update packages USER-SPH, USER-SMTBQ, USER-SDPD, USER-TALLY, USER-UEF, USER-YAFF

src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp

@@ -18,9 +18,8 @@
     references: Espanol and Revenga, Phys Rev E 67, 026705 (2003)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sdpd_taitwater_isothermal.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"

src/USER-SMTBQ/pair_smtbq.cpp

@@ -38,25 +38,24 @@
    <http://www.gnu.org/licenses/>.
    ------------------------------------------------------------------------- */
 
+#include "pair_smtbq.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
+#include <algorithm>
 #include <vector>
-#include "pair_smtbq.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "group.h"
 #include "update.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
-#include "domain.h"
 
 #include <fstream>
 #include <iomanip>

src/USER-SPH/compute_meso_e_atom.cpp

@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_meso_e_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 

src/USER-SPH/compute_meso_rho_atom.cpp

@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_meso_rho_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 

src/USER-SPH/compute_meso_t_atom.cpp

@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_meso_t_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 

src/USER-SPH/fix_meso.cpp

@@ -11,23 +11,11 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
-#include <cmath>
-#include <cstdlib>
 #include "fix_meso.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"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-SPH/fix_meso_stationary.cpp

@@ -11,23 +11,11 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
-#include <cmath>
-#include <cstdlib>
 #include "fix_meso_stationary.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"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-SPH/pair_sph_heatconduction.cpp

@@ -11,12 +11,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_heatconduction.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "memory.h"
 #include "error.h"
 #include "neigh_list.h"

src/USER-SPH/pair_sph_idealgas.cpp

@@ -11,12 +11,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_idealgas.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"

src/USER-SPH/pair_sph_lj.cpp

@@ -11,12 +11,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_lj.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"

src/USER-SPH/pair_sph_rhosum.cpp

@@ -11,8 +11,6 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_rhosum.h"
 #include "atom.h"
 #include "force.h"

src/USER-SPH/pair_sph_taitwater.cpp

@@ -11,9 +11,8 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_taitwater.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"

src/USER-SPH/pair_sph_taitwater_morris.cpp

@@ -11,9 +11,8 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_taitwater_morris.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"

src/USER-TALLY/compute_force_tally.cpp

@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cmath>
 #include "compute_force_tally.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"

src/USER-TALLY/compute_heat_flux_tally.cpp

@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_heat_flux_tally.h"
+#include <mpi.h>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"

src/USER-TALLY/compute_pe_mol_tally.cpp

@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_pe_mol_tally.h"
+#include <mpi.h>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"
 #include "update.h"
-#include "memory.h"
 #include "error.h"
 #include "force.h"
 #include "comm.h"

src/USER-TALLY/compute_pe_tally.cpp

@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_pe_tally.h"
+#include <mpi.h>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"

src/USER-TALLY/compute_stress_tally.cpp

@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_stress_tally.h"
+#include <mpi.h>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"

src/USER-UEF/compute_pressure_uef.cpp

@@ -13,21 +13,14 @@
    Contributing author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
-#include <cstdlib>
 #include "compute_pressure_uef.h"
+#include <cstring>
 #include "fix_nh_uef.h"
 #include "update.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
 #include "force.h"
-#include "pair.h"
-#include "bond.h"
-#include "angle.h"
-#include "dihedral.h"
-#include "improper.h"
 #include "kspace.h"
 #include "error.h"
 

src/USER-UEF/compute_temp_uef.cpp

@@ -13,11 +13,9 @@
    Contributing author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "compute_temp_uef.h"
+#include <cstring>
 #include "fix_nh_uef.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "error.h"

src/USER-UEF/dump_cfg_uef.cpp

@@ -13,15 +13,11 @@
    Contributing Author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "dump_cfg.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "domain.h"
 #include "modify.h"
-#include "compute.h"
 #include "fix.h"
 #include "error.h"
 #include "uef_utils.h"

src/USER-UEF/fix_nh_uef.cpp

@@ -13,19 +13,16 @@
    Contributing author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_nh_uef.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "group.h"
 #include "comm.h"
 #include "citeme.h"
 #include "irregular.h"
 #include "modify.h"
 #include "compute.h"
-#include "kspace.h"
 #include "update.h"
 #include "domain.h"
 #include "error.h"

src/USER-YAFF/angle_cross.cpp

@@ -15,10 +15,8 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
 #include "angle_cross.h"
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/USER-YAFF/angle_cross.h

@@ -20,7 +20,6 @@ AngleStyle(cross,AngleCross)
 #ifndef LMP_ANGLE_CROSS_H
 #define LMP_ANGLE_CROSS_H
 
-#include <stdio.h>
 #include "angle.h"
 
 namespace LAMMPS_NS {

src/USER-YAFF/angle_mm3.cpp

@@ -15,10 +15,9 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
 #include "angle_mm3.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/USER-YAFF/angle_mm3.h

@@ -20,7 +20,6 @@ AngleStyle(mm3,AngleMM3)
 #ifndef LMP_ANGLE_MM3_H
 #define LMP_ANGLE_MM3_H
 
-#include <stdio.h>
 #include "angle.h"
 
 namespace LAMMPS_NS {

src/USER-YAFF/bond_mm3.cpp

@@ -15,12 +15,11 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <stdlib.h>
 #include "bond_mm3.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/USER-YAFF/bond_mm3.h

@@ -20,7 +20,6 @@ BondStyle(mm3,BondMM3)
 #ifndef LMP_BOND_MM3_H
 #define LMP_BOND_MM3_H
 
-#include <stdio.h>
 #include "bond.h"
 
 namespace LAMMPS_NS {

src/USER-YAFF/improper_distharm.cpp

@@ -16,16 +16,14 @@
    improper_distance code by Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
 #include "improper_distharm.h"
+#include <mpi.h>
+#include <cmath>
 #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-YAFF/improper_distharm.h

@@ -20,7 +20,6 @@ ImproperStyle(distharm,ImproperDistHarm)
 #ifndef LMP_IMPROPER_DISTHARM_H
 #define LMP_IMPROPER_DISTHARM_H
 
-#include <stdio.h>
 #include "improper.h"
 
 namespace LAMMPS_NS {

src/USER-YAFF/improper_sqdistharm.cpp

@@ -16,16 +16,14 @@
    improper_distance code by Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
 #include "improper_sqdistharm.h"
+#include <mpi.h>
+#include <cmath>
 #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-YAFF/improper_sqdistharm.h

@@ -20,7 +20,6 @@ ImproperStyle(sqdistharm,ImproperSQDistHarm)
 #ifndef LMP_IMPROPER_SQDISTHARM_H
 #define LMP_IMPROPER_SQDISTHARM_H
 
-#include <stdio.h>
 #include "improper.h"
 
 namespace LAMMPS_NS {

src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp

@@ -15,17 +15,15 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
 #include "pair_lj_switch3_coulgauss_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-YAFF/pair_mm3_switch3_coulgauss_long.cpp

@@ -15,17 +15,15 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
 #include "pair_mm3_switch3_coulgauss_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"