silence compiler warnings

src/BPM/fix_update_special_bonds.cpp

@@ -154,7 +154,7 @@ void FixUpdateSpecialBonds::pre_exchange()
 
 void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
 {
-  int ilist, nlist, i1, i2, j, jj, jnum;
+  int i1, i2, j, jj, jnum;
   int *jlist, *numneigh, **firstneigh;
   tagint tag1, tag2;
   NeighList *list;

src/EXTRA-COMPUTE/compute_rattlers_atom.h

@@ -38,8 +38,7 @@ class ComputeRattlersAtom : public Compute {
   void unpack_reverse_comm(int, int *, double *) override;
 
  private:
-  int pstyle, cutstyle;
+  int cutstyle, ncontacts_rattler, max_tries, nmax, invoked_peratom;
-  int ncontacts_rattler, max_tries, nmax, invoked_peratom;
   int *ncontacts;
   double *rattler;
   class NeighList *list;

src/EXTRA-COMPUTE/compute_slcsa_atom.cpp

@@ -33,21 +33,20 @@
 
 #include <cmath>
 #include <cstring>
-#include <iostream>
 
 using namespace LAMMPS_NS;
 
 static const char cite_compute_slcsa_atom_c[] =
-    "compute slcsa/atom command: doi:10.1088/0965-0393/21/5/055020\n\n"
+    "compute slcsa/atom command: doi:10.1016/j.commatsci.2023.112534\n\n"
     "@Article{Lafourcade2023,\n"
     " author = {P. Lafourcade and J.-B. Maillet and C. Denoual and E. Duval and A. Allera and A. "
     "M. Goryaeva and M.-C. Marinica},\n"
     " title = {Robust crystal structure identification at extreme conditions using a "
     "density-independent spectral descriptor and supervised learning},\n"
     " journal = {Computational Materials Science},\n"
-    " year =    2023,\n"
+    " year = 2023,\n"
-    " volume =  XX,\n"
+    " volume = 230,\n"
-    " pages =   {XXXXXX}\n"
+    " pages = 112534\n"
     "}\n\n";
 
 /* ---------------------------------------------------------------------- */
@@ -79,6 +78,8 @@ ComputeSLCSAAtom::ComputeSLCSAAtom(LAMMPS *lmp, int narg, char **arg) :
   // # LR bias vector
   // vector with 1 row x nclasses cols
 
+  if (lmp->citeme) lmp->citeme->add(cite_compute_slcsa_atom_c);
+
   if (narg != 11) utils::missing_cmd_args(FLERR, "compute slcsa/atom", error);
 
   int twojmax = utils::inumeric(FLERR, arg[3], false, lmp);

src/EXTRA-COMPUTE/compute_slcsa_atom.h

@@ -53,14 +53,12 @@ class ComputeSLCSAAtom : public Compute {
   value_t descriptorval;
   int nmax;
   int ncols;
-  int nevery;
   int ncomps;
   int nclasses;
   const char *database_mean_descriptor_file;
   const char *lda_scalings_file;
   const char *lr_decision_file;
   const char *lr_bias_file;
-  const char *covmat_file;
   const char *maha_file;
   class NeighList *list;
 

src/EXTRA-FIX/fix_nonaffine_displacement.cpp

@@ -202,7 +202,7 @@ void FixNonaffineDisplacement::init()
     // need an occasional half neighbor list
 
     if (cut_style == RADIUS) {
-      auto req = neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_OCCASIONAL);
+      neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_OCCASIONAL);
     } else {
       auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
       if (cut_style == CUSTOM) {
@@ -233,7 +233,7 @@ void FixNonaffineDisplacement::init_list(int /*id*/, NeighList *ptr)
 
 /* ---------------------------------------------------------------------- */
 
-void FixNonaffineDisplacement::setup(int vflag)
+void FixNonaffineDisplacement::setup(int /*vflag*/)
 {
   post_force(0); // Save state if needed before starting the 1st timestep
 }
@@ -285,7 +285,6 @@ void FixNonaffineDisplacement::restart(char *buf)
 
 void FixNonaffineDisplacement::integrate_velocity()
 {
-  int i,n;
   dtv = update->dt;
 
   double **v = atom->v;
@@ -306,7 +305,6 @@ void FixNonaffineDisplacement::integrate_velocity()
 
 void FixNonaffineDisplacement::save_reference_state()
 {
-  int i, n;
   double **x = atom->x;
 
   int *mask = atom->mask;
@@ -354,15 +352,14 @@ void FixNonaffineDisplacement::calculate_D2Min()
 
   int i, j, k, l, ii, jj, inum, jnum, itype, jtype;
   double evol, j2, edev;
-  double r[3], r0[3], rsq, rsq0, radsum, temp[3];
+  double r[3], r0[3], rsq, radsum, temp[3];
   double X_tmp[3][3], Y_tmp[3][3], F_tmp[3][3], E[3][3];
-  double Y_inv[3][3] = {0.0}; // Zero for 2d since not all entries used
+  double Y_inv[3][3] = {{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; // Zero for 2d since not all entries used
   int *ilist, *jlist, *numneigh, **firstneigh;
 
   double **x = atom->x;
   double **x0 = array_atom;
   double *radius = atom->radius;
-  tagint *tag = atom->tag;
   int *type = atom->type;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;

src/EXTRA-MOLECULE/dihedral_quadratic.cpp

@@ -338,7 +338,7 @@ void DihedralQuadratic::born_matrix(int nd, int i1, int i2, int i3, int i4,
   double sb1,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
   double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
   double c2mag,sc1,sc2,s12,c;
-  double s1,s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2;
+  double cx,cy,cz,cmag,dx,phi,si,siinv,sin2;
 
   int **dihedrallist = neighbor->dihedrallist;
   double **x = atom->x;
@@ -405,8 +405,6 @@ void DihedralQuadratic::born_matrix(int nd, int i1, int i2, int i3, int i4,
   if (sc2 < SMALL) sc2 = SMALL;
   sc2 = 1.0/sc2;
 
-  s1 = sc1 * sc1;
-  s2 = sc2 * sc2;
   s12 = sc1 * sc2;
   c = (c0 + c1mag*c2mag) * s12;