git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1656 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/compute_temp_asphere.cpp

@@ -37,7 +37,8 @@ using namespace LAMMPS_NS;
 ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
-  if (narg != 3) error->all("Illegal compute temp command");
+  if (narg != 3 || narg != 4)
+    error->all("Illegal compute temp/asphere command");
 
   if (!atom->quat_flag || !atom->angmom_flag)
     error->all("Compute temp/asphere requires atom attributes quat, angmom");
@@ -48,6 +49,15 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
   extvector = 1;
   tempflag = 1;
 
+  tempbias = 0;
+  id_bias = NULL;
+  if (narg == 4) {
+    tempbias = 1;
+    int n = strlen(arg[3]) + 1;
+    id_bias = new char[n];
+    strcpy(id_bias,arg[3]);
+  }
+
   vector = new double[6];
   inertia = 
     memory->create_2d_double_array(atom->ntypes+1,3,"fix_temp_sphere:inertia");
@@ -57,6 +67,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeTempAsphere::~ComputeTempAsphere()
 {
+  delete [] id_bias;
   delete [] vector;
   memory->destroy_2d_double_array(inertia);
 }
@@ -65,20 +76,25 @@ ComputeTempAsphere::~ComputeTempAsphere()
 
 void ComputeTempAsphere::init()
 {
+  if (tempbias) {
+    int i = modify->find_compute(id_bias);
+    if (i < 0) error->all("Could not find compute ID for temperature bias");
+    tbias = modify->compute[i];
+    if (tbias->tempflag == 0)
+      error->all("Bias compute does not calculate temperature");
+    if (tbias->tempbias == 0)
+      error->all("Bias compute does not calculate a velocity bias");
+    if (tbias->igroup != igroup)
+      error->all("Bias compute group does not match compute group");
+    tbias->init();
+    if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
+  }
+
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   dof_compute();
 
-  tempbias = 0;
-  tbias = NULL;
-  if (id_bias) {
-    tempbias = 1;
-    int i = modify->find_compute(id_bias);
-    if (i < 0) error->all("Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
-  }
-
   calculate_inertia();
 }
 
@@ -89,10 +105,10 @@ void ComputeTempAsphere::dof_compute()
   double natoms = group->count(igroup);
   int dimension = domain->dimension;
   dof = dimension * natoms;
-  if (tbias) dof -= tbias->dof_remove(natoms);
-  dof -= extra_dof + fix_dof;
 
-  // add rotational degrees of freedom
+  if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms;
+
+  // rotational degrees of freedom
   // 0 for sphere, 2 for uniaxial, 3 for biaxial
 
   double **shape = atom->shape;
@@ -101,27 +117,30 @@ void ComputeTempAsphere::dof_compute()
   int nlocal = atom->nlocal;
 
   int itype;
-  int rot_dof = 0;
+  int count = 0;
+
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
+      if (tempbias == 2 && tbias->dof_remove(i)) continue;
       itype = type[i];
       if (dimension == 2) {
 	if (shape[itype][0] == shape[itype][1]) continue;
-	else rot_dof += 1;
+	else count++;
       } else {
 	if (shape[itype][0] == shape[itype][1] && 
 	    shape[itype][1] == shape[itype][2]) continue;
 	else if (shape[itype][0] == shape[itype][1] || 
 		 shape[itype][1] == shape[itype][2] ||
-		 shape[itype][0] == shape[itype][2]) rot_dof += 2;
+		 shape[itype][0] == shape[itype][2]) count += 2;
-	else rot_dof += 3;
+	else count += 3;
       }
     }
 
-  int rot_total;
+  int count_all;
-  MPI_Allreduce(&rot_dof,&rot_total,1,MPI_INT,MPI_SUM,world);
+  MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
-  dof += rot_total;
+  dof += count_all;
     
+  dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
 }
@@ -132,7 +151,7 @@ double ComputeTempAsphere::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
 
-  if (tbias) {
+  if (tempbias) {
     if (!(tbias->invoked & INVOKED_SCALAR))
       double tmp = tbias->compute_scalar();
     tbias->remove_bias_all();
@@ -179,10 +198,10 @@ double ComputeTempAsphere::compute_scalar()
       }
     }
 
-  if (tbias) tbias->restore_bias_all();
+  if (tempbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic || tbias) dof_compute();
+  if (dynamic || tempbias == 2) dof_compute();
   scalar *= tfactor;
   return scalar;
 }
@@ -195,7 +214,7 @@ void ComputeTempAsphere::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
-  if (tbias) {
+  if (tempbias) {
     if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
     tbias->remove_bias_all();
   }
@@ -246,7 +265,7 @@ void ComputeTempAsphere::compute_vector()
       t[5] += inertia[itype][2]*wbody[1]*wbody[2];
     }
 
-  if (tbias) tbias->restore_bias_all();
+  if (tempbias) tbias->restore_bias_all();
 
   MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
   for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
@@ -280,15 +299,6 @@ void ComputeTempAsphere::remove_bias(int i, double *v)
   if (tbias) tbias->remove_bias(i,v);
 }
 
-/* ----------------------------------------------------------------------
-   remove velocity bias from all atoms to leave thermal velocity
-------------------------------------------------------------------------- */
-
-void ComputeTempAsphere::remove_bias_all()
-{
-  if (tbias) tbias->remove_bias_all();
-}
-
 /* ----------------------------------------------------------------------
    add back in velocity bias to atom I removed by remove_bias()
    assume remove_bias() was previously called
@@ -298,13 +308,3 @@ void ComputeTempAsphere::restore_bias(int i, double *v)
 {
   if (tbias) tbias->restore_bias(i,v);
 }
-
-/* ----------------------------------------------------------------------
-   add back in velocity bias to all atoms removed by remove_bias_all()
-   assume remove_bias_all() was previously called
-------------------------------------------------------------------------- */
-
-void ComputeTempAsphere::restore_bias_all()
-{
-  if (tbias) tbias->restore_bias_all();
-}

src/ASPHERE/compute_temp_asphere.h

@@ -27,15 +27,13 @@ class ComputeTempAsphere : public Compute {
   void compute_vector();
 
   void remove_bias(int, double *);
-  void remove_bias_all();
   void restore_bias(int, double *);
-  void restore_bias_all();
 
  private:
   int fix_dof;
   double tfactor;
   double **inertia;
-
+  char *id_bias;
   Compute *tbias;     // ptr to additional bias compute
 
   void dof_compute();

src/compute.cpp

@@ -62,9 +62,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   scalar_flag = vector_flag = peratom_flag = 0;
   tempflag = pressflag = peflag = 0;
   pressatomflag = peatomflag = 0;
-
   tempbias = 0;
-  id_bias = NULL;
 
   id_pre = NULL;
   timeflag = 0;
@@ -90,7 +88,6 @@ Compute::~Compute()
 {
   delete [] id;
   delete [] style;
-  delete [] id_bias;
   delete [] id_pre;
 
   memory->sfree(tlist);
@@ -120,21 +117,6 @@ void Compute::modify_params(int narg, char **arg)
       else if (strcmp(arg[iarg+1],"yes") == 0) thermoflag = 1;
       else error->all("Illegal compute_modify command");
       iarg += 2;
-    } else if (strcmp(arg[iarg],"bias") == 0) {
-      if (iarg+2 > narg) error->all("Illegal compute_modify command");
-      delete [] id_bias;
-      if (strcmp(arg[iarg+1],"NULL") == 0) id_bias = NULL;
-      else {
-	int n = strlen(arg[iarg+1]) + 1;
-	id_bias = new char[n];
-	strcpy(id_bias,arg[iarg+1]);
-	int icompute = modify->find_compute(id_bias);
-	if (icompute < 0) error->all("Could not find compute_modify bias ID");
-	Compute *temperature = modify->compute[icompute];
-	if (temperature->igroup != igroup && comm->me == 0)
-	  error->warning("Group for compute_modify bias != compute group");
-      }
-      iarg += 2;
     } else error->all("Illegal compute_modify command");
   }
 }

src/compute.h

@@ -45,9 +45,7 @@ class Compute : protected Pointers {
   int peflag;         // 1 if Compute calculates PE (uses Force energies)
   int peatomflag;     // 1 if Compute calculates per-atom PE
 
-  int tempbias;       // 0/1 if Compute temp includes
+  int tempbias;       // 0/1 if Compute temp includes self/extra bias
-                      // self or extra bias via compute_modify
-  char *id_bias;      // ID of extra Compute temp that adds bias
 
   char *id_pre;       // ID of pre-compute the Compute may store
 
@@ -77,7 +75,7 @@ class Compute : protected Pointers {
   virtual int pack_reverse_comm(int, int, double *) {return 0;}
   virtual void unpack_reverse_comm(int, int *, double *) {}
 
-  virtual double dof_remove(double &) {return 0.0;}
+  virtual int dof_remove(int) {return 0;}
   virtual void remove_bias(int, double *) {}
   virtual void remove_bias_all() {}
   virtual void restore_bias(int, double *) {}

src/compute_temp.cpp

@@ -38,6 +38,7 @@ ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 0;
   extvector = 1;
   tempflag = 1;
+  tempbias = 0;
 
   vector = new double[6];
 }
@@ -57,15 +58,6 @@ void ComputeTemp::init()
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   dof_compute();
-
-  tempbias = 0;
-  tbias = NULL;
-  if (id_bias) {
-    tempbias = 1;
-    int i = modify->find_compute(id_bias);
-    if (i < 0) error->all("Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
-  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -74,7 +66,6 @@ void ComputeTemp::dof_compute()
 {
   double natoms = group->count(igroup);
   dof = domain->dimension * natoms;
-  if (tbias) dof -= tbias->dof_remove(natoms);
   dof -= extra_dof + fix_dof;
   if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
@@ -86,12 +77,6 @@ double ComputeTemp::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_SCALAR))
-      double tmp = tbias->compute_scalar();
-    tbias->remove_bias_all();
-  }
-
   double **v = atom->v;
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -112,10 +97,8 @@ double ComputeTemp::compute_scalar()
 	t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
   }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic || tbias) dof_compute();
+  if (dynamic) dof_compute();
   scalar *= tfactor;
   return scalar;
 }
@@ -128,11 +111,6 @@ void ComputeTemp::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
-    tbias->remove_bias_all();
-  }
-
   double **v = atom->v;
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -155,46 +133,6 @@ void ComputeTemp::compute_vector()
       t[5] += massone * v[i][1]*v[i][2];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
   for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
 }
-
-/* ----------------------------------------------------------------------
-   remove velocity bias from atom I to leave thermal velocity
-------------------------------------------------------------------------- */
-
-void ComputeTemp::remove_bias(int i, double *v)
-{
-  if (tbias) tbias->remove_bias(i,v);
-}
-
-/* ----------------------------------------------------------------------
-   remove velocity bias from all atoms to leave thermal velocity
-------------------------------------------------------------------------- */
-
-void ComputeTemp::remove_bias_all()
-{
-  if (tbias) tbias->remove_bias_all();
-}
-
-/* ----------------------------------------------------------------------
-   add back in velocity bias to atom I removed by remove_bias()
-   assume remove_bias() was previously called
-------------------------------------------------------------------------- */
-
-void ComputeTemp::restore_bias(int i, double *v)
-{
-  if (tbias) tbias->restore_bias(i,v);
-}
-
-/* ----------------------------------------------------------------------
-   add back in velocity bias to all atoms removed by remove_bias_all()
-   assume remove_bias_all() was previously called
-------------------------------------------------------------------------- */
-
-void ComputeTemp::restore_bias_all()
-{
-  if (tbias) tbias->restore_bias_all();
-}

src/compute_temp.h

@@ -26,17 +26,10 @@ class ComputeTemp : public Compute {
   double compute_scalar();
   void compute_vector();
 
-  void remove_bias(int, double *);
-  void remove_bias_all();
-  void restore_bias(int, double *);
-  void restore_bias_all();
-
  private:
   int fix_dof;
   double tfactor;
 
-  Compute *tbias;     // ptr to additional bias compute
-
   void dof_compute();
 };
 

src/compute_temp_com.cpp

@@ -64,14 +64,8 @@ void ComputeTempCOM::init()
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   dof_compute();
-  masstotal = group->mass(igroup);
 
-  tbias = NULL;
+  masstotal = group->mass(igroup);
-  if (id_bias) {
-    int i = modify->find_compute(id_bias);
-    if (i < 0) error->all("Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
-  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -79,8 +73,8 @@ void ComputeTempCOM::init()
 void ComputeTempCOM::dof_compute()
 {
   double natoms = group->count(igroup);
-  dof = domain->dimension * natoms;
+  int nper = domain->dimension;
-  if (tbias) dof -= tbias->dof_remove(natoms);
+  dof = nper * natoms;
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
@@ -94,12 +88,6 @@ double ComputeTempCOM::compute_scalar()
 
   invoked |= INVOKED_SCALAR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_SCALAR))
-      double tmp = tbias->compute_scalar();
-    tbias->remove_bias_all();
-  }
-
   if (dynamic) masstotal = group->mass(igroup);
   group->vcm(igroup,masstotal,vbias);
 
@@ -124,10 +112,8 @@ double ComputeTempCOM::compute_scalar()
 	      vthermal[2]*vthermal[2]) * rmass[i];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic || tbias) dof_compute();
+  if (dynamic) dof_compute();
   scalar *= tfactor;
   return scalar;
 }
@@ -141,11 +127,6 @@ void ComputeTempCOM::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
-    tbias->remove_bias_all();
-  }
-
   if (dynamic) masstotal = group->mass(igroup);
   group->vcm(igroup,masstotal,vbias);
 
@@ -176,8 +157,6 @@ void ComputeTempCOM::compute_vector()
       t[5] += massone * vthermal[1]*vthermal[2];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
   for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
 }
@@ -188,13 +167,10 @@ void ComputeTempCOM::compute_vector()
 
 void ComputeTempCOM::remove_bias(int i, double *v)
 {
-  if (tbias) tbias->remove_bias(i,v);
-  if (atom->mask[i] & groupbit) {
   v[0] -= vbias[0];
   v[1] -= vbias[1];
   v[2] -= vbias[2];
 }
-}
 
 /* ----------------------------------------------------------------------
    remove velocity bias from all atoms to leave thermal velocity
@@ -202,8 +178,6 @@ void ComputeTempCOM::remove_bias(int i, double *v)
 
 void ComputeTempCOM::remove_bias_all()
 {
-  if (tbias) tbias->remove_bias_all();
-
   double **v = atom->v;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
@@ -223,13 +197,10 @@ void ComputeTempCOM::remove_bias_all()
 
 void ComputeTempCOM::restore_bias(int i, double *v)
 {
-  if (atom->mask[i] & groupbit) {
   v[0] += vbias[0];
   v[1] += vbias[1];
   v[2] += vbias[2];
 }
-  if (tbias) tbias->restore_bias(i,v);
-}
 
 /* ----------------------------------------------------------------------
    add back in velocity bias to all atoms removed by remove_bias_all()
@@ -248,6 +219,4 @@ void ComputeTempCOM::restore_bias_all()
       v[i][1] += vbias[1];
       v[i][2] += vbias[2];
     }
-
-  if (tbias) tbias->restore_bias_all();
 }

src/compute_temp_com.h

@@ -34,11 +34,10 @@ class ComputeTempCOM : public Compute {
  private:
   int fix_dof;
   double tfactor,masstotal;
-
   double vbias[3];    // stored velocity bias for one atom
-  Compute *tbias;     // ptr to additional bias compute
 
   void dof_compute();
+
 };
 
 }

src/compute_temp_deform.cpp

@@ -73,13 +73,6 @@ void ComputeTempDeform::init()
     fix_dof += modify->fix[i]->dof(igroup);
   dof_compute();
 
-  tbias = NULL;
-  if (id_bias) {
-    int i = modify->find_compute(id_bias);
-    if (i < 0) error->all("Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
-  }
-
   // check fix deform remap settings
 
   for (i = 0; i < modify->nfix; i++)
@@ -99,7 +92,6 @@ void ComputeTempDeform::dof_compute()
 {
   double natoms = group->count(igroup);
   dof = domain->dimension * natoms;
-  if (tbias) dof -= tbias->dof_remove(natoms);
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
@@ -113,12 +105,6 @@ double ComputeTempDeform::compute_scalar()
 
   invoked |= INVOKED_SCALAR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_SCALAR))
-      double tmp = tbias->compute_scalar();
-    tbias->remove_bias_all();
-  }
-
   double **x = atom->x;
   double **v = atom->v;
   double *mass = atom->mass;
@@ -154,10 +140,8 @@ double ComputeTempDeform::compute_scalar()
 	      vthermal[2]*vthermal[2]) * rmass[i];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic || tbias) dof_compute();
+  if (dynamic) dof_compute();
   scalar *= tfactor;
   return scalar;
 }
@@ -170,11 +154,6 @@ void ComputeTempDeform::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
-    tbias->remove_bias_all();
-  }
-
   double **x = atom->x;
   double **v = atom->v;
   double *mass = atom->mass;
@@ -210,8 +189,6 @@ void ComputeTempDeform::compute_vector()
       t[5] += massone * vthermal[1]*vthermal[2];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
   for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
 }
@@ -222,9 +199,6 @@ void ComputeTempDeform::compute_vector()
 
 void ComputeTempDeform::remove_bias(int i, double *v)
 {
-  if (tbias) tbias->remove_bias(i,v);
-
-  if (atom->mask[i] & groupbit) {
   double lamda[3];
   double *h_rate = domain->h_rate;
   double *h_ratelo = domain->h_ratelo;
@@ -238,7 +212,6 @@ void ComputeTempDeform::remove_bias(int i, double *v)
   v[1] -= vbias[1];
   v[2] -= vbias[2];
 }
-}
 
 /* ----------------------------------------------------------------------
    remove velocity bias from all atoms to leave thermal velocity
@@ -246,8 +219,6 @@ void ComputeTempDeform::remove_bias(int i, double *v)
 
 void ComputeTempDeform::remove_bias_all()
 {
-  if (tbias) tbias->remove_bias_all();
-
   double **v = atom->v;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
@@ -283,13 +254,10 @@ void ComputeTempDeform::remove_bias_all()
 
 void ComputeTempDeform::restore_bias(int i, double *v)
 {
-  if (atom->mask[i] & groupbit) {
   v[0] += vbias[0];
   v[1] += vbias[1];
   v[2] += vbias[2];
 }
-  if (tbias) tbias->restore_bias(i,v);
-}
 
 /* ----------------------------------------------------------------------
    add back in velocity bias to all atoms removed by remove_bias_all()
@@ -308,8 +276,6 @@ void ComputeTempDeform::restore_bias_all()
       v[i][1] += vbiasall[i][1];
       v[i][2] += vbiasall[i][2];
     }
-
-  if (tbias) tbias->restore_bias_all();
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_deform.h

@@ -35,11 +35,9 @@ class ComputeTempDeform : public Compute {
  private:
   int fix_dof;
   double tfactor;
-
   double vbias[3];    // stored velocity bias for one atom
   double **vbiasall;  // stored velocity bias for all atoms
   int maxbias;        // size of vbiasall array
-  Compute *tbias;     // ptr to additional bias compute
 
   void dof_compute();
 };

src/compute_temp_partial.cpp

@@ -67,13 +67,6 @@ void ComputeTempPartial::init()
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   dof_compute();
-
-  tbias = NULL;
-  if (id_bias) {
-    int i = modify->find_compute(id_bias);
-    if (i < 0) error->all("Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
-  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -81,8 +74,9 @@ void ComputeTempPartial::init()
 void ComputeTempPartial::dof_compute()
 {
   double natoms = group->count(igroup);
-  dof = (xflag+yflag+zflag) * natoms;
+  int nper = xflag+yflag+zflag;
-  if (tbias) dof -= tbias->dof_remove(natoms);
+  if (domain->dimension == 2) nper = xflag+yflag;
+  dof = nper * natoms;
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
@@ -90,14 +84,9 @@ void ComputeTempPartial::dof_compute()
 
 /* ---------------------------------------------------------------------- */
 
-double ComputeTempPartial::dof_remove(double &natoms)
+int ComputeTempPartial::dof_remove(int i)
 {
-  double rmdof = 0.0;
+  return 0;
-  if (tbias) rmdof = tbias->dof_remove(natoms);
-  int activedim = xflag+yflag+zflag;
-  if (domain->dimension == 2) activedim = xflag+yflag;
-  rmdof += (domain->dimension - activedim) * natoms;
-  return rmdof;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -106,12 +95,6 @@ double ComputeTempPartial::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_SCALAR))
-      double tmp = tbias->compute_scalar();
-    tbias->remove_bias_all();
-  }
-
   double **v = atom->v;
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -133,10 +116,8 @@ double ComputeTempPartial::compute_scalar()
 	      zflag*v[i][2]*v[i][2]) * rmass[i];
   }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic || tbias) dof_compute();
+  if (dynamic) dof_compute();
   scalar *= tfactor;
   return scalar;
 }
@@ -149,11 +130,6 @@ void ComputeTempPartial::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
-    tbias->remove_bias_all();
-  }
-
   double **v = atom->v;
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -176,8 +152,6 @@ void ComputeTempPartial::compute_vector()
       t[5] += massone * yflag*zflag*v[i][1]*v[i][2];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
   for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
 }
@@ -188,9 +162,6 @@ void ComputeTempPartial::compute_vector()
 
 void ComputeTempPartial::remove_bias(int i, double *v)
 {
-  if (tbias) tbias->remove_bias(i,v);
-
-  if (atom->mask[i] & groupbit) {
   if (!xflag) {
     vbias[0] = v[0];
     v[0] = 0.0;
@@ -204,7 +175,6 @@ void ComputeTempPartial::remove_bias(int i, double *v)
     v[2] = 0.0;
   }
 }
-}
 
 /* ----------------------------------------------------------------------
    remove velocity bias from all atoms to leave thermal velocity
@@ -212,8 +182,6 @@ void ComputeTempPartial::remove_bias(int i, double *v)
 
 void ComputeTempPartial::remove_bias_all()
 {
-  if (tbias) tbias->remove_bias_all();
-
   double **v = atom->v;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
@@ -249,12 +217,9 @@ void ComputeTempPartial::remove_bias_all()
 
 void ComputeTempPartial::restore_bias(int i, double *v)
 {
-  if (atom->mask[i] & groupbit) {
+  if (!xflag) v[0] += vbias[0];
-    v[0] += vbias[0];
+  if (!yflag) v[1] += vbias[1];
-    v[1] += vbias[1];
+  if (!zflag) v[2] += vbias[2];
-    v[2] += vbias[2];
-  }
-  if (tbias) tbias->restore_bias(i,v);
 }
 
 /* ----------------------------------------------------------------------
@@ -270,12 +235,10 @@ void ComputeTempPartial::restore_bias_all()
 
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      v[i][0] += vbiasall[i][0];
+      if (!xflag) v[i][0] += vbiasall[i][0];
-      v[i][1] += vbiasall[i][1];
+      if (!yflag) v[i][1] += vbiasall[i][1];
-      v[i][2] += vbiasall[i][2];
+      if (!zflag) v[i][2] += vbiasall[i][2];
     }
-
-  if (tbias) tbias->restore_bias_all();
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_partial.h

@@ -26,7 +26,7 @@ class ComputeTempPartial : public Compute {
   double compute_scalar();
   void compute_vector();
 
-  double dof_remove(double &);
+  int dof_remove(int);
   void remove_bias(int, double *);
   void remove_bias_all();
   void restore_bias(int, double *);
@@ -37,11 +37,9 @@ class ComputeTempPartial : public Compute {
   int xflag,yflag,zflag;
   int fix_dof;
   double tfactor;
-
   double vbias[3];    // stored velocity bias for one atom
   double **vbiasall;  // stored velocity bias for all atoms
   int maxbias;        // size of vbiasall array
-  Compute *tbias;     // ptr to additional bias compute
 
   void dof_compute();
 };

src/compute_temp_ramp.cpp

@@ -131,13 +131,6 @@ void ComputeTempRamp::init()
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   dof_compute();
-
-  tbias = NULL;
-  if (id_bias) {
-    int i = modify->find_compute(id_bias);
-    if (i < 0) error->all("Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
-  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -145,8 +138,8 @@ void ComputeTempRamp::init()
 void ComputeTempRamp::dof_compute()
 {
   double natoms = group->count(igroup);
-  dof = domain->dimension * natoms;
+  int nper = domain->dimension;
-  if (tbias) dof -= tbias->dof_remove(natoms);
+  dof = nper * natoms;
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
@@ -160,12 +153,6 @@ double ComputeTempRamp::compute_scalar()
 
   invoked |= INVOKED_SCALAR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_SCALAR))
-      double tmp = tbias->compute_scalar();
-    tbias->remove_bias_all();
-  }
-
   double **x = atom->x;
   double **v = atom->v;
   double *mass = atom->mass;
@@ -193,10 +180,8 @@ double ComputeTempRamp::compute_scalar()
 	      vthermal[2]*vthermal[2]) * rmass[i];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic || tbias) dof_compute();
+  if (dynamic) dof_compute();
   scalar *= tfactor;
   return scalar;
 }
@@ -210,11 +195,6 @@ void ComputeTempRamp::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
-    tbias->remove_bias_all();
-  }
-
   double **x = atom->x;
   double **v = atom->v;
   double *mass = atom->mass;
@@ -247,8 +227,6 @@ void ComputeTempRamp::compute_vector()
       t[5] += massone * vthermal[1]*vthermal[2];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
   for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
 }
@@ -259,17 +237,12 @@ void ComputeTempRamp::compute_vector()
 
 void ComputeTempRamp::remove_bias(int i, double *v)
 {
-  if (tbias) tbias->remove_bias(i,v);
+  double fraction = (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
-
-  if (atom->mask[i] & groupbit) {
-    double fraction = 
-      (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
   fraction = MAX(fraction,0.0);
   fraction = MIN(fraction,1.0);
   vbias[v_dim] = v_lo + fraction*(v_hi - v_lo);
   v[v_dim] -= vbias[v_dim];
 }
-}
 
 /* ----------------------------------------------------------------------
    remove velocity bias from all atoms to leave thermal velocity
@@ -277,8 +250,6 @@ void ComputeTempRamp::remove_bias(int i, double *v)
 
 void ComputeTempRamp::remove_bias_all()
 {
-  if (tbias) tbias->remove_bias_all();
-
   double **v = atom->v;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
@@ -308,8 +279,7 @@ void ComputeTempRamp::remove_bias_all()
 
 void ComputeTempRamp::restore_bias(int i, double *v)
 {
-  if (atom->mask[i] & groupbit) v[v_dim] += vbias[v_dim];
+  v[v_dim] += vbias[v_dim];
-  if (tbias) tbias->restore_bias(i,v);
 }
 
 /* ----------------------------------------------------------------------
@@ -326,8 +296,6 @@ void ComputeTempRamp::restore_bias_all()
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit)
       v[i][v_dim] += vbiasall[i][v_dim];
-
-  if (tbias) tbias->restore_bias_all();
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_ramp.h

@@ -39,11 +39,9 @@ class ComputeTempRamp : public Compute {
   double v_lo,v_hi;
   int scaleflag,fix_dof;
   double tfactor,xscale,yscale,zscale;
-
   double vbias[3];    // stored velocity bias for one atom
   double **vbiasall;  // stored velocity bias for all atoms
   int maxbias;        // size of vbiasall array
-  Compute *tbias;     // ptr to additional bias compute
 
   void dof_compute();
 };

src/compute_temp_region.cpp

@@ -61,25 +61,16 @@ ComputeTempRegion::~ComputeTempRegion()
 
 void ComputeTempRegion::init()
 {
-  dof = 0;
+  dof = 0.0;
-
-  tbias = NULL;
-  if (id_bias) {
-    int i = modify->find_compute(id_bias);
-    if (i < 0) error->all("Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
-  }
 }
 
 /* ---------------------------------------------------------------------- */
 
-double ComputeTempRegion::dof_remove(double &natoms)
+int ComputeTempRegion::dof_remove(int i)
 {
-  double rmdof = 0.0;
+  double *x = atom->x[i];
-  if (tbias) rmdof = tbias->dof_remove(natoms);
+  if (domain->regions[iregion]->match(x[0],x[1],x[2])) return 0;
-  natoms -= natoms_region;
+  return 1;
-  rmdof += domain->dimension * natoms;
-  return rmdof;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -88,12 +79,6 @@ double ComputeTempRegion::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_SCALAR))
-      double tmp = tbias->compute_scalar();
-    tbias->remove_bias_all();
-  }
-
   double **x = atom->x;
   double **v = atom->v;
   double *mass = atom->mass;
@@ -102,34 +87,30 @@ double ComputeTempRegion::compute_scalar()
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
+  Region *region = domain->regions[iregion];
   int count = 0;
   double t = 0.0;
 
   if (mass) {
     for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit &&
+      if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
-	  domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
 	count++;
 	t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * 
 	  mass[type[i]];
       }
   } else {
     for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit &&
+      if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
-	  domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
 	count++;
 	t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
       }
   }
 
-  if (tbias) tbias->restore_bias_all();
-
   double tarray[2],tarray_all[2];
   tarray[0] = count;
   tarray[1] = t;
   MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
-  natoms_region = tarray_all[0];
+  dof = domain->dimension * tarray_all[0] - extra_dof;
-  dof = domain->dimension * natoms_region - extra_dof;
   if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
   else scalar = 0.0;
   return scalar;
@@ -143,11 +124,6 @@ void ComputeTempRegion::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
-  if (tbias) {
-    if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
-    tbias->remove_bias_all();
-  }
-
   double **x = atom->x;
   double **v = atom->v;
   double *mass = atom->mass;
@@ -156,12 +132,12 @@ void ComputeTempRegion::compute_vector()
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
+  Region *region = domain->regions[iregion];
   double massone,t[6];
   for (i = 0; i < 6; i++) t[i] = 0.0;
 
   for (i = 0; i < nlocal; i++)
-    if (mask[i] & groupbit && 
+    if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
-	domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
       if (mass) massone = mass[type[i]];
       else massone = rmass[i];
       t[0] += massone * v[i][0]*v[i][0];
@@ -172,8 +148,6 @@ void ComputeTempRegion::compute_vector()
       t[5] += massone * v[i][1]*v[i][2];
     }
 
-  if (tbias) tbias->restore_bias_all();
-
   MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
   for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
 }
@@ -184,9 +158,6 @@ void ComputeTempRegion::compute_vector()
 
 void ComputeTempRegion::remove_bias(int i, double *v)
 {
-  if (tbias) tbias->remove_bias(i,v);
-
-  if (atom->mask[i] & groupbit) {
   double *x = atom->x[i];
   if (domain->regions[iregion]->match(x[0],x[1],x[2]))
     vbias[0] = vbias[1] = vbias[2] = 0.0;
@@ -197,7 +168,6 @@ void ComputeTempRegion::remove_bias(int i, double *v)
     v[0] = v[1] = v[2] = 0.0;
   }
 }
-}
 
 /* ----------------------------------------------------------------------
    remove velocity bias from all atoms to leave thermal velocity
@@ -205,8 +175,6 @@ void ComputeTempRegion::remove_bias(int i, double *v)
 
 void ComputeTempRegion::remove_bias_all()
 {
-  if (tbias) tbias->remove_bias_all();
-
   double **x = atom->x;
   double **v = atom->v;
   int *mask = atom->mask;
@@ -219,9 +187,11 @@ void ComputeTempRegion::remove_bias_all()
 					      "compute/temp:vbiasall");
   }
   
+  Region *region = domain->regions[iregion];
+
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
+      if (region->match(x[i][0],x[i][1],x[i][2]))
 	vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0;
       else {
 	vbiasall[i][0] = v[i][0];
@@ -239,13 +209,10 @@ void ComputeTempRegion::remove_bias_all()
 
 void ComputeTempRegion::restore_bias(int i, double *v)
 {
-  if (atom->mask[i] & groupbit) {
   v[0] += vbias[0];
   v[1] += vbias[1];
   v[2] += vbias[2];
 }
-  if (tbias) tbias->restore_bias(i,v);
-}
 
 /* ----------------------------------------------------------------------
    add back in velocity bias to all atoms removed by remove_bias_all()
@@ -264,8 +231,6 @@ void ComputeTempRegion::restore_bias_all()
       v[i][1] += vbiasall[i][1];
       v[i][2] += vbiasall[i][2];
     }
-
-  if (tbias) tbias->restore_bias_all();
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_region.h

@@ -26,7 +26,7 @@ class ComputeTempRegion : public Compute {
   double compute_scalar();
   void compute_vector();
 
-  double dof_remove(double &);
+  int dof_remove(int);
   void remove_bias(int, double *);
   void remove_bias_all();
   void restore_bias(int, double *);
@@ -35,12 +35,9 @@ class ComputeTempRegion : public Compute {
 
  private:
   int iregion;
-  double natoms_region;
-
   double vbias[3];    // stored velocity bias for one atom
   double **vbiasall;  // stored velocity bias for all atoms
   int maxbias;        // size of vbiasall array
-  Compute *tbias;     // ptr to additional bias compute
 };
 
 }

src/compute_temp_sphere.cpp

@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "mpi.h"
+#include "string.h"
 #include "compute_temp_sphere.h"
 #include "atom.h"
 #include "force.h"
@@ -33,7 +34,8 @@ using namespace LAMMPS_NS;
 ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) : 
   Compute(lmp, narg, arg)
 {
-  if (narg != 3) error->all("Illegal compute temp command");
+  if (narg != 3 || narg != 4)
+    error->all("Illegal compute temp/sphere command");
 
   scalar_flag = vector_flag = 1;
   size_vector = 6;
@@ -41,6 +43,15 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
   extvector = 1;
   tempflag = 1;
 
+  tempbias = 0;
+  id_bias = NULL;
+  if (narg == 4) {
+    tempbias = 1;
+    int n = strlen(arg[3]) + 1;
+    id_bias = new char[n];
+    strcpy(id_bias,arg[3]);
+  }
+
   vector = new double[6];
   inertia = new double[atom->ntypes+1];
 }
@@ -57,20 +68,26 @@ ComputeTempSphere::~ComputeTempSphere()
 
 void ComputeTempSphere::init()
 {
+  if (tempbias) {
+    int i = modify->find_compute(id_bias);
+    if (i < 0) error->all("Could not find compute ID for temperature bias");
+    tbias = modify->compute[i];
+    if (tbias->tempflag == 0)
+      error->all("Bias compute does not calculate temperature");
+    if (tbias->tempbias == 0)
+      error->all("Bias compute does not calculate a velocity bias");
+    if (tbias->igroup != igroup)
+      error->all("Bias compute group does not match compute group");
+    tbias->init();
+    if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
+    else tempbias = 1;
+  }
+
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   dof_compute();
 
-  tempbias = 0;
-  tbias = NULL;
-  if (id_bias) {
-    tempbias = 1;
-    int i = modify->find_compute(id_bias);
-    if (i < 0) error->all("Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
-  }
-
   if (atom->mass) {
     double *mass = atom->mass;
     double **shape = atom->shape;
@@ -88,9 +105,25 @@ void ComputeTempSphere::init()
 void ComputeTempSphere::dof_compute()
 {
   double natoms = group->count(igroup);
-  if (domain->dimension == 3) dof = 6.0 * natoms;
+  int nper = 6;
-  else dof = 3.0 * natoms;
+  if (domain->dimension == 2) nper = 3;
-  if (tbias) dof -= tbias->dof_remove(natoms);
+  dof = nper * natoms;
+
+  if (tempbias) {
+    if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms;
+    else {
+      int *mask = atom->mask;
+      int nlocal = atom->nlocal;
+      int count = 0;
+      for (int i = 0; i < nlocal; i++)
+	if (mask[i] & groupbit)
+	  if (tbias->dof_remove(i)) count++;
+      int count_all;
+      MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
+      dof -= nper * count_all;
+    }
+  }
+
   dof -= extra_dof + fix_dof;
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
@@ -102,7 +135,7 @@ double ComputeTempSphere::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
 
-  if (tbias) {
+  if (tempbias) {
     if (!(tbias->invoked & INVOKED_SCALAR))
       double tmp = tbias->compute_scalar();
     tbias->remove_bias_all();
@@ -136,10 +169,10 @@ double ComputeTempSphere::compute_scalar()
       }
   }
 
-  if (tbias) tbias->restore_bias_all();
+  if (tempbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic || tbias) dof_compute();
+  if (dynamic || tempbias == 2) dof_compute();
   scalar *= tfactor;
   return scalar;
 }
@@ -152,7 +185,7 @@ void ComputeTempSphere::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
-  if (tbias) {
+  if (tempbias) {
     if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
     tbias->remove_bias_all();
   }
@@ -209,7 +242,7 @@ void ComputeTempSphere::compute_vector()
       }
   }
 
-  if (tbias) tbias->restore_bias_all();
+  if (tempbias) tbias->restore_bias_all();
 
   MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
   for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
@@ -221,16 +254,7 @@ void ComputeTempSphere::compute_vector()
 
 void ComputeTempSphere::remove_bias(int i, double *v)
 {
-  if (tbias) tbias->remove_bias(i,v);
+  tbias->remove_bias(i,v);
-}
-
-/* ----------------------------------------------------------------------
-   remove velocity bias from all atoms to leave thermal velocity
-------------------------------------------------------------------------- */
-
-void ComputeTempSphere::remove_bias_all()
-{
-  if (tbias) tbias->remove_bias_all();
 }
 
 /* ----------------------------------------------------------------------
@@ -240,16 +264,5 @@ void ComputeTempSphere::remove_bias_all()
 
 void ComputeTempSphere::restore_bias(int i, double *v)
 {
-  if (tbias) tbias->restore_bias(i,v);
+  tbias->restore_bias(i,v);
 }
-
-/* ----------------------------------------------------------------------
-   add back in velocity bias to all atoms removed by remove_bias_all()
-   assume remove_bias_all() was previously called
-------------------------------------------------------------------------- */
-
-void ComputeTempSphere::restore_bias_all()
-{
-  if (tbias) tbias->restore_bias_all();
-}
-

src/compute_temp_sphere.h

@@ -27,15 +27,13 @@ class ComputeTempSphere : public Compute {
   void compute_vector();
 
   void remove_bias(int, double *);
-  void remove_bias_all();
   void restore_bias(int, double *);
-  void restore_bias_all();
 
  private:
   int fix_dof;
   double tfactor;
   double *inertia;
-
+  char *id_bias;
   Compute *tbias;     // ptr to additional bias compute
 
   void dof_compute();