}

  dof -= extra_dof + fix_dof;

  if (dof < 0.0 && natoms > 0.0) 

    error->all(FLERR,"Temperature compute degrees of freedom < 0");

  if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);

  else tfactor = 0.0;

}

  MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);

  if (dynamic || tempbias == 2) dof_compute();

  if (tfactor == 0.0 && atom->natoms != 0) 

    error->all(FLERR,"Temperature compute degrees of freedom < 0");

  scalar *= tfactor;

  return scalar;

}

  dof = nper * natoms;

  dof -= nper * nshells;

  dof -= extra_dof + fix_dof;

  if (dof < 0.0 && natoms > 0.0) 

    error->all(FLERR,"Temperature compute degrees of freedom < 0");

  if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);

  else tfactor = 0.0;

}

  MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);

  if (dynamic) dof_compute();

  if (tfactor == 0.0 && atom->natoms != 0) 

    error->all(FLERR,"Temperature compute degrees of freedom < 0");

  scalar *= tfactor;

  return scalar;

}

/* ----------------------------------------------------------------------

   setup static/dynamic properties of rigid bodies, using current atom info

   allows resetting of atom properties like mass between runs

   only do static initialization once if using an infile

   only do static initialization must be done once

     do not do again if using an infile or mol keyword

     this is b/c the infile and Molecule class define the COM, etc

       so should not reset those values

   cannot do this until now, b/c requires comm->setup() to have setup stencil

   invoke pre_neighbor() to insure body xcmimage flags are reset

     needed if Verlet::setup::pbc() has remapped/migrated atoms for 2nd run

void FixRigidSmall::setup_pre_neighbor()

{

  if (!staticflag || !infile) setup_bodies_static();

  if (!staticflag || (!infile && !onemols)) setup_bodies_static();

  else pre_neighbor();

  setup_bodies_dynamic();

  //if (!staticflag || (!infile)) setup_bodies_static();

  //else pre_neighbor();

  //setup_bodies_dynamic();

  if (!onemols) setup_bodies_dynamic();

}

/* ----------------------------------------------------------------------

     due to first-time definition of rigid body in setup_bodies_static()

     or due to box flip

   also adjust imagebody = rigid body image flags, due to xcm remap

   also adjust rgdimage flags of all atoms in bodies for two effects

   then communicate bodies so other procs will know of changes to body xcm

   then adjust xcmimage flags of all atoms in bodies via image_shift()

     for two effects

     (1) change in true image flags due to pbc() call during exchange

     (2) change in imagebody due to xcm remap

   rgdimage flags are always -1,0,-1 so that body can be unwrapped

   xcmimage flags are always -1,0,-1 so that body can be unwrapped

     around in-box xcm and stay close to simulation box

   if don't do this, then a body could end up very far away

     when unwrapped by true image flags, and set_xv() will

     compute huge displacements every step to reset coords of 

   if just inferred unwrapped from atom image flags, 

     then a body could end up very far away

     when unwrapped by true image flags

   then set_xv() will compute huge displacements every step to reset coords of 

     all the body atoms to be back inside the box, ditto for triclinic box flip

     note: so just want to avoid that numeric probem?

------------------------------------------------------------------------- */

void FixRigidSmall::pre_neighbor()

{

  // acquire ghost bodies via forward comm

  // also gets new remapflags needed for adjusting atom image flags

  // reset atom2body for owned atoms

  // forward comm sets atom2body for ghost atoms

  for (int ibody = 0; ibody < nlocal_body; ibody++) {

    Body *b = &body[ibody];

    domain->remap(b->xcm,b->image);

  }  

  nghost_body = 0;

  commflag = FULL_BODY;

  reset_atom2body();

  //check(4);

  for (int ibody = 0; ibody < nlocal_body; ibody++) {

    Body *b = &body[ibody];

    domain->remap(b->xcm,b->image);

  }  

  image_shift();

}

/* ----------------------------------------------------------------------

   initialization of rigid body attributes

   called at setup, so body/atom properties can be changed between runs

   unless reading from infile, in which case only called once

   unless reading from infile or defined by Molecule class,

     in which case only called once

   sets extended flags, masstotal, center-of-mass

   sets Cartesian and diagonalized inertia tensor

   sets body image flags, but only on first call

   one-time initialization of dynamic rigid body attributes

   vcm and angmom, computed explicitly from constituent particles

   even if wrong for overlapping particles, is OK,

     since is just setting initial time=0 Vcm and angmom of the body

     since is just setting initial time=0 vcm and angmom of the body

     which can be estimated value

------------------------------------------------------------------------- */

else the rigid fix contribution to the pressure virial is

incorrect.

W: Cannot count rigid body degrees-of-freedom before bodies are fully initialized

W: Cannot count rigid body degrees-of-freedom before bodies are fully initialized h

This means the temperature associated with the rigid bodies may be

incorrect on this timestep.

  dof -= domain->dimension * nelectrons;

  if (dof < 0.0 && natoms > 0.0) 

    error->all(FLERR,"Temperature compute degrees of freedom < 0");

  if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);

  else tfactor = 0.0;

}

  MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);

  if (dynamic) dof_compute();

  if (tfactor == 0.0 && atom->natoms != 0) 

    error->all(FLERR,"Temperature compute degrees of freedom < 0");

  scalar *= tfactor;

  return scalar;

}