git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12664 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/GRANULAR/fix_pour.cpp

@@ -217,7 +217,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
   // volume_one = volume of inserted particle (with max possible radius)
   // in 3d, insure dy >= 1, for quasi-2d simulations
 
-  double volume,volume_one;
+  double volume,volume_one=1.0;
 
   molradius_max = 0.0;
   if (mode == MOLECULE) {

src/MC/fix_bond_create.cpp

@@ -1398,25 +1398,28 @@ void FixBondCreate::print_bb()
   for (int i = 0; i < atom->nlocal; i++) {
     printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]);
     for (int j = 0; j < atom->num_bond[i]; j++) {
-      printf(" %d",atom->bond_atom[i][j]);
+      printf(" " TAGINT_FORMAT,atom->bond_atom[i][j]);
     }
     printf("\n");
     printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]);
     for (int j = 0; j < atom->num_angle[i]; j++) {
-      printf(" %d %d %d,",atom->angle_atom1[i][j],
+      printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",",
-	     atom->angle_atom2[i][j],atom->angle_atom3[i][j]);
+             atom->angle_atom1[i][j], atom->angle_atom2[i][j],
+             atom->angle_atom3[i][j]);
     }
     printf("\n");
     printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
     for (int j = 0; j < atom->num_dihedral[i]; j++) {
-      printf(" %d %d %d %d,",atom->dihedral_atom1[i][j],
+      printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " 
+             TAGINT_FORMAT ",", atom->dihedral_atom1[i][j],
 	     atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
 	     atom->dihedral_atom4[i][j]);
     }
     printf("\n");
     printf("TAG " TAGINT_FORMAT ": %d nimpropers: ",atom->tag[i],atom->num_improper[i]);
     for (int j = 0; j < atom->num_improper[i]; j++) {
-      printf(" %d %d %d %d,",atom->improper_atom1[i][j],
+      printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " 
+             TAGINT_FORMAT ",",atom->improper_atom1[i][j],
 	     atom->improper_atom2[i][j],atom->improper_atom3[i][j],
 	     atom->improper_atom4[i][j]);
     }
@@ -1424,7 +1427,7 @@ void FixBondCreate::print_bb()
     printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
 	   atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
     for (int j = 0; j < atom->nspecial[i][2]; j++) {
-      printf(" %d",atom->special[i][j]);
+      printf(" " TAGINT_FORMAT,atom->special[i][j]);
     }
     printf("\n");
   }
@@ -1435,7 +1438,7 @@ void FixBondCreate::print_bb()
 void FixBondCreate::print_copy(const char *str, tagint m, 
                               int n1, int n2, int n3, int *v)
 {
-  printf("%s %i: %d %d %d nspecial: ",str,m,n1,n2,n3);
+  printf("%s " TAGINT_FORMAT ": %d %d %d nspecial: ",str,m,n1,n2,n3);
   for (int j = 0; j < n3; j++) printf(" %d",v[j]);
   printf("\n");
 }

src/RIGID/fix_rigid_small.cpp

@@ -1734,11 +1734,11 @@ void FixRigidSmall::setup_bodies_static()
   // dorientflag = 1 if any particle stores dipole orientation
 
   if (extended) {
-    grow_arrays(atom->nmax);
     if (atom->ellipsoid_flag) orientflag = 4;
     if (atom->line_flag) orientflag = 1;
     if (atom->tri_flag) orientflag = 4;
     if (atom->mu_flag) dorientflag = 1;
+    grow_arrays(atom->nmax);
 
     for (i = 0; i < nlocal; i++) {
       eflags[i] = 0;

src/SNAP/pair_snap.cpp

@@ -163,10 +163,10 @@ void PairSNAP::compute(int eflag, int vflag)
 
 void PairSNAP::compute_regular(int eflag, int vflag)
 {
-  int i,j,inum,jnum,ninside;
+  int i,j,jnum,ninside;
   double delx,dely,delz,evdwl,rsq;
   double fij[3];
-  int *ilist,*jlist,*numneigh,**firstneigh;
+  int *jlist,*numneigh,**firstneigh;
   evdwl = 0.0;
 
   if (eflag || vflag) ev_setup(eflag,vflag);
@@ -179,8 +179,6 @@ void PairSNAP::compute_regular(int eflag, int vflag)
   int newton_pair = force->newton_pair;
   class SNA* snaptr = sna[0];
 
-  inum = list->inum;
-  ilist = list->ilist;
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
@@ -425,10 +423,10 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
     }
 
     int ielem;
-    int jj,k,inum,jnum,jtype,ninside;
+    int jj,k,jnum,jtype,ninside;
     double delx,dely,delz,evdwl,rsq;
     double fij[3];
-    int *ilist,*jlist,*numneigh,**firstneigh;
+    int *jlist,*numneigh,**firstneigh;
     evdwl = 0.0;
 
 #if defined(_OPENMP)
@@ -450,8 +448,6 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
     int nlocal = atom->nlocal;
     int newton_pair = force->newton_pair;
 
-    inum = list->inum;
-    ilist = list->ilist;
     numneigh = list->numneigh;
     firstneigh = list->firstneigh;
 
@@ -1020,17 +1016,16 @@ void PairSNAP::build_per_atom_arrays()
   clock_gettime(CLOCK_REALTIME,&starttime);
 #endif
 
-  int i_list[list->inum+ghostinum];
   int count = 0;
   int neighmax = 0;
   for (int ii = 0; ii < list->inum; ii++)
     if ((do_load_balance <= 0) || ilistmask[ii]) {
       neighmax=MAX(neighmax,list->numneigh[list->ilist[ii]]);
-      i_list[count++]=list->ilist[ii];
+      ++count;
     }
   for (int ii = 0; ii < ghostinum; ii++) {
     neighmax=MAX(neighmax,ghostnumneigh[ghostilist[ii]]);
-    i_list[count++]=ghostilist[ii];
+    ++count;
   }
 
   if (i_max < count || i_neighmax < neighmax) {

src/citeme.cpp

@@ -47,10 +47,12 @@ CiteMe::~CiteMe()
 
   delete cs;
 
-  if (screen) fprintf(screen,cite_nagline);
+  if (fp) {
-  if (logfile) fprintf(logfile,cite_nagline);
+    if (screen) fprintf(screen,cite_nagline);
+    if (logfile) fprintf(logfile,cite_nagline);
 
-  if (fp) fclose(fp);
+    fclose(fp);
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -65,7 +67,7 @@ void CiteMe::add(const char *ref)
 
   if (!fp) {
     fp = fopen("log.cite","w");
-    if (!fp) error->universe_one(FLERR,"Cannot open log.cite file");
+    if (!fp) return;
     fputs(cite_header,fp);
     fflush(fp);
   }

src/fix_recenter.cpp

@@ -20,10 +20,12 @@
 #include "fix_recenter.h"
 #include "atom.h"
 #include "group.h"
+#include "update.h"
 #include "domain.h"
 #include "lattice.h"
 #include "modify.h"
 #include "comm.h"
+#include "respa.h"
 #include "error.h"
 #include "force.h"
 
@@ -110,6 +112,7 @@ int FixRecenter::setmask()
 {
   int mask = 0;
   mask |= INITIAL_INTEGRATE;
+  mask |= INITIAL_INTEGRATE_RESPA;
   return mask;
 }
 
@@ -139,6 +142,9 @@ void FixRecenter::init()
     yinit = xcm[1];
     zinit = xcm[2];
   }
+
+  if (strstr(update->integrate_style,"respa"))
+    nlevels_respa = ((Respa *) update->integrate)->nlevels;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -214,3 +220,13 @@ double FixRecenter::compute_vector(int n)
   return shift[n];
 }
 
+/* ---------------------------------------------------------------------- */
+
+void FixRecenter::initial_integrate_respa(int vflag, int ilevel, int iloop)
+{
+  // outermost level - operate recenter
+  // all other levels - nothing
+
+  if (ilevel == nlevels_respa-1) initial_integrate(vflag);
+}
+