remove dead code and silence compiler warnings

src/BODY/pair_body_rounded_polygon.cpp

@@ -107,7 +107,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
   int nei,nej,iefirst,jefirst;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl;
   double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij;
-  double xi[3],xj[3],facc[3];
+  double facc[3];
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = 0.0;

src/MISC/pair_nm_cut.cpp

@@ -274,14 +274,6 @@ double PairNMCut::init_one(int i, int j)
     }
     MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
 
-    double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
-    double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
-    double p1 = 1-nn[i][j];
-    double p2 = 1-mm[i][j];
-
-    double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
-    double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
-
     double cut3 = cut[i][j]*cut[i][j]*cut[i][j];
     ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut3 *
       (pow(r0[i][j]/cut[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut[i][j],mm[i][j])/(mm[i][j]-3));

src/MISC/pair_nm_cut_coul_cut.cpp

@@ -324,14 +324,6 @@ double PairNMCutCoulCut::init_one(int i, int j)
     }
     MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
 
-    double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
-    double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
-    double p1 = 1-nn[i][j];
-    double p2 = 1-mm[i][j];
-
-    double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
-    double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
-
     double cut_lj3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
     ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut_lj3 *
       (pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3));

src/MISC/pair_nm_cut_coul_long.cpp

@@ -371,14 +371,6 @@ double PairNMCutCoulLong::init_one(int i, int j)
     }
     MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
 
-    double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
-    double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
-    double p1 = 1-nn[i][j];
-    double p2 = 1-mm[i][j];
-
-    double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
-    double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
-
     double cut_lj3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
     ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut_lj3 *
       (pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3));

src/MOLECULE/fix_cmap.cpp

@@ -943,7 +943,7 @@ double FixCMAP::dihedral_angle_atan2(double fx, double fy, double fz,
 {
   // calculate the dihedral angle
 
-  double angle, arg1, arg2;
+  double angle = 0.0, arg1, arg2;
 
   arg1 = absg*(fx*bx+fy*by+fz*bz);
   arg2 = ax*bx+ay*by+az*bz;

src/POEMS/fix_poems.cpp

@@ -748,19 +748,9 @@ void FixPOEMS::initial_integrate(int vflag)
 
 /* ---------------------------------------------------------------------- */
 
-void FixPOEMS::post_force(int vflag)
+void FixPOEMS::post_force(int /* vflag */)
 {
   if (earlyflag) compute_forces_and_torques();
-
-  /*
-  for (int ibody = 0; ibody < nbody; ibody++) {
-    if (ibody == 0) {
-    printf("PFF %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]);
-    printf("PFT %d %g %g %g\n",ibody,
-           torque[ibody][0],torque[ibody][1],torque[ibody][2]);
-    }
-  }
-  */
 }
 
 /* ----------------------------------------------------------------------
@@ -850,7 +840,7 @@ void FixPOEMS::final_integrate()
 
 /* ---------------------------------------------------------------------- */
 
-void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int /* iloop */)
 {
   dtv = step_respa[ilevel];
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -862,14 +852,14 @@ void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int iloop)
 
 /* ---------------------------------------------------------------------- */
 
-void FixPOEMS::post_force_respa(int vflag, int ilevel, int iloop)
+void FixPOEMS::post_force_respa(int vflag, int ilevel, int /* iloop */)
 {
   if (ilevel == nlevels_respa-1) post_force(vflag);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void FixPOEMS::final_integrate_respa(int ilevel, int iloop)
+void FixPOEMS::final_integrate_respa(int ilevel, int /* iloop */)
 {
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
   final_integrate();
@@ -949,7 +939,7 @@ int FixPOEMS::dof(int igroup)
          thus this routine does nothing for now
 ------------------------------------------------------------------------- */
 
-void FixPOEMS::deform(int flag) {}
+void FixPOEMS::deform(int /* flag */) {}
 
 /* ---------------------------------------------------------------------- */
 
@@ -1607,7 +1597,7 @@ void FixPOEMS::grow_arrays(int nmax)
    copy values within local atom-based arrays
 ------------------------------------------------------------------------- */
 
-void FixPOEMS::copy_arrays(int i, int j, int delflag)
+void FixPOEMS::copy_arrays(int i, int j, int /* delflag */)
 {
   natom2body[j] = natom2body[i];
   for (int k = 0; k < natom2body[j]; k++) atom2body[j][k] = atom2body[i][k];

src/REPLICA/fix_hyper_local.cpp

@@ -716,7 +716,7 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
     if (update->ntimestep % histo_print == 0) {
       MPI_Allreduce(histo,allhisto,histo_count+2,MPI_LMP_BIGINT,MPI_SUM,world);
 
-      bigint total;
+      bigint total = 0;
       for (i = 0; i < histo_count+2; i++) total += allhisto[i];
 
       if (me == 0) {

src/REPLICA/fix_hyper_local.h

@@ -87,7 +87,7 @@ class FixHyperLocal : public FixHyper {
   int nevent;                // # of events that trigger bond rebuild
   int nevent_atom;           // # of atoms that experienced an event
   double cutbondsq,dcutsq;
-  double beta,t_hyper,invqfactorsq;
+  double beta,invqfactorsq;
   double mybias;
   double maxbondlen;         // cummulative max length of any bond
   double maxdriftsq;         // max distance any atom drifts from original pos
@@ -147,7 +147,7 @@ class FixHyperLocal : public FixHyper {
 
   // histogramming of bond boost cooeficients
 
-  int histo_flag,histo_every,histo_count,histo_print,histo_steps;
+  int histo_every,histo_count,histo_print,histo_steps;
   double histo_delta,invhisto_delta,histo_lo;
   bigint *histo,*allhisto;
 };

src/SPIN/pair_spin_exchange.cpp

@@ -323,7 +323,7 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
   double **x = atom->x;
   double **sp = atom->sp;
   double local_cut2;
-  double xi[3], rij[3];
+  double xi[3];
   double delx,dely,delz;
   double spj[3];
 

src/USER-CGDNA/pair_oxdna2_coaxstk.cpp

@@ -103,9 +103,9 @@ PairOxdna2Coaxstk::~PairOxdna2Coaxstk()
 void PairOxdna2Coaxstk::compute(int eflag, int vflag)
 {
 
-  double delf[3],delt[3],delta[3],deltb[3]; // force, torque increment;
+  double delf[3],delta[3],deltb[3]; // force, torque increment;
   double evdwl,fpair,finc,tpair,factor_lj;
-  double v1tmp[3],v2tmp[3],v3tmp[3];
+  double v1tmp[3];
   double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
   double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
   double theta1,theta1p,t1dir[3],cost1;
@@ -114,12 +114,6 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
   double theta6,theta6p,t6dir[3],cost6;
   double cosphi3;
 
-  double gamma,gammacub,rinv_ss_cub,fac;
-  double aybx,azbx,rax,ray,raz,rbx;
-  double dcdr,dcdrbx;
-  double dcdaxbx,dcdaybx,dcdazbx;
-  double dcdrax,dcdray,dcdraz;
-
   // distances COM-backbone site, COM-stacking site
   double d_cs=-0.4, d_cst=+0.34;
   // vectors COM-backbone site, COM-stacking site in lab frame

src/USER-MISC/compute_stress_mop.cpp

@@ -210,7 +210,7 @@ void ComputeStressMop::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeStressMop::init_list(int id, NeighList *ptr)
+void ComputeStressMop::init_list(int /* id */, NeighList *ptr)
 {
   list = ptr;
 }
@@ -246,9 +246,9 @@ void ComputeStressMop::compute_vector()
 void ComputeStressMop::compute_pairs()
 
 {
-  int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
+  int i,j,m,ii,jj,inum,jnum,itype,jtype;
   double delx,dely,delz;
-  double rsq,eng,fpair,factor_coul,factor_lj;
+  double rsq,fpair,factor_coul,factor_lj;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   double *mass = atom->mass;
@@ -363,8 +363,7 @@ void ComputeStressMop::compute_pairs()
     // counts local particles transfers across the plane
 
     if (which[m] == KIN || which[m] == TOTAL){
-      double vcm[3];
+      double sgn;
-      double masstotal,sgn;
 
       for (int i = 0; i < nlocal; i++){
 

src/USER-MISC/compute_stress_mop_profile.cpp

@@ -211,7 +211,7 @@ void ComputeStressMopProfile::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeStressMopProfile::init_list(int id, NeighList *ptr)
+void ComputeStressMopProfile::init_list(int /* id */, NeighList *ptr)
 {
   list = ptr;
 }
@@ -253,11 +253,11 @@ void ComputeStressMopProfile::compute_array()
 void ComputeStressMopProfile::compute_pairs()
 
 {
-  int i,j,m,n,ii,jj,inum,jnum,itype,jtype,ibin;
+  int i,j,m,ii,jj,inum,jnum,itype,jtype,ibin;
   double delx,dely,delz;
-  double rsq,eng,fpair,factor_coul,factor_lj;
+  double rsq,fpair,factor_coul,factor_lj;
   int *ilist,*jlist,*numneigh,**firstneigh;
-  double pos,pos1,pos_temp;    
+  double pos,pos1;    
 
   double *mass = atom->mass;
   int *type = atom->type;
@@ -385,8 +385,7 @@ void ComputeStressMopProfile::compute_pairs()
 
     if (which[m] == KIN || which[m] == TOTAL){
 
-      double vcm[3];
+      double sgn;
-      double masstotal,sgn;
 
       for (int i = 0; i < nlocal; i++){
 
@@ -449,8 +448,8 @@ void ComputeStressMopProfile::compute_pairs()
 
 void ComputeStressMopProfile::setup_bins()
 {
-  int i,j,k,m,n;
+  int i,n;
-  double lo,hi,coord1,coord2;
+  double lo = 0.0, hi = 0.0;
 
   double *boxlo,*boxhi,*prd;
   boxlo = domain->boxlo;

src/USER-MISC/compute_stress_mop_profile.h

@@ -50,7 +50,6 @@ namespace LAMMPS_NS {
     double **coord,**coordp;
     double **values_local,**values_global;
 
-    int ndim;
     double dt,nktv2p,ftm2v;
     double area;
     class NeighList *list;

src/USER-MISC/fix_ffl.cpp

@@ -108,8 +108,6 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) :
   }
 
   t_target=t_start;
-  const double kT = t_target * force->boltz / force->mvv2e;
-
 
   // initialize Marsaglia RNG with processor-unique seed
   // NB: this means runs will not be the same with different numbers of processors
@@ -298,7 +296,7 @@ void FixFFL::ffl_integrate() {
 
 }
 
-void FixFFL::initial_integrate(int vflag) {
+void FixFFL::initial_integrate(int /* vflag */) {
   double dtfm;
 
   // update v and x of atoms in group
@@ -391,7 +389,7 @@ void FixFFL::final_integrate() {
 }
 /* ---------------------------------------------------------------------- */
 
-void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) {
+void FixFFL::initial_integrate_respa(int vflag, int ilevel, int /* iloop */) {
   dtv = step_respa[ilevel];
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
 
@@ -406,7 +404,7 @@ void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) {
   }
 }
 
-void FixFFL::final_integrate_respa(int ilevel, int iloop) {
+void FixFFL::final_integrate_respa(int ilevel, int /* iloop */) {
 
   dtv = step_respa[ilevel];
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;

src/USER-MISC/fix_filter_corotate.cpp

@@ -592,14 +592,13 @@ void FixFilterCorotate::pre_neighbor()
       double c = (del2[0])*(del3[1]) - (del2[1])*(del3[0]);
       int signum = sgn(a*(del1[0]) + b*(del1[1]) + c*(del1[2]));
 
-      if (fabs(signum)!= 1)
+      if (abs(signum) != 1)
         error->all(FLERR,"Wrong orientation in cluster of size 4"
           "in fix filter/corotate!");
       clist_q0[i][8] *= signum;
       clist_q0[i][11] *= signum;
 
-    } else if (N == 5)
+    } else if (N == 5) {
-    {
       oxy = atom->map(shake_atom[m][0]);
       atom1 = atom->map(shake_atom[m][1]);
       atom2 = atom->map(shake_atom[m][2]);
@@ -666,14 +665,12 @@ void FixFilterCorotate::pre_neighbor()
       double c = (del2[0])*(del3[1]) - (del2[1])*(del3[0]);
       int signum = sgn(a*(del1[0]) + b*(del1[1]) + c*(del1[2]));
 
-      if (fabs(signum)!= 1)
+      if (abs(signum)!= 1)
         error->all(FLERR,"Wrong orientation in cluster of size 5"
           "in fix filter/corotate!");
       clist_q0[i][8] *= signum;
       clist_q0[i][11] *= signum;
-    }
+    } else {
-    else
-    {
       error->all(FLERR,"Fix filter/corotate cluster with size > 5"
         "not yet configured...");
     }

src/USER-OMP/fix_omp.cpp

@@ -80,7 +80,9 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg)
   if (nthreads < 1)
     error->all(FLERR,"Illegal number of OpenMP threads requested");
 
+#if defined(_OPENMP)
   int reset_thr = 0;
+#endif
   if (nthreads != comm->nthreads) {
 #if defined(_OPENMP)
     reset_thr = 1;

src/USER-OMP/thr_omp.h

@@ -185,6 +185,7 @@ static inline void loop_setup_thr(int &ifrom, int &ito, int &tid,
   tid = 0;
   ifrom = 0;
   ito = inum;
+  nthreads = 1;
 #endif
 }
 

src/compute_chunk_atom.cpp

@@ -66,7 +66,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
 
   // chunk style and its args
 
-  int iarg;
+  int iarg = 0;
 
   binflag = 0;
   ncoord = 0;
@@ -248,7 +248,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
     } else if (strcmp(arg[iarg],"bound") == 0) {
       if (iarg+4 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
-      int idim;
+      int idim = 0;
       if (strcmp(arg[iarg+1],"x") == 0) idim = 0;
       else if (strcmp(arg[iarg+1],"y") == 0) idim = 1;
       else if (strcmp(arg[iarg+1],"z") == 0) idim = 2;

src/compute_dihedral_local.h

@@ -33,7 +33,7 @@ class ComputeDihedralLocal : public Compute {
   double memory_usage();
 
  private:
-  int nvalues,nvar,ncount,setflag,tflag;
+  int nvalues,nvar,ncount,setflag;
 
   int pvar;
   int *bstyle,*vvar;

src/create_bonds.cpp

@@ -54,7 +54,7 @@ void CreateBonds::command(int narg, char **arg)
 
   int style;
 
-  int iarg;
+  int iarg = 0;
   if (strcmp(arg[0],"many") == 0) {
     style = MANY;
     if (narg != 6) error->all(FLERR,"Illegal create_bonds command");

src/displace_atoms.cpp

@@ -118,7 +118,7 @@ void DisplaceAtoms::command(int narg, char **arg)
 
   if (style == RAMP) {
 
-    int d_dim;
+    int d_dim = 0;
     if (strcmp(arg[2],"x") == 0) d_dim = 0;
     else if (strcmp(arg[2],"y") == 0) d_dim = 1;
     else if (strcmp(arg[2],"z") == 0) d_dim = 2;
@@ -136,7 +136,7 @@ void DisplaceAtoms::command(int narg, char **arg)
       d_hi = zscale*force->numeric(FLERR,arg[4]);
     }
 
-    int coord_dim;
+    int coord_dim = 0;
     if (strcmp(arg[5],"x") == 0) coord_dim = 0;
     else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
     else if (strcmp(arg[5],"z") == 0) coord_dim = 2;

src/dump_image.cpp

@@ -1290,7 +1290,7 @@ int DumpImage::modify_param(int narg, char **arg)
   if (strcmp(arg[0],"amap") == 0) {
     if (narg < 6) error->all(FLERR,"Illegal dump_modify command");
     if (strlen(arg[3]) != 2) error->all(FLERR,"Illegal dump_modify command");
-    int factor;
+    int factor = 0;
     if (arg[3][0] == 's') factor = 1;
     else if (arg[3][0] == 'c') factor = 2;
     else if (arg[3][0] == 'd') factor = 3;

src/fix_deform.cpp

@@ -802,7 +802,7 @@ void FixDeform::end_of_step()
       // tilt_target can be large positive or large negative value
       // add/subtract box lengths until tilt_target is closest to current value
 
-      int idenom;
+      int idenom = 0;
       if (i == 5) idenom = 0;
       else if (i == 4) idenom = 0;
       else if (i == 3) idenom = 1;

src/fix_move.cpp

@@ -68,7 +68,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
 
   // parse args
 
-  int iarg;
+  int iarg = 0;
 
   if (strcmp(arg[3],"linear") == 0) {
     if (narg < 7) error->all(FLERR,"Illegal fix move command");

src/input.cpp

@@ -1138,7 +1138,7 @@ void Input::partition()
 {
   if (narg < 3) error->all(FLERR,"Illegal partition command");
 
-  int yesflag;
+  int yesflag = 0;
   if (strcmp(arg[0],"yes") == 0) yesflag = 1;
   else if (strcmp(arg[0],"no") == 0) yesflag = 0;
   else error->all(FLERR,"Illegal partition command");

src/set.cpp

@@ -890,7 +890,7 @@ void Set::set(int keyword)
     // enforce quat rotation vector in z dir for 2d systems
 
     else if (keyword == QUAT) {
-      double *quat;
+      double *quat = NULL;
       if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
         quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
       else if (avec_tri && atom->tri[i] >= 0)

src/variable.cpp

@@ -182,7 +182,7 @@ void Variable::set(int narg, char **arg)
     if (find(arg[0]) >= 0) return;
     if (nvar == maxvar) grow();
     style[nvar] = LOOP;
-    int nfirst,nlast;
+    int nfirst = 0,nlast = 0;
     if (narg == 3 || (narg == 4 && strcmp(arg[3],"pad") == 0)) {
       nfirst = 1;
       nlast = force->inumeric(FLERR,arg[2]);
@@ -3983,7 +3983,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
       strcmp(word,"max") == 0 || strcmp(word,"ave") == 0 ||
       strcmp(word,"trap") == 0 || strcmp(word,"slope") == 0) {
 
-    int method;
+    int method = 0;
     if (strcmp(word,"sum") == 0) method = SUM;
     else if (strcmp(word,"min") == 0) method = XMIN;
     else if (strcmp(word,"max") == 0) method = XMAX;

src/velocity.cpp

@@ -641,7 +641,7 @@ void Velocity::ramp(int /*narg*/, char **arg)
 
   // parse args
 
-  int v_dim;
+  int v_dim = 0;
   if (strcmp(arg[0],"vx") == 0) v_dim = 0;
   else if (strcmp(arg[0],"vy") == 0) v_dim = 1;
   else if (strcmp(arg[0],"vz") == 0) v_dim = 2;
@@ -662,7 +662,7 @@ void Velocity::ramp(int /*narg*/, char **arg)
     v_hi = zscale*force->numeric(FLERR,arg[2]);
   }
 
-  int coord_dim;
+  int coord_dim = 0;
   if (strcmp(arg[3],"x") == 0) coord_dim = 0;
   else if (strcmp(arg[3],"y") == 0) coord_dim = 1;
   else if (strcmp(arg[3],"z") == 0) coord_dim = 2;

src/write_dump.cpp

@@ -45,7 +45,7 @@ void WriteDump::command(int narg, char **arg)
   // create the Dump instance
   // create dump command line with extra required args
 
-  Dump *dump;
+  Dump *dump = NULL;
 
   char **dumpargs = new char*[modindex+2];
   dumpargs[0] = (char *) "WRITE_DUMP"; // dump id