git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3414 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/atom_vec_ellipsoid.cpp

@@ -87,6 +87,18 @@ void AtomVecEllipsoid::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::grow_reset()
+{
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  quat = atom->quat; angmom = atom->angmom; torque = atom->torque;
+}
+
 /* ---------------------------------------------------------------------- */
 
 void AtomVecEllipsoid::copy(int i, int j)

src/ASPHERE/atom_vec_ellipsoid.h

@@ -23,6 +23,7 @@ class AtomVecEllipsoid : public AtomVec {
   AtomVecEllipsoid(class LAMMPS *, int, char **);
   virtual ~AtomVecEllipsoid() {}
   void grow(int);
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/COLLOID/atom_vec_colloid.cpp

@@ -81,6 +81,18 @@ void AtomVecColloid::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecColloid::grow_reset()
+{
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  omega = atom->omega; torque = atom->torque;
+}
+
 /* ---------------------------------------------------------------------- */
 
 void AtomVecColloid::copy(int i, int j)

src/COLLOID/atom_vec_colloid.h

@@ -23,6 +23,7 @@ class AtomVecColloid : public AtomVec {
   AtomVecColloid(class LAMMPS *, int, char **);
   virtual ~AtomVecColloid() {}
   void grow(int);
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/DIPOLE/atom_vec_dipole.cpp

@@ -84,6 +84,19 @@ void AtomVecDipole::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecDipole::grow_reset()
+{
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  q = atom->q; mu = atom->mu;
+  omega = atom->omega; torque = atom->torque;
+}
+
 /* ---------------------------------------------------------------------- */
 
 void AtomVecDipole::copy(int i, int j)

src/DIPOLE/atom_vec_dipole.h

@@ -22,6 +22,7 @@ class AtomVecDipole : public AtomVec {
  public:
   AtomVecDipole(class LAMMPS *, int, char **);
   void grow(int);
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/GRANULAR/atom_vec_granular.cpp

@@ -90,6 +90,19 @@ void AtomVecGranular::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecGranular::grow_reset()
+{
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  radius = atom->radius; density = atom->density; rmass = atom->rmass;
+  omega = atom->omega; torque = atom->torque;
+}
+
 /* ---------------------------------------------------------------------- */
 
 void AtomVecGranular::copy(int i, int j)

src/GRANULAR/atom_vec_granular.h

@@ -23,6 +23,7 @@ class AtomVecGranular : public AtomVec {
   AtomVecGranular(class LAMMPS *, int, char **);
   ~AtomVecGranular() {}
   void grow(int);
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/MOLECULE/atom_vec_angle.cpp

@@ -110,11 +110,22 @@ void AtomVecAngle::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
 
-void AtomVecAngle::reset_special()
+void AtomVecAngle::grow_reset()
 {
-  special = atom->special;
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  molecule = atom->molecule;
+  nspecial = atom->nspecial; special = atom->special;
+  num_bond = atom->num_bond; bond_type = atom->bond_type;
+  bond_atom = atom->bond_atom;
+  num_angle = atom->num_angle; angle_type = atom->angle_type;
+  angle_atom1 = atom->angle_atom1; angle_atom2 = atom->angle_atom2;
+  angle_atom3 = atom->angle_atom3;
 }
 
 /* ---------------------------------------------------------------------- */

src/MOLECULE/atom_vec_angle.h

@@ -22,7 +22,7 @@ class AtomVecAngle : public AtomVec {
  public:
   AtomVecAngle(class LAMMPS *, int, char **);
   void grow(int);
-  void reset_special();
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/MOLECULE/atom_vec_bond.cpp

@@ -95,11 +95,19 @@ void AtomVecBond::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
 
-void AtomVecBond::reset_special()
+void AtomVecBond::grow_reset()
 {
-  special = atom->special;
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  molecule = atom->molecule;
+  nspecial = atom->nspecial; special = atom->special;
+  num_bond = atom->num_bond; bond_type = atom->bond_type;
+  bond_atom = atom->bond_atom;
 }
 
 /* ---------------------------------------------------------------------- */

src/MOLECULE/atom_vec_bond.h

@@ -22,7 +22,7 @@ class AtomVecBond : public AtomVec {
  public:
   AtomVecBond(class LAMMPS *, int, char **);
   void grow(int);
-  void reset_special();
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/MOLECULE/atom_vec_full.cpp

@@ -148,11 +148,28 @@ void AtomVecFull::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
 
-void AtomVecFull::reset_special()
+void AtomVecFull::grow_reset()
 {
-  special = atom->special;
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  q = atom->q; molecule = atom->molecule;
+  nspecial = atom->nspecial; special = atom->special;
+  num_bond = atom->num_bond; bond_type = atom->bond_type;
+  bond_atom = atom->bond_atom;
+  num_angle = atom->num_angle; angle_type = atom->angle_type;
+  angle_atom1 = atom->angle_atom1; angle_atom2 = atom->angle_atom2;
+  angle_atom3 = atom->angle_atom3;
+  num_dihedral = atom->num_dihedral; dihedral_type = atom->dihedral_type;
+  dihedral_atom1 = atom->dihedral_atom1; dihedral_atom2 = atom->dihedral_atom2;
+  dihedral_atom3 = atom->dihedral_atom3; dihedral_atom4 = atom->dihedral_atom4;
+  num_improper = atom->num_improper; improper_type = atom->improper_type;
+  improper_atom1 = atom->improper_atom1; improper_atom2 = atom->improper_atom2;
+  improper_atom3 = atom->improper_atom3; improper_atom4 = atom->improper_atom4;
 }
 
 /* ---------------------------------------------------------------------- */

src/MOLECULE/atom_vec_full.h

@@ -22,7 +22,7 @@ class AtomVecFull : public AtomVec {
  public:
   AtomVecFull(class LAMMPS *, int, char **);
   void grow(int);
-  void reset_special();
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/MOLECULE/atom_vec_molecular.cpp

@@ -146,11 +146,28 @@ void AtomVecMolecular::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
 
-void AtomVecMolecular::reset_special()
+void AtomVecMolecular::grow_reset()
 {
-  special = atom->special;
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  molecule = atom->molecule;
+  nspecial = atom->nspecial; special = atom->special;
+  num_bond = atom->num_bond; bond_type = atom->bond_type;
+  bond_atom = atom->bond_atom;
+  num_angle = atom->num_angle; angle_type = atom->angle_type;
+  angle_atom1 = atom->angle_atom1; angle_atom2 = atom->angle_atom2;
+  angle_atom3 = atom->angle_atom3;
+  num_dihedral = atom->num_dihedral; dihedral_type = atom->dihedral_type;
+  dihedral_atom1 = atom->dihedral_atom1; dihedral_atom2 = atom->dihedral_atom2;
+  dihedral_atom3 = atom->dihedral_atom3; dihedral_atom4 = atom->dihedral_atom4;
+  num_improper = atom->num_improper; improper_type = atom->improper_type;
+  improper_atom1 = atom->improper_atom1; improper_atom2 = atom->improper_atom2;
+  improper_atom3 = atom->improper_atom3; improper_atom4 = atom->improper_atom4;
 }
 
 /* ---------------------------------------------------------------------- */

src/MOLECULE/atom_vec_molecular.h

@@ -22,7 +22,7 @@ class AtomVecMolecular : public AtomVec {
  public:
   AtomVecMolecular(class LAMMPS *, int, char **);
   void grow(int);
-  void reset_special();
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/PERI/atom_vec_peri.cpp

@@ -88,6 +88,19 @@ void AtomVecPeri::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecPeri::grow_reset()
+{
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  vfrac = atom->vfrac; density = atom->density; rmass = atom->rmass;
+  s0 = atom->s0; x0 = atom->x0;
+}
+
 /* ---------------------------------------------------------------------- */
 
 void AtomVecPeri::copy(int i, int j)

src/PERI/atom_vec_peri.h

@@ -22,6 +22,7 @@ class AtomVecPeri : public AtomVec {
  public:
   AtomVecPeri(class LAMMPS *, int, char **);
   void grow(int);
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/atom_vec.h

@@ -43,7 +43,7 @@ class AtomVec : protected Pointers {
   virtual void init() {}
 
   virtual void grow(int) = 0;
-  virtual void reset_special() {}
+  virtual void grow_reset() = 0;
   virtual void copy(int, int) = 0;
 
   virtual int pack_comm(int, int *, double *, int, int *) = 0;

src/atom_vec_atomic.cpp

@@ -71,6 +71,17 @@ void AtomVecAtomic::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecAtomic::grow_reset()
+{
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+}
+
 /* ---------------------------------------------------------------------- */
 
 void AtomVecAtomic::copy(int i, int j)

src/atom_vec_atomic.h

@@ -23,6 +23,7 @@ class AtomVecAtomic : public AtomVec {
   AtomVecAtomic(class LAMMPS *, int, char **);
   ~AtomVecAtomic() {}
   void grow(int);
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/atom_vec_charge.cpp

@@ -76,6 +76,18 @@ void AtomVecCharge::grow(int n)
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecCharge::grow_reset()
+{
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  q = atom->q;
+}
+
 /* ---------------------------------------------------------------------- */
 
 void AtomVecCharge::copy(int i, int j)

src/atom_vec_charge.h

@@ -22,6 +22,7 @@ class AtomVecCharge : public AtomVec {
  public:
   AtomVecCharge(class LAMMPS *, int, char **);
   void grow(int);
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/atom_vec_hybrid.cpp

@@ -118,29 +118,27 @@ void AtomVecHybrid::grow(int n)
   for (int k = 0; k < nstyles; k++) styles[k]->grow(nmax);
   atom->nextra_grow = tmp;
 
-  // pointers for arrays used directly by hybrid style
+  // insure sub-style ptrs and hybrid local ptrs are up to date
+  // for sub-styles, is in case sub-style reallocs actually realloced
 
-  tag = atom->tag;
-  type = atom->type;
-  mask = atom->mask;
-  image = atom->image;
-  x = atom->x;
-  v = atom->v;
-  f = atom->f;
-
-  omega = atom->omega;
-  angmom = atom->angmom;
+  for (int k = 0; k < nstyles; k++) styles[k]->grow_reset();
+  grow_reset();
 
   if (atom->nextra_grow)
     for (int iextra = 0; iextra < atom->nextra_grow; iextra++) 
       modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   reset local array ptrs
+------------------------------------------------------------------------- */
 
-void AtomVecHybrid::reset_special()
+void AtomVecHybrid::grow_reset()
 {
-  for (int k = 0; k < nstyles; k++) styles[k]->reset_special();
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  omega = atom->omega; angmom = atom->angmom;
 }
 
 /* ----------------------------------------------------------------------

src/atom_vec_hybrid.h

@@ -27,7 +27,7 @@ class AtomVecHybrid : public AtomVec {
   AtomVecHybrid(class LAMMPS *, int, char **);
   ~AtomVecHybrid();
   void grow(int);
-  void reset_special();
+  void grow_reset();
   void copy(int, int);
   int pack_comm(int, int *, double *, int, int *);
   int pack_comm_vel(int, int *, double *, int, int *);

src/special.cpp

@@ -639,7 +639,7 @@ void Special::combine()
 
   atom->special = 
     memory->create_2d_int_array(atom->nmax,atom->maxspecial,"atom:special");
-  atom->avec->reset_special();
+  atom->avec->grow_reset();
   int **special = atom->special;
 
   // ----------------------------------------------------