cleaning up include file handling in packages MOLECULE and PERI

src/MOLECULE/angle_charmm.cpp

@@ -16,8 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_charmm.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/MOLECULE/angle_cosine.cpp

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/MOLECULE/angle_cosine_delta.cpp

@@ -17,14 +17,10 @@
 
 #include "angle_cosine_delta.h"
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
-#include "comm.h"
 #include "force.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 

src/MOLECULE/angle_cosine_periodic.cpp

@@ -16,8 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine_periodic.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/MOLECULE/angle_cosine_squared.cpp

@@ -16,8 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine_squared.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/MOLECULE/angle_harmonic.cpp

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_harmonic.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"

src/MOLECULE/angle_table.cpp

@@ -16,6 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_table.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>

src/MOLECULE/atom_vec_template.cpp

@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "atom_vec_template.h"
-#include <cstring>
 #include <cstdlib>
 #include "atom.h"
 #include "molecule.h"

src/MOLECULE/bond_fene.cpp

@@ -12,11 +12,10 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_fene.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"

src/MOLECULE/bond_fene_expand.cpp

@@ -12,11 +12,10 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_fene_expand.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"

src/MOLECULE/bond_gromos.cpp

@@ -16,12 +16,10 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_gromos.h"
-#include <cmath>
-#include <cstdlib>
+#include <mpi.h>
 #include <cstring>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/MOLECULE/bond_harmonic.cpp

@@ -12,12 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_harmonic.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/MOLECULE/bond_morse.cpp

@@ -16,11 +16,10 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_morse.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/MOLECULE/bond_nonlinear.cpp

@@ -12,11 +12,10 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_nonlinear.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/MOLECULE/bond_quartic.cpp

@@ -16,13 +16,11 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_quartic.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
-#include "update.h"
 #include "force.h"
 #include "pair.h"
 #include "memory.h"

src/MOLECULE/bond_table.cpp

@@ -16,12 +16,12 @@
 ------------------------------------------------------------------------- */
 
 #include "bond_table.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"

src/MOLECULE/dihedral_charmm.cpp

@@ -18,12 +18,10 @@
 #include "dihedral_charmm.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "pair.h"
 #include "update.h"

src/MOLECULE/dihedral_charmmfsw.cpp

@@ -21,12 +21,10 @@
 #include "dihedral_charmmfsw.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "pair.h"
 #include "update.h"

src/MOLECULE/dihedral_harmonic.cpp

@@ -18,11 +18,9 @@
 #include "dihedral_harmonic.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"

src/MOLECULE/dihedral_helix.cpp

@@ -19,10 +19,8 @@
 #include "dihedral_helix.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "update.h"

src/MOLECULE/dihedral_multi_harmonic.cpp

@@ -16,11 +16,10 @@
 ------------------------------------------------------------------------- */
 
 #include "dihedral_multi_harmonic.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "update.h"

src/MOLECULE/dihedral_opls.cpp

@@ -16,12 +16,11 @@
 ------------------------------------------------------------------------- */
 
 #include "dihedral_opls.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"

src/MOLECULE/fix_cmap.cpp

@@ -32,15 +32,11 @@
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include <cstdio>
 #include "atom.h"
-#include "atom_vec.h"
 #include "update.h"
 #include "respa.h"
-#include "modify.h"
 #include "domain.h"
 #include "force.h"
-#include "group.h"
 #include "comm.h"
 #include "math_const.h"
 #include "memory.h"

src/MOLECULE/improper_cvff.cpp

@@ -14,11 +14,9 @@
 #include "improper_cvff.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"

src/MOLECULE/improper_harmonic.cpp

@@ -14,11 +14,9 @@
 #include "improper_harmonic.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "math_const.h"

src/MOLECULE/improper_umbrella.cpp

@@ -18,11 +18,9 @@
 #include "improper_umbrella.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "math_const.h"

src/MOLECULE/pair_hbond_dreiding_lj.cpp

@@ -17,13 +17,10 @@
 
 #include "pair_hbond_dreiding_lj.h"
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_request.h"

src/MOLECULE/pair_hbond_dreiding_morse.cpp

@@ -17,13 +17,10 @@
 
 #include "pair_hbond_dreiding_morse.h"
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_request.h"

src/MOLECULE/pair_lj_charmm_coul_charmm.cpp

@@ -16,9 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_charmm_coul_charmm.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "comm.h"

src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp

@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_charmm_coul_charmm_implicit.h"
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "neigh_list.h"

src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp

@@ -20,9 +20,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_charmmfsw_coul_charmmfsh.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "update.h"

src/MOLECULE/pair_lj_cut_tip4p_cut.cpp

@@ -16,8 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_tip4p_cut.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "force.h"

src/MOLECULE/pair_tip4p_cut.cpp

@@ -16,8 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tip4p_cut.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include "atom.h"
 #include "force.h"
 #include "neighbor.h"
@@ -26,12 +26,10 @@
 #include "angle.h"
 #include "bond.h"
 #include "comm.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 

src/PERI/compute_damage_atom.cpp

@@ -21,8 +21,6 @@
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
-#include "pair_peri_pmb.h"
 #include "fix_peri_neigh.h"
 #include "memory.h"
 #include "error.h"

src/PERI/compute_dilatation_atom.cpp

@@ -21,13 +21,11 @@
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
+#include "fix.h"
 #include "force.h"
-#include "pair.h"
 #include "pair_peri_lps.h"
-#include "pair_peri_pmb.h"
 #include "pair_peri_ves.h"
 #include "pair_peri_eps.h"
-#include "fix_peri_neigh.h"
 #include "memory.h"
 #include "error.h"
 

src/PERI/compute_plasticity_atom.cpp

@@ -21,9 +21,8 @@
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
-#include "pair_peri_pmb.h"
 #include "fix_peri_neigh.h"
+#include "force.h"
 #include "memory.h"
 #include "error.h"
 

src/PERI/fix_peri_neigh.cpp

@@ -16,8 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_peri_neigh.h"
+#include <mpi.h>
 #include <cmath>
-#include "pair_peri_pmb.h"
 #include "pair_peri_lps.h"
 #include "pair_peri_ves.h"
 #include "pair_peri_eps.h"
@@ -25,7 +25,6 @@
 #include "domain.h"
 #include "force.h"
 #include "comm.h"
-#include "update.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"

src/PERI/pair_peri_eps.cpp

@@ -16,14 +16,13 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_peri_eps.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "lattice.h"
 #include "force.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_peri_neigh.h"
@@ -32,7 +31,6 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "update.h"
 
 using namespace LAMMPS_NS;
 
@@ -451,12 +449,12 @@ void PairPeriEPS::coeff(int narg, char **arg)
   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
 
-  double bulkmodulus_one = atof(arg[2]);
-  double shearmodulus_one = atof(arg[3]);
-  double cut_one = atof(arg[4]);
-  double s00_one = atof(arg[5]);
-  double alpha_one = atof(arg[6]);
-  double myieldstress_one = atof(arg[7]);
+  double bulkmodulus_one = force->numeric(FLERR,arg[2]);
+  double shearmodulus_one = force->numeric(FLERR,arg[3]);
+  double cut_one = force->numeric(FLERR,arg[4]);
+  double s00_one = force->numeric(FLERR,arg[5]);
+  double alpha_one = force->numeric(FLERR,arg[6]);
+  double myieldstress_one = force->numeric(FLERR,arg[7]);
 
   int count = 0;
   for (int i = ilo; i <= ihi; i++) {

src/PERI/pair_peri_lps.cpp

@@ -16,14 +16,13 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_peri_lps.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "lattice.h"
 #include "force.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_peri_neigh.h"
@@ -32,7 +31,6 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "update.h"
 #include "math_const.h"
 
 using namespace LAMMPS_NS;

src/PERI/pair_peri_pmb.cpp

@@ -16,22 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_peri_pmb.h"
+#include <mpi.h>
 #include <cmath>
 #include <cfloat>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "lattice.h"
 #include "force.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_peri_neigh.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 

src/PERI/pair_peri_ves.cpp

@@ -16,6 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_peri_ves.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
@@ -23,7 +24,6 @@
 #include "domain.h"
 #include "lattice.h"
 #include "force.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_peri_neigh.h"
@@ -428,13 +428,13 @@ void PairPeriVES::coeff(int narg, char **arg)
   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
 
-  double bulkmodulus_one = atof(arg[2]);
-  double shearmodulus_one = atof(arg[3]);
-  double cut_one = atof(arg[4]);
-  double s00_one = atof(arg[5]);
-  double alpha_one = atof(arg[6]);
-  double mlambdai_one = atof(arg[7]);
-  double mtaui_one = atof(arg[8]);
+  double bulkmodulus_one = force->numeric(FLERR,arg[2]);
+  double shearmodulus_one = force->numeric(FLERR,arg[3]);
+  double cut_one = force->numeric(FLERR,arg[4]);
+  double s00_one = force->numeric(FLERR,arg[5]);
+  double alpha_one = force->numeric(FLERR,arg[6]);
+  double mlambdai_one = force->numeric(FLERR,arg[7]);
+  double mtaui_one = force->numeric(FLERR,arg[8]);
 
   int count = 0;
   for (int i = ilo; i <= ihi; i++) {