git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9380 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/atom_vec_body.cpp

@@ -219,8 +219,9 @@ void AtomVecBody::copy(int i, int j, int delflag)
   }
 
   // if atom I has bonus data, reset I's bonus.ilocal to loc J
+  // do NOT do this if self-copy (I=J) since I's bonus data is already deleted
 
-  if (body[i] >= 0) bonus[body[i]].ilocal = j;
+  if (body[i] >= 0 && i != j) bonus[body[i]].ilocal = j;
   body[j] = body[i];
 
   if (atom->nextra_grow)
@@ -230,13 +231,13 @@ void AtomVecBody::copy(int i, int j, int delflag)
 
 /* ----------------------------------------------------------------------
    copy bonus data from I to J, effectively deleting the J entry
-   insure index pointers between per-atom and bonus data are updated
+   also reset body that points to I to now point to J
 ------------------------------------------------------------------------- */
 
 void AtomVecBody::copy_bonus(int i, int j)
 {
+  body[bonus[i].ilocal] = j;
   memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
-  body[bonus[j].ilocal] = j;
 }
 
 /* ----------------------------------------------------------------------
@@ -1407,3 +1408,52 @@ bigint AtomVecBody::memory_usage()
 
   return bytes;
 }
+
+/* ----------------------------------------------------------------------
+   debug method for sanity checking of own/bonus data pointers
+------------------------------------------------------------------------- */
+
+/*
+void AtomVecBody::check(int flag)
+{
+  for (int i = 0; i < atom->nlocal; i++) {
+    if (atom->body[i] >= 0 && atom->body[i] >= nlocal_bonus) {
+      printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
+      error->one(FLERR,"BAD AAA");
+    }
+  }
+  for (int i = atom->nlocal; i < atom->nlocal+atom->nghost; i++) {
+    if (atom->body[i] >= 0 && 
+        (atom->body[i] < nlocal_bonus || 
+         atom->body[i] >= nlocal_bonus+nghost_bonus)) {
+      printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
+      error->one(FLERR,"BAD BBB");
+    }
+  }
+  for (int i = 0; i < nlocal_bonus; i++) {
+    if (bonus[i].ilocal < 0 || bonus[i].ilocal >= atom->nlocal) {
+      printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
+      error->one(FLERR,"BAD CCC");
+    }
+  }
+  for (int i = 0; i < nlocal_bonus; i++) {
+    if (atom->body[bonus[i].ilocal] != i) {
+      printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
+      error->one(FLERR,"BAD DDD");
+    }
+  }
+  for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
+    if (bonus[i].ilocal < atom->nlocal || 
+        bonus[i].ilocal >= atom->nlocal+atom->nghost) {
+      printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
+      error->one(FLERR,"BAD EEE");
+    }
+  }
+  for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
+    if (atom->body[bonus[i].ilocal] != i) {
+      printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
+      error->one(FLERR,"BAD FFF");
+    }
+  }
+}
+*/

src/atom_vec_body.h

@@ -25,6 +25,12 @@ AtomStyle(body,AtomVecBody)
 namespace LAMMPS_NS {
 
 class AtomVecBody : public AtomVec {
+    friend class Comm;
+
+
+
+
+
  public:
   class Body *bptr;
 
@@ -96,6 +102,7 @@ class AtomVecBody : public AtomVec {
 
   void grow_bonus();
   void copy_bonus(int, int);
+  //void check(int);
 };
 
 }

src/atom_vec_ellipsoid.cpp

@@ -153,8 +153,9 @@ void AtomVecEllipsoid::copy(int i, int j, int delflag)
   }
 
   // if atom I has bonus data, reset I's bonus.ilocal to loc J
+  // do NOT do this if self-copy (I=J) since I's bonus data is already deleted
 
-  if (ellipsoid[i] >= 0) bonus[ellipsoid[i]].ilocal = j;
+  if (ellipsoid[i] >= 0 && i != j) bonus[ellipsoid[i]].ilocal = j;
   ellipsoid[j] = ellipsoid[i];
 
   if (atom->nextra_grow)
@@ -164,13 +165,13 @@ void AtomVecEllipsoid::copy(int i, int j, int delflag)
 
 /* ----------------------------------------------------------------------
    copy bonus data from I to J, effectively deleting the J entry
-   insure index pointers between per-atom and bonus data are updated
+   also reset ellipsoid that points to I to now point to J
 ------------------------------------------------------------------------- */
 
 void AtomVecEllipsoid::copy_bonus(int i, int j)
 {
+  ellipsoid[bonus[i].ilocal] = j;
   memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
-  ellipsoid[bonus[j].ilocal] = j;
 }
 
 /* ----------------------------------------------------------------------

src/atom_vec_line.cpp

@@ -163,8 +163,9 @@ void AtomVecLine::copy(int i, int j, int delflag)
   }
 
   // if atom I has bonus data, reset I's bonus.ilocal to loc J
+  // do NOT do this if self-copy (I=J) since I's bonus data is already deleted
 
-  if (line[i] >= 0) bonus[line[i]].ilocal = j;
+  if (line[i] >= 0 && i != j) bonus[line[i]].ilocal = j;
   line[j] = line[i];
 
   if (atom->nextra_grow)
@@ -174,13 +175,13 @@ void AtomVecLine::copy(int i, int j, int delflag)
 
 /* ----------------------------------------------------------------------
    copy bonus data from I to J, effectively deleting the J entry
-   insure index pointers between per-atom and bonus data are updated
+   also reset ine that points to I to now point to J
 ------------------------------------------------------------------------- */
 
 void AtomVecLine::copy_bonus(int i, int j)
 {
+  line[bonus[i].ilocal] = j;
   memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
-  line[bonus[j].ilocal] = j;
 }
 
 /* ----------------------------------------------------------------------

src/atom_vec_tri.cpp

@@ -165,8 +165,9 @@ void AtomVecTri::copy(int i, int j, int delflag)
   }
 
   // if atom I has bonus data, reset I's bonus.ilocal to loc J
+  // do NOT do this if self-copy (I=J) since I's bonus data is already deleted
 
-  if (tri[i] >= 0) bonus[tri[i]].ilocal = j;
+  if (tri[i] >= 0 && i != j) bonus[tri[i]].ilocal = j;
   tri[j] = tri[i];
 
   if (atom->nextra_grow)
@@ -176,13 +177,13 @@ void AtomVecTri::copy(int i, int j, int delflag)
 
 /* ----------------------------------------------------------------------
    copy bonus data from I to J, effectively deleting the J entry
-   insure index pointers between per-atom and bonus data are updated
+   also reset tri that points to I to now point to J
 ------------------------------------------------------------------------- */
 
 void AtomVecTri::copy_bonus(int i, int j)
 {
+  tri[bonus[i].ilocal] = j;
   memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
-  tri[bonus[j].ilocal] = j;
 }
 
 /* ----------------------------------------------------------------------