git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4320 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/atom.cpp

@@ -1336,7 +1336,7 @@ void Atom::first_reorder()
 
 void Atom::sort()
 {
-  int i,m,n,ix,iy,iz,ibin,empty,ndone;
+  int i,m,n,ix,iy,iz,ibin,empty;
 
   // re-setup sort bins if needed
 

src/change_box.cpp

@@ -38,6 +38,7 @@ void ChangeBox::command(int narg, char **arg)
   int style;
   if (strcmp(arg[0],"ortho") == 0) style = ORTHO;
   else if (strcmp(arg[0],"triclinic") == 0) style = TRICLINIC;
+  else error->all("Illegal change_box command");
 
   if (style == ORTHO && domain->triclinic == 0)
     error->all("Change_box operation is invalid");

src/compute_erotate_sphere.cpp

@@ -102,12 +102,14 @@ double ComputeERotateSphere::compute_scalar()
 		      omega[i][2]*omega[i][2]) * radius[i]*radius[i]*rmass[i];
     } else {
       for (i = 0; i < nlocal; i++)
-	if (mask[i] & groupbit)
+	if (mask[i] & groupbit) {
+	  itype = type[i];
 	  erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] + 
 		      omega[i][2]*omega[i][2]) * 
 	    radius[i]*radius[i]*mass[itype];
+	}
     }
-
+    
   } else {
     if (rmass) {
       for (i = 0; i < nlocal; i++) 

src/compute_improper_local.cpp

@@ -117,7 +117,6 @@ int ComputeImproperLocal::compute_impropers(int flag)
   int **improper_atom2 = atom->improper_atom2;
   int **improper_atom3 = atom->improper_atom3;
   int **improper_atom4 = atom->improper_atom4;
-  int **improper_type = atom->improper_type;
   int *tag = atom->tag;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;

src/compute_property_local.cpp

@@ -281,7 +281,7 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag)
 {
   int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz;
-  double rsq,eng,fpair,factor_coul,factor_lj;
+  double rsq,factor_coul,factor_lj;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   double **x = atom->x;
@@ -306,7 +306,6 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag)
   // loop over neighbors of my atoms
   // skip if I or J are not in group
 
-  Pair *pair = force->pair;
   double **cutsq = force->pair->cutsq;
 
   m = n = 0;
@@ -453,7 +452,6 @@ int ComputePropertyLocal::count_dihedrals(int flag)
   int **dihedral_atom2 = atom->dihedral_atom2;
   int **dihedral_atom3 = atom->dihedral_atom3;
   int **dihedral_atom4 = atom->dihedral_atom4;
-  int **dihedral_type = atom->dihedral_type;
   int *tag = atom->tag;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
@@ -497,7 +495,6 @@ int ComputePropertyLocal::count_impropers(int flag)
   int **improper_atom2 = atom->improper_atom2;
   int **improper_atom3 = atom->improper_atom3;
   int **improper_atom4 = atom->improper_atom4;
-  int **improper_type = atom->improper_type;
   int *tag = atom->tag;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;

src/compute_temp_profile.cpp

@@ -171,7 +171,6 @@ double ComputeTempProfile::compute_scalar()
 
   bin_average();
 
-  double **x = atom->x;
   double **v = atom->v;
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -215,7 +214,6 @@ void ComputeTempProfile::compute_vector()
 
   bin_average();
 
-  double **x = atom->x;
   double **v = atom->v;
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -277,7 +275,6 @@ void ComputeTempProfile::remove_bias(int i, double *v)
 
 void ComputeTempProfile::remove_bias_all()
 {
-  double **x = atom->x;
   double **v = atom->v;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
@@ -367,7 +364,6 @@ void ComputeTempProfile::bin_average()
 
   // sum each particle's velocity to appropriate bin
 
-  double **x = atom->x;
   double **v = atom->v;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;

src/read_restart.cpp

@@ -481,10 +481,6 @@ void ReadRestart::header()
 	}
       }
 
-      int flag = 0;
-      if ((xperiodic != domain->xperiodic || yperiodic != domain->yperiodic ||
-	   zperiodic != domain->zperiodic)) flag = 1;
-
       domain->boundary[0][0] = boundary[0][0];
       domain->boundary[0][1] = boundary[0][1];
       domain->boundary[1][0] = boundary[1][0];

src/region.cpp

@@ -181,8 +181,6 @@ int Region::dynamic_check()
 
 int Region::match(double x, double y, double z)
 {
-  double a[3],b[3],c[3],d[3];
-
   if (dynamic) {
     double delta = (update->ntimestep - time_origin) * dt;
     if (dynamic == VELOCITY) {

src/region_block.cpp

@@ -197,7 +197,6 @@ int RegBlock::surface_interior(double *x, double cutoff)
 int RegBlock::surface_exterior(double *x, double cutoff)
 {
   double xp,yp,zp;
-  double delta;
 
   // x is far enough from block that there is no contact
   // x is interior to block

src/region_cone.cpp

@@ -262,18 +262,18 @@ int RegCone::surface_interior(double *x, double cutoff)
     }
 
   } else if (axis == 'y') {
-    delx = x[0] - c1;
+    del1 = x[0] - c1;
-    delz = x[2] - c2;
+    del2 = x[2] - c2;
-    r = sqrt(delx*delx + delz*delz);
+    r = sqrt(del1*del1 + del2*del2);
     currentradius = radiuslo + (x[1]-lo)*(radiushi-radiuslo)/(hi-lo);
 
-    // x is exterior to cone
+    // y is exterior to cone
     
     if (r > currentradius || x[1] < lo || x[1] > hi) return 0;
 
-    // x is interior to cone or on its surface
+    // y is interior to cone or on its surface
-    // surflo = pt on outer circle of bottom end plane, same dir as x vs axis
+    // surflo = pt on outer circle of bottom end plane, same dir as y vs axis
-    // surfhi = pt on outer circle of top end plane, same dir as x vs axis
+    // surfhi = pt on outer circle of top end plane, same dir as y vs axis
 
     if (r > 0.0) {
       surflo[0] = c1 + del1*radiuslo/r;
@@ -312,18 +312,18 @@ int RegCone::surface_interior(double *x, double cutoff)
     }
 
   } else {
-    delx = x[0] - c1;
+    del1 = x[0] - c1;
-    dely = x[1] - c2;
+    del2 = x[1] - c2;
-    r = sqrt(delx*delx + dely*dely);
+    r = sqrt(del1*del1 + del2*del2);
     currentradius = radiuslo + (x[2]-lo)*(radiushi-radiuslo)/(hi-lo);
 
     // x is exterior to cone
     
     if (r > currentradius || x[2] < lo || x[2] > hi) return 0;
 
-    // x is interior to cone or on its surface
+    // z is interior to cone or on its surface
-    // surflo = pt on outer circle of bottom end plane, same dir as x vs axis
+    // surflo = pt on outer circle of bottom end plane, same dir as z vs axis
-    // surfhi = pt on outer circle of top end plane, same dir as x vs axis
+    // surfhi = pt on outer circle of top end plane, same dir as z vs axis
 
     if (r > 0.0) {
       surflo[0] = c1 + del1*radiuslo/r;
@@ -427,17 +427,17 @@ int RegCone::surface_exterior(double *x, double cutoff)
     r = sqrt(del1*del1 + del2*del2);
     currentradius = radiuslo + (x[1]-lo)*(radiushi-radiuslo)/(hi-lo);
 
-    // x is far enough from cone that there is no contact
+    // y is far enough from cone that there is no contact
-    // x is interior to cone
+    // y is interior to cone
 
     if (r >= maxradius+cutoff || 
 	x[1] <= lo-cutoff || x[1] >= hi+cutoff) return 0;
     if (r < currentradius && x[1] > lo && x[1] < hi) return 0;
 
-    // x is exterior to cone or on its surface
+    // y is exterior to cone or on its surface
-    // corner1234 = 4 corner pts of half trapezoid = cone surf in plane of x
+    // corner1234 = 4 corner pts of half trapezoid = cone surf in plane of y
     // project x to 3 line segments in half trapezoid (4th is axis of cone)
-    // nearest = point on surface of cone that x is closest to
+    // nearest = point on surface of cone that y is closest to
     //           could be edge of cone
     // do not add contact point if r >= cutoff
 
@@ -472,17 +472,17 @@ int RegCone::surface_exterior(double *x, double cutoff)
     r = sqrt(del1*del1 + del2*del2);
     currentradius = radiuslo + (x[2]-lo)*(radiushi-radiuslo)/(hi-lo);
 
-    // x is far enough from cone that there is no contact
+    // z is far enough from cone that there is no contact
-    // x is interior to cone
+    // z is interior to cone
 
     if (r >= maxradius+cutoff || 
 	x[2] <= lo-cutoff || x[2] >= hi+cutoff) return 0;
     if (r < currentradius && x[2] > lo && x[2] < hi) return 0;
 
-    // x is exterior to cone or on its surface
+    // z is exterior to cone or on its surface
-    // corner1234 = 4 corner pts of half trapezoid = cone surf in plane of x
+    // corner1234 = 4 corner pts of half trapezoid = cone surf in plane of z
     // project x to 3 line segments in half trapezoid (4th is axis of cone)
-    // nearest = point on surface of cone that x is closest to
+    // nearest = point on surface of cone that z is closest to
     //           could be edge of cone
     // do not add contact point if r >= cutoff
 

src/region_cylinder.cpp

@@ -231,11 +231,11 @@ int RegCylinder::surface_interior(double *x, double cutoff)
     del2 = x[2] - c2;
     r = sqrt(del1*del1 + del2*del2);
 
-    // x is exterior to cylinder
+    // y is exterior to cylinder
     
     if (r > radius || x[1] < lo || x[1] > hi) return 0;
 
-    // x is interior to cylinder or on its surface
+    // y is interior to cylinder or on its surface
 
     delta = radius - r;
     if (delta < cutoff && r > 0.0) {
@@ -265,11 +265,11 @@ int RegCylinder::surface_interior(double *x, double cutoff)
     del2 = x[1] - c2;
     r = sqrt(del1*del1 + del2*del2);
 
-    // x is exterior to cylinder
+    // z is exterior to cylinder
     
     if (r > radius || x[2] < lo || x[2] > hi) return 0;
 
-    // x is interior to cylinder or on its surface
+    // z is interior to cylinder or on its surface
 
     delta = radius - r;
     if (delta < cutoff && r > 0.0) {
@@ -306,7 +306,7 @@ int RegCylinder::surface_interior(double *x, double cutoff)
 
 int RegCylinder::surface_exterior(double *x, double cutoff)
 {
-  double del1,del2,r,delta;
+  double del1,del2,r;
   double xp,yp,zp;
 
   if (axis == 'x') {
@@ -345,13 +345,13 @@ int RegCylinder::surface_exterior(double *x, double cutoff)
     del2 = x[2] - c2;
     r = sqrt(del1*del1 + del2*del2);
 
-    // x is far enough from cylinder that there is no contact
+    // y is far enough from cylinder that there is no contact
-    // x is interior to cylinder
+    // y is interior to cylinder
 
     if (r >= radius+cutoff || x[1] <= lo-cutoff || x[1] >= hi+cutoff) return 0;
     if (r < radius && x[1] > lo && x[1] < hi) return 0;
 
-    // x is exterior to cylinder or on its surface
+    // y is exterior to cylinder or on its surface
     // xp,yp,zp = point on surface of cylinder that x is closest to
     //            could be edge of cylinder
     // do not add contact point if r >= cutoff
@@ -376,13 +376,13 @@ int RegCylinder::surface_exterior(double *x, double cutoff)
     del2 = x[1] - c2;
     r = sqrt(del1*del1 + del2*del2);
 
-    // x is far enough from cylinder that there is no contact
+    // z is far enough from cylinder that there is no contact
-    // x is interior to cylinder
+    // z is interior to cylinder
 
     if (r >= radius+cutoff || x[2] <= lo-cutoff || x[2] >= hi+cutoff) return 0;
     if (r < radius && x[2] > lo && x[2] < hi) return 0;
 
-    // x is exterior to cylinder or on its surface
+    // z is exterior to cylinder or on its surface
     // xp,yp,zp = point on surface of cylinder that x is closest to
     //            could be edge of cylinder
     // do not add contact point if r >= cutoff

src/region_prism.cpp

@@ -304,7 +304,7 @@ int RegPrism::surface_interior(double *x, double cutoff)
 int RegPrism::surface_exterior(double *x, double cutoff)
 {
   int i;
-  double dot,delta;
+  double dot;
   double *corner;
   double xp,yp,zp;
 

src/special.cpp

@@ -705,7 +705,6 @@ void Special::dihedral_trim()
   MPI_Request request;
   MPI_Status status;
 
-  int *tag = atom->tag;
   int *num_dihedral = atom->num_dihedral;
   int **dihedral_atom1 = atom->dihedral_atom1;
   int **dihedral_atom4 = atom->dihedral_atom4;

src/temper.cpp

@@ -176,7 +176,7 @@ void Temper::command(int narg, char **arg)
   // setup tempering runs
 
   int i,which,partner,swap,partner_set_temp,partner_world;
-  double pe,pe_partner,ke,boltz_factor,new_temp;
+  double pe,pe_partner,boltz_factor,new_temp;
   MPI_Status status;
 
   if (me_universe == 0 && universe->uscreen)