fix some minor bugs write data file writing and remove dead code and silence compiler warnings

src/USER-COLVARS/group_ndx.cpp

@@ -50,7 +50,7 @@ static int cmptagint(const void *p1, const void *p2)
 static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
                         int np, MPI_Comm world, FILE *screen, FILE *logfile)
 {
-  char fmt[8];
+  char fmt[16];
   tagint *sendlist, *recvlist;
   bigint num = group->count(gid);
   int lnum, cols;
@@ -73,7 +73,7 @@ static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
       ++i;
       j /= 10;
     }
-    sprintf(fmt,"%%%dd ", i);
+    snprintf(fmt,16,"%%%dd ", i);
     cols = 80 / (i+1);
   }
 

src/USER-DPD/fix_rx.cpp

@@ -758,8 +758,10 @@ void FixRX::pre_force(int /*vflag*/)
     memory->create( diagnosticCounterPerODE[FuncSum], nlocal, "FixRX::diagnosticCounterPerODE");
   }
 
-  //#pragma omp parallel \
-  //   reduction(+: nSteps, nIters, nFuncs, nFails )
+#if 0
+  #pragma omp parallel \
+     reduction(+: nSteps, nIters, nFuncs, nFails )
+#endif
   {
     double *rwork = new double[8*nspecies];
 

src/USER-MISC/compute_stress_mop_profile.cpp

@@ -451,10 +451,9 @@ void ComputeStressMopProfile::setup_bins()
   int i,n;
   double lo = 0.0, hi = 0.0;
 
-  double *boxlo,*boxhi,*prd;
+  double *boxlo,*boxhi;
   boxlo = domain->boxlo;
   boxhi = domain->boxhi;
-  prd = domain->prd;
 
   if (originflag == LOWER) origin = boxlo[dir];
   else if (originflag == UPPER) origin = boxhi[dir];

src/USER-MOFFF/angle_class2_p6.cpp

@@ -429,7 +429,7 @@ void AngleClass2P6::read_restart(FILE *fp)
 void AngleClass2P6::write_data(FILE *fp)
 {
   for (int i = 1; i <= atom->nangletypes; i++)
-    fprintf(fp,"%d %g %g %g %g\n",
+    fprintf(fp,"%d %g %g %g %g %g %g\n",
             i,theta0[i]/MY_PI*180.0,k2[i],k3[i],k4[i],k5[i],k6[i]);
 
   fprintf(fp,"\nBondBond Coeffs\n\n");

src/USER-MOFFF/angle_cosine_buck6d.cpp

@@ -353,7 +353,7 @@ void AngleCosineBuck6d::read_restart(FILE *fp)
 void AngleCosineBuck6d::write_data(FILE *fp)
 {
   for (int i = 1; i <= atom->nangletypes; i++) {
-    fprintf(fp,"%d %g %d %d\n",i,k[i],multiplicity[i],th0[i]);
+    fprintf(fp,"%d %g %d %g\n",i,k[i],multiplicity[i],th0[i]);
   }
 }
 

src/USER-MOFFF/improper_inversion_harmonic.cpp

@@ -241,8 +241,8 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
     f[i4][2] += f4[2];
   }
 
-  double rb3x, rb3y, rb3z;
-  if (evflag)
+  if (evflag) {
+    double rb3x, rb3y, rb3z;
 
     rb3x = vb1x - vb2x;
     rb3y = vb1y - vb2y;
@@ -252,6 +252,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
              vb3x,vb3y,vb3z,
              vb2x,vb2y,vb2z,
              rb3x,rb3y,rb3z);
+  }
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp

@@ -83,7 +83,7 @@ void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag)
   double r,rsq,r2inv,r6inv,r14inv,rexp,forcecoul,forcebuck6d,factor_coul,factor_lj;
   double term1,term2,term3,term4,term5;
   double rcu,rqu,sme,smf,ebuck6d;
-  double prefactor,erfcc,erfcd,t,arg;
+  double prefactor,erfcc,erfcd,arg;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = ecoul = 0.0;

src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp

@@ -85,7 +85,7 @@ void PairBuck6dCoulGaussLong::compute(int eflag, int vflag)
   double grij,expm2,erf;
   double term1,term2,term3,term4,term5;
   double rcu,rqu,sme,smf,ebuck6d,ealpha;
-  double prefactor,erfa,expa,t,arg,falpha;
+  double prefactor,erfa,expa,arg,falpha;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = ecoul = 0.0;