diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp
index 8e85f1dffd..4128c508d6 100644
--- a/src/USER-DRUDE/fix_drude_transform.cpp
+++ b/src/USER-DRUDE/fix_drude_transform.cpp
@@ -13,6 +13,7 @@
 
 /** Fix Drude Transform ******************************************************/
 #include "fix_drude_transform.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include "fix_drude.h"
diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp
index 1a16c3df96..d413c31bd7 100644
--- a/src/USER-DRUDE/fix_langevin_drude.cpp
+++ b/src/USER-DRUDE/fix_langevin_drude.cpp
@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_langevin_drude.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
 #include "fix_drude.h"
diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp
index 8e07e390fa..e9295ea680 100644
--- a/src/USER-EFF/compute_temp_eff.cpp
+++ b/src/USER-EFF/compute_temp_eff.cpp
@@ -17,6 +17,7 @@
 
 #include "compute_temp_eff.h"
 #include <mpi.h>
+#include <cstdlib>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp
index 31c54aee76..8ad3dbe33e 100644
--- a/src/USER-LB/fix_lb_fluid.cpp
+++ b/src/USER-LB/fix_lb_fluid.cpp
@@ -20,15 +20,14 @@
 #include <cmath>
 #include <mpi.h>
 #include <cstdlib>
-#include <cstdio>
 #include <cstring>
+#include <algorithm>
+#include <utility>
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
 #include "domain.h"
 #include "atom.h"
-#include <iostream>
-#include <iomanip>
 #include "group.h"
 #include "random_mars.h"
 #include "update.h"
diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp
index df17561380..10fffed018 100644
--- a/src/USER-LB/fix_lb_momentum.cpp
+++ b/src/USER-LB/fix_lb_momentum.cpp
@@ -18,16 +18,15 @@
    Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
 ------------------------------------------------------------------------- */
 
+#include "fix_lb_momentum.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
-#include "fix_lb_momentum.h"
 #include "atom.h"
-#include "domain.h"
 #include "group.h"
 #include "error.h"
 #include "fix_lb_fluid.h"
 #include "modify.h"
-#include "comm.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp
index ce6ca0c9a1..d61692419a 100644
--- a/src/USER-LB/fix_lb_pc.cpp
+++ b/src/USER-LB/fix_lb_pc.cpp
@@ -15,17 +15,14 @@
    Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_lb_pc.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "memory.h"
-#include "comm.h"
 #include "domain.h"
 #include "fix_lb_fluid.h"
 #include "modify.h"
diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
index 83dc751631..af1b01043d 100644
--- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
+++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
@@ -16,21 +16,18 @@
    Based on fix_rigid (version from 2008).
 ------------------------------------------------------------------------- */
 
+#include "fix_lb_rigid_pc_sphere.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "fix_lb_rigid_pc_sphere.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "domain.h"
 #include "update.h"
-#include "respa.h"
 #include "modify.h"
 #include "group.h"
 #include "comm.h"
 #include "force.h"
-#include "output.h"
 #include "memory.h"
 #include "error.h"
 #include "fix_lb_fluid.h"
diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp
index afe23477be..59fddebd67 100644
--- a/src/USER-LB/fix_lb_viscous.cpp
+++ b/src/USER-LB/fix_lb_viscous.cpp
@@ -15,10 +15,8 @@
    Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_lb_viscous.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h
index 3e861a0198..ff71edc9f3 100644
--- a/src/USER-MGPT/pair_mgpt.h
+++ b/src/USER-MGPT/pair_mgpt.h
@@ -30,8 +30,6 @@ PairStyle(mgpt,PairMGPT)
 #ifndef LMP_PAIR_MGPT_H
 #define LMP_PAIR_MGPT_H
 
-#include <new>
-#include <cmath>
 #include <cstdlib>
 #include <cassert>
 
diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp
index 732fea74bd..d9d8ec3c97 100644
--- a/src/USER-MOLFILE/dump_molfile.cpp
+++ b/src/USER-MOLFILE/dump_molfile.cpp
@@ -15,15 +15,14 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
+#include "dump_molfile.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "dump_molfile.h"
 #include "domain.h"
 #include "atom.h"
 #include "comm.h"
 #include "update.h"
-#include "output.h"
 #include "group.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp
index ca1a61850c..5cff56753b 100644
--- a/src/USER-MOLFILE/reader_molfile.cpp
+++ b/src/USER-MOLFILE/reader_molfile.cpp
@@ -15,11 +15,9 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
+#include "reader_molfile.h"
 #include <cstdlib>
 #include <cmath>
-#include "reader_molfile.h"
-#include "atom.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp
index 55e2b73812..f7945b5579 100644
--- a/src/USER-OMP/fix_qeq_reax_omp.cpp
+++ b/src/USER-OMP/fix_qeq_reax_omp.cpp
@@ -42,6 +42,7 @@
 #include "memory.h"
 #include "error.h"
 #include "reaxc_defs.h"
+#include "reaxc_types.h"
 
 #if defined(_OPENMP)
 #include <omp.h>
diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h
index ad8c368aaf..0cae28f56b 100644
--- a/src/USER-OMP/pair_reaxc_omp.h
+++ b/src/USER-OMP/pair_reaxc_omp.h
@@ -22,7 +22,6 @@ PairStyle(reax/c/omp,PairReaxCOMP)
 
 #include "pair_reaxc.h"
 #include "thr_omp.h"
-#include "suffix.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp
index 17715c6e26..d581819e00 100644
--- a/src/USER-OMP/reaxc_bond_orders_omp.cpp
+++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp
@@ -27,6 +27,9 @@
   ----------------------------------------------------------------------*/
 
 #include "reaxc_bond_orders_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
 #include "reaxc_defs.h"
 #include "pair_reaxc_omp.h"
 #include "reaxc_types.h"
diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp
index 12ba1dcbfe..b6a76b3f3a 100644
--- a/src/USER-OMP/reaxc_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_bonds_omp.cpp
@@ -27,13 +27,12 @@
   ----------------------------------------------------------------------*/
 
 #include "reaxc_bonds_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
 #include "reaxc_defs.h"
-#include "reaxc_bond_orders_omp.h"
 #include "pair_reaxc_omp.h"
-
 #include "reaxc_list.h"
-#include "reaxc_tool_box.h"
-#include "reaxc_vector.h"
 
 #if defined(_OPENMP)
 #include  <omp.h>
diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp
index 1ada5e7e71..971667cc2d 100644
--- a/src/USER-OMP/reaxc_forces_omp.cpp
+++ b/src/USER-OMP/reaxc_forces_omp.cpp
@@ -27,19 +27,18 @@
   ----------------------------------------------------------------------*/
 
 #include "reaxc_forces_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
 #include "reaxc_defs.h"
 #include "pair_reaxc_omp.h"
-#include "thr_data.h"
 
 #include "reaxc_bond_orders_omp.h"
 #include "reaxc_bonds_omp.h"
 #include "reaxc_hydrogen_bonds_omp.h"
-#include "reaxc_io_tools.h"
 #include "reaxc_list.h"
-#include "reaxc_lookup.h"
 #include "reaxc_multi_body_omp.h"
 #include "reaxc_nonbonded_omp.h"
-#include "reaxc_tool_box.h"
 #include "reaxc_torsion_angles_omp.h"
 #include "reaxc_valence_angles_omp.h"
 #include "reaxc_vector.h"
diff --git a/src/USER-OMP/reaxc_forces_omp.h b/src/USER-OMP/reaxc_forces_omp.h
index d1e2a5c65a..6df0288656 100644
--- a/src/USER-OMP/reaxc_forces_omp.h
+++ b/src/USER-OMP/reaxc_forces_omp.h
@@ -30,7 +30,6 @@
 #define __FORCES_OMP_H_
 
 #include "reaxc_types.h"
-#include "reaxc_defs.h"
 
 void Init_Force_FunctionsOMP( control_params* );
 void Compute_ForcesOMP( reax_system*, control_params*, simulation_data*,
diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
index e3c034a12e..d06966a92d 100644
--- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
@@ -27,9 +27,11 @@
   ----------------------------------------------------------------------*/
 
 #include "reaxc_hydrogen_bonds_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
 #include "pair_reaxc_omp.h"
 #include "reaxc_defs.h"
-#include "reaxc_bond_orders_omp.h"
 #include "reaxc_list.h"
 #include "reaxc_valence_angles.h"     // To access Calculate_Theta()
 #include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP()
diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp
index 847e916666..9d40479ddf 100644
--- a/src/USER-OMP/reaxc_init_md_omp.cpp
+++ b/src/USER-OMP/reaxc_init_md_omp.cpp
@@ -27,18 +27,15 @@
   ----------------------------------------------------------------------*/
 
 #include "reaxc_init_md_omp.h"
-#include "pair_reaxc_omp.h"
+#include <cstdlib>
 #include "reaxc_defs.h"
-#include "reaxc_allocate.h"
 #include "reaxc_forces.h"
 #include "reaxc_forces_omp.h"
 #include "reaxc_io_tools.h"
 #include "reaxc_list.h"
 #include "reaxc_lookup.h"
-#include "reaxc_reset_tools.h"
-#include "reaxc_system_props.h"
 #include "reaxc_tool_box.h"
-#include "reaxc_vector.h"
+#include "error.h"
 
 // Functions defined in reaxc_init_md.cpp
 extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*);
diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp
index 9cd716b594..68bacb7202 100644
--- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp
+++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp
@@ -27,14 +27,13 @@
   ----------------------------------------------------------------------*/
 
 #include "reaxc_torsion_angles_omp.h"
+#include <mpi.h>
+#include "fix_omp.h"
 #include "pair_reaxc_omp.h"
-#include "thr_data.h"
 
 #include "reaxc_defs.h"
 #include "reaxc_types.h"
-#include "reaxc_bond_orders_omp.h"
 #include "reaxc_list.h"
-#include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
 
 #if defined(_OPENMP)
diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp
index b50e5c4333..cedd35126d 100644
--- a/src/USER-PTM/ptm_index.cpp
+++ b/src/USER-PTM/ptm_index.cpp
@@ -22,6 +22,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #include <cmath>
 #include <cstdio>
 #include <cstring>
+#include <stdint.h>
 
 static double calculate_interatomic_distance(int type, double scale) {
         assert(type >= 1 && type <= 8);
diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp
index 1f0a5c94af..ff8245fe44 100644
--- a/src/USER-PTM/ptm_initialize_data.cpp
+++ b/src/USER-PTM/ptm_initialize_data.cpp
@@ -8,6 +8,10 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 */
 
 #include "ptm_initialize_data.h"
+#include "ptm_canonical_coloured.h"
+#include "ptm_convex_hull_incremental.h"
+#include "ptm_graph_tools.h"
+#include "ptm_neighbour_ordering.h"
 #include <cassert>
 
 
diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h
index 20c9921962..4e7f3e8f0a 100644
--- a/src/USER-PTM/ptm_initialize_data.h
+++ b/src/USER-PTM/ptm_initialize_data.h
@@ -12,12 +12,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 
 #include "ptm_graph_data.h"
-#include "ptm_graph_tools.h"
 #include "ptm_deformation_gradient.h"
 #include "ptm_fundamental_mappings.h"
-#include "ptm_neighbour_ordering.h"
-#include "ptm_canonical_coloured.h"
-#include "ptm_convex_hull_incremental.h"
 #include "ptm_alt_templates.h"