git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9437 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_temp_com.cpp

@@ -159,7 +159,7 @@ void ComputeTempCOM::compute_vector()
    remove velocity bias from atom I to leave thermal velocity
 ------------------------------------------------------------------------- */
 
-void ComputeTempCOM::remove_bias(int i, double *v)
+void ComputeTempCOM::remove_bias(int, double *v)
 {
   v[0] -= vbias[0];
   v[1] -= vbias[1];
@@ -189,7 +189,7 @@ void ComputeTempCOM::remove_bias_all()
    assume remove_bias() was previously called
 ------------------------------------------------------------------------- */
 
-void ComputeTempCOM::restore_bias(int i, double *v)
+void ComputeTempCOM::restore_bias(int, double *v)
 {
   v[0] += vbias[0];
   v[1] += vbias[1];

src/compute_temp_com.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -40,9 +40,9 @@ class ComputeTempCOM : public Compute {
  private:
   int fix_dof;
   double tfactor,masstotal;
-  double vbias[3];    // stored velocity bias for one atom
 
   void dof_compute();
+
 };
 
 }

src/compute_temp_deform.cpp

@@ -83,7 +83,8 @@ void ComputeTempDeform::init()
       break;
     }
   if (i == modify->nfix && comm->me == 0)
-    error->warning(FLERR,"Using compute temp/deform with no fix deform defined");
+    error->warning(FLERR,
+                   "Using compute temp/deform with no fix deform defined");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -281,6 +282,6 @@ void ComputeTempDeform::restore_bias_all()
 
 double ComputeTempDeform::memory_usage()
 {
-  double bytes = maxbias * sizeof(double);
+  double bytes = 3*maxbias * sizeof(double);
   return bytes;
 }

src/compute_temp_deform.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -41,9 +41,6 @@ class ComputeTempDeform : public Compute {
  protected:
   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
 
   virtual void dof_compute();
 };

src/compute_temp_partial.cpp

@@ -262,6 +262,6 @@ void ComputeTempPartial::restore_bias_all()
 
 double ComputeTempPartial::memory_usage()
 {
-  double bytes = maxbias * sizeof(double);
+  double bytes = 3*maxbias * sizeof(double);
   return bytes;
 }

src/compute_temp_profile.cpp

@@ -140,9 +140,6 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
 
   maxatom = 0;
   bin = NULL;
-
-  maxbias = 0;
-  vbiasall = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -152,7 +149,6 @@ ComputeTempProfile::~ComputeTempProfile()
   memory->destroy(vbin);
   memory->destroy(binave);
   memory->destroy(bin);
-  memory->destroy(vbiasall);
   if (outflag == TENSOR) delete [] vector;
   else {
     memory->destroy(tbin);
@@ -348,18 +344,9 @@ void ComputeTempProfile::compute_array()
 void ComputeTempProfile::remove_bias(int i, double *v)
 {
   int ibin = bin[i];
-  if (xflag) {
-    vbias[0] = binave[ibin][ivx];
-    v[0] -= vbias[0];
-  }
-  if (yflag) {
-    vbias[1] = binave[ibin][ivy];
-    v[1] -= vbias[1];
-  }
-  if (zflag) {
-    vbias[2] = binave[ibin][ivz];
-    v[2] -= vbias[2];
-  }
+  if (xflag) v[0] -= binave[ibin][ivx];
+  if (yflag) v[1] -= binave[ibin][ivy];
+  if (zflag) v[2] -= binave[ibin][ivz];
 }
 
 /* ----------------------------------------------------------------------
@@ -372,28 +359,13 @@ void ComputeTempProfile::remove_bias_all()
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
-  if (nlocal > maxbias) {
-    memory->destroy(vbiasall);
-    maxbias = atom->nmax;
-    memory->create(vbiasall,maxbias,3,"temp/profile:vbiasall");
-  }
-
   int ibin;
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
       ibin = bin[i];
-      if (xflag) {
-        vbiasall[i][0] = binave[ibin][ivx];
-        v[i][0] -= vbiasall[i][0];
-      }
-      if (yflag) {
-        vbiasall[i][1] = binave[ibin][ivy];
-        v[i][1] -= vbiasall[i][1];
-      }
-      if (zflag) {
-        vbiasall[i][2] = binave[ibin][ivz];
-        v[i][2] -= vbiasall[i][2];
-      }
+      if (xflag) v[i][0] -= binave[ibin][ivx];
+      if (yflag) v[i][1] -= binave[ibin][ivy];
+      if (zflag) v[i][2] -= binave[ibin][ivz];
     }
 }
 
@@ -404,9 +376,10 @@ void ComputeTempProfile::remove_bias_all()
 
 void ComputeTempProfile::restore_bias(int i, double *v)
 {
-  if (xflag) v[0] += vbias[0];
-  if (yflag) v[1] += vbias[1];
-  if (zflag) v[2] += vbias[2];
+  int ibin = bin[i];
+  if (xflag) v[0] += binave[ibin][ivx];
+  if (yflag) v[1] += binave[ibin][ivy];
+  if (zflag) v[2] += binave[ibin][ivz];
 }
 
 /* ----------------------------------------------------------------------
@@ -420,21 +393,14 @@ void ComputeTempProfile::restore_bias_all()
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
-  if (xflag) {
-    for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit)
-        v[i][0] += vbiasall[i][0];
-  }
-  if (yflag) {
-    for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit)
-        v[i][1] += vbiasall[i][1];
-  }
-  if (zflag) {
-    for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit)
-        v[i][2] += vbiasall[i][2];
-  }
+  int ibin;
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      ibin = bin[i];
+      if (xflag) v[i][0] += binave[ibin][ivx];
+      if (yflag) v[i][1] += binave[ibin][ivy];
+      if (zflag) v[i][2] += binave[ibin][ivz];
+    }
 }
 
 /* ----------------------------------------------------------------------
@@ -563,8 +529,7 @@ void ComputeTempProfile::bin_assign()
 
 double ComputeTempProfile::memory_usage()
 {
-  double bytes = maxbias * sizeof(double);
-  bytes += maxatom * sizeof(int);
+  double bytes = maxatom * sizeof(int);
   bytes += nbins*(ncount+1) * sizeof(double);
   return bytes;
 }

src/compute_temp_ramp.cpp

@@ -294,6 +294,6 @@ void ComputeTempRamp::restore_bias_all()
 
 double ComputeTempRamp::memory_usage()
 {
-  double bytes = maxbias * sizeof(double);
+  double bytes = 3*maxbias * sizeof(double);
   return bytes;
 }

src/compute_temp_region.cpp

@@ -245,6 +245,6 @@ void ComputeTempRegion::restore_bias_all()
 
 double ComputeTempRegion::memory_usage()
 {
-  double bytes = maxbias * sizeof(double);
+  double bytes = 3*maxbias * sizeof(double);
   return bytes;
 }

src/verlet.cpp

@@ -243,6 +243,7 @@ void Verlet::run(int n)
       comm->forward_comm();
       timer->stamp(TIME_COMM);
     } else {
+      printf("RENEIGH %ld\n",ntimestep);
       if (n_pre_exchange) modify->pre_exchange();
       if (triclinic) domain->x2lamda(atom->nlocal);
       domain->pbc();