update include lists in packages USER-MISC, USER-MOFF, USER-PTM, and USER-SMD

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>
 

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"

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"
 

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"

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"

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"

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;
 
 /* ---------------------------------------------------------------------- */
 

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"

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"

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"
 

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 {
 

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"

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"

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"

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"

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

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"

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"

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 {
 

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"

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 {
 

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"

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"

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"

src/USER-MISC/pair_list.cpp

@@ -16,18 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_list.h"
-#include "atom.h"
+#include <mpi.h>
-#include "comm.h"
-#include "domain.h"
-#include "force.h"
-#include "memory.h"
-
-#include "error.h"
-
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include <cmath>
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
 
 using namespace LAMMPS_NS;
 

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"

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"

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"

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"

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"

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"

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"

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"

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"

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;

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;

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"

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
 

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"

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"

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
 

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"

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"
 

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) {

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])

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 {

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 {
 

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>
 
 

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"

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 {
 

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
 

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"
 

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"
 

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"
 

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"
 

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"
 

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"
 

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;

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"

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"

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"

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;
 

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;
 

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"

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"
 

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"
 

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;

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;

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;

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"

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"

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 {
 

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"

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"

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"

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"

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"

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"