diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index cef875ed7c..67342d91d6 100755
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -79,8 +79,9 @@ PairPolymorphic::~PairPolymorphic()
 
 void PairPolymorphic::compute(int eflag, int vflag)
 {
+  tagint itag,jtag;
   int i,j,k,ii,jj,kk,inum,jnum;
-  int itag,jtag,iel,jel,kel,iparam_ij,iparam_ik,iparam_ijk;
+  int iel,jel,kel,iparam_ij,iparam_ik,iparam_ijk;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,rsq1,rsq2,r0,r1,r2;
   double delr1[3],delr2[3],fi[3],fj[3],fk[3];
@@ -94,7 +95,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
 
   double **x = atom->x;
   double **f = atom->f;
-  int *tag = atom->tag;
+  tagint *tag = atom->tag;
   int *type = atom->type;
   int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
@@ -512,7 +513,7 @@ void PairPolymorphic::read_file(char *file, char** elements)
   // open file on proc 0
   FILE *fp=NULL;
   if (comm->me == 0) {
-    fp = fopen(file,"r");
+    fp = force->open_potential(file);
     if (fp == NULL) {
       char str[128];
       sprintf(str,"Cannot open polymorphic potential file %s",file);
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index f9af5d3d92..6b61b5c1ef 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -146,7 +146,6 @@ void AtomVecSMD::grow_reset() {
 	radius = atom->radius;
 	rmass = atom->rmass;
 
-	molecule = atom->molecule;
 	vfrac = atom->vfrac;
 	x0 = atom->x0;
 	contact_radius = atom->contact_radius;
@@ -657,7 +656,7 @@ void AtomVecSMD::unpack_border_vel(int n, int first, double *buf) {
 		tag[i] = (tagint) ubuf(buf[m++]).i;
 		type[i] = (int) ubuf(buf[m++]).i;
 		mask[i] = (int) ubuf(buf[m++]).i;
-		molecule[i] = (int) ubuf(buf[m++]).i; // 10
+		molecule[i] = (tagint) ubuf(buf[m++]).i; // 10
 
 		radius[i] = buf[m++];
 		rmass[i] = buf[m++];
@@ -698,7 +697,7 @@ int AtomVecSMD::unpack_border_hybrid(int n, int first, double *buf) {
 		x0[i][0] = buf[m++];
 		x0[i][1] = buf[m++];
 		x0[i][2] = buf[m++]; // 3
-		molecule[i] = (int) ubuf(buf[m++]).i; // 4
+		molecule[i] = (tagint) ubuf(buf[m++]).i; // 4
 		radius[i] = buf[m++];
 		rmass[i] = buf[m++];
 		vfrac[i] = buf[m++];
@@ -790,7 +789,7 @@ int AtomVecSMD::unpack_exchange(double *buf) {
 	type[nlocal] = (int) ubuf(buf[m++]).i;
 	mask[nlocal] = (int) ubuf(buf[m++]).i;
 	image[nlocal] = (imageint) ubuf(buf[m++]).i;
-	molecule[nlocal] = (int) ubuf(buf[m++]).i; // 11
+	molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
 
 	radius[nlocal] = buf[m++];
 	rmass[nlocal] = buf[m++];
@@ -920,7 +919,7 @@ int AtomVecSMD::unpack_restart(double *buf) {
 	type[nlocal] = (int) ubuf(buf[m++]).i;
 	mask[nlocal] = (int) ubuf(buf[m++]).i;
 	image[nlocal] = (imageint) ubuf(buf[m++]).i;
-	molecule[nlocal] = (int) ubuf(buf[m++]).i; // 11
+	molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
 
 	radius[nlocal] = buf[m++];
 	rmass[nlocal] = buf[m++];
@@ -1034,7 +1033,7 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) {
 	if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
 		error->one(FLERR, "Invalid atom type in Atoms section of data file");
 
-	molecule[nlocal] = atoi(values[2]);
+	molecule[nlocal] = ATOTAGINT(values[2]);
 	if (molecule[nlocal] <= 0)
 		error->one(FLERR, "Invalid molecule in Atoms section of data file");
 
diff --git a/src/USER-SMD/atom_vec_smd.h b/src/USER-SMD/atom_vec_smd.h
index c79c60c352..cea9a31f86 100644
--- a/src/USER-SMD/atom_vec_smd.h
+++ b/src/USER-SMD/atom_vec_smd.h
@@ -88,7 +88,7 @@ class AtomVecSMD : public AtomVec {
   double **x,**v,**f;
   double *radius,*rmass;
 
-  int *molecule;
+  tagint *molecule;
   double *vfrac,**x0,*contact_radius, **smd_data_9, *e, *de, **vest;
   double **tlsph_stress;
   double *eff_plastic_strain;
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index 407eabf452..ab81caeba3 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -255,7 +255,7 @@ void FixSMDMoveTriSurf::initial_integrate(int vflag) {
 	double **v = atom->v;
 	double **vest = atom->vest;
 	double **smd_data_9 = atom->smd_data_9;
-	int *mol = atom->molecule;
+	tagint *mol = atom->molecule;
 
 	int *mask = atom->mask;
 	int nlocal = atom->nlocal;
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index 776acff7a8..41866b1d3e 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -437,7 +437,7 @@ void FixSMDWallSurface::read_triangles(int pass) {
 			 * due to calling grow() in create_atoms() above;
 			 */
 
-			int *mol = atom->molecule;
+			tagint *mol = atom->molecule;
 			int *type = atom->type;
 			double *radius = atom->radius;
 			double *contact_radius = atom->contact_radius;
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index 77a45ee754..9b293d77d8 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -137,7 +137,7 @@ PairTlsph::~PairTlsph() {
  ---------------------------------------------------------------------- */
 
 void PairTlsph::PreCompute() {
-	int *mol = atom->molecule;
+	tagint *mol = atom->molecule;
 	double *vfrac = atom->vfrac;
 	double *radius = atom->radius;
 	double **x0 = atom->x0;
@@ -145,7 +145,7 @@ void PairTlsph::PreCompute() {
 	double **v = atom->vest; // extrapolated velocities corresponding to current positions
 	double **vint = atom->v; // Velocity-Verlet algorithm velocities
 	double *damage = atom->damage;
-	int *tag = atom->tag;
+	tagint *tag = atom->tag;
 	int *type = atom->type;
 	int nlocal = atom->nlocal;
 	int jnum, jj, i, j, itype, idim;
@@ -417,7 +417,7 @@ void PairTlsph::compute(int eflag, int vflag) {
 }
 
 void PairTlsph::ComputeForces(int eflag, int vflag) {
-	int *mol = atom->molecule;
+	tagint *mol = atom->molecule;
 	double **x = atom->x;
 	double **v = atom->vest;
 	double **x0 = atom->x0;
@@ -702,7 +702,7 @@ void PairTlsph::ComputeForces(int eflag, int vflag) {
  shape matrix correction
  ------------------------------------------------------------------------- */
 void PairTlsph::AssembleStress() {
-	int *mol = atom->molecule;
+	tagint *mol = atom->molecule;
 	double *eff_plastic_strain = atom->eff_plastic_strain;
 	double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
 	double **tlsph_stress = atom->smd_stress;
@@ -1842,7 +1842,7 @@ void *PairTlsph::extract(const char *str, int &i) {
 
 int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
 	int i, j, m;
-	int *mol = atom->molecule;
+	tagint *mol = atom->molecule;
 	double *damage = atom->damage;
 	double *eff_plastic_strain = atom->eff_plastic_strain;
 	double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
@@ -1885,7 +1885,7 @@ int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, in
 
 void PairTlsph::unpack_forward_comm(int n, int first, double *buf) {
 	int i, m, last;
-	int *mol = atom->molecule;
+	tagint *mol = atom->molecule;
 	double *damage = atom->damage;
 	double *eff_plastic_strain = atom->eff_plastic_strain;
 	double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index 9fc057e1db..6d27187260 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -101,7 +101,7 @@ void PairTriSurf::compute(int eflag, int vflag) {
 	else
 		evflag = vflag_fdotr = 0;
 
-	int *mol = atom->molecule;
+	tagint *mol = atom->molecule;
 	double **f = atom->f;
 	double **smd_data_9 = atom->smd_data_9;
 	double **x = atom->x;
diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp
index f5f0f55f63..4746a22c0b 100644
--- a/src/atom_vec_tri.cpp
+++ b/src/atom_vec_tri.cpp
@@ -1433,7 +1433,7 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
 
   // size = length of one edge
 
-  double c2mc1[2],c3mc1[3];
+  double c2mc1[3],c3mc1[3];
   MathExtra::sub3(c2,c1,c2mc1);
   MathExtra::sub3(c3,c1,c3mc1);
   double size = MAX(MathExtra::len3(c2mc1),MathExtra::len3(c3mc1));
@@ -1557,7 +1557,7 @@ int AtomVecTri::data_vel_hybrid(int m, char **values)
 
 void AtomVecTri::pack_data(double **buf)
 {
-  double c2mc1[2],c3mc1[3],norm[3];
+  double c2mc1[3],c3mc1[3],norm[3];
   double area;
 
   int nlocal = atom->nlocal;
@@ -1595,7 +1595,7 @@ int AtomVecTri::pack_data_hybrid(int i, double *buf)
   else buf[1] = ubuf(1).d;
   if (tri[i] < 0) buf[2] = rmass[i];
   else {
-    double c2mc1[2],c3mc1[3],norm[3];
+    double c2mc1[3],c3mc1[3],norm[3];
     MathExtra::sub3(bonus[tri[i]].c2,bonus[tri[i]].c1,c2mc1);
     MathExtra::sub3(bonus[tri[i]].c3,bonus[tri[i]].c1,c3mc1);
     MathExtra::cross3(c2mc1,c3mc1,norm);
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index d5a7a8abf1..0aaa3713ae 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -722,9 +722,9 @@ void DeleteAtoms::options(int narg, char **arg)
       iarg += 2;
     } else if (strcmp(arg[iarg],"mol") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
-      if (atom->molecular == 0) 
-        error->all(FLERR,"Cannot delete_atoms mol yes for "
-                   "non-molecular systems");
+      if (atom->molecule_flag == 0) 
+        error->all(FLERR,"Delete_atoms mol yes requires "
+                   "atom attribute molecule");
       if (strcmp(arg[iarg+1],"yes") == 0) mol_flag = 1;
       else if (strcmp(arg[iarg+1],"no") == 0) mol_flag = 0;
       else error->all(FLERR,"Illegal delete_atoms command");
diff --git a/src/math_extra.cpp b/src/math_extra.cpp
index dda3205817..eb2afcea2c 100644
--- a/src/math_extra.cpp
+++ b/src/math_extra.cpp
@@ -61,7 +61,7 @@ int mldivide3(const double m[3][3], const double *v, double *ans)
       }
     }
 
-    while (aug[p][i] == 0.0 && p < 3) p++;
+    while (p < 3 && aug[p][i] == 0.0) p++;
 
     if (p == 3) return 1;
     else
diff --git a/src/set.cpp b/src/set.cpp
index 737568a085..d8cbbf6806 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -642,7 +642,7 @@ void Set::set(int keyword)
         double *c1 = avec_tri->bonus[atom->tri[i]].c1;
         double *c2 = avec_tri->bonus[atom->tri[i]].c2;
         double *c3 = avec_tri->bonus[atom->tri[i]].c3;
-        double c2mc1[2],c3mc1[3];
+        double c2mc1[3],c3mc1[3];
         MathExtra::sub3(c2,c1,c2mc1);
         MathExtra::sub3(c3,c1,c3mc1);
         double norm[3];