3cd91..4895c1f081 100644
--- a/src/region_plane.cpp
+++ b/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;
 
diff --git a/src/region_prism.cpp b/src/region_prism.cpp
index 5d7c5bce1f..af270cc47f 100644
--- a/src/region_prism.cpp
+++ b/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;
 
diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp
index 44db951fde..4256af4213 100644
--- a/src/region_sphere.cpp
+++ b/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;
 
diff --git a/src/region_union.cpp b/src/region_union.cpp
index 30f563df2c..677f1022f9 100644
--- a/src/region_union.cpp
+++ b/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;
 
diff --git a/src/replicate.cpp b/src/replicate.cpp
index 9c915d08c0..374d7113b2 100644
--- a/src/replicate.cpp
+++ b/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;
 
diff --git a/src/rerun.cpp b/src/rerun.cpp
index a63fd1ea55..51c0f6fdb2 100644
--- a/src/rerun.cpp
+++ b/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;
 
diff --git a/src/reset_atom_ids.cpp b/src/reset_atom_ids.cpp
index 526de60cba..0b7cf9879f 100644
--- a/src/reset_atom_ids.cpp
+++ b/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;
 
diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp
index a6cfb69185..0d9fe55e07 100644
--- a/src/reset_mol_ids.cpp
+++ b/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;
 
diff --git a/src/respa.cpp b/src/respa.cpp
index 1dcc4b898a..c970c63a19 100644
--- a/src/respa.cpp
+++ b/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;
 
diff --git a/src/run.cpp b/src/run.cpp
index 91e2db5c6b..166955d6ac 100644
--- a/src/run.cpp
+++ b/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;
 
diff --git a/src/set.cpp b/src/set.cpp
index b4a82e5c72..3b2cd44ad0 100644
--- a/src/set.cpp
+++ b/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;
diff --git a/src/special.cpp b/src/special.cpp
index 3780fab5c0..eb74f534f7 100644
--- a/src/special.cpp
+++ b/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;
 
diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp
index 917aea7d49..50843c119e 100644
--- a/src/table_file_reader.cpp
+++ b/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"
 
diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp
index 1e1e5e2ec1..3c63bba5fb 100644
--- a/src/text_file_reader.cpp
+++ b/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>
 
diff --git a/src/text_file_reader.h b/src/text_file_reader.h
index b64407701f..e74a285961 100644
--- a/src/text_file_reader.h
+++ b/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
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 96de72b4ab..787b0cdda8 100644
--- a/src/thermo.cpp
+++ b/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;
diff --git a/src/write_data.cpp b/src/write_data.cpp
index d549d8bf77..53d277b723 100644
--- a/src/write_data.cpp
+++ b/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;