git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1651 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/compute_erotate_asphere.cpp

@@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-ComputeERotateASphere::ComputeERotateASphere(LAMMPS *lmp, int narg, char **arg) :
+ComputeERotateAsphere::ComputeERotateAsphere(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
   if (narg != 3) error->all("Illegal compute erotate/asphere command");
@@ -42,14 +42,14 @@ ComputeERotateASphere::ComputeERotateASphere(LAMMPS *lmp, int narg, char **arg)
 
 /* ---------------------------------------------------------------------- */
 
-ComputeERotateASphere::~ComputeERotateASphere()
+ComputeERotateAsphere::~ComputeERotateAsphere()
 {
   memory->destroy_2d_double_array(inertia);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeERotateASphere::init()
+void ComputeERotateAsphere::init()
 {
   pfactor = 0.5 * force->mvv2e;
 
@@ -61,7 +61,7 @@ void ComputeERotateASphere::init()
 
 /* ---------------------------------------------------------------------- */
 
-double ComputeERotateASphere::compute_scalar()
+double ComputeERotateAsphere::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
 
@@ -102,7 +102,7 @@ double ComputeERotateASphere::compute_scalar()
    principal moments of inertia for ellipsoids
 ------------------------------------------------------------------------- */
 
-void ComputeERotateASphere::calculate_inertia()
+void ComputeERotateAsphere::calculate_inertia()
 {
   double *mass = atom->mass;
   double **shape = atom->shape;

src/ASPHERE/compute_erotate_asphere.h

@@ -18,10 +18,10 @@
 
 namespace LAMMPS_NS {
 
-class ComputeERotateASphere : public Compute {
+class ComputeERotateAsphere : public Compute {
  public:
-  ComputeERotateASphere(class LAMMPS *, int, char **);
+  ComputeERotateAsphere(class LAMMPS *, int, char **);
-  ~ComputeERotateASphere();
+  ~ComputeERotateAsphere();
   void init();
   double compute_scalar();
 

src/ASPHERE/compute_temp_asphere.cpp

@@ -70,6 +70,13 @@ void ComputeTempAsphere::init()
     fix_dof += modify->fix[i]->dof(igroup);
   recount();
 
+  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];
+  } else tempbias = 0;
+
   calculate_inertia();
 }
 
@@ -122,6 +129,12 @@ double ComputeTempAsphere::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 **quat = atom->quat;
   double **angmom = atom->angmom;
@@ -163,6 +176,8 @@ double ComputeTempAsphere::compute_scalar()
       }
     }
 
+  if (tbias) tbias->restore_bias_all();
+
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
   if (dynamic) recount();
   scalar *= tfactor;
@@ -177,6 +192,11 @@ void ComputeTempAsphere::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
+  if (tbias) {
+    if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
+    tbias->remove_bias_all();
+  }
+
   double **v = atom->v;
   double **quat = atom->quat;
   double **angmom = atom->angmom;
@@ -223,6 +243,8 @@ void ComputeTempAsphere::compute_vector()
       t[5] += inertia[itype][2]*wbody[1]*wbody[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;
 }
@@ -245,3 +267,42 @@ void ComputeTempAsphere::calculate_inertia()
       (shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]) / 5.0;
   }
 }
+
+/* ----------------------------------------------------------------------
+   remove velocity bias from atom I to leave thermal velocity
+------------------------------------------------------------------------- */
+
+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
+------------------------------------------------------------------------- */
+
+void ComputeTempAsphere::restore_bias(double *v)
+{
+  if (tbias) tbias->restore_bias(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

@@ -26,11 +26,18 @@ class ComputeTempAsphere : public Compute {
   double compute_scalar();
   void compute_vector();
 
+  void remove_bias(int, double *);
+  void remove_bias_all();
+  void restore_bias(double *);
+  void restore_bias_all();
+
  private:
   int fix_dof;
   double tfactor;
   double **inertia;
 
+  Compute *tbias;     // ptr to additional bias compute
+
   void recount();
   void calculate_inertia();
 };

src/ASPHERE/fix_npt_asphere.cpp

@@ -35,7 +35,7 @@ enum{NOBIAS,BIAS};
 
 /* ---------------------------------------------------------------------- */
 
-FixNPTASphere::FixNPTASphere(LAMMPS *lmp, int narg, char **arg) :
+FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
   FixNPT(lmp, narg, arg)
 {
   if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
@@ -46,7 +46,7 @@ FixNPTASphere::FixNPTASphere(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-void FixNPTASphere::init()
+void FixNPTAsphere::init()
 {
   FixNPT::init();
   dtq = 0.5 * update->dt;
@@ -56,7 +56,7 @@ void FixNPTASphere::init()
    1st half of Verlet update 
 ------------------------------------------------------------------------- */
 
-void FixNPTASphere::initial_integrate(int vflag)
+void FixNPTAsphere::initial_integrate(int vflag)
 {
   int i;
   double dtfm;
@@ -168,7 +168,7 @@ void FixNPTASphere::initial_integrate(int vflag)
    2nd half of Verlet update 
 ------------------------------------------------------------------------- */
 
-void FixNPTASphere::final_integrate()
+void FixNPTAsphere::final_integrate()
 {
   int i;
   double dtfm;
@@ -251,7 +251,7 @@ void FixNPTASphere::final_integrate()
 
 /* ---------------------------------------------------------------------- */
 
-void FixNPTASphere::reset_dt()
+void FixNPTAsphere::reset_dt()
 {
   FixNPT::reset_dt();
   dtq = 0.5 * update->dt;
@@ -261,7 +261,7 @@ void FixNPTASphere::reset_dt()
    Richardson iteration to update quaternion accurately
 ------------------------------------------------------------------------- */
 
-void FixNPTASphere::richardson(double *q, double *m, double *moments)
+void FixNPTAsphere::richardson(double *q, double *m, double *moments)
 {
   // compute omega at 1/2 step from m at 1/2 step and q at 0
 
@@ -320,7 +320,7 @@ void FixNPTASphere::richardson(double *q, double *m, double *moments)
      and divide by principal moments
 ------------------------------------------------------------------------- */
 
-void FixNPTASphere::omega_from_mq(double *q, double *m, double *inertia,
+void FixNPTAsphere::omega_from_mq(double *q, double *m, double *inertia,
 				  double *w)
 {
   double rot[3][3];
@@ -339,7 +339,7 @@ void FixNPTASphere::omega_from_mq(double *q, double *m, double *inertia,
    shape = x,y,z radii in body frame
 ------------------------------------------------------------------------- */
 
-void FixNPTASphere::calculate_inertia(double mass, double *shape,
+void FixNPTAsphere::calculate_inertia(double mass, double *shape,
 				      double *inertia)
 {
   inertia[0] = mass*(shape[1]*shape[1]+shape[2]*shape[2])/5.0;

src/ASPHERE/fix_npt_asphere.h

@@ -18,9 +18,9 @@
 
 namespace LAMMPS_NS {
 
-class FixNPTASphere : public FixNPT {
+class FixNPTAsphere : public FixNPT {
  public:
-  FixNPTASphere(class LAMMPS *, int, char **);
+  FixNPTAsphere(class LAMMPS *, int, char **);
   void init();
   void initial_integrate(int);
   void final_integrate();

src/ASPHERE/fix_nve_asphere.cpp

@@ -34,7 +34,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-FixNVEASphere::FixNVEASphere(LAMMPS *lmp, int narg, char **arg) : 
+FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) : 
   FixNVE(lmp, narg, arg)
 {
   if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
@@ -47,14 +47,14 @@ FixNVEASphere::FixNVEASphere(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-FixNVEASphere::~FixNVEASphere()
+FixNVEAsphere::~FixNVEAsphere()
 {
   memory->destroy_2d_double_array(inertia);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVEASphere::init()
+void FixNVEAsphere::init()
 {
   FixNVE::init();
   calculate_inertia();
@@ -62,7 +62,7 @@ void FixNVEASphere::init()
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVEASphere::initial_integrate(int vflag)
+void FixNVEAsphere::initial_integrate(int vflag)
 {
   double dtfm;
 
@@ -102,7 +102,7 @@ void FixNVEASphere::initial_integrate(int vflag)
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVEASphere::final_integrate()
+void FixNVEAsphere::final_integrate()
 {
   double dtfm;
 
@@ -133,7 +133,7 @@ void FixNVEASphere::final_integrate()
    Richardson iteration to update quaternion accurately
 ------------------------------------------------------------------------- */
 
-void FixNVEASphere::richardson(double *q, double *m, double *moments)
+void FixNVEAsphere::richardson(double *q, double *m, double *moments)
 {
   // compute omega at 1/2 step from m at 1/2 step and q at 0
 
@@ -192,7 +192,7 @@ void FixNVEASphere::richardson(double *q, double *m, double *moments)
      and divide by principal moments
 ------------------------------------------------------------------------- */
 
-void FixNVEASphere::omega_from_mq(double *q, double *m, double *moments,
+void FixNVEAsphere::omega_from_mq(double *q, double *m, double *moments,
 				  double *w)
 {
   double rot[3][3];
@@ -210,7 +210,7 @@ void FixNVEASphere::omega_from_mq(double *q, double *m, double *moments,
    principal moments of inertia for ellipsoids
 ------------------------------------------------------------------------- */
 
-void FixNVEASphere::calculate_inertia()
+void FixNVEAsphere::calculate_inertia()
 {
   double *mass = atom->mass;
   double **shape = atom->shape;

src/ASPHERE/fix_nve_asphere.h

@@ -18,10 +18,10 @@
 
 namespace LAMMPS_NS {
 
-class FixNVEASphere : public FixNVE {
+class FixNVEAsphere : public FixNVE {
  public:
-  FixNVEASphere(class LAMMPS *, int, char **);
+  FixNVEAsphere(class LAMMPS *, int, char **);
-  ~FixNVEASphere();
+  ~FixNVEAsphere();
   void init();
   void initial_integrate(int);
   void final_integrate();

src/ASPHERE/fix_nvt_asphere.cpp

@@ -36,7 +36,7 @@ enum{NOBIAS,BIAS};
 
 /* ---------------------------------------------------------------------- */
 
-FixNVTASphere::FixNVTASphere(LAMMPS *lmp, int narg, char **arg) :
+FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) :
   FixNVT(lmp, narg, arg)
 {
   if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
@@ -47,7 +47,7 @@ FixNVTASphere::FixNVTASphere(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVTASphere::init()
+void FixNVTAsphere::init()
 {
   FixNVT::init();
   dtq = 0.5 * update->dt;
@@ -55,7 +55,7 @@ void FixNVTASphere::init()
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVTASphere::initial_integrate(int vflag)
+void FixNVTAsphere::initial_integrate(int vflag)
 {
   double dtfm;
 
@@ -141,7 +141,7 @@ void FixNVTASphere::initial_integrate(int vflag)
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVTASphere::final_integrate()
+void FixNVTAsphere::final_integrate()
 {
   double dtfm;
 
@@ -199,7 +199,7 @@ void FixNVTASphere::final_integrate()
 
 /* ---------------------------------------------------------------------- */
 
-void FixNVTASphere::reset_dt()
+void FixNVTAsphere::reset_dt()
 {
   FixNVT::reset_dt();
   dtq = 0.5 * update->dt;
@@ -209,7 +209,7 @@ void FixNVTASphere::reset_dt()
    Richardson iteration to update quaternion accurately
 ------------------------------------------------------------------------- */
 
-void FixNVTASphere::richardson(double *q, double *m, double *moments)
+void FixNVTAsphere::richardson(double *q, double *m, double *moments)
 {
   // compute omega at 1/2 step from m at 1/2 step and q at 0
 
@@ -268,7 +268,7 @@ void FixNVTASphere::richardson(double *q, double *m, double *moments)
      and divide by principal moments
 ------------------------------------------------------------------------- */
 
-void FixNVTASphere::omega_from_mq(double *q, double *m, double *inertia,
+void FixNVTAsphere::omega_from_mq(double *q, double *m, double *inertia,
 				  double *w)
 {
   double rot[3][3];
@@ -287,7 +287,7 @@ void FixNVTASphere::omega_from_mq(double *q, double *m, double *inertia,
    shape = x,y,z radii in body frame
 ------------------------------------------------------------------------- */
 
-void FixNVTASphere::calculate_inertia(double mass, double *shape,
+void FixNVTAsphere::calculate_inertia(double mass, double *shape,
 				      double *inertia)
 {
   inertia[0] = mass*(shape[1]*shape[1]+shape[2]*shape[2])/5.0;

src/ASPHERE/fix_nvt_asphere.h

@@ -18,9 +18,9 @@
 
 namespace LAMMPS_NS {
 
-class FixNVTASphere : public FixNVT {
+class FixNVTAsphere : public FixNVT {
  public:
-  FixNVTASphere(class LAMMPS *, int, char **);
+  FixNVTAsphere(class LAMMPS *, int, char **);
   void init();
   void initial_integrate(int);
   void final_integrate();

src/ASPHERE/style_asphere.h

@@ -25,7 +25,7 @@ AtomStyle(ellipsoid,AtomVecEllipsoid)
 #endif
 
 #ifdef ComputeClass
-ComputeStyle(erotate/asphere,ComputeERotateASphere)
+ComputeStyle(erotate/asphere,ComputeERotateAsphere)
 ComputeStyle(temp/asphere,ComputeTempAsphere)
 #endif
 
@@ -36,9 +36,9 @@ ComputeStyle(temp/asphere,ComputeTempAsphere)
 #endif
 
 #ifdef FixClass
-FixStyle(nve/asphere,FixNVEASphere)
+FixStyle(nve/asphere,FixNVEAsphere)
-FixStyle(nvt/asphere,FixNVTASphere)
+FixStyle(nvt/asphere,FixNVTAsphere)
-FixStyle(npt/asphere,FixNPTASphere)
+FixStyle(npt/asphere,FixNPTAsphere)
 #endif
 
 #ifdef PairInclude

src/compute.cpp

@@ -60,7 +60,10 @@ 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;
   invoked = 0;
@@ -83,6 +86,7 @@ Compute::~Compute()
 {
   delete [] id;
   delete [] style;
+  delete [] id_bias;
   delete [] id_pre;
 
   memory->sfree(tlist);
@@ -112,6 +116,16 @@ 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]);
+      }
+      iarg += 2;
     } else error->all("Illegal compute_modify command");
   }
 }
@@ -163,15 +177,3 @@ int Compute::matchstep(int ntimestep)
   }
   return 0;
 }
-
-/* ----------------------------------------------------------------------
-   add back in velocity bias removed by remove_bias() to leave thermal temp
-   assume remove_bias() was previously called for this atom
-------------------------------------------------------------------------- */
-
-void Compute::restore_bias(double *v)
-{
-  v[0] += vbias[0];
-  v[1] += vbias[1];
-  v[2] += vbias[2];
-}

src/compute.h

@@ -45,8 +45,9 @@ 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 has bias routines for isolating thermal temp
+  int tempbias;       // 0/1 if Compute temp includes
-  double vbias[3];    // stored velocity bias for one atom
+                      // 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 +78,9 @@ class Compute : protected Pointers {
   virtual void unpack_reverse_comm(int, int *, double *) {}
 
   virtual void remove_bias(int, double *) {}
-  void restore_bias(double *);
+  virtual void remove_bias_all() {}
+  virtual void restore_bias(double *) {}
+  virtual void restore_bias_all() {}
 
   void addstep(int);
   int matchstep(int);

src/compute_temp.cpp

@@ -57,6 +57,13 @@ void ComputeTemp::init()
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   recount();
+
+  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];
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -76,6 +83,12 @@ double ComputeTemp::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
 
+  if (tbias) {
+    if (!(tbias->invoked & INVOKED_SCALAR))
+      double tmp = tbias->compute_scalar();
+    tbias->remove_bias_all();
+  } else tempbias = 0;
+
   double **v = atom->v;
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -96,6 +109,8 @@ 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) recount();
   scalar *= tfactor;
@@ -110,6 +125,11 @@ 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;
@@ -132,6 +152,46 @@ 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(double *v)
+{
+  if (tbias) tbias->restore_bias(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

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

src/compute_temp_com.cpp

@@ -45,7 +45,6 @@ ComputeTempCOM::ComputeTempCOM(LAMMPS *lmp, int narg, char **arg) :
   extvector = 1;
   tempflag = 1;
   tempbias = 1;
-  vbias[0] = vbias[1] = vbias[2] = 0.0;
 
   vector = new double[6];
 }
@@ -66,6 +65,12 @@ void ComputeTempCOM::init()
     fix_dof += modify->fix[i]->dof(igroup);
   recount();
   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];
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -87,6 +92,12 @@ 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);
 
@@ -111,6 +122,8 @@ 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) recount();
   scalar *= tfactor;
@@ -126,6 +139,11 @@ 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);
 
@@ -156,15 +174,74 @@ 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;
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   remove velocity bias from atom I to leave thermal velocity
+------------------------------------------------------------------------- */
 
 void ComputeTempCOM::remove_bias(int i, double *v)
 {
-  v[0] = v[0] - vbias[0];
+  if (tbias) tbias->remove_bias(i,v);
-  v[1] = v[1] - vbias[1];
+  v[0] -= vbias[0];
-  v[2] = v[2] - vbias[2];
+  v[1] -= vbias[1];
+  v[2] -= vbias[2];
+}
+
+/* ----------------------------------------------------------------------
+   remove velocity bias from all atoms to leave thermal velocity
+------------------------------------------------------------------------- */
+
+void ComputeTempCOM::remove_bias_all()
+{
+  if (tbias) tbias->remove_bias_all();
+
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      v[i][0] -= vbias[0];
+      v[i][1] -= vbias[1];
+      v[i][2] -= vbias[2];
+    }
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to atom I removed by remove_bias()
+   assume remove_bias() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempCOM::restore_bias(double *v)
+{
+  v[0] += vbias[0];
+  v[1] += vbias[1];
+  v[2] += vbias[2];
+  if (tbias) tbias->restore_bias(v);
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to all atoms removed by remove_bias_all()
+   assume remove_bias_all() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempCOM::restore_bias_all()
+{
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      v[i][0] += vbias[0];
+      v[i][1] += vbias[1];
+      v[i][2] += vbias[2];
+    }
+
+  if (tbias) tbias->restore_bias_all();
 }

src/compute_temp_com.h

@@ -25,12 +25,19 @@ class ComputeTempCOM : public Compute {
   void init();
   double compute_scalar();
   void compute_vector();
+
   void remove_bias(int, double *);
+  void remove_bias_all();
+  void restore_bias(double *);
+  void restore_bias_all();
 
  private:
   int fix_dof;
   double tfactor,masstotal;
 
+  double vbias[3];    // stored velocity bias for one atom
+  Compute *tbias;     // ptr to additional bias compute
+
   void recount();
 };
 

src/compute_temp_deform.cpp

@@ -26,6 +26,7 @@
 #include "fix_deform.h"
 #include "group.h"
 #include "comm.h"
+#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -48,6 +49,8 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
   tempflag = 1;
   tempbias = 1;
 
+  maxbias = 0;
+  vbiasall = NULL;
   vector = new double[6];
 }
 
@@ -55,6 +58,7 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeTempDeform::~ComputeTempDeform()
 {
+  memory->destroy_2d_double_array(vbiasall);
   delete [] vector;
 }
 
@@ -69,6 +73,12 @@ void ComputeTempDeform::init()
     fix_dof += modify->fix[i]->dof(igroup);
   recount();
 
+  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++)
@@ -101,6 +111,12 @@ 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;
@@ -118,35 +134,25 @@ double ComputeTempDeform::compute_scalar()
 
   double t = 0.0;
 
-  if (mass) {
+  for (int i = 0; i < nlocal; i++)
-    for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
-      if (mask[i] & groupbit) {
+      domain->x2lamda(x[i],lamda);
-	domain->x2lamda(x[i],lamda);
+      vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] + 
-	vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] + 
+	h_rate[4]*lamda[2] + h_ratelo[0];
-	  h_rate[4]*lamda[2] + h_ratelo[0];
+      vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
-	vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
+      vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
-	vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
+      vthermal[0] = v[i][0] - vstream[0];
-	vthermal[0] = v[i][0] - vstream[0];
+      vthermal[1] = v[i][1] - vstream[1];
-	vthermal[1] = v[i][1] - vstream[1];
+      vthermal[2] = v[i][2] - vstream[2];
-	vthermal[2] = v[i][2] - vstream[2];
+      if (mass)
 	t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] + 
 	      vthermal[2]*vthermal[2]) * mass[type[i]];
-      }
+      else 
-  }
-  else
-    for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit) {
-	domain->x2lamda(x[i],lamda);
-	vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] + 
-	  h_rate[4]*lamda[2] + h_ratelo[0];
-	vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
-	vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
-	vthermal[0] = v[i][0] - vstream[0];
-	vthermal[1] = v[i][1] - vstream[1];
-	vthermal[2] = v[i][2] - vstream[2];
 	t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] + 
 	      vthermal[2]*vthermal[2]) * rmass[i];
-      }
+    }
+
+  if (tbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
   scalar *= tfactor;
@@ -161,6 +167,11 @@ 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;
@@ -196,14 +207,20 @@ 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;
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   remove velocity bias from atom I to leave thermal velocity
+------------------------------------------------------------------------- */
 
 void ComputeTempDeform::remove_bias(int i, double *v)
 {
+  if (tbias) tbias->remove_bias(i,v);
+
   double lamda[3];
   double *h_rate = domain->h_rate;
   double *h_ratelo = domain->h_ratelo;
@@ -217,3 +234,81 @@ 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
+------------------------------------------------------------------------- */
+
+void ComputeTempDeform::remove_bias_all()
+{
+  if (tbias) tbias->remove_bias_all();
+
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  if (nlocal > maxbias) {
+    memory->destroy_2d_double_array(vbiasall);
+    maxbias = atom->nmax;
+    vbiasall = memory->create_2d_double_array(maxbias,3,
+					      "compute/temp:vbiasall");
+  }
+
+  double lamda[3];
+  double *h_rate = domain->h_rate;
+  double *h_ratelo = domain->h_ratelo;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      domain->x2lamda(atom->x[i],lamda);
+      vbiasall[i][0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] + 
+	h_rate[4]*lamda[2] + h_ratelo[0];
+      vbiasall[i][1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
+      vbiasall[i][2] = h_rate[2]*lamda[2] + h_ratelo[2];
+      v[i][0] -= vbiasall[i][0];
+      v[i][1] -= vbiasall[i][1];
+      v[i][2] -= vbiasall[i][2];
+    }
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to atom I removed by remove_bias()
+   assume remove_bias() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempDeform::restore_bias(double *v)
+{
+  v[0] += vbias[0];
+  v[1] += vbias[1];
+  v[2] += vbias[2];
+  if (tbias) tbias->restore_bias(v);
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to all atoms removed by remove_bias_all()
+   assume remove_bias_all() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempDeform::restore_bias_all()
+{
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      v[i][0] += vbiasall[i][0];
+      v[i][1] += vbiasall[i][1];
+      v[i][2] += vbiasall[i][2];
+    }
+
+  if (tbias) tbias->restore_bias_all();
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeTempDeform::memory_usage()
+{
+  double bytes = maxbias * sizeof(double);
+  return bytes;
+}

src/compute_temp_deform.h

@@ -25,12 +25,22 @@ class ComputeTempDeform : public Compute {
   void init();
   double compute_scalar();
   void compute_vector();
+
   void remove_bias(int, double *);
+  void remove_bias_all();
+  void restore_bias(double *);
+  void restore_bias_all();
+  double memory_usage();
 
  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 recount();
 };
 

src/compute_temp_partial.cpp

@@ -19,6 +19,7 @@
 #include "modify.h"
 #include "fix.h"
 #include "group.h"
+#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -43,8 +44,9 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
   extvector = 1;
   tempflag = 1;
   tempbias = 1;
-  vbias[0] = vbias[1] = vbias[2] = 0.0;
 
+  maxbias = 0;
+  vbiasall = NULL;
   vector = new double[6];
 }
 
@@ -52,6 +54,7 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeTempPartial::~ComputeTempPartial()
 {
+  memory->destroy_2d_double_array(vbiasall);
   delete [] vector;
 }
 
@@ -63,6 +66,12 @@ void ComputeTempPartial::init()
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   recount();
+
+  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];
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -82,6 +91,12 @@ 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;
@@ -102,7 +117,9 @@ double ComputeTempPartial::compute_scalar()
 	t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] + 
 	      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) recount();
   scalar *= tfactor;
@@ -117,6 +134,11 @@ 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;
@@ -139,14 +161,20 @@ 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;
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   remove velocity bias from atom I to leave thermal velocity
+------------------------------------------------------------------------- */
 
 void ComputeTempPartial::remove_bias(int i, double *v)
 {
+  if (tbias) tbias->remove_bias(i,v);
+
   if (!xflag) {
     vbias[0] = v[0];
     v[0] = 0.0;
@@ -160,3 +188,81 @@ void ComputeTempPartial::remove_bias(int i, double *v)
     v[2] = 0.0;
   }
 }
+
+/* ----------------------------------------------------------------------
+   remove velocity bias from all atoms to leave thermal velocity
+------------------------------------------------------------------------- */
+
+void ComputeTempPartial::remove_bias_all()
+{
+  if (tbias) tbias->remove_bias_all();
+
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  if (nlocal > maxbias) {
+    memory->destroy_2d_double_array(vbiasall);
+    maxbias = atom->nmax;
+    vbiasall = memory->create_2d_double_array(maxbias,3,
+					      "compute/temp:vbiasall");
+  }
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (!xflag) {
+	vbiasall[i][0] = v[i][0];
+	v[i][0] = 0.0;
+      }
+      if (!yflag) {
+	vbiasall[i][1] = v[i][1];
+	v[i][1] = 0.0;
+      }
+      if (!zflag) {
+	vbiasall[i][2] = v[i][2];
+	v[i][2] = 0.0;
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to atom I removed by remove_bias()
+   assume remove_bias() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempPartial::restore_bias(double *v)
+{
+  v[0] += vbias[0];
+  v[1] += vbias[1];
+  v[2] += vbias[2];
+  if (tbias) tbias->restore_bias(v);
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to all atoms removed by remove_bias_all()
+   assume remove_bias_all() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempPartial::restore_bias_all()
+{
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      v[i][0] += vbiasall[i][0];
+      v[i][1] += vbiasall[i][1];
+      v[i][2] += vbiasall[i][2];
+    }
+
+  if (tbias) tbias->restore_bias_all();
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeTempPartial::memory_usage()
+{
+  double bytes = maxbias * sizeof(double);
+  return bytes;
+}

src/compute_temp_partial.h

@@ -25,13 +25,23 @@ class ComputeTempPartial : public Compute {
   void init();
   double compute_scalar();
   void compute_vector();
+
   void remove_bias(int, double *);
+  void remove_bias_all();
+  void restore_bias(double *);
+  void restore_bias_all();
+  double memory_usage();
 
  private:
   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 recount();
 };
 

src/compute_temp_ramp.cpp

@@ -22,6 +22,7 @@
 #include "fix.h"
 #include "domain.h"
 #include "lattice.h"
+#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -108,8 +109,9 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
   extvector = 1;
   tempflag = 1;
   tempbias = 1;
-  vbias[0] = vbias[1] = vbias[2] = 0.0;
 
+  maxbias = 0;
+  vbiasall = NULL;
   vector = new double[6];
 }
 
@@ -117,6 +119,7 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeTempRamp::~ComputeTempRamp()
 {
+  memory->destroy_2d_double_array(vbiasall);
   delete [] vector;
 }
 
@@ -128,6 +131,12 @@ void ComputeTempRamp::init()
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
   recount();
+
+  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];
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -149,6 +158,12 @@ 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;
@@ -176,6 +191,8 @@ 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) recount();
   scalar *= tfactor;
@@ -191,6 +208,11 @@ 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;
@@ -223,17 +245,90 @@ 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;
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   remove velocity bias from atom I to leave thermal velocity
+------------------------------------------------------------------------- */
 
 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);
   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
+------------------------------------------------------------------------- */
+
+void ComputeTempRamp::remove_bias_all()
+{
+  if (tbias) tbias->remove_bias_all();
+
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  if (nlocal > maxbias) {
+    memory->destroy_2d_double_array(vbiasall);
+    maxbias = atom->nmax;
+    vbiasall = memory->create_2d_double_array(maxbias,3,
+					      "compute/temp:vbiasall");
+  }
+
+  double fraction;
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      fraction = (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
+      fraction = MAX(fraction,0.0);
+      fraction = MIN(fraction,1.0);
+      vbiasall[i][v_dim] = v_lo + fraction*(v_hi - v_lo);
+      v[i][v_dim] -= vbiasall[i][v_dim];
+    }
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to atom I removed by remove_bias()
+   assume remove_bias() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempRamp::restore_bias(double *v)
+{
+  v[v_dim] += vbias[v_dim];
+  if (tbias) tbias->restore_bias(v);
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to all atoms removed by remove_bias_all()
+   assume remove_bias_all() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempRamp::restore_bias_all()
+{
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  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();
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeTempRamp::memory_usage()
+{
+  double bytes = maxbias * sizeof(double);
+  return bytes;
+}

src/compute_temp_ramp.h

@@ -25,7 +25,12 @@ class ComputeTempRamp : public Compute {
   void init();
   double compute_scalar();
   void compute_vector();
+
   void remove_bias(int, double *);
+  void remove_bias_all();
+  void restore_bias(double *);
+  void restore_bias_all();
+  double memory_usage();
 
  private:
   int coord_dim;
@@ -35,6 +40,11 @@ class ComputeTempRamp : public Compute {
   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 recount();
 };
 

src/compute_temp_region.cpp

@@ -16,8 +16,10 @@
 #include "compute_temp_region.h"
 #include "atom.h"
 #include "force.h"
+#include "modify.h"
 #include "domain.h"
 #include "region.h"
+#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -42,6 +44,8 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
   tempflag = 1;
   tempbias = 1;
 
+  maxbias = 0;
+  vbiasall = NULL;
   vector = new double[6];
 }
 
@@ -49,6 +53,7 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeTempRegion::~ComputeTempRegion()
 {
+  memory->destroy_2d_double_array(vbiasall);
   delete [] vector;
 }
 
@@ -57,6 +62,12 @@ ComputeTempRegion::~ComputeTempRegion()
 void ComputeTempRegion::init()
 {
   dof = 0;
+
+  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];
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -65,6 +76,12 @@ 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;
@@ -93,6 +110,8 @@ double ComputeTempRegion::compute_scalar()
       }
   }
   
+  if (tbias) tbias->restore_bias_all();
+
   double tarray[2],tarray_all[2];
   tarray[0] = count;
   tarray[1] = t;
@@ -111,6 +130,11 @@ 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;
@@ -135,14 +159,20 @@ 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;
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   remove velocity bias from atom I to leave thermal velocity
+------------------------------------------------------------------------- */
 
 void ComputeTempRegion::remove_bias(int i, double *v)
 {
+  if (tbias) tbias->remove_bias(i,v);
+
   double *x = atom->x[i];
   if (atom->mask[i] & groupbit && 
       domain->regions[iregion]->match(x[0],x[1],x[2]))
@@ -154,3 +184,79 @@ 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
+------------------------------------------------------------------------- */
+
+void ComputeTempRegion::remove_bias_all()
+{
+  if (tbias) tbias->remove_bias_all();
+
+  double **x = atom->x;
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  if (nlocal > maxbias) {
+    memory->destroy_2d_double_array(vbiasall);
+    maxbias = atom->nmax;
+    vbiasall = memory->create_2d_double_array(maxbias,3,
+					      "compute/temp:vbiasall");
+  }
+  
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (atom->mask[i] & groupbit && 
+	  domain->regions[iregion]->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];
+	vbiasall[i][1] = v[i][1];
+	vbiasall[i][2] = v[i][2];
+	v[i][0] = v[i][1] = v[i][2] = 0.0;
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to atom I removed by remove_bias()
+   assume remove_bias() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempRegion::restore_bias(double *v)
+{
+  v[0] += vbias[0];
+  v[1] += vbias[1];
+  v[2] += vbias[2];
+  if (tbias) tbias->restore_bias(v);
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to all atoms removed by remove_bias_all()
+   assume remove_bias_all() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempRegion::restore_bias_all()
+{
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      v[i][0] += vbiasall[i][0];
+      v[i][1] += vbiasall[i][1];
+      v[i][2] += vbiasall[i][2];
+    }
+
+  if (tbias) tbias->restore_bias_all();
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeTempRegion::memory_usage()
+{
+  double bytes = maxbias * sizeof(double);
+  return bytes;
+}

src/compute_temp_region.h

@@ -25,10 +25,20 @@ class ComputeTempRegion : public Compute {
   void init();
   double compute_scalar();
   void compute_vector();
+
   void remove_bias(int, double *);
+  void remove_bias_all();
+  void restore_bias(double *);
+  void restore_bias_all();
+  double memory_usage();
 
  private:
   int iregion;
+
+  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

@@ -62,6 +62,13 @@ void ComputeTempSphere::init()
     fix_dof += modify->fix[i]->dof(igroup);
   recount();
 
+  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];
+  } else tempbias = 0;
+
   if (atom->mass) {
     double *mass = atom->mass;
     double **shape = atom->shape;
@@ -92,6 +99,12 @@ double ComputeTempSphere::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 **omega = atom->omega;
   double *mass = atom->mass;
@@ -120,6 +133,8 @@ double ComputeTempSphere::compute_scalar()
       }
   }
 
+  if (tbias) tbias->restore_bias_all();
+
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
   if (dynamic) recount();
   scalar *= tfactor;
@@ -134,6 +149,11 @@ void ComputeTempSphere::compute_vector()
 
   invoked |= INVOKED_VECTOR;
 
+  if (tbias) {
+    if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
+    tbias->remove_bias_all();
+  }
+
   double **v = atom->v;
   double **omega = atom->omega;
   double *mass = atom->mass;
@@ -186,6 +206,47 @@ void ComputeTempSphere::compute_vector()
       }
   }
 
+  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 ComputeTempSphere::remove_bias(int i, double *v)
+{
+  if (tbias) 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();
+}
+
+/* ----------------------------------------------------------------------
+   add back in velocity bias to atom I removed by remove_bias()
+   assume remove_bias() was previously called
+------------------------------------------------------------------------- */
+
+void ComputeTempSphere::restore_bias(double *v)
+{
+  if (tbias) tbias->restore_bias(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

@@ -26,11 +26,18 @@ class ComputeTempSphere : public Compute {
   double compute_scalar();
   void compute_vector();
 
+  void remove_bias(int, double *);
+  void remove_bias_all();
+  void restore_bias(double *);
+  void restore_bias_all();
+
  private:
   int fix_dof;
   double tfactor;
   double *inertia;
 
+  Compute *tbias;     // ptr to additional bias compute
+
   void recount();
 };
 

src/style_asphere.h

@@ -25,7 +25,7 @@ AtomStyle(ellipsoid,AtomVecEllipsoid)
 #endif
 
 #ifdef ComputeClass
-ComputeStyle(erotate/asphere,ComputeERotateASphere)
+ComputeStyle(erotate/asphere,ComputeERotateAsphere)
 ComputeStyle(temp/asphere,ComputeTempAsphere)
 #endif
 
@@ -36,9 +36,9 @@ ComputeStyle(temp/asphere,ComputeTempAsphere)
 #endif
 
 #ifdef FixClass
-FixStyle(nve/asphere,FixNVEASphere)
+FixStyle(nve/asphere,FixNVEAsphere)
-FixStyle(nvt/asphere,FixNVTASphere)
+FixStyle(nvt/asphere,FixNVTAsphere)
-FixStyle(npt/asphere,FixNPTASphere)
+FixStyle(npt/asphere,FixNPTAsphere)
 #endif
 
 #ifdef PairInclude