fix bugs found by or avoid warnings from coverity scan

src/BODY/fix_wall_body_polygon.cpp

@@ -59,6 +59,7 @@ FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) :
 
   restart_peratom = 1;
   create_attribute = 1;
+  wallstyle = -1;
 
   // wall/particle coefficients
 
@@ -96,7 +97,7 @@ FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) :
     lo = hi = 0.0;
     cylradius = utils::numeric(FLERR,arg[iarg+1],false,lmp);
     iarg += 2;
-  }
+  } else error->all(FLERR,fmt::format("Unknown wall style {}",arg[iarg]));
 
   // check for trailing keyword/values
 

src/BODY/fix_wall_body_polyhedron.cpp

@@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;
 
-enum{XPLANE=0,YPLANE=1,ZPLANE};    // XYZ PLANE need to be 0,1,2
+enum{XPLANE=0,YPLANE=1,ZPLANE=2};    // XYZ PLANE need to be 0,1,2
 enum{HOOKE,HOOKE_HISTORY};
 
 enum {INVALID=0,NONE=1,VERTEX=2};
@@ -59,6 +59,7 @@ FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg)
 
   restart_peratom = 1;
   create_attribute = 1;
+  wallstyle = -1;
 
   // wall/particle coefficients
 

src/COLLOID/pair_colloid.cpp

@@ -473,6 +473,7 @@ double PairColloid::single(int /*i*/, int /*j*/, int itype, int jtype, double rs
   double K[9],h[4],g[4];
   double r,r2inv,r6inv,forcelj,c1,c2,phi,fR,dUR,dUA;
 
+  phi = 0.0;
   switch (form[itype][jtype]) {
   case SMALL_SMALL:
     r2inv = 1.0/rsq;

src/MC/fix_tfmc.cpp

@@ -56,6 +56,7 @@ FixTFMC::FixTFMC(LAMMPS *lmp, int narg, char **arg) :
 
   comflag = 0;
   rotflag = 0;
+  xflag = yflag = zflag = 0;
 
   int iarg = 6;
   while (iarg < narg) {

src/SHOCK/fix_append_atoms.cpp

@@ -49,6 +49,7 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
   scaleflag = 1;
   spatflag=0;
   spatialid = nullptr;
+  size = 0.0;
   xloflag = xhiflag = yloflag = yhiflag = zloflag = zhiflag = 0;
 
   tempflag = 0;

src/SHOCK/fix_wall_piston.cpp

@@ -43,6 +43,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
   tempflag = 0;
   scaleflag = 1;
   roughflag = 0;
+  roughdist = 0.0;
   rampflag = 0;
   rampNL1flag = 0;
   rampNL2flag = 0;

src/compute_chunk_atom.cpp

@@ -386,7 +386,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
   // apply scaling factors and cylinder dims orthogonal to axis
 
   if (binflag) {
-    double scale;
+    double scale = 1.0;
     if (which == ArgInfo::BIN1D || which == ArgInfo::BIN2D
         || which == ArgInfo::BIN3D || which == ArgInfo::BINCYLINDER) {
       if (which == ArgInfo::BIN1D || which == ArgInfo::BINCYLINDER) ndim = 1;

src/compute_global_atom.cpp

@@ -50,7 +50,7 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
   indexref = argi.get_index1();
   idref = argi.copy_name();
 
-  if ((whichref == ArgInfo::UNKNOWN) || (which[nvalues] == ArgInfo::NONE)
+  if ((whichref == ArgInfo::UNKNOWN) || (whichref == ArgInfo::NONE)
       || (argi.get_dim() > 1))
     error->all(FLERR,"Illegal compute global/atom command");
 

src/fix_ave_histo_weight.cpp

@@ -51,7 +51,7 @@ FixAveHistoWeight::FixAveHistoWeight(LAMMPS *lmp, int narg, char **arg) :
 
   // check that length of 2 values is the same
 
-  int size[2];
+  int size[2] = {0,0};
 
   for (int i = 0; i < nvalues; i++) {
     if (which[i] == ArgInfo::X || which[i] == ArgInfo::V || which[i] == ArgInfo::F) {

src/update.cpp

@@ -54,6 +54,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
   eflag_atom = vflag_atom = 0;
 
   dt_default = 1;
+  dt = 0.0;
   unit_style = nullptr;
   set_units("lj");