git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1655 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/compute_temp_asphere.cpp

@@ -68,7 +68,7 @@ void ComputeTempAsphere::init()
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
-  recount();
+  dof_compute();
 
   tempbias = 0;
   tbias = NULL;
@@ -84,11 +84,12 @@ void ComputeTempAsphere::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeTempAsphere::recount()
+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
@@ -181,7 +182,7 @@ double ComputeTempAsphere::compute_scalar()
   if (tbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic) recount();
+  if (dynamic || tbias) dof_compute();
   scalar *= tfactor;
   return scalar;
 }

src/ASPHERE/compute_temp_asphere.h

@@ -38,7 +38,7 @@ class ComputeTempAsphere : public Compute {
 
   Compute *tbias;     // ptr to additional bias compute
 
-  void recount();
+  void dof_compute();
   void calculate_inertia();
 };
 

src/compute.cpp

@@ -17,6 +17,7 @@
 #include "ctype.h"
 #include "comm.h"
 #include "compute.h"
+#include "domain.h"
 #include "group.h"
 #include "modify.h"
 #include "lattice.h"
@@ -71,7 +72,9 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   comm_forward = comm_reverse = 0;
 
   // set modify defaults
+  // should change 3 to dimension
 
+  //extra_dof = domain->dimension;
   extra_dof = 3;
   dynamic = 0;
 

src/compute.h

@@ -77,6 +77,7 @@ 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 void remove_bias(int, double *) {}
   virtual void remove_bias_all() {}
   virtual void restore_bias(int, double *) {}

src/compute_temp.cpp

@@ -56,7 +56,7 @@ void ComputeTemp::init()
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
-  recount();
+  dof_compute();
 
   tempbias = 0;
   tbias = NULL;
@@ -70,12 +70,13 @@ void ComputeTemp::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeTemp::recount()
+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) tfactor = force->mvv2e / (dof * force->boltz);
+  if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
 }
 
@@ -89,7 +90,7 @@ double ComputeTemp::compute_scalar()
     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;
@@ -114,7 +115,7 @@ double ComputeTemp::compute_scalar()
   if (tbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic) recount();
+  if (dynamic || tbias) dof_compute();
   scalar *= tfactor;
   return scalar;
 }

src/compute_temp.h

@@ -37,7 +37,7 @@ class ComputeTemp : public Compute {
 
   Compute *tbias;     // ptr to additional bias compute
 
-  void recount();
+  void dof_compute();
 };
 
 }

src/compute_temp_com.cpp

@@ -63,7 +63,7 @@ void ComputeTempCOM::init()
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
-  recount();
+  dof_compute();
   masstotal = group->mass(igroup);
 
   tbias = NULL;
@@ -76,10 +76,11 @@ void ComputeTempCOM::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeTempCOM::recount()
+void ComputeTempCOM::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;
@@ -126,7 +127,7 @@ double ComputeTempCOM::compute_scalar()
   if (tbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic) recount();
+  if (dynamic || tbias) dof_compute();
   scalar *= tfactor;
   return scalar;
 }

src/compute_temp_com.h

@@ -38,7 +38,7 @@ class ComputeTempCOM : public Compute {
   double vbias[3];    // stored velocity bias for one atom
   Compute *tbias;     // ptr to additional bias compute
 
-  void recount();
+  void dof_compute();
 };
 
 }

src/compute_temp_deform.cpp

@@ -71,7 +71,7 @@ void ComputeTempDeform::init()
   fix_dof = 0;
   for (i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
-  recount();
+  dof_compute();
 
   tbias = NULL;
   if (id_bias) {
@@ -95,10 +95,11 @@ void ComputeTempDeform::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeTempDeform::recount()
+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;
@@ -156,6 +157,7 @@ double ComputeTempDeform::compute_scalar()
   if (tbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
+  if (dynamic || tbias) dof_compute();
   scalar *= tfactor;
   return scalar;
 }

src/compute_temp_deform.h

@@ -41,7 +41,7 @@ class ComputeTempDeform : public Compute {
   int maxbias;        // size of vbiasall array
   Compute *tbias;     // ptr to additional bias compute
 
-  void recount();
+  void dof_compute();
 };
 
 }

src/compute_temp_partial.cpp

@@ -16,6 +16,7 @@
 #include "compute_temp_partial.h"
 #include "atom.h"
 #include "force.h"
+#include "domain.h"
 #include "modify.h"
 #include "fix.h"
 #include "group.h"
@@ -65,7 +66,7 @@ void ComputeTempPartial::init()
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
-  recount();
+  dof_compute();
 
   tbias = NULL;
   if (id_bias) {
@@ -77,10 +78,11 @@ void ComputeTempPartial::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeTempPartial::recount()
+void ComputeTempPartial::dof_compute()
 {
   double natoms = group->count(igroup);
   dof = (xflag+yflag+zflag) * 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;
@@ -88,6 +90,18 @@ void ComputeTempPartial::recount()
 
 /* ---------------------------------------------------------------------- */
 
+double ComputeTempPartial::dof_remove(double &natoms)
+{
+  double rmdof = 0.0;
+  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;
+}
+
+/* ---------------------------------------------------------------------- */
+
 double ComputeTempPartial::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
@@ -122,7 +136,7 @@ double ComputeTempPartial::compute_scalar()
   if (tbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic) recount();
+  if (dynamic || tbias) dof_compute();
   scalar *= tfactor;
   return scalar;
 }

src/compute_temp_partial.h

@@ -26,6 +26,7 @@ class ComputeTempPartial : public Compute {
   double compute_scalar();
   void compute_vector();
 
+  double dof_remove(double &);
   void remove_bias(int, double *);
   void remove_bias_all();
   void restore_bias(int, double *);
@@ -42,7 +43,7 @@ class ComputeTempPartial : public Compute {
   int maxbias;        // size of vbiasall array
   Compute *tbias;     // ptr to additional bias compute
 
-  void recount();
+  void dof_compute();
 };
 
 }

src/compute_temp_ramp.cpp

@@ -130,7 +130,7 @@ void ComputeTempRamp::init()
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
-  recount();
+  dof_compute();
 
   tbias = NULL;
   if (id_bias) {
@@ -142,10 +142,11 @@ void ComputeTempRamp::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeTempRamp::recount()
+void ComputeTempRamp::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;
@@ -195,7 +196,7 @@ double ComputeTempRamp::compute_scalar()
   if (tbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic) recount();
+  if (dynamic || tbias) dof_compute();
   scalar *= tfactor;
   return scalar;
 }

src/compute_temp_ramp.h

@@ -45,7 +45,7 @@ class ComputeTempRamp : public Compute {
   int maxbias;        // size of vbiasall array
   Compute *tbias;     // ptr to additional bias compute
 
-  void recount();
+  void dof_compute();
 };
 
 }

src/compute_temp_region.cpp

@@ -73,6 +73,17 @@ void ComputeTempRegion::init()
 
 /* ---------------------------------------------------------------------- */
 
+double ComputeTempRegion::dof_remove(double &natoms)
+{
+  double rmdof = 0.0;
+  if (tbias) rmdof = tbias->dof_remove(natoms);
+  natoms -= natoms_region;
+  rmdof += domain->dimension * natoms;
+  return rmdof;
+}
+
+/* ---------------------------------------------------------------------- */
+
 double ComputeTempRegion::compute_scalar()
 {
   invoked |= INVOKED_SCALAR;
@@ -117,7 +128,8 @@ double ComputeTempRegion::compute_scalar()
   tarray[0] = count;
   tarray[1] = t;
   MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
-  dof = domain->dimension * tarray_all[0] - extra_dof;
+  natoms_region = tarray_all[0];
+  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;

src/compute_temp_region.h

@@ -26,6 +26,7 @@ class ComputeTempRegion : public Compute {
   double compute_scalar();
   void compute_vector();
 
+  double dof_remove(double &);
   void remove_bias(int, double *);
   void remove_bias_all();
   void restore_bias(int, double *);
@@ -34,6 +35,7 @@ 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

src/compute_temp_sphere.cpp

@@ -60,7 +60,7 @@ void ComputeTempSphere::init()
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);
-  recount();
+  dof_compute();
 
   tempbias = 0;
   tbias = NULL;
@@ -85,11 +85,12 @@ void ComputeTempSphere::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeTempSphere::recount()
+void ComputeTempSphere::dof_compute()
 {
   double natoms = group->count(igroup);
   if (domain->dimension == 3) dof = 6.0 * natoms;
   else dof = 3.0 * 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;
@@ -138,7 +139,7 @@ double ComputeTempSphere::compute_scalar()
   if (tbias) tbias->restore_bias_all();
 
   MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
-  if (dynamic) recount();
+  if (dynamic || tbias) dof_compute();
   scalar *= tfactor;
   return scalar;
 }

src/compute_temp_sphere.h

@@ -38,7 +38,7 @@ class ComputeTempSphere : public Compute {
 
   Compute *tbias;     // ptr to additional bias compute
 
-  void recount();
+  void dof_compute();
 };
 
 }