From 6284969800724e4ea42e71ec31825a37080a4110 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 18 Apr 2011 22:16:33 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5973
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/atom_vec_ellipsoid.cpp | 1262 ++++++++++++++++++++++++++++++++++++
 src/atom_vec_ellipsoid.h   |   91 +++
 2 files changed, 1353 insertions(+)
 create mode 100755 src/atom_vec_ellipsoid.cpp
 create mode 100755 src/atom_vec_ellipsoid.h

diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp
new file mode 100755
index 0000000000..5e00a4f24b
--- /dev/null
+++ b/src/atom_vec_ellipsoid.cpp
@@ -0,0 +1,1262 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Mike Brown (SNL)
+------------------------------------------------------------------------- */
+
+#include "lmptype.h"
+#include "stdlib.h"
+#include "atom_vec_ellipsoid.h"
+#include "math_extra.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+#define DELTA_BONUS 10000
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp, int narg, char **arg) :
+  AtomVec(lmp, narg, arg)
+{
+  molecular = 0;
+
+  comm_x_only = comm_f_only = 0;
+  size_forward = 7;
+  size_reverse = 6;
+  size_border = 14;
+  size_velocity = 6;
+  size_data_atom = 7;
+  size_data_vel = 7;
+  size_data_bonus = 8;
+  xcol_data = 5;
+
+  atom->ellipsoid_flag = 1;
+  atom->rmass_flag = atom->angmom_flag = atom->torque_flag = 1;
+
+  PI = 4.0*atan(1.0);
+
+  nlocal_bonus = nghost_bonus = nmax_bonus = 0;
+  bonus = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecEllipsoid::~AtomVecEllipsoid()
+{
+  memory->sfree(bonus);
+}
+
+/* ----------------------------------------------------------------------
+   grow atom arrays
+   n = 0 grows arrays by DELTA
+   n > 0 allocates arrays to size n
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::grow(int n)
+{
+  if (n == 0) nmax += DELTA;
+  else nmax = n;
+  atom->nmax = nmax;
+  if (nmax < 0 || nmax > MAXSMALLINT)
+    error->one("Per-processor system is too big");
+
+  tag = memory->grow(atom->tag,nmax,"atom:tag");
+  type = memory->grow(atom->type,nmax,"atom:type");
+  mask = memory->grow(atom->mask,nmax,"atom:mask");
+  image = memory->grow(atom->image,nmax,"atom:image");
+  x = memory->grow(atom->x,nmax,3,"atom:x");
+  v = memory->grow(atom->v,nmax,3,"atom:v");
+  f = memory->grow(atom->f,nmax,3,"atom:f");
+
+  rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
+  angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");
+  torque = memory->grow(atom->torque,nmax,3,"atom:torque");
+  ellipsoid = memory->grow(atom->ellipsoid,nmax,"atom:ellipsoid");
+
+  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 AtomVecEllipsoid::grow_reset()
+{
+  tag = atom->tag; type = atom->type;
+  mask = atom->mask; image = atom->image;
+  x = atom->x; v = atom->v; f = atom->f;
+  rmass = atom->rmass; angmom = atom->angmom; torque = atom->torque;
+}
+
+/* ----------------------------------------------------------------------
+   grow bonus data structure
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::grow_bonus()
+{
+  nmax_bonus += DELTA_BONUS;
+  if (nmax_bonus < 0 || nmax_bonus > MAXSMALLINT)
+    error->one("Per-processor system is too big");
+
+  bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
+				     "atom:bonus");
+}
+
+/* ----------------------------------------------------------------------
+   copy atom I info to atom J
+   if delflag and atom J has bonus data, then delete it
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::copy(int i, int j, int delflag)
+{
+  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];
+
+  rmass[j] = rmass[i];
+  angmom[j][0] = angmom[i][0];
+  angmom[j][1] = angmom[i][1];
+  angmom[j][2] = angmom[i][2];
+
+  if (delflag && ellipsoid[j] >= 0) {
+    copy_bonus(nlocal_bonus-1,ellipsoid[j]);
+    nlocal_bonus--;
+  }
+  ellipsoid[j] = ellipsoid[i];
+  if (ellipsoid[j] >= 0) bonus[ellipsoid[j]].ilocal = j;
+
+  if (atom->nextra_grow)
+    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+      modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
+}
+
+/* ----------------------------------------------------------------------
+   copy bonus data from I to J, effectively deleting the J entry
+   insure index pointers between per-atom and bonus data are updated
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::copy_bonus(int i, int j)
+{
+  double *ishape = bonus[i].shape;
+  double *iquat = bonus[i].quat;
+  double *jshape = bonus[j].shape;
+  double *jquat = bonus[j].quat;
+  jshape[0] = ishape[0];
+  jshape[1] = ishape[1];
+  jshape[2] = ishape[2];
+  jquat[0] = iquat[0];
+  jquat[1] = iquat[1];
+  jquat[2] = iquat[2];
+  jquat[3] = iquat[3];
+  int m = bonus[i].ilocal;
+  bonus[j].ilocal = m;
+  ellipsoid[m] = j;
+}
+
+/* ----------------------------------------------------------------------
+   set shape values in bonus data for particle I
+   this may create or delete entry in bonus data
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::set_bonus(int i, 
+				 double shapex, double shapey, double shapez)
+{
+  if (ellipsoid[i] < 0) {
+    if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) return;
+    if (nlocal_bonus == nmax_bonus) grow_bonus();
+    double *shape = bonus[nlocal_bonus].shape;
+    double *quat = bonus[nlocal_bonus].quat;
+    shape[0] = shapex;
+    shape[1] = shapey;
+    shape[2] = shapez;
+    quat[0] = 1.0;
+    quat[1] = 0.0;
+    quat[2] = 0.0;
+    quat[3] = 0.0;
+    bonus[nlocal_bonus].ilocal = i;
+    ellipsoid[i] = nlocal_bonus++;
+  } else if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) {
+    copy_bonus(nlocal_bonus-1,ellipsoid[i]);
+    nlocal_bonus--;
+    ellipsoid[i] = -1;
+  } else {
+    double *shape = bonus[ellipsoid[i]].shape;
+    shape[0] = shapex;
+    shape[1] = shapey;
+    shape[2] = shapez;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   clear ghost info in bonus data
+   called before ghosts are recommunicated in comm and irregular
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::clear_bonus()
+{
+  nghost_bonus = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
+			     int pbc_flag, int *pbc)
+{
+  int i,j,m;
+  double dx,dy,dz;
+  double *quat;
+
+  m = 0;
+  if (pbc_flag == 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];
+      if (ellipsoid[j] >= 0) {
+	quat = bonus[ellipsoid[j]].quat;
+	buf[m++] = quat[0];
+	buf[m++] = quat[1];
+	buf[m++] = quat[2];
+	buf[m++] = quat[3];
+      }
+    }
+  } else {
+    if (domain->triclinic == 0) {
+      dx = pbc[0]*domain->xprd;
+      dy = pbc[1]*domain->yprd;
+      dz = pbc[2]*domain->zprd;
+    } else {
+      dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+      dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+      dz = pbc[2]*domain->zprd;
+    }
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      buf[m++] = x[j][0] + dx;
+      buf[m++] = x[j][1] + dy;
+      buf[m++] = x[j][2] + dz;
+      if (ellipsoid[j] >= 0) {
+	quat = bonus[ellipsoid[j]].quat;
+	buf[m++] = quat[0];
+	buf[m++] = quat[1];
+	buf[m++] = quat[2];
+	buf[m++] = quat[3];
+      }
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_comm_vel(int n, int *list, double *buf,
+				    int pbc_flag, int *pbc)
+{
+  int i,j,m;
+  double dx,dy,dz,dvx,dvy,dvz;
+  double *quat;
+
+  m = 0;
+  if (pbc_flag == 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];
+      if (ellipsoid[j] >= 0) {
+	quat = bonus[ellipsoid[j]].quat;
+	buf[m++] = quat[0];
+	buf[m++] = quat[1];
+	buf[m++] = quat[2];
+	buf[m++] = quat[3];
+      }
+      buf[m++] = v[j][0];
+      buf[m++] = v[j][1];
+      buf[m++] = v[j][2];
+      buf[m++] = angmom[j][0];
+      buf[m++] = angmom[j][1];
+      buf[m++] = angmom[j][2];
+    }
+  } else {
+    if (domain->triclinic == 0) {
+      dx = pbc[0]*domain->xprd;
+      dy = pbc[1]*domain->yprd;
+      dz = pbc[2]*domain->zprd;
+    } else {
+      dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+      dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+      dz = pbc[2]*domain->zprd;
+    }
+    if (!deform_vremap) {
+      for (i = 0; i < n; i++) {
+	j = list[i];
+	buf[m++] = x[j][0] + dx;
+	buf[m++] = x[j][1] + dy;
+	buf[m++] = x[j][2] + dz;
+	if (ellipsoid[j] >= 0) {
+	  quat = bonus[ellipsoid[j]].quat;
+	  buf[m++] = quat[0];
+	  buf[m++] = quat[1];
+	  buf[m++] = quat[2];
+	  buf[m++] = quat[3];
+	}
+	buf[m++] = v[j][0];
+	buf[m++] = v[j][1];
+	buf[m++] = v[j][2];
+	buf[m++] = angmom[j][0];
+	buf[m++] = angmom[j][1];
+	buf[m++] = angmom[j][2];
+      }
+    } else {
+      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+      dvz = pbc[2]*h_rate[2];
+      for (i = 0; i < n; i++) {
+	j = list[i];
+	buf[m++] = x[j][0] + dx;
+	buf[m++] = x[j][1] + dy;
+	buf[m++] = x[j][2] + dz;
+	if (ellipsoid[j] >= 0) {
+	  quat = bonus[ellipsoid[j]].quat;
+	  buf[m++] = quat[0];
+	  buf[m++] = quat[1];
+	  buf[m++] = quat[2];
+	  buf[m++] = quat[3];
+	}
+	if (mask[i] & deform_groupbit) {
+	  buf[m++] = v[j][0] + dvx;
+	  buf[m++] = v[j][1] + dvy;
+	  buf[m++] = v[j][2] + dvz;
+	} else {
+	  buf[m++] = v[j][0];
+	  buf[m++] = v[j][1];
+	  buf[m++] = v[j][2];
+	}
+	buf[m++] = angmom[j][0];
+	buf[m++] = angmom[j][1];
+	buf[m++] = angmom[j][2];
+      }
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_comm_hybrid(int n, int *list, double *buf)
+{
+  int i,j,m;
+  double *quat;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    if (ellipsoid[j] >= 0) {
+      quat = bonus[ellipsoid[j]].quat;
+      buf[m++] = quat[0];
+      buf[m++] = quat[1];
+      buf[m++] = quat[2];
+      buf[m++] = quat[3];
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::unpack_comm(int n, int first, double *buf)
+{
+  int i,m,last;
+  double *quat;
+
+  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++];
+    if (ellipsoid[i] >= 0) {
+      quat = bonus[ellipsoid[i]].quat;
+      quat[0] = buf[m++];
+      quat[1] = buf[m++];
+      quat[2] = buf[m++];
+      quat[3] = buf[m++];
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::unpack_comm_vel(int n, int first, double *buf)
+{
+  int i,m,last;
+  double *quat;
+
+  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++];
+    if (ellipsoid[i] >= 0) {
+      quat = bonus[ellipsoid[i]].quat;
+      quat[0] = buf[m++];
+      quat[1] = buf[m++];
+      quat[2] = buf[m++];
+      quat[3] = buf[m++];
+    }
+    v[i][0] = buf[m++];
+    v[i][1] = buf[m++];
+    v[i][2] = buf[m++];
+    angmom[i][0] = buf[m++];
+    angmom[i][1] = buf[m++];
+    angmom[i][2] = buf[m++];
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::unpack_comm_hybrid(int n, int first, double *buf)
+{
+  int i,m,last;
+  double *quat;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    if (ellipsoid[i] >= 0) {
+      quat = bonus[ellipsoid[i]].quat;
+      quat[0] = buf[m++];
+      quat[1] = buf[m++];
+      quat[2] = buf[m++];
+      quat[3] = buf[m++];
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::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];
+    buf[m++] = torque[i][0];
+    buf[m++] = torque[i][1];
+    buf[m++] = torque[i][2];
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_reverse_hybrid(int n, int first, double *buf)
+{
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    buf[m++] = torque[i][0];
+    buf[m++] = torque[i][1];
+    buf[m++] = torque[i][2];
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::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++];
+    torque[j][0] += buf[m++];
+    torque[j][1] += buf[m++];
+    torque[j][2] += buf[m++];
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::unpack_reverse_hybrid(int n, int *list, double *buf)
+{
+  int i,j,m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    torque[j][0] += buf[m++];
+    torque[j][1] += buf[m++];
+    torque[j][2] += buf[m++];
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
+				  int pbc_flag, int *pbc)
+{
+  int i,j,m;
+  double dx,dy,dz;
+  double *shape,*quat;
+
+  m = 0;
+  if (pbc_flag == 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];
+      if (ellipsoid[j] < 0) buf[m++] = 0;
+      else {
+	buf[m++] = 1;
+	shape = bonus[ellipsoid[j]].shape;
+	quat = bonus[ellipsoid[j]].quat;
+	buf[m++] = shape[0];
+	buf[m++] = shape[1];
+	buf[m++] = shape[2];
+	buf[m++] = quat[0];
+	buf[m++] = quat[1];
+	buf[m++] = quat[2];
+	buf[m++] = quat[3];
+      }
+    }
+  } else {
+    if (domain->triclinic == 0) {
+      dx = pbc[0]*domain->xprd;
+      dy = pbc[1]*domain->yprd;
+      dz = pbc[2]*domain->zprd;
+    } else {
+      dx = pbc[0];
+      dy = pbc[1];
+      dz = pbc[2];
+    }
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      buf[m++] = x[j][0] + dx;
+      buf[m++] = x[j][1] + dy;
+      buf[m++] = x[j][2] + dz;
+      buf[m++] = tag[j];
+      buf[m++] = type[j];
+      buf[m++] = mask[j];
+      if (ellipsoid[j] < 0) buf[m++] = 0;
+      else {
+	buf[m++] = 1;
+	shape = bonus[ellipsoid[j]].shape;
+	quat = bonus[ellipsoid[j]].quat;
+	buf[m++] = shape[0];
+	buf[m++] = shape[1];
+	buf[m++] = shape[2];
+	buf[m++] = quat[0];
+	buf[m++] = quat[1];
+	buf[m++] = quat[2];
+	buf[m++] = quat[3];
+      }
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
+				      int pbc_flag, int *pbc)
+{
+  int i,j,m;
+  double dx,dy,dz,dvx,dvy,dvz;
+  double *shape,*quat;
+
+  m = 0;
+  if (pbc_flag == 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];
+      if (ellipsoid[j] < 0) buf[m++] = 0;
+      else {
+	buf[m++] = 1;
+	shape = bonus[ellipsoid[j]].shape;
+	quat = bonus[ellipsoid[j]].quat;
+	buf[m++] = shape[0];
+	buf[m++] = shape[1];
+	buf[m++] = shape[2];
+	buf[m++] = quat[0];
+	buf[m++] = quat[1];
+	buf[m++] = quat[2];
+	buf[m++] = quat[3];
+      }
+      buf[m++] = v[j][0];
+      buf[m++] = v[j][1];
+      buf[m++] = v[j][2];
+      buf[m++] = angmom[j][0];
+      buf[m++] = angmom[j][1];
+      buf[m++] = angmom[j][2];
+    }
+  } else {
+    if (domain->triclinic == 0) {
+      dx = pbc[0]*domain->xprd;
+      dy = pbc[1]*domain->yprd;
+      dz = pbc[2]*domain->zprd;
+    } else {
+      dx = pbc[0];
+      dy = pbc[1];
+      dz = pbc[2];
+    }
+    if (!deform_vremap) {
+      for (i = 0; i < n; i++) {
+	j = list[i];
+	buf[m++] = x[j][0] + dx;
+	buf[m++] = x[j][1] + dy;
+	buf[m++] = x[j][2] + dz;
+	buf[m++] = tag[j];
+	buf[m++] = type[j];
+	buf[m++] = mask[j];
+	if (ellipsoid[j] < 0) buf[m++] = 0;
+	else {
+	  buf[m++] = 1;
+	  quat = bonus[ellipsoid[j]].quat;
+	  buf[m++] = shape[0];
+	  buf[m++] = shape[1];
+	  buf[m++] = shape[2];
+	  buf[m++] = quat[0];
+	  buf[m++] = quat[1];
+	  buf[m++] = quat[2];
+	  buf[m++] = quat[3];
+	}
+	buf[m++] = v[j][0];
+	buf[m++] = v[j][1];
+	buf[m++] = v[j][2];
+	buf[m++] = angmom[j][0];
+	buf[m++] = angmom[j][1];
+	buf[m++] = angmom[j][2];
+      }
+    } else {
+      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+      dvz = pbc[2]*h_rate[2];
+      for (i = 0; i < n; i++) {
+	j = list[i];
+	buf[m++] = x[j][0] + dx;
+	buf[m++] = x[j][1] + dy;
+	buf[m++] = x[j][2] + dz;
+	buf[m++] = tag[j];
+	buf[m++] = type[j];
+	buf[m++] = mask[j];
+	if (ellipsoid[j] < 0) buf[m++] = 0;
+	else {
+	  buf[m++] = 1;
+	  shape = bonus[ellipsoid[j]].shape;
+	  quat = bonus[ellipsoid[j]].quat;
+	  buf[m++] = shape[0];
+	  buf[m++] = shape[1];
+	  buf[m++] = shape[2];
+	  buf[m++] = quat[0];
+	  buf[m++] = quat[1];
+	  buf[m++] = quat[2];
+	  buf[m++] = quat[3];
+	}
+	if (mask[i] & deform_groupbit) {
+	  buf[m++] = v[j][0] + dvx;
+	  buf[m++] = v[j][1] + dvy;
+	  buf[m++] = v[j][2] + dvz;
+	} else {
+	  buf[m++] = v[j][0];
+	  buf[m++] = v[j][1];
+	  buf[m++] = v[j][2];
+	}
+	buf[m++] = angmom[j][0];
+	buf[m++] = angmom[j][1];
+	buf[m++] = angmom[j][2];
+      }
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_border_hybrid(int n, int *list, double *buf)
+{
+  int i,j,m;
+  double *shape,*quat;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    if (ellipsoid[j] < 0) buf[m++] = 0;
+    else {
+      buf[m++] = 1;
+      shape = bonus[ellipsoid[j]].shape;
+      quat = bonus[ellipsoid[j]].quat;
+      buf[m++] = shape[0];
+      buf[m++] = shape[1];
+      buf[m++] = shape[2];
+      buf[m++] = quat[0];
+      buf[m++] = quat[1];
+      buf[m++] = quat[2];
+      buf[m++] = quat[3];
+    }
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::unpack_border(int n, int first, double *buf)
+{
+  int i,j,m,last;
+  double *shape,*quat;
+
+  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++]);
+    ellipsoid[i] = static_cast<int> (buf[m++]);
+    if (ellipsoid[i] < 0) ellipsoid[i] = 0;
+    else {
+      j = nlocal_bonus + nghost_bonus;
+      if (j == nmax_bonus) grow_bonus();
+      shape = bonus[j].shape;
+      quat = bonus[j].quat;
+      shape[0] = buf[m++];
+      shape[1] = buf[m++];
+      shape[2] = buf[m++];
+      quat[0] = buf[m++];
+      quat[1] = buf[m++];
+      quat[2] = buf[m++];
+      quat[3] = buf[m++];
+      bonus[j].ilocal = i;
+      ellipsoid[i] = j;
+      nghost_bonus++;
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::unpack_border_vel(int n, int first, double *buf)
+{
+  int i,j,m,last;
+  double *shape,*quat;
+
+  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++]);
+    ellipsoid[i] = static_cast<int> (buf[m++]);
+    if (ellipsoid[i] < 0) ellipsoid[i] = 0;
+    else {
+      j = nlocal_bonus + nghost_bonus;
+      if (j == nmax_bonus) grow_bonus();
+      shape = bonus[j].shape;
+      quat = bonus[j].quat;
+      shape[0] = buf[m++];
+      shape[1] = buf[m++];
+      shape[2] = buf[m++];
+      quat[0] = buf[m++];
+      quat[1] = buf[m++];
+      quat[2] = buf[m++];
+      quat[3] = buf[m++];
+      bonus[j].ilocal = i;
+      ellipsoid[i] = j;
+      nghost_bonus++;
+    }
+    v[i][0] = buf[m++];
+    v[i][1] = buf[m++];
+    v[i][2] = buf[m++];
+    angmom[i][0] = buf[m++];
+    angmom[i][1] = buf[m++];
+    angmom[i][2] = buf[m++];
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::unpack_border_hybrid(int n, int first, double *buf)
+{
+  int i,j,m,last;
+  double *shape,*quat;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    ellipsoid[i] = static_cast<int> (buf[m++]);
+    if (ellipsoid[i] < 0) ellipsoid[i] = 0;
+    else {
+      j = nlocal_bonus + nghost_bonus;
+      if (j == nmax_bonus) grow_bonus();
+      shape = bonus[j].shape;
+      quat = bonus[j].quat;
+      shape[0] = buf[m++];
+      shape[1] = buf[m++];
+      shape[2] = buf[m++];
+      quat[0] = buf[m++];
+      quat[1] = buf[m++];
+      quat[2] = buf[m++];
+      quat[3] = buf[m++];
+      bonus[j].ilocal = i;
+      ellipsoid[i] = j;
+      nghost_bonus++;
+    }
+  }
+  return m;
+}
+
+/* ----------------------------------------------------------------------
+   pack data for atom I for sending to another proc
+   xyz must be 1st 3 values, so comm::exchange() can test on them
+------------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_exchange(int i, double *buf)
+{
+  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++] = rmass[i];
+  buf[m++] = angmom[i][0];
+  buf[m++] = angmom[i][1];
+  buf[m++] = angmom[i][2];
+
+  if (ellipsoid[i] < 0) buf[m++] = 0;
+  else {
+    buf[m++] = 1;
+    int j = ellipsoid[i];
+    buf[m++] = bonus[j].shape[0];
+    buf[m++] = bonus[j].shape[1];
+    buf[m++] = bonus[j].shape[2];
+    buf[m++] = bonus[j].quat[0];
+    buf[m++] = bonus[j].quat[1];
+    buf[m++] = bonus[j].quat[2];
+    buf[m++] = bonus[j].quat[3];
+  }
+  
+  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 AtomVecEllipsoid::unpack_exchange(double *buf)
+{
+  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++]);
+
+  rmass[nlocal] = buf[m++];
+  angmom[nlocal][0] = buf[m++];
+  angmom[nlocal][1] = buf[m++];
+  angmom[nlocal][2] = buf[m++];
+
+  ellipsoid[nlocal] = static_cast<int> (buf[m++]);
+  if (ellipsoid[nlocal]) {
+    if (nlocal_bonus == nmax_bonus) grow_bonus();
+    double *shape = bonus[nlocal_bonus].shape;
+    double *quat = bonus[nlocal_bonus].quat;
+    shape[0] = buf[m++];
+    shape[1] = buf[m++];
+    shape[2] = buf[m++];
+    quat[0] = buf[m++];
+    quat[1] = buf[m++];
+    quat[2] = buf[m++];
+    quat[3] = buf[m++];
+    bonus[nlocal_bonus].ilocal = nlocal;
+    ellipsoid[nlocal] = nlocal_bonus++;
+  }
+
+  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 AtomVecEllipsoid::size_restart()
+{
+  int i;
+
+  int n = 0;
+  int nlocal = atom->nlocal;
+  for (i = 0; i < nlocal; i++)
+    if (ellipsoid[i] >= 0) n += 23;
+    else n += 16;
+
+  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;
+}
+
+/* ----------------------------------------------------------------------
+   pack atom I's data for restart file including bonus data
+   xyz must be 1st 3 values, so that read_restart can test on them
+   molecular types may be negative, but write as positive
+------------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::pack_restart(int i, double *buf)
+{
+  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++] = rmass[i];
+  buf[m++] = angmom[i][0];
+  buf[m++] = angmom[i][1];
+  buf[m++] = angmom[i][2];
+
+  if (ellipsoid[i] < 0) buf[m++] = 0;
+  else {
+    buf[m++] = 1;
+    int j = ellipsoid[i];
+    buf[m++] = bonus[j].shape[0];
+    buf[m++] = bonus[j].shape[1];
+    buf[m++] = bonus[j].shape[2];
+    buf[m++] = bonus[j].quat[0];
+    buf[m++] = bonus[j].quat[1];
+    buf[m++] = bonus[j].quat[2];
+    buf[m++] = bonus[j].quat[3];
+  }
+
+  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 bonus data
+------------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::unpack_restart(double *buf)
+{
+  int nlocal = atom->nlocal;
+  if (nlocal == nmax) {
+    grow(0);
+    if (atom->nextra_store) 
+      memory->grow(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++];
+
+  rmass[nlocal] = buf[m++];
+  angmom[nlocal][0] = buf[m++];
+  angmom[nlocal][1] = buf[m++];
+  angmom[nlocal][2] = buf[m++];
+
+  ellipsoid[nlocal] = static_cast<int> (buf[m++]);
+  if (ellipsoid[nlocal]) {
+    if (nlocal_bonus == nmax_bonus) grow_bonus();
+    double *shape = bonus[nlocal_bonus].shape;
+    double *quat = bonus[nlocal_bonus].quat;
+    shape[0] = buf[m++];
+    shape[1] = buf[m++];
+    shape[2] = buf[m++];
+    quat[0] = buf[m++];
+    quat[1] = buf[m++];
+    quat[2] = buf[m++];
+    quat[3] = buf[m++];
+    bonus[nlocal_bonus].ilocal = nlocal;
+    ellipsoid[nlocal] = nlocal_bonus++;
+  }
+  
+  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 itype at coord
+   set other values to defaults
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::create_atom(int itype, double *coord)
+{
+  int nlocal = atom->nlocal;
+  if (nlocal == nmax) grow(0);
+
+  tag[nlocal] = 0;
+  type[nlocal] = itype;
+  x[nlocal][0] = coord[0];
+  x[nlocal][1] = coord[1];
+  x[nlocal][2] = coord[2];
+  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;
+  
+  rmass[nlocal] = 1.0;
+  angmom[nlocal][0] = 0.0;
+  angmom[nlocal][1] = 0.0;
+  angmom[nlocal][2] = 0.0;
+  ellipsoid[nlocal] = -1;
+
+  atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+   unpack one line from Atoms section of data file
+   initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::data_atom(double *coord, int imagetmp, char **values)
+{
+  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");
+
+  type[nlocal] = atoi(values[1]);
+  if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
+    error->one("Invalid atom type in Atoms section of data file");
+
+  ellipsoid[nlocal] = atoi(values[2]);
+  if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1;
+  else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0;
+  else error->one("Invalid atom type in Atoms section of data file");
+
+  rmass[nlocal] = atof(values[3]);
+  if (rmass[nlocal] <= 0.0)
+    error->one("Invalid density in Atoms section of data file");
+
+  x[nlocal][0] = coord[0];
+  x[nlocal][1] = coord[1];
+  x[nlocal][2] = coord[2];
+
+  image[nlocal] = imagetmp;
+
+  mask[nlocal] = 1;
+  v[nlocal][0] = 0.0;
+  v[nlocal][1] = 0.0;
+  v[nlocal][2] = 0.0;
+  angmom[nlocal][0] = 0.0;
+  angmom[nlocal][1] = 0.0;
+  angmom[nlocal][2] = 0.0;
+
+  atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+   unpack hybrid quantities from one line in Atoms section of data file
+   initialize other atom quantities for this sub-style
+------------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::data_atom_hybrid(int nlocal, char **values)
+{
+  ellipsoid[nlocal] = atoi(values[0]);
+  if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1;
+  else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0;
+  else error->one("Invalid atom type in Atoms section of data file");
+
+  rmass[nlocal] = atof(values[1]);
+  if (rmass[nlocal] <= 0.0)
+    error->one("Invalid density in Atoms section of data file");
+
+  return 2;
+}
+
+/* ----------------------------------------------------------------------
+   unpack one line from Ellipsoids section of data file
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::data_atom_bonus(int m, char **values)
+{
+  if (ellipsoid[m])
+    error->one("Assigning ellipsoid parameters to non-ellipsoid atom");
+
+  if (nlocal_bonus == nmax_bonus) grow_bonus();
+
+  double *shape = bonus[nlocal_bonus].shape;
+  shape[0] = 0.5 * atof(values[0]);
+  shape[1] = 0.5 * atof(values[1]);
+  shape[2] = 0.5 * atof(values[2]);
+  if (shape[0] <= 0.0 || shape[1] <= 0.0 || shape[2] <= 0.0)
+    error->one("Invalid shape in Ellipsoids section of data file");
+
+  double *quat = bonus[nlocal_bonus].quat;
+  quat[0] = atof(values[3]);
+  quat[1] = atof(values[4]);
+  quat[2] = atof(values[5]);
+  quat[3] = atof(values[6]);
+  MathExtra::normalize4(quat);
+
+  // reset ellipsoid mass
+  // previously stored density in rmass
+
+  rmass[m] *= 4.0*PI/3.0 * shape[0]*shape[1]*shape[2];
+
+  bonus[nlocal_bonus].ilocal = m;
+  ellipsoid[m] = nlocal_bonus++;
+}
+
+/* ----------------------------------------------------------------------
+   unpack one line from Velocities section of data file
+------------------------------------------------------------------------- */
+
+void AtomVecEllipsoid::data_vel(int m, char **values)
+{
+  v[m][0] = atof(values[0]);
+  v[m][1] = atof(values[1]);
+  v[m][2] = atof(values[2]);
+  angmom[m][0] = atof(values[3]);
+  angmom[m][1] = atof(values[4]);
+  angmom[m][2] = atof(values[5]);
+}
+
+/* ----------------------------------------------------------------------
+   unpack hybrid quantities from one line in Velocities section of data file
+------------------------------------------------------------------------- */
+
+int AtomVecEllipsoid::data_vel_hybrid(int m, char **values)
+{
+  angmom[m][0] = atof(values[0]);
+  angmom[m][1] = atof(values[1]);
+  angmom[m][2] = atof(values[2]);
+  return 3;
+}
+
+/* ----------------------------------------------------------------------
+   return # of bytes of allocated memory 
+------------------------------------------------------------------------- */
+
+bigint AtomVecEllipsoid::memory_usage()
+{
+  bigint bytes = 0;
+
+  if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
+  if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
+  if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
+  if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
+  if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
+  if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
+  if (atom->memcheck("f")) bytes += memory->usage(f,nmax,3);
+
+  if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
+  if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
+  if (atom->memcheck("torque")) bytes += memory->usage(torque,nmax,3);
+  if (atom->memcheck("ellipsoid")) bytes += memory->usage(ellipsoid,nmax);
+  
+  bytes += nmax_bonus*sizeof(Bonus);
+
+  return bytes;
+}
diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h
new file mode 100755
index 0000000000..f0b176e150
--- /dev/null
+++ b/src/atom_vec_ellipsoid.h
@@ -0,0 +1,91 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef ATOM_CLASS
+
+AtomStyle(ellipsoid,AtomVecEllipsoid)
+
+#else
+
+#ifndef LMP_ATOM_VEC_ELLIPSOID_H
+#define LMP_ATOM_VEC_ELLIPSOID_H
+
+#include "atom_vec.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecEllipsoid : public AtomVec {
+ public:
+  struct Bonus {
+    double shape[3];
+    double quat[4];
+    int ilocal;
+  };
+  struct Bonus *bonus;
+
+  AtomVecEllipsoid(class LAMMPS *, int, char **);
+  ~AtomVecEllipsoid();
+  void grow(int);
+  void grow_reset();
+  void copy(int, int, int);
+  int pack_comm(int, int *, double *, int, int *);
+  int pack_comm_vel(int, int *, double *, int, int *);
+  int pack_comm_hybrid(int, int *, double *);
+  void unpack_comm(int, int, double *);
+  void unpack_comm_vel(int, int, double *);
+  int unpack_comm_hybrid(int, int, double *);
+  int pack_reverse(int, int, double *);
+  int pack_reverse_hybrid(int, int, double *);
+  void unpack_reverse(int, int *, double *);
+  int unpack_reverse_hybrid(int, int *, double *);
+  int pack_border(int, int *, double *, int, int *);
+  int pack_border_vel(int, int *, double *, int, int *);
+  int pack_border_hybrid(int, int *, double *);
+  void unpack_border(int, int, double *);
+  void unpack_border_vel(int, int, double *);
+  int unpack_border_hybrid(int, int, double *);
+  int pack_exchange(int, double *);
+  int unpack_exchange(double *);
+  int size_restart();
+  int pack_restart(int, double *);
+  int unpack_restart(double *);
+  void create_atom(int, double *);
+  void data_atom(double *, int, char **);
+  int data_atom_hybrid(int, char **);
+  void data_vel(int, char **);
+  int data_vel_hybrid(int, char **);
+  bigint memory_usage();
+
+  // manipulate Bonus data structure for extra atom info
+
+  void grow_bonus();
+  void copy_bonus(int, int);
+  void set_bonus(int, double, double, double);
+  void clear_bonus();
+  void data_atom_bonus(int, char **);
+
+ private:
+  double PI;
+  int *tag,*type,*mask,*image;
+  double **x,**v,**f;
+  double *rmass;
+  double **angmom,**torque;
+  int *ellipsoid;
+
+  int nlocal_bonus,nghost_bonus,nmax_bonus;
+};
+
+}
+
+#endif
+#endif