git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@642 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/atom_vec_ellipsoid.cpp

@@ -48,14 +48,6 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp, int narg, char **arg) :
   atom->angmom_flag = atom->torque_flag = atom->quat_flag = 1;
 }
 
-/* ---------------------------------------------------------------------- */
-
-void AtomVecEllipsoid::init()
-{
-  if (force->dimension == 2)
-    error->all("Cannot use atom style ellipsoid for 2d simulation");
-}
-
 /* ----------------------------------------------------------------------
    grow atom arrays
    n = 0 grows arrays by DELTA

src/ASPHERE/atom_vec_ellipsoid.h

@@ -22,7 +22,6 @@ class AtomVecEllipsoid : public AtomVec {
  public:
   AtomVecEllipsoid(class LAMMPS *, int, char **);
   virtual ~AtomVecEllipsoid() {}
-  void init();
   void grow(int);
   void copy(int, int);
   virtual int pack_comm(int, int *, double *, int, int *);

src/ASPHERE/compute_temp_asphere.cpp

@@ -20,6 +20,7 @@
 #include "math_extra.h"
 #include "atom.h"
 #include "force.h"
+#include "domain.h"
 #include "modify.h"
 #include "fix.h"
 #include "group.h"
@@ -73,7 +74,7 @@ void ComputeTempAsphere::init()
 void ComputeTempAsphere::recount()
 {
   double natoms = group->count(igroup);
-  dof = force->dimension * natoms;
+  dof = domain->dimension * natoms;
   dof -= extra_dof + fix_dof;
 
   // add rotational degrees of freedom

src/DIPOLE/compute_temp_dipole.cpp

@@ -15,6 +15,7 @@
 #include "compute_temp_dipole.h"
 #include "atom.h"
 #include "force.h"
+#include "domain.h"
 #include "group.h"
 #include "modify.h"
 #include "fix.h"
@@ -76,7 +77,7 @@ void ComputeTempDipole::init()
 void ComputeTempDipole::recount()
 {
   double natoms = group->count(igroup);
-  dof = 2.0 * force->dimension * natoms;
+  dof = 2.0 * domain->dimension * natoms;
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;

src/GRANULAR/atom_vec_granular.cpp

@@ -40,7 +40,7 @@ AtomVecGranular::AtomVecGranular(LAMMPS *lmp, int narg, char **arg) :
   xcol_data = 5;
 
   atom->radius_flag = atom->density_flag = atom->rmass_flag = 1;
-  atom->xphi_flag = atom->omega_flag = atom->torque_flag = 1;
+  atom->xorient_flag = atom->omega_flag = atom->torque_flag = 1;
 
   PI = 4.0*atan(1.0);
 }
@@ -76,8 +76,8 @@ void AtomVecGranular::grow(int n)
   rmass = atom->rmass = (double *)
     memory->srealloc(atom->rmass,nmax*sizeof(double),"atom:rmass");
 
-  xphi = atom->xphi = 
+  xorient = atom->xorient = 
-    memory->grow_2d_double_array(atom->xphi,nmax,3,"atom:xphi");
+    memory->grow_2d_double_array(atom->xorient,nmax,3,"atom:xorient");
   omega = atom->omega = 
     memory->grow_2d_double_array(atom->omega,nmax,3,"atom:omega");
   torque = atom->torque =
@@ -106,9 +106,9 @@ void AtomVecGranular::copy(int i, int j)
   radius[j] = radius[i];
   density[j] = density[i];
   rmass[j] = rmass[i];
-  xphi[j][0] = xphi[i][0];
+  xorient[j][0] = xorient[i][0];
-  xphi[j][1] = xphi[i][1];
+  xorient[j][1] = xorient[i][1];
-  xphi[j][2] = xphi[i][2];
+  xorient[j][2] = xorient[i][2];
   omega[j][0] = omega[i][0];
   omega[j][1] = omega[i][1];
   omega[j][2] = omega[i][2];
@@ -407,9 +407,9 @@ int AtomVecGranular::pack_exchange(int i, double *buf)
   buf[m++] = radius[i];
   buf[m++] = density[i];
   buf[m++] = rmass[i];
-  buf[m++] = xphi[i][0];
+  buf[m++] = xorient[i][0];
-  buf[m++] = xphi[i][1];
+  buf[m++] = xorient[i][1];
-  buf[m++] = xphi[i][2];
+  buf[m++] = xorient[i][2];
   buf[m++] = omega[i][0];
   buf[m++] = omega[i][1];
   buf[m++] = omega[i][2];
@@ -444,9 +444,9 @@ int AtomVecGranular::unpack_exchange(double *buf)
   radius[nlocal] = buf[m++];
   density[nlocal] = buf[m++];
   rmass[nlocal] = buf[m++];
-  xphi[nlocal][0] = buf[m++];
+  xorient[nlocal][0] = buf[m++];
-  xphi[nlocal][1] = buf[m++];
+  xorient[nlocal][1] = buf[m++];
-  xphi[nlocal][2] = buf[m++];
+  xorient[nlocal][2] = buf[m++];
   omega[nlocal][0] = buf[m++];
   omega[nlocal][1] = buf[m++];
   omega[nlocal][2] = buf[m++];
@@ -502,9 +502,9 @@ int AtomVecGranular::pack_restart(int i, double *buf)
 
   buf[m++] = radius[i];
   buf[m++] = density[i];
-  buf[m++] = xphi[i][0];
+  buf[m++] = xorient[i][0];
-  buf[m++] = xphi[i][1];
+  buf[m++] = xorient[i][1];
-  buf[m++] = xphi[i][2];
+  buf[m++] = xorient[i][2];
   buf[m++] = omega[i][0];
   buf[m++] = omega[i][1];
   buf[m++] = omega[i][2];
@@ -546,15 +546,15 @@ int AtomVecGranular::unpack_restart(double *buf)
 
   radius[nlocal] = buf[m++];
   density[nlocal] = buf[m++];
-  if (force->dimension == 3) 
+  if (domain->dimension == 3) 
     rmass[nlocal] = 4.0*PI/3.0 * 
       radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];
   else
     rmass[nlocal] = PI * radius[nlocal]*radius[nlocal] * density[nlocal];
 
-  xphi[nlocal][0] = buf[m++];
+  xorient[nlocal][0] = buf[m++];
-  xphi[nlocal][1] = buf[m++];
+  xorient[nlocal][1] = buf[m++];
-  xphi[nlocal][2] = buf[m++];
+  xorient[nlocal][2] = buf[m++];
   omega[nlocal][0] = buf[m++];
   omega[nlocal][1] = buf[m++];
   omega[nlocal][2] = buf[m++];
@@ -592,14 +592,14 @@ void AtomVecGranular::create_atom(int itype, double *coord)
 
   radius[nlocal] = 0.5;
   density[nlocal] = 1.0;
-  if (force->dimension == 3)
+  if (domain->dimension == 3)
     rmass[nlocal] = 4.0*PI/3.0 *
       radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];
   else
     rmass[nlocal] = PI * radius[nlocal]*radius[nlocal] * density[nlocal];
-  xphi[nlocal][0] = 0.0;
+  xorient[nlocal][0] = 0.0;
-  xphi[nlocal][1] = 0.0;
+  xorient[nlocal][1] = 0.0;
-  xphi[nlocal][2] = 0.0;
+  xorient[nlocal][2] = 0.0;
   omega[nlocal][0] = 0.0;
   omega[nlocal][1] = 0.0;
   omega[nlocal][2] = 0.0;
@@ -627,7 +627,7 @@ void AtomVecGranular::data_atom(double *coord, int imagetmp, char **values)
 
   radius[nlocal] = 0.5 * atof(values[2]);
   density[nlocal] = atof(values[3]);
-  if (force->dimension == 3)
+  if (domain->dimension == 3)
     rmass[nlocal] = 4.0*PI/3.0 *
       radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];
   else
@@ -643,9 +643,9 @@ void AtomVecGranular::data_atom(double *coord, int imagetmp, char **values)
   v[nlocal][0] = 0.0;
   v[nlocal][1] = 0.0;
   v[nlocal][2] = 0.0;
-  xphi[nlocal][0] = 0.0;
+  xorient[nlocal][0] = 1.0;
-  xphi[nlocal][1] = 0.0;
+  xorient[nlocal][1] = 0.0;
-  xphi[nlocal][2] = 0.0;
+  xorient[nlocal][2] = 0.0;
   omega[nlocal][0] = 0.0;
   omega[nlocal][1] = 0.0;
   omega[nlocal][2] = 0.0;
@@ -662,7 +662,7 @@ int AtomVecGranular::data_atom_hybrid(int nlocal, char **values)
 {
   radius[nlocal] = 0.5 * atof(values[0]);
   density[nlocal] = atof(values[1]);
-  if (force->dimension == 3)
+  if (domain->dimension == 3)
     rmass[nlocal] = 4.0*PI/3.0 *
       radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];
   else
@@ -671,9 +671,9 @@ int AtomVecGranular::data_atom_hybrid(int nlocal, char **values)
   v[nlocal][0] = 0.0;
   v[nlocal][1] = 0.0;
   v[nlocal][2] = 0.0;
-  xphi[nlocal][0] = 0.0;
+  xorient[nlocal][0] = 1.0;
-  xphi[nlocal][1] = 0.0;
+  xorient[nlocal][1] = 0.0;
-  xphi[nlocal][2] = 0.0;
+  xorient[nlocal][2] = 0.0;
   omega[nlocal][0] = 0.0;
   omega[nlocal][1] = 0.0;
   omega[nlocal][2] = 0.0;
@@ -726,7 +726,7 @@ int AtomVecGranular::memory_usage()
   if (atom->memcheck("radius")) bytes += nmax * sizeof(double);
   if (atom->memcheck("density")) bytes += nmax * sizeof(double);
   if (atom->memcheck("rmass")) bytes += nmax * sizeof(double);
-  if (atom->memcheck("xphi")) bytes += nmax*3 * sizeof(double);
+  if (atom->memcheck("xorient")) bytes += nmax*3 * sizeof(double);
   if (atom->memcheck("omega")) bytes += nmax*3 * sizeof(double);
   if (atom->memcheck("torque")) bytes += nmax*3 * sizeof(double);
 

src/GRANULAR/atom_vec_granular.h

@@ -53,7 +53,7 @@ class AtomVecGranular : public AtomVec {
   int *tag,*type,*mask,*image;
   double **x,**v,**f;
   double *radius,*density,*rmass;
-  double **xphi,**omega,**torque;
+  double **xorient,**omega,**torque;
 };
 
 }

src/GRANULAR/fix_nve_gran.cpp

@@ -17,6 +17,7 @@
 #include "atom.h"
 #include "update.h"
 #include "force.h"
+#include "domain.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -33,9 +34,9 @@ FixNVEGran::FixNVEGran(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all("Illegal fix nve/gran command");
 
-  if (!atom->xphi_flag || !atom->omega_flag || !atom->torque_flag)
+  if (!atom->xorient_flag || !atom->omega_flag || !atom->torque_flag)
     error->all("Fix nve/gran requires atom attributes "
-	       "xphi, omega, torque");
+	       "xorient, omega, torque");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -54,8 +55,8 @@ void FixNVEGran::init()
 {
   dtv = update->dt;
   dtf = 0.5 * update->dt * force->ftm2v;
-  if (force->dimension == 3) dtfphi = dtf / INERTIA3D;
+  if (domain->dimension == 3) dtfrotate = dtf / INERTIA3D;
-  else dtfphi = dtf / INERTIA2D;
+  else dtfrotate = dtf / INERTIA2D;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -67,7 +68,7 @@ void FixNVEGran::initial_integrate()
   double **x = atom->x;
   double **v = atom->v;
   double **f = atom->f;
-  double **xphi = atom->xphi;
+  double **xorient = atom->xorient;
   double **omega = atom->omega;
   double **torque = atom->torque;
   double *rmass = atom->rmass;
@@ -85,13 +86,13 @@ void FixNVEGran::initial_integrate()
       x[i][1] += dtv * v[i][1];
       x[i][2] += dtv * v[i][2];
 
-      dtfm = dtfphi / (radius[i]*radius[i]*rmass[i]);
+      dtfm = dtfrotate / (radius[i]*radius[i]*rmass[i]);
       omega[i][0] += dtfm * torque[i][0];
       omega[i][1] += dtfm * torque[i][1];
       omega[i][2] += dtfm * torque[i][2];
-      xphi[i][0] += dtv * omega[i][0];
+      xorient[i][0] += dtv * omega[i][0];
-      xphi[i][1] += dtv * omega[i][1];
+      xorient[i][1] += dtv * omega[i][1];
-      xphi[i][2] += dtv * omega[i][2];
+      xorient[i][2] += dtv * omega[i][2];
     }
   }
 }
@@ -118,7 +119,7 @@ void FixNVEGran::final_integrate()
       v[i][1] += dtfm * f[i][1];
       v[i][2] += dtfm * f[i][2];
 
-      dtfm = dtfphi / (radius[i]*radius[i]*rmass[i]);
+      dtfm = dtfrotate / (radius[i]*radius[i]*rmass[i]);
       omega[i][0] += dtfm * torque[i][0];
       omega[i][1] += dtfm * torque[i][1];
       omega[i][2] += dtfm * torque[i][2];

src/GRANULAR/fix_nve_gran.h

@@ -27,7 +27,7 @@ class FixNVEGran : public Fix {
   void final_integrate();
 
  private:
-  double dtv,dtf,dtfphi;
+  double dtv,dtf,dtfrotate;
 };
 
 }

src/GRANULAR/fix_pour.cpp

@@ -94,7 +94,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
       rate = atof(arg[iarg+1]);
       iarg += 2;
     } else if (strcmp(arg[iarg],"vel") == 0) {
-      if (force->dimension == 3) {
+      if (domain->dimension == 3) {
 	if (iarg+6 > narg) error->all("Illegal fix pour command");
 	vxlo = atof(arg[iarg+1]);
 	vxhi = atof(arg[iarg+2]);
@@ -150,7 +150,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
       error->all("Insertion region extends outside simulation box");
   } else error->all("Must use a block or cylinder region with fix pour");
 
-  if (region_style == 2 && force->dimension == 2)
+  if (region_style == 2 && domain->dimension == 2)
     error->all("Must use a block region with fix pour for 2d simulations");
 
   // random number generator, same for all procs
@@ -171,7 +171,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
 
   double v_relative,delta;
   double g = 1.0;
-  if (force->dimension == 3) {
+  if (domain->dimension == 3) {
     v_relative = vz - rate;
     delta = v_relative + sqrt(v_relative*v_relative + 2.0*g*(zhi-zlo)) / g;
   } else {
@@ -192,7 +192,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
   // in 3d, insure dy >= 1, for quasi-2d simulations
 
   double volume,volume_one;
-  if (force->dimension == 3) {
+  if (domain->dimension == 3) {
     if (region_style == 1) {
       double dy = yhi - ylo;
       if (dy < 1.0) dy = 1.0;
@@ -261,7 +261,7 @@ void FixPour::init()
   double ygrav = sin(degree2rad * theta) * sin(degree2rad * phi);
   double zgrav = cos(degree2rad * theta);
 
-  if (force->dimension == 3) {
+  if (domain->dimension == 3) {
     if (fabs(xgrav) > EPSILON || fabs(ygrav) > EPSILON ||
 	fabs(zgrav+1.0) > EPSILON)
       error->all("Gravity must point in -z to use with fix pour in 3d");
@@ -299,7 +299,7 @@ void FixPour::pre_exchange()
 
   // lo/hi current = z (or y) bounds of insertion region this timestep
 
-  if (force->dimension == 3) {
+  if (domain->dimension == 3) {
     lo_current = zlo + (update->ntimestep - nfirst) * update->dt * rate;
     hi_current = zhi + (update->ntimestep - nfirst) * update->dt * rate;
   } else {
@@ -430,7 +430,7 @@ void FixPour::pre_exchange()
     coord[2] = xnear[i][2];
     radtmp = xnear[i][3];
     denstmp = density_lo + random->uniform() * (density_hi-density_lo);
-    if (force->dimension == 3) {
+    if (domain->dimension == 3) {
       vxtmp = vxlo + random->uniform() * (vxhi-vxlo);
       vytmp = vylo + random->uniform() * (vyhi-vylo);
       vztmp = vz - sqrt(2.0*g*(hi_current-coord[2]));
@@ -444,11 +444,11 @@ void FixPour::pre_exchange()
     if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
 	coord[1] >= sublo[1] && coord[1] < subhi[1] &&
 	coord[2] >= sublo[2] && coord[2] < subhi[2]) flag = 1;
-    else if (force->dimension == 3 && coord[2] >= domain->boxhi[2] &&
+    else if (domain->dimension == 3 && coord[2] >= domain->boxhi[2] &&
 	     comm->myloc[2] == comm->procgrid[2]-1 &&
 	     coord[0] >= sublo[0] && coord[0] < subhi[0] &&
 	     coord[1] >= sublo[1] && coord[1] < subhi[1]) flag = 1;
-    else if (force->dimension == 2 && coord[1] >= domain->boxhi[1] &&
+    else if (domain->dimension == 2 && coord[1] >= domain->boxhi[1] &&
 	     comm->myloc[1] == comm->procgrid[1]-1 &&
 	     coord[0] >= sublo[0] && coord[0] < subhi[0]) flag = 1;
 
@@ -458,7 +458,7 @@ void FixPour::pre_exchange()
       atom->type[m] = ntype;
       atom->radius[m] = radtmp;
       atom->density[m] = denstmp;
-      if (force->dimension == 3) 
+      if (domain->dimension == 3) 
 	atom->rmass[m] = 4.0*PI/3.0 * radtmp*radtmp*radtmp * denstmp;
       else
 	atom->rmass[m] = PI * radtmp*radtmp * denstmp;
@@ -505,7 +505,7 @@ int FixPour::overlap(int i)
   double delta = radius_hi + atom->radius[i];
   double **x = atom->x;
 
-  if (force->dimension == 3) {
+  if (domain->dimension == 3) {
     if (region_style == 1) {
       if (x[i][0] < xlo-delta || x[i][0] > xhi+delta ||
 	  x[i][1] < ylo-delta || x[i][1] > yhi+delta ||
@@ -530,7 +530,7 @@ int FixPour::overlap(int i)
 
 void FixPour::xyz_random(double h, double *coord)
 {
-  if (force->dimension == 3) {
+  if (domain->dimension == 3) {
     if (region_style == 1) {
       coord[0] = xlo + random->uniform() * (xhi-xlo);
       coord[1] = ylo + random->uniform() * (yhi-ylo);

src/KSPACE/ewald.cpp

@@ -81,7 +81,7 @@ void Ewald::init()
   // error check
 
   if (domain->triclinic) error->all("Cannot use Ewald with triclinic box");
-  if (force->dimension == 2) error->all("Cannot use Ewald with 2d simulation");
+  if (domain->dimension == 2) error->all("Cannot use Ewald with 2d simulation");
 
   if (!atom->q_flag) error->all("Kspace style requires atom attribute q");
 

src/KSPACE/pppm.cpp

@@ -107,7 +107,7 @@ void PPPM::init()
 
   if (domain->triclinic)
     error->all("Cannot (yet) use PPPM with triclinic box");
-  if (force->dimension == 2) error->all("Cannot use PPPM with 2d simulation");
+  if (domain->dimension == 2) error->all("Cannot use PPPM with 2d simulation");
 
   if (!atom->q_flag) error->all("Kspace style requires atom attribute q");
 

src/atom.cpp

@@ -61,7 +61,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   molecule = NULL;
   q = NULL;
   mu = NULL;
-  xphi = quat = omega = angmom = torque = NULL;
+  xorient = quat = omega = angmom = torque = NULL;
   radius = density = rmass = vfrac = NULL;
 
   maxspecial = 1;
@@ -87,7 +87,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
 
   molecule_flag = 0;
   q_flag = mu_flag = 0;
-  xphi_flag = quat_flag = omega_flag = angmom_flag = torque_flag = 0;
+  xorient_flag = quat_flag = omega_flag = angmom_flag = torque_flag = 0;
   radius_flag = density_flag = rmass_flag = vfrac_flag = 0;
 
   // ntype-length arrays
@@ -150,7 +150,7 @@ Atom::~Atom()
 
   memory->sfree(q);
   memory->destroy_2d_double_array(mu);
-  memory->destroy_2d_double_array(xphi);
+  memory->destroy_2d_double_array(xorient);
   memory->destroy_2d_double_array(quat);
   memory->destroy_2d_double_array(omega);
   memory->destroy_2d_double_array(angmom);

src/atom.h

@@ -43,7 +43,7 @@ class Atom : protected Pointers {
 
   int *molecule;
   double *q,**mu;
-  double **xphi,**quat,**omega,**angmom,**torque;
+  double **xorient,**quat,**omega,**angmom,**torque;
   double *radius,*density,*rmass,*vfrac;
 
   int maxspecial;
@@ -70,7 +70,7 @@ class Atom : protected Pointers {
 
   int molecule_flag;
   int q_flag,mu_flag;
-  int xphi_flag,quat_flag,omega_flag,angmom_flag,torque_flag;
+  int xorient_flag,quat_flag,omega_flag,angmom_flag,torque_flag;
   int radius_flag,density_flag,rmass_flag,vfrac_flag;
 
   // extra peratom info in restart file destined for fix & diag 

src/comm.cpp

@@ -166,7 +166,7 @@ void Comm::set_procs()
 
   if (procgrid[0]*procgrid[1]*procgrid[2] != nprocs)
     error->all("Bad grid of processors");
-  if (force->dimension == 2 && procgrid[2] != 1)
+  if (domain->dimension == 2 && procgrid[2] != 1)
     error->all("Proc grid in z != 1 for 2d simulation");
 
   if (grid2proc) memory->destroy_3d_int_array(grid2proc);
@@ -272,7 +272,7 @@ void Comm::setup()
   need[0] = static_cast<int> (cutghost[0] * procgrid[0] / prd[0]) + 1;
   need[1] = static_cast<int> (cutghost[1] * procgrid[1] / prd[1]) + 1;
   need[2] = static_cast<int> (cutghost[2] * procgrid[2] / prd[2]) + 1;
-  if (force->dimension == 2) need[2] = 0;
+  if (domain->dimension == 2) need[2] = 0;
 
   // if non-periodic, do not communicate further than procgrid-1 away
   // this enables very large cutoffs in non-periodic systems
@@ -1300,7 +1300,7 @@ void Comm::procs2box()
       while (ipy <= nremain) {
 	if (nremain % ipy == 0) {
 	  ipz = nremain/ipy;
-	  if (force->dimension == 3 || ipz == 1) {
+	  if (domain->dimension == 3 || ipz == 1) {
 	    surf = area[0]/ipx/ipy + area[1]/ipx/ipz + area[2]/ipy/ipz;
 	    if (surf < bestsurf) {
 	      bestsurf = surf;

src/compute_rotate_dipole.cpp

@@ -14,7 +14,7 @@
 #include "mpi.h"
 #include "compute_rotate_dipole.h"
 #include "atom.h"
-#include "force.h"
+#include "domain.h"
 #include "group.h"
 #include "error.h"
 
@@ -56,7 +56,7 @@ void ComputeRotateDipole::init()
   double *mass = atom->mass;
   double **shape = atom->shape;
 
-  if (force->dimension == 3)
+  if (domain->dimension == 3)
     for (int i = 1; i <= atom->ntypes; i++)
       inertia[i] = INERTIA3D * mass[i] * 0.25*shape[i][0]*shape[i][0];
   else

src/compute_rotate_gran.cpp

@@ -15,6 +15,7 @@
 #include "compute_rotate_gran.h"
 #include "atom.h"
 #include "force.h"
+#include "domain.h"
 #include "group.h"
 #include "error.h"
 
@@ -42,7 +43,7 @@ ComputeRotateGran::ComputeRotateGran(LAMMPS *lmp, int narg, char **arg) :
 
 void ComputeRotateGran::init()
 {
-  if (force->dimension == 3) pfactor = 0.5 * force->mvv2e * INERTIA3D;
+  if (domain->dimension == 3) pfactor = 0.5 * force->mvv2e * INERTIA3D;
   else pfactor = 0.5 * force->mvv2e * INERTIA2D;
 }
 

src/compute_temp.cpp

@@ -15,6 +15,7 @@
 #include "compute_temp.h"
 #include "atom.h"
 #include "force.h"
+#include "domain.h"
 #include "modify.h"
 #include "fix.h"
 #include "group.h"
@@ -59,7 +60,7 @@ void ComputeTemp::init()
 void ComputeTemp::recount()
 {
   double natoms = group->count(igroup);
-  dof = force->dimension * natoms;
+  dof = domain->dimension * natoms;
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;

src/compute_temp_deform.cpp

@@ -83,7 +83,7 @@ void ComputeTempDeform::init()
 void ComputeTempDeform::recount()
 {
   double natoms = group->count(igroup);
-  dof = force->dimension * natoms;
+  dof = domain->dimension * natoms;
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;

src/compute_temp_ramp.cpp

@@ -129,7 +129,7 @@ void ComputeTempRamp::init()
 void ComputeTempRamp::recount()
 {
   double natoms = group->count(igroup);
-  dof = force->dimension * natoms;
+  dof = domain->dimension * natoms;
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;

src/compute_temp_region.cpp

@@ -90,7 +90,7 @@ double ComputeTempRegion::compute_scalar()
   tarray[0] = count;
   tarray[1] = t;
   MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
-  dof = force->dimension * tarray_all[0] - extra_dof;
+  dof = domain->dimension * tarray_all[0] - extra_dof;
   if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
   else scalar = 0.0;
   return scalar;

src/create_box.cpp

@@ -37,7 +37,7 @@ void CreateBox::command(int narg, char **arg)
 
   if (domain->box_exist) 
     error->all("Cannot create_box after simulation box is defined");
-  if (force->dimension == 2 && domain->zperiodic == 0)
+  if (domain->dimension == 2 && domain->zperiodic == 0)
     error->all("Cannot run 2d simulation with nonperiodic Z dimension");
 
   domain->box_exist = 1;

src/domain.cpp

@@ -55,6 +55,7 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
 {
   box_exist = 0;
 
+  dimension = 3;
   nonperiodic = 0;
   xperiodic = yperiodic = zperiodic = 1;
   periodicity[0] = xperiodic;
@@ -132,7 +133,7 @@ void Domain::set_initial_box()
     error->one("Box bounds are invalid");
 
   if (triclinic) {
-    if (force->dimension == 2 && (xz != 0.0 || yz != 0.0))
+    if (domain->dimension == 2 && (xz != 0.0 || yz != 0.0))
       error->all("Cannot skew triclinic box in z for 2d simulation");
     if (xy != 0.0 && (!xperiodic || !yperiodic))
       error->all("Triclinic box must be periodic in skewed dimensions");

src/domain.h

@@ -21,7 +21,7 @@ namespace LAMMPS_NS {
 class Domain : protected Pointers {
  public:
   int box_exist;                         // 0 = not yet created, 1 = exists
-
+  int dimension;                         // 2 = 2d, 3 = 3d
   int nonperiodic;                       // 0 = periodic in all 3 dims
                                          // 1 = periodic or fixed in all 6
                                          // 2 = shrink-wrap in any of 6

src/dump_custom.cpp

@@ -570,7 +570,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
       pack_choice[i] = &DumpCustom::pack_tag;
       vtype[i] = INT;
     } else if (strcmp(arg[iarg],"mol") == 0) {
-      if (atom->molecule == NULL)
+      if (!atom->molecule_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_molecule;
       vtype[i] = INT;
@@ -641,58 +641,58 @@ void DumpCustom::parse_fields(int narg, char **arg)
       vtype[i] = DOUBLE;
 
     } else if (strcmp(arg[iarg],"q") == 0) {
-      if (atom->q == NULL)
+      if (!atom->q_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_q;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"mux") == 0) {
-      if (atom->mu == NULL)
+      if (!atom->mu_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_mux;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"muy") == 0) {
-      if (atom->mu == NULL)
+      if (!atom->mu_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_muy;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"muz") == 0) {
-      if (atom->mu == NULL)
+      if (!atom->mu_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_muz;
       vtype[i] = DOUBLE;
 
     } else if (strcmp(arg[iarg],"quatw") == 0) {
-      if (atom->quat == NULL)
+      if (!atom->quat_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_quatw;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"quati") == 0) {
-      if (atom->quat == NULL)
+      if (!atom->quat_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_quati;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"quatj") == 0) {
-      if (atom->quat == NULL)
+      if (!atom->quat_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_quatj;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"quatk") == 0) {
-      if (atom->quat == NULL)
+      if (!atom->quat_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_quatk;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"tqx") == 0) {
-      if (atom->torque == NULL)
+      if (!atom->torque_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_tqx;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"tqy") == 0) {
-      if (atom->torque == NULL)
+      if (!atom->torque_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_tqy;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"tqz") == 0) {
-      if (atom->torque == NULL)
+      if (!atom->torque_flag)
 	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_tqz;
       vtype[i] = DOUBLE;

src/fix_deform.cpp

@@ -162,20 +162,24 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
   if (set[5].style && (domain->xperiodic == 0 || domain->yperiodic == 0))
     error->all("Cannot fix deform on a non-periodic boundary");
 
-  // setup scaling
+  // apply scaling to FINAL,DELTA,VEL since they have distance/vel units
 
-  if (scaleflag && domain->lattice == NULL)
+  int flag = 0;
+  for (int i = 0; i < 6; i++)
+    if (set[i].style == FINAL || set[i].style == DELTA || 
+	set[i].style == VEL) flag = 1;
+
+  if (flag && scaleflag && domain->lattice == NULL)
     error->all("Use of fix deform with undefined lattice");
 
-  if (scaleflag) {
+  if (flag && scaleflag) {
     xscale = domain->lattice->xlattice;
     yscale = domain->lattice->ylattice;
     zscale = domain->lattice->zlattice;
   }
   else xscale = yscale = zscale = 1.0;
 
-  // apply scaling to input parameters with dist/vel units
+  // for 3,4,5 scaling is in 1st dimension, e.g. x for xz
-  // for 3,4,5 scale is in 1st dimension, e.g. x for xz
 
   double map[6];
   map[0] = xscale; map[1] = yscale; map[2] = zscale;

src/fix_deposit.cpp

@@ -88,7 +88,7 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
 
   // apply scaling to all input parameters with dist/vel units
 
-  if (force->dimension == 2) {
+  if (domain->dimension == 2) {
     lo *= yscale;
     hi *= yscale;
     rate *= yscale;
@@ -191,7 +191,7 @@ void FixDeposit::pre_exchange()
 
     // adjust vertical coord by offset
 
-    if (force->dimension == 2) coord[1] += offset;
+    if (domain->dimension == 2) coord[1] += offset;
     else coord[2] += offset;
 
     // if global, reset vertical coord to be lo-hi above highest atom
@@ -202,7 +202,7 @@ void FixDeposit::pre_exchange()
       int dim;
       double max,maxall,delx,dely,delz,rsq;
 
-      if (force->dimension == 2) {
+      if (domain->dimension == 2) {
 	dim = 1;
 	max = domain->boxlo[1];
       } else {
@@ -218,7 +218,7 @@ void FixDeposit::pre_exchange()
 	  dely = coord[1] - x[i][1];
 	  delz = 0.0;
 	  domain->minimum_image(delx,dely,delz);
-	  if (force->dimension == 2) rsq = delx*delx;
+	  if (domain->dimension == 2) rsq = delx*delx;
 	  else rsq = delx*delx + dely*dely;
 	  if (rsq > deltasq) continue;
 	}
@@ -226,7 +226,7 @@ void FixDeposit::pre_exchange()
       }
 
       MPI_Allreduce(&max,&maxall,1,MPI_DOUBLE,MPI_MAX,world);
-      if (force->dimension == 2)
+      if (domain->dimension == 2)
 	coord[1] = maxall + lo + random->uniform()*(hi-lo);
       else
 	coord[2] = maxall + lo + random->uniform()*(hi-lo);
@@ -271,11 +271,11 @@ void FixDeposit::pre_exchange()
     if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
 	newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
 	newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
-    else if (force->dimension == 3 && newcoord[2] >= domain->boxhi[2] &&
+    else if (domain->dimension == 3 && newcoord[2] >= domain->boxhi[2] &&
 	     comm->myloc[2] == comm->procgrid[2]-1 &&
 	     newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
 	     newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
-    else if (force->dimension == 2 && newcoord[1] >= domain->boxhi[1] &&
+    else if (domain->dimension == 2 && newcoord[1] >= domain->boxhi[1] &&
 	     comm->myloc[1] == comm->procgrid[1]-1 &&
 	     newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
 

src/fix_enforce2d.cpp

@@ -67,9 +67,7 @@ void FixEnforce2D::min_setup()
 void FixEnforce2D::post_force(int vflag)
 {
   double **v = atom->v;
-  double **omega = atom->omega;
   double **f = atom->f;
-  double **torque = atom->torque;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
@@ -79,9 +77,10 @@ void FixEnforce2D::post_force(int vflag)
       f[i][2] = 0.0;
     }
 
-  // for omega/torque systems, zero xy rotation
+  // for systems with omega/angmom/torque, zero x and y components
 
-  if (omega) {
+  if (atom->omega_flag) {
+    double **omega = atom->omega;
     for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
 	omega[i][0] = 0.0;
@@ -89,7 +88,17 @@ void FixEnforce2D::post_force(int vflag)
       }
   }
 
-  if (torque) {
+  if (atom->angmom_flag) {
+    double **angmom = atom->angmom;
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+	angmom[i][0] = 0.0;
+	angmom[i][1] = 0.0;
+      }
+  }
+
+  if (atom->torque_flag) {
+    double **torque = atom->torque;
     for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
 	torque[i][0] = 0.0;

src/fix_nvt.cpp

@@ -71,7 +71,7 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
   newarg[1] = group->names[igroup];
   if (strcmp(style,"nvt") == 0) newarg[2] = "temp";
   else if (strcmp(style,"nvt/asphere") == 0) newarg[2] = "temp/asphere";
-  else if (strcmp(style,"nvt/deform") == 0) newarg[2] = "temp/deform";
+  else if (strcmp(style,"nvt/sllod") == 0) newarg[2] = "temp/deform";
   modify->add_compute(3,newarg);
   delete [] newarg;
   tflag = 1;

src/force.cpp

@@ -51,7 +51,6 @@ using namespace LAMMPS_NS;
 
 Force::Force(LAMMPS *lmp) : Pointers(lmp)
 {
-  dimension = 3;
   newton = newton_pair = newton_bond = 1;
 
   special_lj[1] = special_lj[2] = special_lj[3] = 0.0;

src/force.h

@@ -29,7 +29,6 @@ class Force : protected Pointers {
   double dielectric;                 // dielectric constant
   double qqrd2e;                     // q^2/r to energy w/ dielectric constant
 
-  int dimension;                        // 2 = 2d, 3 = 3d
   int newton,newton_pair,newton_bond;   // Newton's 3rd law settings
 
   class Pair *pair;

src/input.cpp

@@ -795,7 +795,7 @@ void Input::dimension()
   if (narg != 1) error->all("Illegal dimension command");
   if (domain->box_exist) 
     error->all("Dimension command after simulation box is defined");
-  force->dimension = atoi(arg[0]);
+  domain->dimension = atoi(arg[0]);
 }
 
 /* ---------------------------------------------------------------------- */

src/lattice.cpp

@@ -16,7 +16,7 @@
 #include "stdlib.h"
 #include "lattice.h"
 #include "update.h"
-#include "force.h"
+#include "domain.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
@@ -59,7 +59,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   // check that lattice matches dimension
   // style CUSTOM can be either 2d or 3d
 
-  int dimension = force->dimension;
+  int dimension = domain->dimension;
   if (dimension == 2) {
     if (style == SC || style == BCC || style == FCC || style == DIAMOND)
       error->all("Lattice style incompatible with simulation dimension");

src/neighbor.cpp

@@ -520,19 +520,19 @@ void Neighbor::init()
       } else if (style == BIN) {
 	if (force->newton_pair == 0) {
 	  half_build = &Neighbor::granular_bin_no_newton;
-	  if (force->dimension == 3)
+	  if (domain->dimension == 3)
 	    half_stencil = &Neighbor::stencil_half_3d_no_newton;
 	  else
 	    half_stencil = &Neighbor::stencil_half_2d_no_newton;
 	} else if (triclinic) {
 	  half_build = &Neighbor::granular_bin_newton_tri;
-	  if (force->dimension == 3)
+	  if (domain->dimension == 3)
 	    half_stencil = &Neighbor::stencil_half_3d_newton_tri;
 	  else
 	    half_stencil = &Neighbor::stencil_half_2d_newton_tri;
 	} else {
 	  half_build = &Neighbor::granular_bin_newton;
-	  if (force->dimension == 3)
+	  if (domain->dimension == 3)
 	    half_stencil = &Neighbor::stencil_half_3d_newton;
 	  else
 	    half_stencil = &Neighbor::stencil_half_2d_newton;
@@ -547,19 +547,19 @@ void Neighbor::init()
       } else if (style == BIN) {
 	if (force->newton_pair == 0) {
 	  half_build = &Neighbor::respa_bin_no_newton;
-	  if (force->dimension == 3)
+	  if (domain->dimension == 3)
 	    half_stencil = &Neighbor::stencil_half_3d_no_newton;
 	  else
 	    half_stencil = &Neighbor::stencil_half_2d_no_newton;
 	} else if (triclinic) {
 	  half_build = &Neighbor::respa_bin_newton_tri;
-	  if (force->dimension == 3)
+	  if (domain->dimension == 3)
 	    half_stencil = &Neighbor::stencil_half_3d_newton_tri;
 	  else
 	    half_stencil = &Neighbor::stencil_half_2d_newton_tri;
 	} else {
 	  half_build = &Neighbor::respa_bin_newton;
-	  if (force->dimension == 3)
+	  if (domain->dimension == 3)
 	    half_stencil = &Neighbor::stencil_half_3d_newton;
 	  else
 	    half_stencil = &Neighbor::stencil_half_2d_newton;
@@ -582,7 +582,7 @@ void Neighbor::init()
 	    half_stencil = &Neighbor::stencil_none;
 	  } else {
 	    half_build = &Neighbor::half_bin_no_newton;
-	    if (force->dimension == 3)
+	    if (domain->dimension == 3)
 	      half_stencil = &Neighbor::stencil_half_3d_no_newton;
 	    else
 	      half_stencil = &Neighbor::stencil_half_2d_no_newton;
@@ -593,13 +593,13 @@ void Neighbor::init()
 	    half_stencil = &Neighbor::stencil_none;
 	  } else if (triclinic) {
 	    half_build = &Neighbor::half_bin_newton_tri;
-	    if (force->dimension == 3)
+	    if (domain->dimension == 3)
 	      half_stencil = &Neighbor::stencil_half_3d_newton_tri;
 	    else
 	      half_stencil = &Neighbor::stencil_half_2d_newton_tri;
 	  } else {
 	    half_build = &Neighbor::half_bin_newton;
-	    if (force->dimension == 3)
+	    if (domain->dimension == 3)
 	      half_stencil = &Neighbor::stencil_half_3d_newton;
 	    else
 	      half_stencil = &Neighbor::stencil_half_2d_newton;
@@ -612,7 +612,7 @@ void Neighbor::init()
 	    half_stencil = &Neighbor::stencil_none;
 	  } else {
 	    half_build = &Neighbor::half_bin_no_newton_multi;
-	    if (force->dimension == 3)
+	    if (domain->dimension == 3)
 	      half_stencil = &Neighbor::stencil_half_3d_no_newton_multi;
 	    else
 	      half_stencil = &Neighbor::stencil_half_2d_no_newton_multi;
@@ -623,13 +623,13 @@ void Neighbor::init()
 	    half_stencil = &Neighbor::stencil_none;
 	  } else if (triclinic) {
 	    half_build = &Neighbor::half_bin_newton_multi_tri;
-	    if (force->dimension == 3)
+	    if (domain->dimension == 3)
 	      half_stencil = &Neighbor::stencil_half_3d_newton_multi_tri;
 	    else
 	      half_stencil = &Neighbor::stencil_half_2d_newton_multi_tri;
 	  } else {
 	    half_build = &Neighbor::half_bin_newton_multi;
-	    if (force->dimension == 3)
+	    if (domain->dimension == 3)
 	      half_stencil = &Neighbor::stencil_half_3d_newton_multi;
 	    else
 	      half_stencil = &Neighbor::stencil_half_2d_newton_multi;
@@ -644,13 +644,13 @@ void Neighbor::init()
     if (style == NSQ) full_build = &Neighbor::full_nsq;
     else if (style == BIN) {
       full_build = &Neighbor::full_bin;
-      if (force->dimension == 3)
+      if (domain->dimension == 3)
 	full_stencil = &Neighbor::stencil_full_3d;
       else
 	full_stencil = &Neighbor::stencil_full_2d;
     } else {
       full_build = &Neighbor::full_bin_multi;
-      if (force->dimension == 3)
+      if (domain->dimension == 3)
 	full_stencil = &Neighbor::stencil_full_3d_multi;
       else
 	full_stencil = &Neighbor::stencil_full_2d_multi;
@@ -1001,7 +1001,7 @@ void Neighbor::setup_bins()
 
   nbinx = static_cast<int> (bbox[0]*binsizeinv);
   nbiny = static_cast<int> (bbox[1]*binsizeinv);
-  if (force->dimension == 3)
+  if (domain->dimension == 3)
     nbinz = static_cast<int> (bbox[2]*binsizeinv);
   else nbinz = 1;
 

src/pair.cpp

@@ -117,7 +117,7 @@ void Pair::init()
 
   if (offset_flag && tail_flag)
     error->all("Cannot have both pair_modify shift and tail set to yes");
-  if (tail_flag && force->dimension == 2)
+  if (tail_flag && domain->dimension == 2)
     error->all("Cannot use pair tail corrections with 2d simulations");
   if (tail_flag && domain->nonperiodic && comm->me == 0)
     error->warning("Using pair tail corrections with nonperiodic system");

src/read_data.cpp

@@ -71,7 +71,7 @@ void ReadData::command(int narg, char **arg)
 
   if (domain->box_exist) 
     error->all("Cannot read_data after simulation box is defined");
-  if (force->dimension == 2 && domain->zperiodic == 0)
+  if (domain->dimension == 2 && domain->zperiodic == 0)
     error->all("Cannot run 2d simulation with nonperiodic Z dimension");
 
   // scan data file to determine max topology needed per atom 

src/read_restart.cpp

@@ -378,10 +378,10 @@ void ReadRestart::header()
 
     } else if (flag == DIMENSION) {
       int dimension = read_int();
-      if (dimension != force->dimension && me == 0)
+      if (dimension != domain->dimension && me == 0)
 	error->warning("Resetting dimension to restart file value");
-      force->dimension = dimension;
+      domain->dimension = dimension;
-      if (force->dimension == 2 && domain->zperiodic == 0)
+      if (domain->dimension == 2 && domain->zperiodic == 0)
 	error->all("Cannot run 2d simulation with nonperiodic Z dimension");
 
       // read nprocs_file from restart file, warn if different

src/replicate.cpp

@@ -62,7 +62,7 @@ void Replicate::command(int narg, char **arg)
   // error and warning checks
 
   if (nx <= 0 || ny <= 0 || nz <= 0) error->all("Illegal replicate command");
-  if (force->dimension == 2 && nz != 1)
+  if (domain->dimension == 2 && nz != 1)
     error->all("Cannot replicate 2d simulation in z dimension");
   if ((nx > 1 && domain->xperiodic == 0) || 
       (ny > 1 && domain->yperiodic == 0) ||

src/set.cpp

@@ -26,6 +26,7 @@
 #include "force.h"
 #include "pair.h"
 #include "random_park.h"
+#include "math_extra.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -94,7 +95,7 @@ void Set::command(int narg, char **arg)
     } else if (strcmp(arg[iarg],"mol") == 0) {
       if (iarg+2 > narg) error->all("Illegal set command");
       ivalue = atoi(arg[iarg+1]);
-      if (atom->molecule == NULL)
+      if (!atom->molecule_flag)
 	error->all("Cannot set this attribute for this atom style");
       set(MOLECULE);
       iarg += 2;
@@ -131,7 +132,7 @@ void Set::command(int narg, char **arg)
     } else if (strcmp(arg[iarg],"charge") == 0) {
       if (iarg+2 > narg) error->all("Illegal set command");
       dvalue = atof(arg[iarg+1]);
-      if (atom->q == NULL)
+      if (!atom->q_flag)
 	error->all("Cannot set this attribute for this atom style");
       set(CHARGE);
       iarg += 2;
@@ -140,31 +141,32 @@ void Set::command(int narg, char **arg)
       xvalue = atof(arg[iarg+1]);
       yvalue = atof(arg[iarg+2]);
       zvalue = atof(arg[iarg+3]);
-      if (atom->mu == NULL || atom->dipole == NULL)
+      if (!atom->mu_flag || atom->dipole == NULL)
 	error->all("Cannot set this attribute for this atom style");
       set(DIPOLE);
       iarg += 4;
     } else if (strcmp(arg[iarg],"dipole/random") == 0) {
       if (iarg+2 > narg) error->all("Illegal set command");
       ivalue = atoi(arg[iarg+1]);
-      if (atom->mu == NULL || atom->shape == NULL)
+      if (!atom->mu_flag || atom->shape == NULL)
 	error->all("Cannot set this attribute for this atom style");
       if (ivalue <= 0) error->all("Invalid random number seed in set command");
       setrandom(DIPOLE_RANDOM);
       iarg += 2;
     } else if (strcmp(arg[iarg],"quat") == 0) {
-      if (iarg+4 > narg) error->all("Illegal set command");
+      if (iarg+5 > narg) error->all("Illegal set command");
       xvalue = atof(arg[iarg+1]);
       yvalue = atof(arg[iarg+2]);
       zvalue = atof(arg[iarg+3]);
-      if (atom->quat == NULL)
+      wvalue = atof(arg[iarg+4]);
+      if (!atom->quat_flag)
 	error->all("Cannot set this attribute for this atom style");
       set(QUAT);
-      iarg += 4;
+      iarg += 5;
     } else if (strcmp(arg[iarg],"quat/random") == 0) {
       if (iarg+2 > narg) error->all("Illegal set command");
       ivalue = atoi(arg[iarg+1]);
-      if (atom->quat == NULL)
+      if (!atom->quat_flag)
 	error->all("Cannot set this attribute for this atom style");
       if (ivalue <= 0) error->all("Invalid random number seed in set command");
       setrandom(QUAT_RANDOM);
@@ -305,11 +307,15 @@ void Set::set(int keyword)
 	}
 
       } else if (keyword == QUAT) {
-	// need to set orientation correctly and normalize quat
+	double PI = 4.0*atan(1.0);
+	double theta2 = 0.5 * PI * wvalue/180.0;
+	double sintheta2 = sin(theta2);
 	double **quat = atom->quat;
-	quat[i][0] = xvalue;
+	quat[i][0] = cos(theta2);
-	quat[i][1] = yvalue;
+	quat[i][1] = xvalue * sintheta2;
-	quat[i][2] = zvalue;
+	quat[i][2] = yvalue * sintheta2;
+	quat[i][3] = zvalue * sintheta2;
+	MathExtra::normalize4(quat[i]);
       }
       count++;
     }
@@ -345,55 +351,90 @@ void Set::setrandom(int keyword)
         count++;
       }
 
-  // set dipole moments to random orientations
+  // set dipole moments to random orientations in 3d or 2d
   // dipole length is determined by dipole type array
 
-  } else if (keyword == DIPOLE) {
+  } else if (keyword == DIPOLE_RANDOM) {
     int *type = atom->type;
     double *dipole = atom->dipole;
     double **mu = atom->mu;
     int nlocal = atom->nlocal;
 
     double msq,scale;
-    for (i = 0; i < nlocal; i++)
+
-      if (select[i]) {
+    if (domain->dimension == 3) {
-	if (dipole[type[i]] > 0.0) {
+      for (i = 0; i < nlocal; i++)
-	  random->reset(seed,x[i]);
+	if (select[i]) {
-	  mu[i][0] = random->uniform() - 0.5;
+	  if (dipole[type[i]] > 0.0) {
-	  mu[i][1] = random->uniform() - 0.5;
+	    random->reset(seed,x[i]);
-	  mu[i][2] = random->uniform() - 0.5;
+	    mu[i][0] = random->uniform() - 0.5;
-	  msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
+	    mu[i][1] = random->uniform() - 0.5;
-	  scale = dipole[type[i]]/sqrt(msq);
+	    mu[i][2] = random->uniform() - 0.5;
-	  mu[i][0] *= scale;
+	    msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
-	  mu[i][1] *= scale;
+	    scale = dipole[type[i]]/sqrt(msq);
-	  mu[i][2] *= scale;
+	    mu[i][0] *= scale;
-	  count++;
+	    mu[i][1] *= scale;
+	    mu[i][2] *= scale;
+	    count++;
+	  }
 	}
-      }
 
-  // set quaternions to random orientations
+    } else {
+      for (i = 0; i < nlocal; i++)
+	if (select[i]) {
+	  if (dipole[type[i]] > 0.0) {
+	    random->reset(seed,x[i]);
+	    mu[i][0] = random->uniform() - 0.5;
+	    mu[i][1] = random->uniform() - 0.5;
+	    mu[i][2] = 0.0;
+	    msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1];
+	    scale = dipole[type[i]]/sqrt(msq);
+	    mu[i][0] *= scale;
+	    mu[i][1] *= scale;
+	    count++;
+	  }
+	}
+    }
 
-  } else if (keyword == QUAT) {
+  // set quaternions to random orientations in 3d or 2d
+  // no need to normalize quats since creations algorithms already do
+
+  } else if (keyword == QUAT_RANDOM) {
     double **quat = atom->quat;
     int nlocal = atom->nlocal;
 
-    double s,t1,t2,theta1,theta2;
+    if (domain->dimension == 3) {
-    double PI = 4.0*atan(1.0);
+      double s,t1,t2,theta1,theta2;
+      double PI = 4.0*atan(1.0);
+      for (i = 0; i < nlocal; i++)
+	if (select[i]) {
+	  random->reset(seed,x[i]);
+	  s = random->uniform();
+	  t1 = sqrt(1.0-s);
+	  t2 = sqrt(s);
+	  theta1 = 2.0*PI*random->uniform();
+	  theta2 = 2.0*PI*random->uniform();
+	  quat[i][0] = cos(theta2)*t2;
+	  quat[i][1] = sin(theta1)*t1;
+	  quat[i][2] = cos(theta1)*t1;
+	  quat[i][3] = sin(theta2)*t2;
+	  count++;
+	}
 
-    for (i = 0; i < nlocal; i++)
+    } else {
-      if (select[i]) {
+      double theta2;
-	random->reset(seed,x[i]);
+      double PI = 4.0*atan(1.0);
-	s = random->uniform();
+      for (i = 0; i < nlocal; i++)
-	t1 = sqrt(1.0-s);
+	if (select[i]) {
-	t2 = sqrt(s);
+	  random->reset(seed,x[i]);
-	theta1 = 2.0*PI*random->uniform();
+	  theta2 = PI*random->uniform();
-	theta2 = 2.0*PI*random->uniform();
+	  quat[i][0] = cos(theta2);
-	quat[i][0] = cos(theta2)*t2;
+	  quat[i][1] = 0.0;
-	quat[i][1] = sin(theta1)*t1;
+	  quat[i][2] = 0.0;
-	quat[i][2] = cos(theta1)*t1;
+	  quat[i][3] = sin(theta2);
-	quat[i][3] = sin(theta2)*t2;
+	  count++;
-        count++;
+	}
-      }
+    }
   }
 
   delete random;

src/set.h

@@ -27,7 +27,7 @@ class Set : protected Pointers {
   char *id;
   int *select;
   int style,ivalue,newtype,count;
-  double dvalue,xvalue,yvalue,zvalue,fraction;
+  double dvalue,xvalue,yvalue,zvalue,wvalue,fraction;
 
   void selection(int);
   void set(int);

src/style.h

@@ -154,6 +154,7 @@ DumpStyle(xyz,DumpXYZ)
 #include "fix_nve.h"
 #include "fix_nve_noforce.h"
 #include "fix_nvt.h"
+#include "fix_nvt_sllod.h"
 #include "fix_plane_force.h"
 #include "fix_print.h"
 #include "fix_orient_fcc.h"
@@ -201,6 +202,7 @@ FixStyle(npt,FixNPT)
 FixStyle(nve,FixNVE)
 FixStyle(nve,FixNVENoforce)
 FixStyle(nvt,FixNVT)
+FixStyle(nvt/sllod,FixNVTSlodd)
 FixStyle(orient/fcc,FixOrientFCC)
 FixStyle(print,FixPrint)
 FixStyle(planeforce,FixPlaneForce)

src/velocity.cpp

@@ -176,7 +176,7 @@ void Velocity::create(int narg, char **arg)
   int *mask = atom->mask;
   double *mass = atom->mass;
   double *rmass = atom->rmass;
-  int dimension = force->dimension;
+  int dimension = domain->dimension;
 
   int m;
   double vx,vy,vz,factor;
@@ -360,7 +360,7 @@ void Velocity::set(int narg, char **arg)
   double **v = atom->v;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
-  int dimension = force->dimension;
+  int dimension = domain->dimension;
 
   for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
@@ -427,7 +427,7 @@ void Velocity::ramp(int narg, char **arg)
   else if (strcmp(arg[0],"vz") == 0) v_dim = 2;
   else error->all("Illegal velocity command");
 
-  if (v_dim == 2 && force->dimension == 2) 
+  if (v_dim == 2 && domain->dimension == 2) 
     error->all("Velocity ramp in z for a 2d problem");
 
   double v_lo,v_hi;

src/write_restart.cpp

@@ -242,7 +242,7 @@ void WriteRestart::header()
   write_char(VERSION,universe->version);
   write_char(UNITS,update->unit_style);
   write_int(NTIMESTEP,update->ntimestep);
-  write_int(DIMENSION,force->dimension);
+  write_int(DIMENSION,domain->dimension);
   write_int(NPROCS,nprocs);
   write_int(PROCGRID_0,comm->procgrid[0]);
   write_int(PROCGRID_1,comm->procgrid[1]);