From 956d21ec0ead2d94220c22dd5ba97c0bbe45189f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 10 Jul 2019 15:38:41 -0400
Subject: [PATCH] update include lists in packages USER-MISC, USER-MOFF,
 USER-PTM, and USER-SMD

---
 src/USER-MISC/fix_imd.cpp                       |  2 --
 src/USER-MISC/improper_cossq.cpp                |  4 +---
 src/USER-MISC/improper_distance.cpp             |  4 +---
 src/USER-MISC/improper_fourier.cpp              |  5 +----
 src/USER-MISC/improper_ring.cpp                 |  5 +----
 src/USER-MISC/pair_agni.cpp                     |  6 ++----
 src/USER-MISC/pair_buck_mdf.cpp                 |  9 +++------
 src/USER-MISC/pair_coul_diel.cpp                |  6 ++----
 src/USER-MISC/pair_coul_shield.cpp              |  5 +----
 src/USER-MISC/pair_drip.cpp                     |  6 ++----
 src/USER-MISC/pair_drip.h                       |  2 --
 src/USER-MISC/pair_e3b.cpp                      | 10 ++++------
 src/USER-MISC/pair_edip.cpp                     |  4 ++--
 src/USER-MISC/pair_edip_multi.cpp               |  5 ++---
 src/USER-MISC/pair_extep.cpp                    |  4 ++--
 src/USER-MISC/pair_extep.h                      |  1 -
 src/USER-MISC/pair_gauss_cut.cpp                |  9 ++-------
 src/USER-MISC/pair_ilp_graphene_hbn.cpp         |  3 +--
 src/USER-MISC/pair_ilp_graphene_hbn.h           |  2 --
 src/USER-MISC/pair_kolmogorov_crespi_full.cpp   |  3 +--
 src/USER-MISC/pair_kolmogorov_crespi_full.h     |  2 --
 src/USER-MISC/pair_kolmogorov_crespi_z.cpp      |  4 ++--
 src/USER-MISC/pair_lebedeva_z.cpp               |  4 ++--
 src/USER-MISC/pair_lennard_mdf.cpp              |  8 +++-----
 src/USER-MISC/pair_list.cpp                     | 16 ++++++----------
 src/USER-MISC/pair_lj_expand_coul_long.cpp      |  8 +++-----
 src/USER-MISC/pair_lj_mdf.cpp                   |  8 +++-----
 src/USER-MISC/pair_lj_sf_dipole_sf.cpp          |  6 +++---
 src/USER-MISC/pair_meam_spline.cpp              |  4 +---
 src/USER-MISC/pair_meam_sw_spline.cpp           |  4 +---
 src/USER-MISC/pair_momb.cpp                     |  5 ++---
 src/USER-MISC/pair_morse_smooth_linear.cpp      |  7 +++----
 src/USER-MISC/pair_srp.cpp                      |  4 +++-
 src/USER-MISC/pair_tersoff_table.cpp            |  4 ++--
 src/USER-MISC/temper_grem.cpp                   |  9 ++-------
 src/USER-MISC/temper_npt.cpp                    |  8 ++------
 src/USER-MOFFF/angle_class2_p6.cpp              |  4 ++--
 src/USER-MOFFF/angle_cosine_buck6d.cpp          |  6 ++----
 src/USER-MOFFF/improper_inversion_harmonic.cpp  |  6 +-----
 src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp   |  6 ++----
 src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp  |  9 +++------
 src/USER-PTM/compute_ptm_atom.cpp               |  4 +---
 src/USER-PTM/ptm_convex_hull_incremental.cpp    |  1 -
 src/USER-PTM/ptm_index.cpp                      |  4 ----
 src/USER-PTM/ptm_initialize_data.cpp            |  8 +-------
 src/USER-PTM/ptm_neighbour_ordering.cpp         |  5 ++---
 src/USER-PTM/ptm_polar.h                        |  1 -
 src/USER-PTM/ptm_quat.cpp                       |  2 +-
 src/USER-PTM/ptm_voronoi_cell.cpp               |  2 +-
 src/USER-PTM/ptm_voronoi_cell.h                 |  3 ---
 src/USER-SMD/atom_vec_smd.cpp                   |  5 +----
 src/USER-SMD/compute_smd_contact_radius.cpp     |  3 +--
 src/USER-SMD/compute_smd_damage.cpp             |  3 +--
 src/USER-SMD/compute_smd_internal_energy.cpp    |  1 -
 src/USER-SMD/compute_smd_plastic_strain.cpp     |  3 +--
 .../compute_smd_plastic_strain_rate.cpp         |  3 +--
 src/USER-SMD/compute_smd_rho.cpp                |  3 +--
 src/USER-SMD/compute_smd_tlsph_defgrad.cpp      | 10 +++-------
 src/USER-SMD/compute_smd_tlsph_shape.cpp        |  8 ++------
 src/USER-SMD/compute_smd_tlsph_strain.cpp       |  7 ++-----
 src/USER-SMD/compute_smd_tlsph_stress.cpp       |  3 ++-
 src/USER-SMD/compute_smd_triangle_vertices.cpp  |  9 +--------
 src/USER-SMD/compute_smd_ulsph_strain.cpp       |  9 +--------
 src/USER-SMD/compute_smd_ulsph_stress.cpp       |  3 ++-
 src/USER-SMD/compute_smd_vol.cpp                |  4 ++--
 src/USER-SMD/fix_smd_adjust_dt.cpp              | 11 ++---------
 src/USER-SMD/fix_smd_integrate_tlsph.cpp        | 12 +++---------
 src/USER-SMD/fix_smd_integrate_ulsph.cpp        | 11 +----------
 .../fix_smd_move_triangulated_surface.cpp       | 16 +++-------------
 src/USER-SMD/fix_smd_setvel.cpp                 |  4 ++--
 .../fix_smd_tlsph_reference_configuration.cpp   |  8 ++------
 .../fix_smd_tlsph_reference_configuration.h     |  1 -
 src/USER-SMD/fix_smd_wall_surface.cpp           | 14 ++++----------
 src/USER-SMD/pair_smd_hertz.cpp                 |  7 ++-----
 src/USER-SMD/pair_smd_tlsph.cpp                 | 17 ++++++-----------
 src/USER-SMD/pair_smd_triangulated_surface.cpp  |  9 ++-------
 src/USER-SMD/pair_smd_ulsph.cpp                 | 10 ++--------
 src/USER-SMD/smd_material_models.cpp            |  4 ++++
 78 files changed, 136 insertions(+), 319 deletions(-)

diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp
index 1c3eafdc46..10aaa285a5 100644
--- a/src/USER-MISC/fix_imd.cpp
+++ b/src/USER-MISC/fix_imd.cpp
@@ -58,8 +58,6 @@ negotiate an appropriate license for such distribution."
 #include "group.h"
 #include "memory.h"
 
-#include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 
diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp
index c8eb0808fb..2ea804b95d 100644
--- a/src/USER-MISC/improper_cossq.cpp
+++ b/src/USER-MISC/improper_cossq.cpp
@@ -16,14 +16,12 @@
      gvog@chemeng.ntua.gr
 ------------------------------------------------------------------------- */
 
+#include "improper_cossq.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_cossq.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp
index 50babcc84e..2efab8b5f8 100644
--- a/src/USER-MISC/improper_distance.cpp
+++ b/src/USER-MISC/improper_distance.cpp
@@ -15,16 +15,14 @@
    Contributing author: Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
+#include "improper_distance.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_distance.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp
index 288d888d12..a0ef3a2058 100644
--- a/src/USER-MISC/improper_fourier.cpp
+++ b/src/USER-MISC/improper_fourier.cpp
@@ -16,15 +16,12 @@
    [ based on improper_umbrella.cpp Tod A Pascal (Caltech) ]
 ------------------------------------------------------------------------- */
 
+#include "improper_fourier.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include <cstring>
-#include "improper_fourier.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp
index 36ba73af0f..48db5a41e9 100644
--- a/src/USER-MISC/improper_ring.cpp
+++ b/src/USER-MISC/improper_ring.cpp
@@ -36,16 +36,13 @@
                   of j.
 ------------------------------------------------------------------------- */
 
+#include "improper_ring.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_ring.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 21a6f1deee..b3abc647ef 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -15,18 +15,16 @@
    Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu
 ------------------------------------------------------------------------- */
 
+#include "pair_agni.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_agni.h"
 #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"
diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp
index afd15d7fdb..e977197522 100644
--- a/src/USER-MISC/pair_buck_mdf.cpp
+++ b/src/USER-MISC/pair_buck_mdf.cpp
@@ -15,21 +15,18 @@
    Contributing author: Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck_mdf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.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/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp
index a86921d296..a375901ecd 100644
--- a/src/USER-MISC/pair_coul_diel.cpp
+++ b/src/USER-MISC/pair_coul_diel.cpp
@@ -14,11 +14,9 @@
    Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_diel.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp
index f74dcfe7d8..9264e51287 100644
--- a/src/USER-MISC/pair_coul_shield.cpp
+++ b/src/USER-MISC/pair_coul_shield.cpp
@@ -18,11 +18,8 @@
    [Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_shield.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp
index 118c033b5c..20ec3abcf9 100644
--- a/src/USER-MISC/pair_drip.cpp
+++ b/src/USER-MISC/pair_drip.cpp
@@ -20,19 +20,17 @@
    Phys. Rev. B, 98, 235404 (2018).
 ------------------------------------------------------------------------- */
 
+#include "pair_drip.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include <mpi.h>
-#include "pair_drip.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "my_page.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-MISC/pair_drip.h b/src/USER-MISC/pair_drip.h
index 0a8f90dfc2..3ea6c735a6 100644
--- a/src/USER-MISC/pair_drip.h
+++ b/src/USER-MISC/pair_drip.h
@@ -31,8 +31,6 @@ PairStyle(drip, PairDRIP)
 #define LMP_PAIR_DRIP_H
 
 #include "pair.h"
-#include "my_page.h"
-#include <cmath>
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp
index 43b472594a..aa19849baa 100644
--- a/src/USER-MISC/pair_e3b.cpp
+++ b/src/USER-MISC/pair_e3b.cpp
@@ -14,16 +14,14 @@
    contact: stevene.strong at gmail dot com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-
 #include "pair_e3b.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <algorithm>
 
 #include "atom.h"
 #include "neighbor.h"
-#include "neigh_request.h"
 #include "neigh_list.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index 0b5220fdfd..8dee4a606b 100644
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -21,12 +21,12 @@
        Phys. Rev. B 58, 2539 (1998)
 ------------------------------------------------------------------------- */
 
+#include "pair_edip.h"
+#include <mpi.h>
 #include <cmath>
 #include <cfloat>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_edip.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp
index ab48fbaa73..9f953610de 100644
--- a/src/USER-MISC/pair_edip_multi.cpp
+++ b/src/USER-MISC/pair_edip_multi.cpp
@@ -17,12 +17,11 @@
    Contributing author: Chao Jiang
 ------------------------------------------------------------------------- */
 
+#include "pair_edip_multi.h"
+#include <mpi.h>
 #include <cmath>
-#include <cfloat>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_edip_multi.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp
index bd5da71f4a..8507fd49f6 100644
--- a/src/USER-MISC/pair_extep.cpp
+++ b/src/USER-MISC/pair_extep.cpp
@@ -15,12 +15,12 @@
    Contributing author: Jan Los
 ------------------------------------------------------------------------- */
 
+#include "pair_extep.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <cctype>
-#include "pair_extep.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h
index 535e7261e3..1f127b71e0 100644
--- a/src/USER-MISC/pair_extep.h
+++ b/src/USER-MISC/pair_extep.h
@@ -21,7 +21,6 @@ PairStyle(extep,PairExTeP)
 #define LMP_PAIR_EXTEP_H
 
 #include "pair.h"
-#include "my_page.h"
 
 #define MAXTYPES 8
 #define NSPLINE 5
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index 24d0b191d8..e6cfc02f63 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -15,18 +15,13 @@
    Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_gauss_cut.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "update.h"
-#include "integrate.h"
 #include "memory.h"
 #include "error.h"
 #include "math_const.h"
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index a41c660b7b..b94db6a871 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -20,12 +20,11 @@
    [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
 ------------------------------------------------------------------------- */
 
+#include "pair_ilp_graphene_hbn.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_ilp_graphene_hbn.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h
index 07c3b2e97b..ae4662cdc5 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.h
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.h
@@ -21,8 +21,6 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN)
 #define LMP_PAIR_ILP_GRAPHENE_HBN_H
 
 #include "pair.h"
-#include "my_page.h"
-#include <cmath>
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index e73278968d..0009531ca8 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -20,12 +20,11 @@
    [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
 ------------------------------------------------------------------------- */
 
+#include "pair_kolmogorov_crespi_full.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <mpi.h>
-#include "pair_kolmogorov_crespi_full.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h
index 9923b409a7..68dede0dd5 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.h
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h
@@ -21,8 +21,6 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull)
 #define LMP_PAIR_KolmogorovCrespi_FULL_H
 
 #include "pair.h"
-#include "my_page.h"
-#include <cmath>
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
index 79d6aa3daf..61c326ac87 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
@@ -21,11 +21,11 @@
    The simplification is that all normals are taken along the z-direction
 ------------------------------------------------------------------------- */
 
+#include "pair_kolmogorov_crespi_z.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_kolmogorov_crespi_z.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp
index c9d90e2850..8930042cef 100644
--- a/src/USER-MISC/pair_lebedeva_z.cpp
+++ b/src/USER-MISC/pair_lebedeva_z.cpp
@@ -22,11 +22,11 @@
    [Lebedeva et al., Physica E, 44(6), 949-954, 2012.]
 ------------------------------------------------------------------------- */
 
+#include "pair_lebedeva_z.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lebedeva_z.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp
index e2e81e4943..50f59107a0 100644
--- a/src/USER-MISC/pair_lennard_mdf.cpp
+++ b/src/USER-MISC/pair_lennard_mdf.cpp
@@ -16,15 +16,13 @@
    Contributing author: Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lennard_mdf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp
index 562a60aa99..2f4e886a61 100644
--- a/src/USER-MISC/pair_list.cpp
+++ b/src/USER-MISC/pair_list.cpp
@@ -16,18 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_list.h"
-#include "atom.h"
-#include "comm.h"
-#include "domain.h"
-#include "force.h"
-#include "memory.h"
-
-#include "error.h"
-
-#include <cstdio>
-#include <cstdlib>
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp
index fe21538f2d..ffa828826f 100644
--- a/src/USER-MISC/pair_lj_expand_coul_long.cpp
+++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp
@@ -15,17 +15,15 @@
    Contributing author: Trung Nguyen (Northwestern)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_expand_coul_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp
index cfe125f21f..3fe0fa6bf9 100644
--- a/src/USER-MISC/pair_lj_mdf.cpp
+++ b/src/USER-MISC/pair_lj_mdf.cpp
@@ -16,15 +16,13 @@
    Contributing author: Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_mdf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index af7d23370d..758962ce29 100644
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -16,10 +16,10 @@
                          Samuel Genheden (University of Southampton)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_sf_dipole_sf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index f09919ce0f..79e7ac7e09 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -31,15 +31,13 @@
                        conform with pairing, updated to LAMMPS style
 ------------------------------------------------------------------------- */
 
+#include "pair_meam_spline.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_meam_spline.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index af1e8788bd..eeadacf33a 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -23,15 +23,13 @@
  * 01-Aug-12 - RER: First code version.
 ------------------------------------------------------------------------- */
 
+#include "pair_meam_sw_spline.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_meam_sw_spline.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp
index 1716149a98..29d5715302 100644
--- a/src/USER-MISC/pair_momb.cpp
+++ b/src/USER-MISC/pair_momb.cpp
@@ -16,10 +16,9 @@
                          Ya Zhou (Penn State University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include "pair_momb.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index 7c7973f830..c3cbe39db7 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_morse_smooth_linear.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp
index 01deaf0fbe..416ace8132 100644
--- a/src/USER-MISC/pair_srp.cpp
+++ b/src/USER-MISC/pair_srp.cpp
@@ -25,9 +25,11 @@ There is an example script for this package in examples/USER/srp.
 Please contact Timothy Sirk for questions (tim.sirk@us.army.mil).
 ------------------------------------------------------------------------- */
 
+#include "pair_srp.h"
+#include <mpi.h>
+#include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "pair_srp.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index e0985d1dce..5c4f60f354 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -20,11 +20,11 @@
     1) Tersoff, Phys. Rev. B 39, 5566 (1988)
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff_table.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff_table.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp
index 031a449689..d0e2fa5606 100644
--- a/src/USER-MISC/temper_grem.cpp
+++ b/src/USER-MISC/temper_grem.cpp
@@ -15,26 +15,21 @@
    Contributing author: David Stelter (BU)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "temper_grem.h"
+#include <cmath>
+#include <cstring>
 #include "fix_grem.h"
 #include "universe.h"
 #include "domain.h"
-#include "atom.h"
 #include "update.h"
 #include "integrate.h"
 #include "modify.h"
 #include "compute.h"
 #include "force.h"
-#include "output.h"
-#include "thermo.h"
 #include "fix.h"
 #include "random_park.h"
 #include "finish.h"
 #include "timer.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp
index 7cf8fbab9b..9fd4bd6d06 100644
--- a/src/USER-MISC/temper_npt.cpp
+++ b/src/USER-MISC/temper_npt.cpp
@@ -17,10 +17,9 @@
    Contact Email: amulyapervaje@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "temper_npt.h"
+#include <cmath>
+#include <cstring>
 #include "universe.h"
 #include "domain.h"
 #include "atom.h"
@@ -29,13 +28,10 @@
 #include "modify.h"
 #include "compute.h"
 #include "force.h"
-#include "output.h"
-#include "thermo.h"
 #include "fix.h"
 #include "random_park.h"
 #include "finish.h"
 #include "timer.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp
index e8e6f279de..bb0a01d546 100644
--- a/src/USER-MOFFF/angle_class2_p6.cpp
+++ b/src/USER-MOFFF/angle_class2_p6.cpp
@@ -16,10 +16,10 @@
                         and Rochus Schmid (Ruhr-Universitaet Bochum)
 ------------------------------------------------------------------------- */
 
+#include "angle_class2_p6.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "angle_class2_p6.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index 3829d2b8dc..c17b2a1dba 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -16,9 +16,9 @@
                         and Rochus Schmid (Ruhr-Universitaet Bochum)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_buck6d.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
@@ -26,13 +26,11 @@
 #include "force.h"
 #include "pair.h"
 #include "math_const.h"
-#include "math_special.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
-using namespace MathSpecial;
 
 #define SMALL 0.001
 
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 3f1e61e54a..12f7062ccc 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -19,17 +19,13 @@
    [ abbreviated from and verified via DLPOLY2.0 ]
 ------------------------------------------------------------------------- */
 
+#include "improper_inversion_harmonic.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include <cstring>
-#include "improper_inversion_harmonic.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
index 282bb0c58f..9c917d1c19 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
@@ -18,11 +18,9 @@
                Fennell and Gezelter, JCP 124, 234104 (2006)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck6d_coul_gauss_dsf.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
index d6a4121d21..953507ce21 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
@@ -17,11 +17,10 @@
    References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck6d_coul_gauss_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -29,12 +28,10 @@
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
-#include "math_const.h"
 #include "error.h"
 #include "math_special.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define EWALD_F   1.12837917
 
diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp
index 41e6540b97..ad3d3facdb 100644
--- a/src/USER-PTM/compute_ptm_atom.cpp
+++ b/src/USER-PTM/compute_ptm_atom.cpp
@@ -16,15 +16,14 @@ under
          Contributing author: PM Larsen (MIT)
 ------------------------------------------------------------------------- */
 
+#include "compute_ptm_atom.h"
 #include <algorithm>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include <vector>
 
 #include "atom.h"
 #include "comm.h"
-#include "compute_ptm_atom.h"
 #include "error.h"
 #include "force.h"
 #include "memory.h"
@@ -32,7 +31,6 @@ under
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "neighbor.h"
-#include "pair.h"
 #include "update.h"
 
 #include "ptm_functions.h"
diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp
index 45643ec515..8dd06e8168 100644
--- a/src/USER-PTM/ptm_convex_hull_incremental.cpp
+++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp
@@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #include <cfloat>
 #include <cstring>
 #include <cassert>
-#include <algorithm>
 #include "ptm_convex_hull_incremental.h"
 #include "ptm_constants.h"
 
diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp
index 3068e7a7f6..b50e5c4333 100644
--- a/src/USER-PTM/ptm_index.cpp
+++ b/src/USER-PTM/ptm_index.cpp
@@ -12,19 +12,15 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #include "ptm_convex_hull_incremental.h"
 #include "ptm_deformation_gradient.h"
 #include "ptm_functions.h"
-#include "ptm_graph_data.h"
 #include "ptm_initialize_data.h"
 #include "ptm_neighbour_ordering.h"
 #include "ptm_normalize_vertices.h"
 #include "ptm_polar.h"
 #include "ptm_quat.h"
 #include "ptm_structure_matcher.h"
-#include <algorithm>
 #include <cassert>
-#include <cfloat>
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
 #include <cstring>
 
 static double calculate_interatomic_distance(int type, double scale) {
diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp
index 49dc6f2323..1f0a5c94af 100644
--- a/src/USER-PTM/ptm_initialize_data.cpp
+++ b/src/USER-PTM/ptm_initialize_data.cpp
@@ -7,14 +7,8 @@ The above copyright notice and this permission notice shall be included in all c
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <cmath>
-#include <cfloat>
-#include <cassert>
-#include <algorithm>
 #include "ptm_initialize_data.h"
+#include <cassert>
 
 
 static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3])
diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp
index cb72a43711..1332b8819b 100644
--- a/src/USER-PTM/ptm_neighbour_ordering.cpp
+++ b/src/USER-PTM/ptm_neighbour_ordering.cpp
@@ -9,16 +9,15 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 //todo: normalize vertices
 
-#include <cstdlib>
+#include "ptm_neighbour_ordering.h"
 #include <cmath>
 #include <cstring>
 #include <cassert>
 #include <algorithm>
 #include <set>
+#include <vector>
 #include "ptm_constants.h"
 #include "ptm_voronoi_cell.h"
-#include "ptm_neighbour_ordering.h"
-#include "ptm_normalize_vertices.h"
 
 
 namespace ptm {
diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h
index e03963048b..f11dd98ee9 100644
--- a/src/USER-PTM/ptm_polar.h
+++ b/src/USER-PTM/ptm_polar.h
@@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define PTM_POLAR_H
 
 #include <stdint.h>
-#include <stdbool.h>
 
 namespace ptm {
 
diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp
index 4a93499b3a..527f4d1116 100644
--- a/src/USER-PTM/ptm_quat.cpp
+++ b/src/USER-PTM/ptm_quat.cpp
@@ -7,9 +7,9 @@ The above copyright notice and this permission notice shall be included in all c
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
+#include "ptm_quat.h"
 #include <cstring>
 #include <cmath>
-#include <cfloat>
 #include <algorithm>
 
 
diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp
index dfe61eb24f..dc4ce4e747 100644
--- a/src/USER-PTM/ptm_voronoi_cell.cpp
+++ b/src/USER-PTM/ptm_voronoi_cell.cpp
@@ -52,7 +52,7 @@ such enhancements or derivative works thereof, in binary and source code form.
  * \brief Function implementations for the voronoicell and related classes. */
 
 #include <cmath>
-#include <cstring>
+#include <cstdio>
 #include <cstdlib>
 #include "ptm_voronoi_config.h"
 #include "ptm_voronoi_cell.h"
diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h
index eb091dd36b..69e3b5bdc4 100644
--- a/src/USER-PTM/ptm_voronoi_cell.h
+++ b/src/USER-PTM/ptm_voronoi_cell.h
@@ -56,9 +56,6 @@ such enhancements or derivative works thereof, in binary and source code form.
 #define PTM_VOROPP_CELL_HH
 
 #include <vector>
-#include <cstdio>
-
-#include "ptm_voronoi_config.h"
 
 namespace ptm_voro {
 
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index 93a6f1308f..604504c5a7 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -23,21 +23,18 @@
  ------------------------------------------------------------------------- */
 
 #include "atom_vec_smd.h"
-#include <cmath>
 #include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
-#include "fix_adapt.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "utils.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
+
 #define NMAT_FULL 9
 #define NMAT_SYMM 6
 
diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp
index 8193ad6ccf..46cbc602f2 100644
--- a/src/USER-SMD/compute_smd_contact_radius.cpp
+++ b/src/USER-SMD/compute_smd_contact_radius.cpp
@@ -23,13 +23,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_contact_radius.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-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp
index 9603fd5c64..96a936cd82 100644
--- a/src/USER-SMD/compute_smd_damage.cpp
+++ b/src/USER-SMD/compute_smd_damage.cpp
@@ -23,13 +23,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_damage.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-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp
index d937aa98a4..f88da8bc33 100644
--- a/src/USER-SMD/compute_smd_internal_energy.cpp
+++ b/src/USER-SMD/compute_smd_internal_energy.cpp
@@ -29,7 +29,6 @@
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp
index 67466ebb72..c1c001a5dd 100644
--- a/src/USER-SMD/compute_smd_plastic_strain.cpp
+++ b/src/USER-SMD/compute_smd_plastic_strain.cpp
@@ -23,13 +23,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_plastic_strain.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-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
index 20dfa64edd..272a2c59e5 100644
--- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
@@ -23,13 +23,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_plastic_strain_rate.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-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp
index 5c78e604b6..d9c0a99b07 100644
--- a/src/USER-SMD/compute_smd_rho.cpp
+++ b/src/USER-SMD/compute_smd_rho.cpp
@@ -22,13 +22,12 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_rho.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-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
index 37ad78dcea..09aeeea74a 100644
--- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
@@ -22,20 +22,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "compute_smd_tlsph_defgrad.h"
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
-#include "pair.h"
+
 using namespace Eigen;
 using namespace std;
 using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp
index bbab274b5c..ba1a9306ef 100644
--- a/src/USER-SMD/compute_smd_tlsph_shape.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp
@@ -22,13 +22,9 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
-#include <Eigen/Geometry>
 #include "compute_smd_tlsph_shape.h"
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp
index a94a3cd511..f0061bf7a1 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp
@@ -23,12 +23,9 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "compute_smd_tlsph_strain.h"
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp
index a54b07dd1e..9c78b192ce 100644
--- a/src/USER-SMD/compute_smd_tlsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp
@@ -22,9 +22,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
+#include "compute_smd_tlsph_stress.h"
+#include <cmath>
 #include <cstring>
 #include <Eigen/Eigen>
-#include "compute_smd_tlsph_stress.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp
index b24223b8b5..06706a85ad 100644
--- a/src/USER-SMD/compute_smd_triangle_vertices.cpp
+++ b/src/USER-SMD/compute_smd_triangle_vertices.cpp
@@ -23,22 +23,15 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "compute_smd_triangle_vertices.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
-#include "pair.h"
 
-using namespace Eigen;
 using namespace std;
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp
index 89b85f7bc1..cf1535759c 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp
@@ -23,22 +23,15 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "compute_smd_ulsph_strain.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
-#include "pair.h"
 
-using namespace Eigen;
 using namespace std;
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp
index 7f1bbc4c29..ea477375ce 100644
--- a/src/USER-SMD/compute_smd_ulsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp
@@ -22,9 +22,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
+#include "compute_smd_ulsph_stress.h"
+#include <cmath>
 #include <cstring>
 #include <Eigen/Eigen>
-#include "compute_smd_ulsph_stress.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp
index 17a6b556e8..eb1f144275 100644
--- a/src/USER-SMD/compute_smd_vol.cpp
+++ b/src/USER-SMD/compute_smd_vol.cpp
@@ -22,13 +22,13 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_vol.h"
+#include <mpi.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-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp
index f015c6c4df..ab6dd5ef5c 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.cpp
+++ b/src/USER-SMD/fix_smd_adjust_dt.cpp
@@ -22,21 +22,14 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_smd_adjust_dt.h"
-#include "atom.h"
+#include <mpi.h>
+#include <cstdlib>
 #include "update.h"
-#include "integrate.h"
-#include "domain.h"
-#include "lattice.h"
 #include "force.h"
 #include "pair.h"
 #include "modify.h"
 #include "fix.h"
-#include "output.h"
-#include "dump.h"
 #include "comm.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
index f931ae94ff..8464bed609 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
@@ -22,22 +22,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "fix_smd_integrate_tlsph.h"
+#include <cmath>
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
 #include "pair.h"
-#include "neigh_list.h"
-#include "domain.h"
-#include "neighbor.h"
 #include "comm.h"
-#include "modify.h"
 
 using namespace Eigen;
 using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
index 6c4705eb96..0f0d224f95 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
@@ -22,25 +22,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
+#include "fix_smd_integrate_ulsph.h"
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include <Eigen/Eigen>
-#include "fix_smd_integrate_ulsph.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 "respa.h"
-#include "memory.h"
 #include "error.h"
 #include "pair.h"
-#include "domain.h"
 
 using namespace Eigen;
 using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index fe8695b23e..cbaad9ac4c 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -22,25 +22,15 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
-#include <cmath>
-#include <cstdlib>
-#include <Eigen/Eigen>
 #include "fix_smd_move_triangulated_surface.h"
+#include <cmath>
+#include <cstring>
+#include <Eigen/Eigen>
 #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 "respa.h"
-#include "memory.h"
 #include "error.h"
-#include "pair.h"
-#include "domain.h"
 #include "math_const.h"
 
 using namespace Eigen;
diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp
index 4bc8b5127b..2964ded544 100644
--- a/src/USER-SMD/fix_smd_setvel.cpp
+++ b/src/USER-SMD/fix_smd_setvel.cpp
@@ -23,9 +23,9 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_smd_setvel.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index a2813cc3ca..6aa23fe3b2 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -24,20 +24,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
-#include <cstdio>
-#include <Eigen/Eigen>
 #include "fix_smd_tlsph_reference_configuration.h"
+#include <mpi.h>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "lattice.h"
 #include "force.h"
 #include "pair.h"
 #include "update.h"
-#include "modify.h"
 #include "memory.h"
 #include "error.h"
 #include "domain.h"
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
index 8549621c2f..5f952bde93 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
@@ -35,7 +35,6 @@ FixStyle(SMD_TLSPH_NEIGHBORS,FixSMD_TLSPH_ReferenceConfiguration)
 #define LMP_FIX_SMD_TLSPH_REFERENCE_H
 
 #include "fix.h"
-#include "my_page.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index a37ba67a80..9183bcd9ea 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -15,21 +15,15 @@
    Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdio>
-#include <Eigen/Eigen>
 #include "fix_smd_wall_surface.h"
+#include <mpi.h>
+#include <cstring>
+#include <cstdlib>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
 #include "comm.h"
-#include "update.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "pair.h"
-#include "lattice.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec.h"
diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp
index 541be9f05c..97be94d833 100644
--- a/src/USER-SMD/pair_smd_hertz.cpp
+++ b/src/USER-SMD/pair_smd_hertz.cpp
@@ -26,17 +26,14 @@
    Contributing author: Mike Parks (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_smd_hertz.h"
+#include <mpi.h>
 #include <cmath>
-#include <cfloat>
 #include <cstdlib>
 #include <cstring>
-#include "pair_smd_hertz.h"
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
-#include "modify.h"
-#include "fix.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index 1d7bbca780..0dff905962 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -22,15 +22,13 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cfloat>
-#include <cstdlib>
-#include <cstring>
-#include <cstdio>
-#include <iostream>
-#include <map>
-#include <Eigen/Eigen>
 #include "pair_smd_tlsph.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <string>
+#include <iostream>
+#include <Eigen/Eigen>
 #include "fix_smd_tlsph_reference_configuration.h"
 #include "atom.h"
 #include "domain.h"
@@ -41,12 +39,9 @@
 #include "fix.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "neigh_list.h"
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
-#include "math_special.h"
-#include "update.h"
 #include "smd_material_models.h"
 #include "smd_kernels.h"
 #include "smd_math.h"
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index d3a4983379..f9052be087 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -26,20 +26,15 @@
    Contributing author: Mike Parks (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_smd_triangulated_surface.h"
+#include <mpi.h>
 #include <cmath>
-#include <cfloat>
 #include <cstdlib>
 #include <cstring>
-#include <cstdio>
-#include <iostream>
 #include <Eigen/Eigen>
-#include "pair_smd_triangulated_surface.h"
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
-#include "modify.h"
-#include "fix.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index 2c4a2de989..9e824ded3c 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -22,19 +22,13 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cfloat>
-#include <cstdlib>
-#include <cstring>
-#include <cstdio>
-#include <iostream>
 #include "pair_smd_ulsph.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
 #include "update.h"
-#include "modify.h"
-#include "fix.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp
index 4213428872..5ee67fbb4e 100644
--- a/src/USER-SMD/smd_material_models.cpp
+++ b/src/USER-SMD/smd_material_models.cpp
@@ -21,6 +21,10 @@
 
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
+#include "smd_material_models.h"
+#include <cmath>
+#include <cstdlib>
+#include <utility>
 #include <iostream>
 #include <cstdio>
 #include "math_special.h"