diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp
index 3d7687df90..1355a2f13a 100644
--- a/src/KSPACE/pair_buck_coul_msm.cpp
+++ b/src/KSPACE/pair_buck_coul_msm.cpp
@@ -13,21 +13,15 @@
 
 #include "pair_buck_coul_msm.h"
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp
index 804ae5919d..a93a1275f4 100644
--- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp
@@ -21,7 +21,6 @@
 #include "atom.h"
 #include "force.h"
 #include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp
index 7921c814c3..fb79451b37 100644
--- a/src/KSPACE/pair_lj_cut_coul_long.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_long.cpp
@@ -16,6 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_long.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include "atom.h"
diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp
index f8021cc180..4ebbcb9a3f 100644
--- a/src/KSPACE/pair_lj_cut_coul_msm.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp
@@ -21,7 +21,6 @@
 #include "atom.h"
 #include "force.h"
 #include "kspace.h"
-#include "update.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp
index cde5b6258b..2b663554cc 100644
--- a/src/MPIIO/dump_atom_mpiio.cpp
+++ b/src/MPIIO/dump_atom_mpiio.cpp
@@ -16,11 +16,11 @@
 ------------------------------------------------------------------------- */
 
 #include "dump_atom_mpiio.h"
+#include <cmath>
+#include <cstdlib>
 #include <cstring>
 #include "domain.h"
-#include "atom.h"
 #include "update.h"
-#include "group.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h
index ad49fa1182..36b43e3f08 100644
--- a/src/MPIIO/dump_atom_mpiio.h
+++ b/src/MPIIO/dump_atom_mpiio.h
@@ -21,7 +21,6 @@ DumpStyle(atom/mpiio,DumpAtomMPIIO)
 #define LMP_DUMP_ATOM_MPIIO_H
 
 #include "dump_atom.h"
-#include <cstdlib>
 
 namespace LAMMPS_NS {
 
diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp
index 90f92d094d..31848b550c 100644
--- a/src/MPIIO/dump_cfg_mpiio.cpp
+++ b/src/MPIIO/dump_cfg_mpiio.cpp
@@ -21,12 +21,6 @@
 #include <cstring>
 #include "atom.h"
 #include "domain.h"
-#include "comm.h"
-#include "modify.h"
-#include "compute.h"
-#include "input.h"
-#include "fix.h"
-#include "variable.h"
 #include "update.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp
index 5838c61124..dca5833c5b 100644
--- a/src/MPIIO/dump_custom_mpiio.cpp
+++ b/src/MPIIO/dump_custom_mpiio.cpp
@@ -19,16 +19,11 @@
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "atom.h"
-#include "force.h"
 #include "domain.h"
-#include "region.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "update.h"
 #include "modify.h"
-#include "compute.h"
 #include "fix.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp
index 7b647561bf..ee0532399a 100644
--- a/src/MPIIO/dump_xyz_mpiio.cpp
+++ b/src/MPIIO/dump_xyz_mpiio.cpp
@@ -19,17 +19,10 @@
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "atom.h"
-#include "force.h"
 #include "domain.h"
-#include "region.h"
-#include "group.h"
-#include "input.h"
-#include "variable.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
-#include "fix.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index e0952086dd..936e5ff58e 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -18,7 +18,6 @@
 #include <cstring>
 #include <cstdlib>
 #include <cmath>
-#include "math_extra.h"
 #include "atom.h"
 #include "force.h"
 #include "group.h"
diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp
index 2cd7883600..97005ef5f9 100644
--- a/src/USER-CGDNA/bond_oxdna2_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp
@@ -15,8 +15,6 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_oxdna2_fene.h"
-#include <cmath>
-#include <cstdlib>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp
index 8b94fd6a5a..8314576d63 100644
--- a/src/USER-CGDNA/bond_oxdna_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna_fene.cpp
@@ -16,10 +16,8 @@
 
 #include "bond_oxdna_fene.h"
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp
index 3bf6757df7..ff8e1c0ee2 100644
--- a/src/USER-CGDNA/fix_nve_dot.cpp
+++ b/src/USER-CGDNA/fix_nve_dot.cpp
@@ -15,15 +15,10 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_nve_dot.h"
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "force.h"
 #include "update.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
index 61e3552f11..59def4c812 100644
--- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
+++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
@@ -17,7 +17,6 @@
 
 #include "fix_nve_dotc_langevin.h"
 #include <cmath>
-#include <cstdio>
 #include <cstring>
 #include "math_extra.h"
 #include "atom.h"
@@ -26,7 +25,6 @@
 #include "update.h"
 #include "comm.h"
 #include "random_mars.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index 1d0a2eb494..b96da3fa4a 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -15,9 +15,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna2_coaxstk.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
@@ -25,9 +24,6 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index 22fc79dae4..ea1f4f84f4 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -15,28 +15,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna2_dh.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
-#include "mf_oxdna.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
-using namespace MFOxdna;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp
index de4f8319b9..0a7da8e81a 100644
--- a/src/USER-CGDNA/pair_oxdna2_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp
@@ -15,10 +15,6 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna2_excv.h"
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-CGDNA/pair_oxdna2_stk.cpp b/src/USER-CGDNA/pair_oxdna2_stk.cpp
index 3b9480bff6..26bae766e1 100644
--- a/src/USER-CGDNA/pair_oxdna2_stk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_stk.cpp
@@ -15,10 +15,6 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna2_stk.h"
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
index 7310f60ec3..6e37352ef0 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
@@ -15,9 +15,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna_coaxstk.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
@@ -25,9 +24,6 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp
index 68091f4190..9fb3dd041a 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna_excv.cpp
@@ -15,9 +15,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna_excv.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
@@ -25,17 +24,12 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MFOxdna;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp
index 2de05e66ae..12e4b08c46 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp
@@ -15,9 +15,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna_hbond.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
@@ -25,17 +24,12 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MFOxdna;
 
 // sequence-specific base-pairing strength
diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp
index aaa25039ef..022d94f935 100644
--- a/src/USER-CGDNA/pair_oxdna_stk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_stk.cpp
@@ -15,27 +15,21 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna_stk.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
+#include <utility>
 #include "mf_oxdna.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MFOxdna;
 
 // sequence-specific stacking strength
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp
index 806f8a42c6..384a7768bd 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp
@@ -15,9 +15,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_oxdna_xstk.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
@@ -25,9 +24,6 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp
index 12e6989c00..22741a055d 100644
--- a/src/USER-DPD/pair_dpd_fdt_energy.cpp
+++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp
@@ -15,23 +15,20 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
+#include "pair_dpd_fdt_energy.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
 #include "fix.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "modify.h"
-#include "pair_dpd_fdt_energy.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp
index 13521b52b1..5cf2859ae3 100644
--- a/src/USER-DPD/pair_exp6_rx.cpp
+++ b/src/USER-DPD/pair_exp6_rx.cpp
@@ -11,17 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "pair_exp6_rx.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <cfloat>
-#include "pair_exp6_rx.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neigh_list.h"
-#include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
@@ -29,7 +28,6 @@
 #include "fix.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MathSpecial;
 
 #define MAXLINE 1024
diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp
index aa0dc93809..0db5437c4a 100644
--- a/src/USER-MESO/atom_vec_tdpd.cpp
+++ b/src/USER-MESO/atom_vec_tdpd.cpp
@@ -23,7 +23,6 @@
 #include "update.h"
 #include "memory.h"
 #include "error.h"
-#include "input.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp
index 119e0079d1..9eb6e9752b 100644
--- a/src/USER-MESO/compute_edpd_temp_atom.cpp
+++ b/src/USER-MESO/compute_edpd_temp_atom.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_edpd_temp_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp
index 24bef2b1f7..e62d9a8a79 100644
--- a/src/USER-MESO/fix_edpd_source.cpp
+++ b/src/USER-MESO/fix_edpd_source.cpp
@@ -11,17 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_edpd_source.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
-#include "update.h"
-#include "modify.h"
-#include "domain.h"
-#include "lattice.h"
-#include "input.h"
-#include "variable.h"
 #include "error.h"
 #include "force.h"
 
diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp
index 8719d0d262..bd9cd9cc2a 100644
--- a/src/USER-MESO/fix_mvv_edpd.cpp
+++ b/src/USER-MESO/fix_mvv_edpd.cpp
@@ -29,13 +29,11 @@
    Communications, 2015, 51: 11038-11040.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_mvv_edpd.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp
index 24b1bbcf48..b7fe37d7ee 100644
--- a/src/USER-MESO/fix_mvv_tdpd.cpp
+++ b/src/USER-MESO/fix_mvv_tdpd.cpp
@@ -25,13 +25,11 @@
    -reaction problems". The Journal of Chemical Physics, 2015, 143: 014101.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_mvv_tdpd.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp
index 27252fae89..d5976f85d3 100644
--- a/src/VORONOI/compute_voronoi_atom.cpp
+++ b/src/VORONOI/compute_voronoi_atom.cpp
@@ -19,7 +19,7 @@
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include "voro++.hh"
+#include <voro++.hh>
 #include "atom.h"
 #include "group.h"
 #include "update.h"