git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12348 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/KSPACE/msm.cpp

@@ -1428,6 +1428,9 @@ void MSM::particle_map()
 
   int flag = 0;
 
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   for (int i = 0; i < nlocal; i++) {
 
     // (nx,ny,nz) = global coords of grid pt to "lower left" of charge

src/KSPACE/msm_cg.cpp

@@ -309,6 +309,9 @@ void MSMCG::particle_map()
   int flag = 0;
   int i;
 
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   for (int j = 0; j < num_charged; j++) {
     i = is_charged[j];
 

src/KSPACE/pppm.cpp

@@ -1875,6 +1875,10 @@ void PPPM::particle_map()
   int nlocal = atom->nlocal;
 
   int flag = 0;
+
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   for (int i = 0; i < nlocal; i++) {
 
     // (nx,ny,nz) = global coords of grid pt to "lower left" of charge

src/KSPACE/pppm_cg.cpp

@@ -282,6 +282,9 @@ void PPPMCG::particle_map()
 
   double **x = atom->x;
 
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   int flag = 0;
   for (int j = 0; j < num_charged; j++) {
     int i = is_charged[j];

src/KSPACE/pppm_disp.cpp

@@ -4209,6 +4209,9 @@ void PPPMDisp::particle_map(double delx, double dely, double delz,
   double **x = atom->x;
   int nlocal = atom->nlocal;
 
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   int flag = 0;
   for (int i = 0; i < nlocal; i++) {
     

src/KSPACE/pppm_disp_tip4p.cpp

@@ -78,6 +78,9 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz,
   double **x = atom->x;
   int nlocal = atom->nlocal;
 
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   int flag = 0;
   for (int i = 0; i < nlocal; i++) {
     if (type[i] == typeO) {

src/KSPACE/pppm_stagger.cpp

@@ -679,6 +679,9 @@ void PPPMStagger::particle_map()
   double **x = atom->x;
   int nlocal = atom->nlocal;
 
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   int flag = 0;
   for (int i = 0; i < nlocal; i++) {
 

src/KSPACE/pppm_tip4p.cpp

@@ -73,6 +73,9 @@ void PPPMTIP4P::particle_map()
   double **x = atom->x;
   int nlocal = atom->nlocal;
 
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   int flag = 0;
   for (int i = 0; i < nlocal; i++) {
     if (type[i] == typeO) {

src/MISC/fix_gld.cpp

@@ -57,16 +57,16 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
   // 1 = Group ID         (e.g., all)
   // 2 = gld              (name of this fix)
   // 3 = t_start          (Starting target temperature)
-  t_start = atof(arg[3]);
+  t_start = force->numeric(FLERR,arg[3]);
 
   // 4 = t_stop           (Stopping target temperature)
-  t_stop = atof(arg[4]);
+  t_stop = force->numeric(FLERR,arg[4]);
 
   // 5 = prony_terms      (number of terms in Prony series)
-  prony_terms = atoi(arg[5]);
+  prony_terms = force->inumeric(FLERR,arg[5]);
 
   // 6 = seed             (random seed)
-  int seed    = atoi(arg[6]);
+  int seed    = force->inumeric(FLERR,arg[6]);
 
   // 7 = series type
   if(strcmp(arg[7],"pprony") == 0) {
@@ -101,8 +101,8 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
   int iarg = narg_min;
   int icoeff = 0;
   while (iarg < narg && icoeff < prony_terms) {
-    double pc = atof(arg[iarg]);
+    double pc = force->numeric(FLERR,arg[iarg]);
-    double ptau = atof(arg[iarg+1]);
+    double ptau = force->numeric(FLERR,arg[iarg+1]);
 
     if (pc < 0)
       error->all(FLERR,"Fix gld c coefficients must be >= 0");

src/SHOCK/fix_wall_piston.cpp

@@ -135,14 +135,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
 
   // setup scaling
 
-  double xscale,yscale,zscale;
+  const double zscale = (scaleflag) ? domain->lattice->zlattice : 1.0;
-  if (scaleflag) {
-    xscale = domain->lattice->xlattice;
-    yscale = domain->lattice->ylattice;
-    zscale = domain->lattice->zlattice;
-  }
-  else xscale = yscale = zscale = 1.0;
-
   vz *= zscale;
   z0 *= zscale;
   roughdist *= zscale;

src/USER-OMP/pppm_disp_omp.cpp

@@ -354,6 +354,9 @@ void PPPMDispOMP::particle_map(double dxinv, double dyinv,
   const int nyhi_out = nyhi_o;
   const int nzhi_out = nzhi_o;
 
+  if (!isfinite(boxlo[0]) || !isfinite(boxlo[1]) || !isfinite(boxlo[2]))
+    error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
+
   int i, flag = 0;
 #if defined(_OPENMP)
 #pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static)

src/comm_tiled.cpp

@@ -775,11 +775,10 @@ void CommTiled::exchange()
 
 void CommTiled::borders()
 {
-  int i,m,n,irecv,nlast,nsend,nrecv,ngroup,ncount,ncountall;
+  int i,m,n,nlast,nsend,nrecv,ngroup,ncount,ncountall;
   double xlo,xhi,ylo,yhi,zlo,zhi;
   double *bbox;
   double **x;
-  MPI_Status status;
   AtomVec *avec = atom->avec;
 
   // send/recv max one = max # of atoms in single send/recv for any swap
@@ -1371,7 +1370,7 @@ void CommTiled::reverse_comm_dump(Dump *dump)
 
 void CommTiled::forward_comm_array(int nsize, double **array)
 { 
-  int i,j,k,m,n,iatom,last,irecv,nsend,nrecv;
+  int i,j,k,m,iatom,last,irecv,nsend,nrecv;
   MPI_Status status;
 
   // insure send/recv bufs are big enough for nsize
@@ -1732,7 +1731,6 @@ int CommTiled::point_drop_tiled(int idim, double *x)
       if (!done) proc = point_drop_tiled_recurse(xnew,0,nprocs-1);
     }
   } else if (idim == 1) {
-    int done = 1;
     if (rcbinfo[proc].mysplit[2][0] == rcbinfo[me].mysplit[2][1]) {
       xnew[2] -= EPSILON * (subhi[2]-sublo[2]);
       proc = point_drop_tiled_recurse(xnew,0,nprocs-1);

src/compute_temp_partial.cpp

@@ -38,9 +38,9 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
   tempflag = 1;
   tempbias = 1;
 
-  xflag = atoi(arg[3]);
+  xflag = force->inumeric(FLERR,arg[3]);
-  yflag = atoi(arg[4]);
+  yflag = force->inumeric(FLERR,arg[4]);
-  zflag = atoi(arg[5]);
+  zflag = force->inumeric(FLERR,arg[5]);
   if (zflag && domain->dimension == 2)
     error->all(FLERR,"Compute temp/partial cannot use vz for 2d systemx");
 

src/compute_temp_profile.cpp

@@ -41,9 +41,9 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
   tempflag = 1;
   tempbias = 1;
 
-  xflag = atoi(arg[3]);
+  xflag = force->inumeric(FLERR,arg[3]);
-  yflag = atoi(arg[4]);
+  yflag = force->inumeric(FLERR,arg[4]);
-  zflag = atoi(arg[5]);
+  zflag = force->inumeric(FLERR,arg[5]);
   if (zflag && domain->dimension == 2)
     error->all(FLERR,"Compute temp/profile cannot use vz for 2d systemx");
 
@@ -59,44 +59,44 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
   int iarg = 6;
   if (strcmp(arg[iarg],"x") == 0) {
     if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/profile command");
-    nbinx = atoi(arg[iarg+1]);
+    nbinx = force->inumeric(FLERR,arg[iarg+1]);
     iarg += 2;
   } else if (strcmp(arg[iarg],"y") == 0) {
     if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/profile command");
-    nbiny = atoi(arg[iarg+1]);
+    nbiny = force->inumeric(FLERR,arg[iarg+1]);
     iarg += 2;
   } else if (strcmp(arg[iarg],"z") == 0) {
     if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/profile command");
     if (domain->dimension == 2)
       error->all(FLERR,"Compute temp/profile cannot bin z for 2d systems");
-    nbinz = atoi(arg[iarg+1]);
+    nbinz = force->inumeric(FLERR,arg[iarg+1]);
     iarg += 2;
   } else if (strcmp(arg[iarg],"xy") == 0) {
     if (iarg+3 > narg) error->all(FLERR,"Illegal compute temp/profile command");
-    nbinx = atoi(arg[iarg+1]);
+    nbinx = force->inumeric(FLERR,arg[iarg+1]);
-    nbiny = atoi(arg[iarg+2]);
+    nbiny = force->inumeric(FLERR,arg[iarg+2]);
     iarg += 3;
   } else if (strcmp(arg[iarg],"yz") == 0) {
     if (iarg+3 > narg) error->all(FLERR,"Illegal compute temp/profile command");
     if (domain->dimension == 2)
       error->all(FLERR,"Compute temp/profile cannot bin z for 2d systems");
-    nbiny = atoi(arg[iarg+1]);
+    nbiny = force->inumeric(FLERR,arg[iarg+1]);
-    nbinz = atoi(arg[iarg+2]);
+    nbinz = force->inumeric(FLERR,arg[iarg+2]);
     iarg += 3;
   } else if (strcmp(arg[iarg],"xz") == 0) {
     if (iarg+3 > narg) error->all(FLERR,"Illegal compute temp/profile command");
     if (domain->dimension == 2)
       error->all(FLERR,"Compute temp/profile cannot bin z for 2d systems");
-    nbinx = atoi(arg[iarg+1]);
+    nbinx = force->inumeric(FLERR,arg[iarg+1]);
-    nbinz = atoi(arg[iarg+2]);
+    nbinz = force->inumeric(FLERR,arg[iarg+2]);
     iarg += 3;
   } else if (strcmp(arg[iarg],"xyz") == 0) {
     if (iarg+4 > narg) error->all(FLERR,"Illegal compute temp/profile command");
     if (domain->dimension == 2)
       error->all(FLERR,"Compute temp/profile cannot bin z for 2d systems");
-    nbinx = atoi(arg[iarg+1]);
+    nbinx = force->inumeric(FLERR,arg[iarg+1]);
-    nbiny = atoi(arg[iarg+2]);
+    nbiny = force->inumeric(FLERR,arg[iarg+2]);
-    nbinz = atoi(arg[iarg+3]);
+    nbinz = force->inumeric(FLERR,arg[iarg+3]);
     iarg += 4;
   } else error->all(FLERR,"Illegal compute temp/profile command");
 

src/compute_temp_ramp.cpp

@@ -74,14 +74,14 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
   else error->all(FLERR,"Illegal compute temp/ramp command");
 
   if (v_dim == 0) {
-    v_lo = xscale*atof(arg[4]);
+    v_lo = xscale*force->numeric(FLERR,arg[4]);
-    v_hi = xscale*atof(arg[5]);
+    v_hi = xscale*force->numeric(FLERR,arg[5]);
   } else if (v_dim == 1) {
-    v_lo = yscale*atof(arg[4]);
+    v_lo = yscale*force->numeric(FLERR,arg[4]);
-    v_hi = yscale*atof(arg[5]);
+    v_hi = yscale*force->numeric(FLERR,arg[5]);
   } else if (v_dim == 2) {
-    v_lo = zscale*atof(arg[4]);
+    v_lo = zscale*force->numeric(FLERR,arg[4]);
-    v_hi = zscale*atof(arg[5]);
+    v_hi = zscale*force->numeric(FLERR,arg[5]);
   }
 
   if (strcmp(arg[6],"x") == 0) coord_dim = 0;
@@ -90,14 +90,14 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
   else error->all(FLERR,"Illegal compute temp/ramp command");
 
   if (coord_dim == 0) {
-    coord_lo = xscale*atof(arg[7]);
+    coord_lo = xscale*force->numeric(FLERR,arg[7]);
-    coord_hi = xscale*atof(arg[8]);
+    coord_hi = xscale*force->numeric(FLERR,arg[8]);
   } else if (coord_dim == 1) {
-    coord_lo = yscale*atof(arg[7]);
+    coord_lo = yscale*force->numeric(FLERR,arg[7]);
-    coord_hi = yscale*atof(arg[8]);
+    coord_hi = yscale*force->numeric(FLERR,arg[8]);
   } else if (coord_dim == 2) {
-    coord_lo = zscale*atof(arg[7]);
+    coord_lo = zscale*force->numeric(FLERR,arg[7]);
-    coord_hi = zscale*atof(arg[8]);
+    coord_hi = zscale*force->numeric(FLERR,arg[8]);
   }
 
   maxbias = 0;

src/delete_bonds.cpp

@@ -25,6 +25,8 @@
 #include "special.h"
 #include "error.h"
 
+#include <stdlib.h>
+
 using namespace LAMMPS_NS;
 
 enum{MULTI,ATOM,BOND,ANGLE,DIHEDRAL,IMPROPER,STATS};
@@ -80,7 +82,6 @@ void DeleteBonds::command(int narg, char **arg)
   int *tlist = NULL;
 
   int iarg = 2;
-  int which;
   if (style != MULTI && style != STATS) {
     if (narg < 3) error->all(FLERR,"Illegal delete_bonds command");
 

src/rcb.cpp

@@ -176,7 +176,6 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
   // procmid = 1st proc in upper half of partition
 
   int procpartner,procpartner2;
-  int readnumber;                   
 
   int procmid;
   int proclower = 0;
@@ -656,7 +655,6 @@ void median_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
 
 void RCB::invert(int sortflag)
 {
-  Invert *sbuf,*rbuf;
 
   // only create Irregular if not previously created
   // allows Irregular to persist for multiple RCB calls by fix balance

src/read_restart.cpp

@@ -459,7 +459,10 @@ void ReadRestart::command(int narg, char **arg)
     // in case read by different proc than wrote restart file
     // first do map_init() since irregular->migrate_atoms() will do map_clear()
 
-    if (atom->map_style) atom->map_init();
+    if (atom->map_style) {
+      atom->map_init();
+      atom->map_set();
+    }
     if (domain->triclinic) domain->x2lamda(atom->nlocal);
     Irregular *irregular = new Irregular(lmp);
     irregular->migrate_atoms(1);