From 5fdeeabba5282ba6d91e2832c7c587722a34acc3 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 9 Feb 2007 21:26:58 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@279
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/MOLECULE/atom_vec_full.cpp | 888 +++++++++++++++++++++++++++++++++
 src/MOLECULE/atom_vec_full.h   |  68 +++
 2 files changed, 956 insertions(+)
 create mode 100644 src/MOLECULE/atom_vec_full.cpp
 create mode 100644 src/MOLECULE/atom_vec_full.h

diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
new file mode 100644
index 0000000000..7de7dfb748
--- /dev/null
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -0,0 +1,888 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under 
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "stdlib.h"
+#include "atom_vec_full.h"
+#include "atom.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(A,B) ((A) < (B)) ? (A) : (B)
+#define MAX(A,B) ((A) > (B)) ? (A) : (B)
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) : 
+  AtomVec(lmp, narg, arg)
+{
+  molecular = 1;
+  bonds_allow = 1;
+  angles_allow = 1;
+  dihedrals_allow = 1;
+  impropers_allow = 1;
+  mass_type = 1;
+  size_comm = 3;
+  size_reverse = 3;
+  size_border = 8;
+  size_data_atom = 7;
+  size_data_vel = 4;
+  xcol_data = 5;
+}
+
+/* ----------------------------------------------------------------------
+   grow atom arrays
+   n = 0 grows arrays by DELTA
+   n > 0 allocates arrays to size n 
+------------------------------------------------------------------------- */
+
+void AtomVecFull::grow(int n)
+{
+  if (n == 0) nmax += DELTA;
+  else nmax = n;
+  atom->nmax = nmax;
+
+  tag = atom->tag = (int *) 
+    memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
+  type = atom->type = (int *)
+    memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
+  mask = atom->mask = (int *) 
+    memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
+  image = atom->image = (int *) 
+    memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
+  x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
+  v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
+  f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
+
+  q = atom->q = (double *) 
+    memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
+  molecule = atom->molecule = (int *) 
+    memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
+
+  nspecial = atom->nspecial =
+    memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
+  special = atom->special =
+    memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
+			      "atom:special");
+
+  num_bond = atom->num_bond = (int *) 
+    memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
+  bond_type = atom->bond_type = 
+    memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
+			      "atom:bond_type");
+  bond_atom = atom->bond_atom = 
+    memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
+			      "atom:bond_atom");
+
+  num_angle = atom->num_angle = (int *) 
+    memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
+  angle_type = atom->angle_type = 
+    memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
+			      "atom:angle_type");
+  angle_atom1 = atom->angle_atom1 = 
+    memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
+			      "atom:angle_atom1");
+  angle_atom2 = atom->angle_atom2 = 
+    memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
+			      "atom:angle_atom2");
+  angle_atom3 = atom->angle_atom3 = 
+    memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
+			      "atom:angle_atom3");
+
+  num_dihedral = atom->num_dihedral = (int *) 
+    memory->srealloc(atom->num_dihedral,nmax*sizeof(int),"atom:num_dihedral");
+  dihedral_type = atom->dihedral_type = 
+    memory->grow_2d_int_array(atom->dihedral_type,nmax,atom->dihedral_per_atom,
+			      "atom:dihedral_type");
+  dihedral_atom1 = atom->dihedral_atom1 = 
+    memory->grow_2d_int_array(atom->dihedral_atom1,nmax,
+			      atom->dihedral_per_atom,"atom:dihedral_atom1");
+  dihedral_atom2 = atom->dihedral_atom2 = 
+    memory->grow_2d_int_array(atom->dihedral_atom2,nmax,
+			      atom->dihedral_per_atom,"atom:dihedral_atom2");
+  dihedral_atom3 = atom->dihedral_atom3 = 
+    memory->grow_2d_int_array(atom->dihedral_atom3,nmax,
+			      atom->dihedral_per_atom,"atom:dihedral_atom3");
+  dihedral_atom4 = atom->dihedral_atom4 = 
+    memory->grow_2d_int_array(atom->dihedral_atom4,nmax,
+			      atom->dihedral_per_atom,"atom:dihedral_atom4");
+
+  num_improper = atom->num_improper = (int *) 
+    memory->srealloc(atom->num_improper,nmax*sizeof(int),"atom:num_improper");
+  improper_type = atom->improper_type = 
+    memory->grow_2d_int_array(atom->improper_type,nmax,atom->improper_per_atom,
+			      "atom:improper_type");
+  improper_atom1 = atom->improper_atom1 = 
+    memory->grow_2d_int_array(atom->improper_atom1,nmax,
+			      atom->improper_per_atom,"atom:improper_atom1");
+  improper_atom2 = atom->improper_atom2 = 
+    memory->grow_2d_int_array(atom->improper_atom2,nmax,
+			      atom->improper_per_atom,"atom:improper_atom2");
+  improper_atom3 = atom->improper_atom3 = 
+    memory->grow_2d_int_array(atom->improper_atom3,nmax,
+			      atom->improper_per_atom,"atom:improper_atom3");
+  improper_atom4 = atom->improper_atom4 = 
+    memory->grow_2d_int_array(atom->improper_atom4,nmax,
+			      atom->improper_per_atom,"atom:improper_atom4");
+
+  if (atom->nextra_grow)
+    for (int iextra = 0; iextra < atom->nextra_grow; iextra++) 
+      modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFull::reset_ptrs()
+{
+  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;
+}
+
+/* ----------------------------------------------------------------------
+   zero auxiliary data for owned atom I
+   data in copy(), not including tag,type,mask,image,x,v
+------------------------------------------------------------------------- */
+
+void AtomVecFull::zero_owned(int i)
+{
+  q[i] = 0.0;
+  molecule[i] = 0;
+  num_bond[i] = 0;
+  num_angle[i] = 0;
+  num_dihedral[i] = 0;
+  num_improper[i] = 0;
+  nspecial[i][0] = 0;
+  nspecial[i][1] = 0;
+  nspecial[i][2] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   zero auxiliary data for n ghost atoms
+   data in border(), not including x,tag,type,mask
+   grow() is here since zero_ghost called first in hybrid::unpack_border()
+------------------------------------------------------------------------- */
+
+void AtomVecFull::zero_ghost(int n, int first)
+{
+  int last = first + n;
+  for (int i = first; i < last; i++) {
+    if (i == nmax) atom->avec->grow(0);
+    q[i] = 0.0;
+    molecule[i] = 0;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFull::copy(int i, int j)
+{
+  int k;
+
+  tag[j] = tag[i];
+  type[j] = type[i];
+  mask[j] = mask[i];
+  image[j] = image[i];
+  x[j][0] = x[i][0];
+  x[j][1] = x[i][1];
+  x[j][2] = x[i][2];
+  v[j][0] = v[i][0];
+  v[j][1] = v[i][1];
+  v[j][2] = v[i][2];
+
+  q[j] = q[i];
+  molecule[j] = molecule[i];
+
+  num_bond[j] = num_bond[i];
+  for (k = 0; k < num_bond[j]; k++) {
+    bond_type[j][k] = bond_type[i][k];
+    bond_atom[j][k] = bond_atom[i][k];
+  }
+
+  num_angle[j] = num_angle[i];
+  for (k = 0; k < num_angle[j]; k++) {
+    angle_type[j][k] = angle_type[i][k];
+    angle_atom1[j][k] = angle_atom1[i][k];
+    angle_atom2[j][k] = angle_atom2[i][k];
+    angle_atom3[j][k] = angle_atom3[i][k];
+  }
+
+  num_dihedral[j] = num_dihedral[i];
+  for (k = 0; k < num_dihedral[j]; k++) {
+    dihedral_type[j][k] = dihedral_type[i][k];
+    dihedral_atom1[j][k] = dihedral_atom1[i][k];
+    dihedral_atom2[j][k] = dihedral_atom2[i][k];
+    dihedral_atom3[j][k] = dihedral_atom3[i][k];
+    dihedral_atom4[j][k] = dihedral_atom4[i][k];
+  }
+
+  num_improper[j] = num_improper[i];
+  for (k = 0; k < num_improper[j]; k++) {
+    improper_type[j][k] = improper_type[i][k];
+    improper_atom1[j][k] = improper_atom1[i][k];
+    improper_atom2[j][k] = improper_atom2[i][k];
+    improper_atom3[j][k] = improper_atom3[i][k];
+    improper_atom4[j][k] = improper_atom4[i][k];
+  }
+
+  nspecial[j][0] = nspecial[i][0];
+  nspecial[j][1] = nspecial[i][1];
+  nspecial[j][2] = nspecial[i][2];
+  for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
+
+  if (atom->nextra_grow)
+    for (int iextra = 0; iextra < atom->nextra_grow; iextra++) 
+      modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFull::pack_comm(int n, int *list, double *buf, int *pbc_flags)
+{
+  int i,j,m;
+
+  m = 0;
+  if (pbc_flags[0] == 0) {
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      buf[m++] = x[j][0];
+      buf[m++] = x[j][1];
+      buf[m++] = x[j][2];
+    }
+  } else {
+    double xprd = domain->xprd;
+    double yprd = domain->yprd;
+    double zprd = domain->zprd;
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      buf[m++] = x[j][0] + pbc_flags[1]*xprd;
+      buf[m++] = x[j][1] + pbc_flags[2]*yprd;
+      buf[m++] = x[j][2] + pbc_flags[3]*zprd;
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFull::unpack_comm(int n, int first, double *buf)
+{
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    x[i][0] = buf[m++];
+    x[i][1] = buf[m++];
+    x[i][2] = buf[m++];
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFull::pack_reverse(int n, int first, double *buf)
+{
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    buf[m++] = f[i][0];
+    buf[m++] = f[i][1];
+    buf[m++] = f[i][2];
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFull::unpack_reverse(int n, int *list, double *buf)
+{
+  int i,j,m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    f[j][0] += buf[m++];
+    f[j][1] += buf[m++];
+    f[j][2] += buf[m++];
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFull::pack_border(int n, int *list, double *buf,
+				  int *pbc_flags)
+{
+  int i,j,m;
+
+  m = 0;
+  if (pbc_flags[0] == 0) {
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      buf[m++] = x[j][0];
+      buf[m++] = x[j][1];
+      buf[m++] = x[j][2];
+      buf[m++] = tag[j];
+      buf[m++] = type[j];
+      buf[m++] = mask[j];
+      buf[m++] = q[j];
+      buf[m++] = molecule[j];
+    }
+  } else {
+    double xprd = domain->xprd;
+    double yprd = domain->yprd;
+    double zprd = domain->zprd;
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      buf[m++] = x[j][0] + pbc_flags[1]*xprd;
+      buf[m++] = x[j][1] + pbc_flags[2]*yprd;
+      buf[m++] = x[j][2] + pbc_flags[3]*zprd;
+      buf[m++] = tag[j];
+      buf[m++] = type[j];
+      buf[m++] = mask[j];
+      buf[m++] = q[j];
+      buf[m++] = molecule[j];
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFull::pack_border_one(int i, double *buf)
+{
+  buf[0] = q[i];
+  buf[1] = molecule[i];
+  return 2;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFull::unpack_border(int n, int first, double *buf)
+{
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    if (i == nmax) grow(0);
+    x[i][0] = buf[m++];
+    x[i][1] = buf[m++];
+    x[i][2] = buf[m++];
+    tag[i] = static_cast<int> (buf[m++]);
+    type[i] = static_cast<int> (buf[m++]);
+    mask[i] = static_cast<int> (buf[m++]);
+    q[i] = buf[m++];
+    molecule[i] = static_cast<int> (buf[m++]);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFull::unpack_border_one(int i, double *buf)
+{
+  q[i] = buf[0];
+  molecule[i] = static_cast<int> (buf[1]);
+  return 2;
+}
+
+/* ----------------------------------------------------------------------
+   pack data for atom I for sending to another proc
+   xyz must be 1st 3 values, so comm::exchange() can test on them 
+------------------------------------------------------------------------- */
+
+int AtomVecFull::pack_exchange(int i, double *buf)
+{
+  int k;
+
+  int m = 1;
+  buf[m++] = x[i][0];
+  buf[m++] = x[i][1];
+  buf[m++] = x[i][2];
+  buf[m++] = v[i][0];
+  buf[m++] = v[i][1];
+  buf[m++] = v[i][2];
+  buf[m++] = tag[i];
+  buf[m++] = type[i];
+  buf[m++] = mask[i];
+  buf[m++] = image[i];
+
+  buf[m++] = q[i];
+  buf[m++] = molecule[i];
+
+  buf[m++] = num_bond[i];
+  for (k = 0; k < num_bond[i]; k++) {
+    buf[m++] = bond_type[i][k];
+    buf[m++] = bond_atom[i][k];
+  }
+
+  buf[m++] = num_angle[i];
+  for (k = 0; k < num_angle[i]; k++) {
+    buf[m++] = angle_type[i][k];
+    buf[m++] = angle_atom1[i][k];
+    buf[m++] = angle_atom2[i][k];
+    buf[m++] = angle_atom3[i][k];
+  }
+
+  buf[m++] = num_dihedral[i];
+  for (k = 0; k < num_dihedral[i]; k++) {
+    buf[m++] = dihedral_type[i][k];
+    buf[m++] = dihedral_atom1[i][k];
+    buf[m++] = dihedral_atom2[i][k];
+    buf[m++] = dihedral_atom3[i][k];
+    buf[m++] = dihedral_atom4[i][k];
+  }
+
+  buf[m++] = num_improper[i];
+  for (k = 0; k < num_improper[i]; k++) {
+    buf[m++] = improper_type[i][k];
+    buf[m++] = improper_atom1[i][k];
+    buf[m++] = improper_atom2[i][k];
+    buf[m++] = improper_atom3[i][k];
+    buf[m++] = improper_atom4[i][k];
+  }
+
+  buf[m++] = nspecial[i][0];
+  buf[m++] = nspecial[i][1];
+  buf[m++] = nspecial[i][2];
+  for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
+
+  if (atom->nextra_grow)
+    for (int iextra = 0; iextra < atom->nextra_grow; iextra++) 
+      m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
+
+  buf[0] = m;
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFull::unpack_exchange(double *buf)
+{
+  int k;
+
+  int nlocal = atom->nlocal;
+  if (nlocal == nmax) grow(0);
+
+  int m = 1;
+  x[nlocal][0] = buf[m++];
+  x[nlocal][1] = buf[m++];
+  x[nlocal][2] = buf[m++];
+  v[nlocal][0] = buf[m++];
+  v[nlocal][1] = buf[m++];
+  v[nlocal][2] = buf[m++];
+  tag[nlocal] = static_cast<int> (buf[m++]);
+  type[nlocal] = static_cast<int> (buf[m++]);
+  mask[nlocal] = static_cast<int> (buf[m++]);
+  image[nlocal] = static_cast<int> (buf[m++]);
+
+  q[nlocal] = buf[m++];
+  molecule[nlocal] = static_cast<int> (buf[m++]);
+
+  num_bond[nlocal] = static_cast<int> (buf[m++]);
+  for (k = 0; k < num_bond[nlocal]; k++) {
+    bond_type[nlocal][k] = static_cast<int> (buf[m++]);
+    bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
+  }
+
+  num_angle[nlocal] = static_cast<int> (buf[m++]);
+  for (k = 0; k < num_angle[nlocal]; k++) {
+    angle_type[nlocal][k] = static_cast<int> (buf[m++]);
+    angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
+    angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
+    angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
+  }
+
+  num_dihedral[nlocal] = static_cast<int> (buf[m++]);
+  for (k = 0; k < num_dihedral[nlocal]; k++) {
+    dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
+    dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
+    dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
+    dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
+    dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
+  }
+
+  num_improper[nlocal] = static_cast<int> (buf[m++]);
+  for (k = 0; k < num_improper[nlocal]; k++) {
+    improper_type[nlocal][k] = static_cast<int> (buf[m++]);
+    improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
+    improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
+    improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
+    improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
+  }
+
+  nspecial[nlocal][0] = static_cast<int> (buf[m++]);
+  nspecial[nlocal][1] = static_cast<int> (buf[m++]);
+  nspecial[nlocal][2] = static_cast<int> (buf[m++]);
+  for (k = 0; k < nspecial[nlocal][2]; k++)
+    special[nlocal][k] = static_cast<int> (buf[m++]);
+
+  if (atom->nextra_grow)
+    for (int iextra = 0; iextra < atom->nextra_grow; iextra++) 
+      m += modify->fix[atom->extra_grow[iextra]]->
+	unpack_exchange(nlocal,&buf[m]);
+
+  atom->nlocal++;
+  return m;
+}
+
+/* ----------------------------------------------------------------------
+   size of restart data for all atoms owned by this proc
+   include extra data stored by fixes
+------------------------------------------------------------------------- */
+
+int AtomVecFull::size_restart()
+{
+  int i;
+
+  int nlocal = atom->nlocal;
+  int n = 0;
+  for (i = 0; i < nlocal; i++)
+    n += 17 + 2*num_bond[i] + 4*num_angle[i] +
+      5*num_dihedral[i] + 5*num_improper[i];
+
+  if (atom->nextra_restart)
+    for (int iextra = 0; iextra < atom->nextra_restart; iextra++) 
+      for (i = 0; i < nlocal; i++)
+	n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
+  return n;
+}
+
+/* ----------------------------------------------------------------------
+   size of restart data for atom I
+   do not include extra data stored by fixes, included by caller
+------------------------------------------------------------------------- */
+
+int AtomVecFull::size_restart_one(int i)
+{
+  int n = 17 + 2*num_bond[i] + 4*num_angle[i] + 
+    5*num_dihedral[i] + 5*num_improper[i];
+  return n;
+}
+
+/* ----------------------------------------------------------------------
+   pack atom I's data for restart file including extra quantities
+   xyz must be 1st 3 values, so that read_restart can test on them
+   molecular types may be negative, but write as positive   
+------------------------------------------------------------------------- */
+
+int AtomVecFull::pack_restart(int i, double *buf)
+{
+  int k;
+
+  int m = 1;
+  buf[m++] = x[i][0];
+  buf[m++] = x[i][1];
+  buf[m++] = x[i][2];
+  buf[m++] = tag[i];
+  buf[m++] = type[i];
+  buf[m++] = mask[i];
+  buf[m++] = image[i];
+  buf[m++] = v[i][0];
+  buf[m++] = v[i][1];
+  buf[m++] = v[i][2];
+
+  buf[m++] = q[i];
+  buf[m++] = molecule[i];
+ 
+  buf[m++] = num_bond[i];
+  for (k = 0; k < num_bond[i]; k++) {
+    buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
+    buf[m++] = bond_atom[i][k];
+  }
+  
+  buf[m++] = num_angle[i];
+  for (k = 0; k < num_angle[i]; k++) {
+    buf[m++] = MAX(angle_type[i][k],-angle_type[i][k]);
+    buf[m++] = angle_atom1[i][k];
+    buf[m++] = angle_atom2[i][k];
+    buf[m++] = angle_atom3[i][k];
+  }
+
+  buf[m++] = num_dihedral[i];
+  for (k = 0; k < num_dihedral[i]; k++) {
+    buf[m++] = MAX(dihedral_type[i][k],-dihedral_type[i][k]);
+    buf[m++] = dihedral_atom1[i][k];
+    buf[m++] = dihedral_atom2[i][k];
+    buf[m++] = dihedral_atom3[i][k];
+    buf[m++] = dihedral_atom4[i][k];
+  }
+
+  buf[m++] = num_improper[i];
+  for (k = 0; k < num_improper[i]; k++) {
+    buf[m++] = MAX(improper_type[i][k],-improper_type[i][k]);
+    buf[m++] = improper_atom1[i][k];
+    buf[m++] = improper_atom2[i][k];
+    buf[m++] = improper_atom3[i][k];
+    buf[m++] = improper_atom4[i][k];
+  }
+
+  if (atom->nextra_restart)
+    for (int iextra = 0; iextra < atom->nextra_restart; iextra++) 
+      m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
+
+  buf[0] = m;
+  return m;
+}
+
+/* ----------------------------------------------------------------------
+   unpack data for one atom from restart file including extra quantities
+------------------------------------------------------------------------- */
+
+int AtomVecFull::unpack_restart(double *buf)
+{
+  int k;
+
+  int nlocal = atom->nlocal;
+  if (nlocal == nmax) {
+    grow(0);
+    if (atom->nextra_store)
+      atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
+						 atom->nextra_store,
+						 "atom:extra");
+  }
+
+  int m = 1;
+  x[nlocal][0] = buf[m++];
+  x[nlocal][1] = buf[m++];
+  x[nlocal][2] = buf[m++];
+  tag[nlocal] = static_cast<int> (buf[m++]);
+  type[nlocal] = static_cast<int> (buf[m++]);
+  mask[nlocal] = static_cast<int> (buf[m++]);
+  image[nlocal] = static_cast<int> (buf[m++]);
+  v[nlocal][0] = buf[m++];
+  v[nlocal][1] = buf[m++];
+  v[nlocal][2] = buf[m++];
+
+  q[nlocal] = buf[m++];
+  molecule[nlocal] = static_cast<int> (buf[m++]);
+    
+  num_bond[nlocal] = static_cast<int> (buf[m++]);
+  for (k = 0; k < num_bond[nlocal]; k++) {
+    bond_type[nlocal][k] = static_cast<int> (buf[m++]);
+    bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
+  }
+
+  num_angle[nlocal] = static_cast<int> (buf[m++]);
+  for (k = 0; k < num_angle[nlocal]; k++) {
+    angle_type[nlocal][k] = static_cast<int> (buf[m++]);
+    angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
+    angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
+    angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
+  }
+
+  num_dihedral[nlocal] = static_cast<int> (buf[m++]);
+  for (k = 0; k < num_dihedral[nlocal]; k++) {
+    dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
+    dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
+    dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
+    dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
+    dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
+  }
+
+  num_improper[nlocal] = static_cast<int> (buf[m++]);
+  for (k = 0; k < num_improper[nlocal]; k++) {
+    improper_type[nlocal][k] = static_cast<int> (buf[m++]);
+    improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
+    improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
+    improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
+    improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
+  }
+
+  double **extra = atom->extra;
+  if (atom->nextra_store) {
+    int size = static_cast<int> (buf[0]) - m;
+    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
+  }
+
+  atom->nlocal++;
+  return m;
+}
+
+/* ----------------------------------------------------------------------
+   create one atom of type itype at x0,y0,z0
+   set other values to defaults
+------------------------------------------------------------------------- */
+
+void AtomVecFull::create_atom(int itype, double x0, double y0, double z0,
+				   int ihybrid)
+{
+  int nlocal = atom->nlocal;
+  if (nlocal == nmax) grow(0);
+
+  tag[nlocal] = 0;
+  type[nlocal] = itype;
+  x[nlocal][0] = x0;
+  x[nlocal][1] = y0;
+  x[nlocal][2] = z0;
+  mask[nlocal] = 1;
+  image[nlocal] = (512 << 20) | (512 << 10) | 512;
+  v[nlocal][0] = 0.0;
+  v[nlocal][1] = 0.0;
+  v[nlocal][2] = 0.0;
+
+  q[nlocal] = 0.0;
+  molecule[nlocal] = 0;
+  num_bond[nlocal] = 0;
+  num_angle[nlocal] = 0;
+  num_dihedral[nlocal] = 0;
+  num_improper[nlocal] = 0;
+
+  atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+   unpack one line from Atoms section of data file
+   initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecFull::data_atom(double xtmp, double ytmp, double ztmp,
+				 int imagetmp, char **values, int ihybrid)
+{
+  int nlocal = atom->nlocal;
+  if (nlocal == nmax) grow(0);
+
+  tag[nlocal] = atoi(values[0]);
+  if (tag[nlocal] <= 0)
+    error->one("Invalid atom ID in Atoms section of data file");
+
+  molecule[nlocal] = atoi(values[1]);
+
+  type[nlocal] = atoi(values[2]);
+  if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
+    error->one("Invalid atom type in Atoms section of data file");
+
+  q[nlocal] = atof(values[3]);
+
+  x[nlocal][0] = xtmp;
+  x[nlocal][1] = ytmp;
+  x[nlocal][2] = ztmp;
+
+  image[nlocal] = imagetmp;
+
+  mask[nlocal] = 1;
+  v[nlocal][0] = 0.0;
+  v[nlocal][1] = 0.0;
+  v[nlocal][2] = 0.0;
+  num_bond[nlocal] = 0;
+  num_angle[nlocal] = 0;
+  num_dihedral[nlocal] = 0;
+  num_improper[nlocal] = 0;
+
+  atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+   return # of bytes of allocated memory 
+------------------------------------------------------------------------- */
+
+int AtomVecFull::memory_usage()
+{
+  int bytes = 0;
+
+  if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("type")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("image")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
+  if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
+  if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
+
+  if (atom->memcheck("q")) bytes += nmax * sizeof(double);
+  if (atom->memcheck("molecule")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("nspecial")) bytes += nmax*3 * sizeof(int);
+  if (atom->memcheck("special")) bytes += nmax*atom->maxspecial * sizeof(int);
+
+  if (atom->memcheck("num_bond")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("bond_type"))
+    bytes += nmax*atom->bond_per_atom * sizeof(int);
+  if (atom->memcheck("bond_atom"))
+    bytes += nmax*atom->bond_per_atom * sizeof(int);
+
+  if (atom->memcheck("num_angle")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("angle_type"))
+    bytes += nmax*atom->angle_per_atom * sizeof(int);
+  if (atom->memcheck("angle_atom1"))
+    bytes += nmax*atom->angle_per_atom * sizeof(int);
+  if (atom->memcheck("angle_atom2"))
+    bytes += nmax*atom->angle_per_atom * sizeof(int);
+  if (atom->memcheck("angle_atom3"))
+    bytes += nmax*atom->angle_per_atom * sizeof(int);
+
+  if (atom->memcheck("num_dihedral")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("dihedral_type"))
+    bytes += nmax*atom->dihedral_per_atom * sizeof(int);
+  if (atom->memcheck("dihedral_atom1"))
+    bytes += nmax*atom->dihedral_per_atom * sizeof(int);
+  if (atom->memcheck("dihedral_atom2"))
+    bytes += nmax*atom->dihedral_per_atom * sizeof(int);
+  if (atom->memcheck("dihedral_atom3"))
+    bytes += nmax*atom->dihedral_per_atom * sizeof(int);
+  if (atom->memcheck("dihedral_atom4"))
+    bytes += nmax*atom->dihedral_per_atom * sizeof(int);
+
+  if (atom->memcheck("num_improper")) bytes += nmax * sizeof(int);
+  if (atom->memcheck("improper_type"))
+    bytes += nmax*atom->improper_per_atom * sizeof(int);
+  if (atom->memcheck("improper_atom1"))
+    bytes += nmax*atom->improper_per_atom * sizeof(int);
+  if (atom->memcheck("improper_atom2"))
+    bytes += nmax*atom->improper_per_atom * sizeof(int);
+  if (atom->memcheck("improper_atom3"))
+    bytes += nmax*atom->improper_per_atom * sizeof(int);
+  if (atom->memcheck("improper_atom4"))
+    bytes += nmax*atom->improper_per_atom * sizeof(int);
+
+  return bytes;
+}
diff --git a/src/MOLECULE/atom_vec_full.h b/src/MOLECULE/atom_vec_full.h
new file mode 100644
index 0000000000..81f2a6fcca
--- /dev/null
+++ b/src/MOLECULE/atom_vec_full.h
@@ -0,0 +1,68 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under 
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef ATOM_VEC_FULL_H
+#define ATOM_VEC_FULL_H
+
+#include "atom_vec.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecFull : public AtomVec {
+ public:
+  AtomVecFull(class LAMMPS *, int, char **);
+  void grow(int);
+  void reset_ptrs();
+  void zero_owned(int);
+  void zero_ghost(int, int);
+  void copy(int, int);
+  int pack_comm(int, int *, double *, int *);
+  void unpack_comm(int, int, double *);
+  int pack_reverse(int, int, double *);
+  void unpack_reverse(int, int *, double *);
+  int pack_border(int, int *, double *, int *);
+  int pack_border_one(int, double *);
+  void unpack_border(int, int, double *);
+  int unpack_border_one(int, double *);
+  int pack_exchange(int, double *);
+  int unpack_exchange(double *);
+  int size_restart();
+  int size_restart_one(int);
+  int pack_restart(int, double *);
+  int unpack_restart(double *);
+  void create_atom(int, double, double, double, int);
+  void data_atom(double, double, double, int, char **, int);
+  int memory_usage();
+
+ private:
+  int *tag,*type,*mask,*image;
+  double **x,**v,**f;
+  double *q;
+  int *molecule;
+  int **nspecial,**special;
+  int *num_bond;
+  int **bond_type,**bond_atom;
+  int *num_angle;
+  int **angle_type;
+  int **angle_atom1,**angle_atom2,**angle_atom3;
+  int *num_dihedral;
+  int **dihedral_type;
+  int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
+  int *num_improper;
+  int **improper_type;
+  int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
+};
+
+}
+
+#endif