git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3419 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/fix_npt_asphere.cpp

@@ -119,6 +119,12 @@ void FixNPTAsphere::initial_integrate(int vflag)
   }
   factor_rotate = exp(-dthalf*eta_dot);
 
+  // update v of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
+
   double **x = atom->x;
   double **v = atom->v;
   double **f = atom->f;
@@ -140,7 +146,8 @@ void FixNPTAsphere::initial_integrate(int vflag)
 	v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
       }
     }
-  } else if (which == BIAS) {
+  } else {
+    double tmp = temperature->compute_scalar();
     for (i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
 	temperature->remove_bias(i,v[i]);
@@ -157,7 +164,7 @@ void FixNPTAsphere::initial_integrate(int vflag)
 
   remap(0);
 
-  // x update by full step only for atoms in group
+  // update x by full step for atoms in group
 
   for (i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
@@ -171,7 +178,7 @@ void FixNPTAsphere::initial_integrate(int vflag)
 
   dtq = 0.5 * dtv;
 
-  // update angular momentum by 1/2 step for all particles
+  // update angular momentum by 1/2 step for atoms in group
   // update quaternion a full step via Richardson iteration
   // returns new normalized quaternion
 
@@ -199,7 +206,11 @@ void FixNPTAsphere::final_integrate()
   int i;
   double dtfm;
 
-  // update v of only atoms in group
+  // update v,angmom of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
 
   double **v = atom->v;
   double **f = atom->f;
@@ -223,7 +234,8 @@ void FixNPTAsphere::final_integrate()
 	angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * factor_rotate;
       }
     }
-  } else if (which == BIAS) {
+  } else {
+    double tmp = temperature->compute_scalar();
     for (i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
 	temperature->remove_bias(i,v[i]);

src/ASPHERE/fix_nvt_asphere.cpp

@@ -101,6 +101,12 @@ void FixNVTAsphere::initial_integrate(int vflag)
   eta += dtv*eta_dot;
   factor = exp(-dthalf*eta_dot);
 
+  // update v,x,angmom of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
+
   double **x = atom->x;
   double **v = atom->v;
   double **f = atom->f;
@@ -140,7 +146,8 @@ void FixNVTAsphere::initial_integrate(int vflag)
       }
     }
 
-  } else if (which == BIAS) {
+  } else {
+    double tmp = temperature->compute_scalar();
     for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
 	temperature->remove_bias(i,v[i]);
@@ -173,6 +180,12 @@ void FixNVTAsphere::final_integrate()
 {
   double dtfm;
 
+  // update v,angmom of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
+
   double **v = atom->v;
   double **f = atom->f;
   double **angmom = atom->angmom;
@@ -196,7 +209,8 @@ void FixNVTAsphere::final_integrate()
       }
     }
 
-  } else if (which == BIAS) {
+  } else {
+    double tmp = temperature->compute_scalar();
     for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
 	temperature->remove_bias(i,v[i]);

src/fix_langevin.cpp

@@ -195,7 +195,12 @@ void FixLangevin::post_force_no_tally()
   double t_target = t_start + delta * (t_stop-t_start);
   double tsqrt = sqrt(t_target);
 
-  // apply damping and thermostat to appropriate atoms
+  // apply damping and thermostat to atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   test v = 0 since some computes mask non-participating atoms via v = 0
+  //   and added force has extra term not multiplied by v = 0
 
   if (rmass) {
     double boltz = force->boltz;
@@ -216,12 +221,8 @@ void FixLangevin::post_force_no_tally()
 	}
       }
 
-    // invoke temperature since some computes require it to remove bias
-    // test v = 0 since some computes mask non-participating atoms via v = 0
-
     } else if (which == BIAS) {
       double tmp = temperature->compute_scalar();
-      
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  gamma1 = -rmass[i] / t_period / ftm2v;
@@ -252,12 +253,8 @@ void FixLangevin::post_force_no_tally()
 	}
       }
 
-    // invoke temperature since some computes require it to remove bias
-    // test v = 0 since some computes mask non-participating atoms via v = 0
-
     } else if (which == BIAS) {
       double tmp = temperature->compute_scalar();
-      
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  gamma1 = gfactor1[type[i]];
@@ -303,6 +300,11 @@ void FixLangevin::post_force_tally()
   double tsqrt = sqrt(t_target);
 
   // apply damping and thermostat to appropriate atoms
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   test v = 0 since some computes mask non-participating atoms via v = 0
+  //   and added force has extra term not multiplied by v = 0
 
   if (rmass) {
     double boltz = force->boltz;
@@ -326,12 +328,8 @@ void FixLangevin::post_force_tally()
 	}
       }
 
-    // invoke temperature since some computes require it to remove bias
-    // test v = 0 since some computes mask non-participating atoms via v = 0
-
     } else if (which == BIAS) {
       double tmp = temperature->compute_scalar();
-      
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  gamma1 = -rmass[i] / t_period / ftm2v;
@@ -368,12 +366,8 @@ void FixLangevin::post_force_tally()
 	}
       }
 
-    // invoke temperature since some computes require it to remove bias
-    // test v = 0 since some computes mask non-participating atoms via v = 0
-
     } else if (which == BIAS) {
       double tmp = temperature->compute_scalar();
-      
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  gamma1 = gfactor1[type[i]];

src/fix_npt.cpp

@@ -388,6 +388,12 @@ void FixNPT::initial_integrate(int vflag)
     dilation[i] = exp(dthalf*omega_dot[i]);
   }
 
+  // update v and x of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
+
   double **x = atom->x;
   double **v = atom->v;
   double **f = atom->f;
@@ -408,7 +414,8 @@ void FixNPT::initial_integrate(int vflag)
 	  v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -431,7 +438,8 @@ void FixNPT::initial_integrate(int vflag)
 	  v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -449,7 +457,7 @@ void FixNPT::initial_integrate(int vflag)
 
   remap(0);
 
-  // x update by full step only for atoms in group
+  // update x by full step for atoms in group
 
   for (i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
@@ -475,6 +483,12 @@ void FixNPT::final_integrate()
   int i;
   double dtfm;
 
+  // update v of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
+
   double **v = atom->v;
   double **f = atom->f;
   double *rmass = atom->rmass;
@@ -494,7 +508,8 @@ void FixNPT::final_integrate()
 	  v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -517,7 +532,8 @@ void FixNPT::final_integrate()
 	  v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -602,7 +618,7 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
 
   // outermost level - update eta_dot and omega_dot, apply to v, remap box
   // all other levels - NVE update of v
-  // x,v updates only performed for atoms in group
+  // x,v updates performed for atoms in group
 
   if (ilevel == nlevels_respa-1) {
 
@@ -635,7 +651,7 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
       dilation[i] = exp(dthalf*omega_dot[i]);
     }
 
-    // v update only for atoms in group
+    // update v for atoms in group
 
     if (rmass) {
       for (int i = 0; i < nlocal; i++) {
@@ -663,57 +679,31 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
 
   } else {
 
-    // v update only for atoms in group
+    // update v for atoms in group
 
     if (rmass) {
-      if (which == NOBIAS) {
+      for (int i = 0; i < nlocal; i++) {
-	for (int i = 0; i < nlocal; i++) {
+	if (mask[i] & groupbit) {
-	  if (mask[i] & groupbit) {
+	  dtfm = dtf / rmass[i];
-	    dtfm = dtf / rmass[i];
+	  v[i][0] += dtfm*f[i][0];
-	    v[i][0] += dtfm*f[i][0];
+	  v[i][1] += dtfm*f[i][1];
-	    v[i][1] += dtfm*f[i][1];
+	  v[i][2] += dtfm*f[i][2];
-	    v[i][2] += dtfm*f[i][2];
-	  }
-	}
-      } else if (which == BIAS) {
-	for (int i = 0; i < nlocal; i++) {
-	  if (mask[i] & groupbit) {
-	    temperature->remove_bias(i,v[i]);
-	    dtfm = dtf / rmass[i];
-	    v[i][0] += dtfm*f[i][0];
-	    v[i][1] += dtfm*f[i][1];
-	    v[i][2] += dtfm*f[i][2];
-	    temperature->restore_bias(i,v[i]);
-	  }
 	}
       }
 
     } else {
-      if (which == NOBIAS) {
+      for (int i = 0; i < nlocal; i++) {
-	for (int i = 0; i < nlocal; i++) {
+	if (mask[i] & groupbit) {
-	  if (mask[i] & groupbit) {
+	  dtfm = dtf / mass[type[i]];
-	    dtfm = dtf / mass[type[i]];
+	  v[i][0] += dtfm*f[i][0];
-	    v[i][0] += dtfm*f[i][0];
+	  v[i][1] += dtfm*f[i][1];
-	    v[i][1] += dtfm*f[i][1];
+	  v[i][2] += dtfm*f[i][2];
-	    v[i][2] += dtfm*f[i][2];
-	  }
-	}
-      } else if (which == BIAS) {
-	for (int i = 0; i < nlocal; i++) {
-	  if (mask[i] & groupbit) {
-	    temperature->remove_bias(i,v[i]);
-	    dtfm = dtf / mass[type[i]];
-	    v[i][0] += dtfm*f[i][0];
-	    v[i][1] += dtfm*f[i][1];
-	    v[i][2] += dtfm*f[i][2];
-	    temperature->restore_bias(i,v[i]);
-	  }
 	}
       }
     }
   }
 
-  // innermost level - also update x only for atoms in group
+  // innermost level - also update x for atoms in group
 
   if (ilevel == 0) {
     for (int i = 0; i < nlocal; i++) {
@@ -740,12 +730,12 @@ void FixNPT::final_integrate_respa(int ilevel)
   // outermost level - update eta_dot and omega_dot,
   //   apply to v via final_integrate()
   // all other levels - NVE update of v
-  // v update only performed for atoms in group
+  // update v for atoms in group
 
   if (ilevel == nlevels_respa-1) final_integrate();
   else {
 
-    // v update only for atoms in group
+    // update v for atoms in group
 
     double **v = atom->v;
     double **f = atom->f;
@@ -757,48 +747,22 @@ void FixNPT::final_integrate_respa(int ilevel)
     if (igroup == atom->firstgroup) nlocal = atom->nfirst;
 
     if (rmass) {
-      if (which == NOBIAS) {
+      for (int i = 0; i < nlocal; i++) {
-	for (int i = 0; i < nlocal; i++) {
+	if (mask[i] & groupbit) {
-	  if (mask[i] & groupbit) {
+	  dtfm = dtf / rmass[i];
-	    dtfm = dtf / rmass[i];
+	  v[i][0] += dtfm*f[i][0];
-	    v[i][0] += dtfm*f[i][0];
+	  v[i][1] += dtfm*f[i][1];
-	    v[i][1] += dtfm*f[i][1];
+	  v[i][2] += dtfm*f[i][2];
-	    v[i][2] += dtfm*f[i][2];
-	  }
-	}
-      } else if (which == BIAS) {
-	for (int i = 0; i < nlocal; i++) {
-	  if (mask[i] & groupbit) {
-	    temperature->remove_bias(i,v[i]);
-	    dtfm = dtf / rmass[i];
-	    v[i][0] += dtfm*f[i][0];
-	    v[i][1] += dtfm*f[i][1];
-	    v[i][2] += dtfm*f[i][2];
-	    temperature->restore_bias(i,v[i]);
-	  }
 	}
       }
 
     } else {
-      if (which == NOBIAS) {
+      for (int i = 0; i < nlocal; i++) {
-	for (int i = 0; i < nlocal; i++) {
+	if (mask[i] & groupbit) {
-	  if (mask[i] & groupbit) {
+	  dtfm = dtf / mass[type[i]];
-	    dtfm = dtf / mass[type[i]];
+	  v[i][0] += dtfm*f[i][0];
-	    v[i][0] += dtfm*f[i][0];
+	  v[i][1] += dtfm*f[i][1];
-	    v[i][1] += dtfm*f[i][1];
+	  v[i][2] += dtfm*f[i][2];
-	    v[i][2] += dtfm*f[i][2];
-	  }
-	}
-      } else if (which == BIAS) {
-	for (int i = 0; i < nlocal; i++) {
-	  if (mask[i] & groupbit) {
-	    temperature->remove_bias(i,v[i]);
-	    dtfm = dtf / mass[type[i]];
-	    v[i][0] += dtfm*f[i][0];
-	    v[i][1] += dtfm*f[i][1];
-	    v[i][2] += dtfm*f[i][2];
-	    temperature->restore_bias(i,v[i]);
-	  }
 	}
       }
     }

src/fix_npt_sphere.cpp

@@ -122,6 +122,12 @@ void FixNPTSphere::initial_integrate(int vflag)
   }
   factor_rotate = exp(-dthalf*eta_dot);
 
+  // update v of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
+
   double **x = atom->x;
   double **v = atom->v;
   double **f = atom->f;
@@ -146,7 +152,8 @@ void FixNPTSphere::initial_integrate(int vflag)
 	  v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -169,7 +176,8 @@ void FixNPTSphere::initial_integrate(int vflag)
 	  v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -187,7 +195,7 @@ void FixNPTSphere::initial_integrate(int vflag)
 
   remap(0);
 
-  // x update by full step only for atoms in group
+  // update x by full step for atoms in group
 
   for (i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
@@ -282,9 +290,13 @@ void FixNPTSphere::final_integrate()
 
   double dtfrotate = dtf / INERTIA;
 
-  // update v,omega for all particles
+  // update v,omega of atoms in group
   // d_omega/dt = torque / inertia
   // 8 cases depending on radius vs shape, rmass vs mass, bias vs nobias
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
 
   if (radius) {
     if (rmass) {
@@ -305,7 +317,8 @@ void FixNPTSphere::final_integrate()
 	      factor_rotate;
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    temperature->remove_bias(i,v[i]);
@@ -345,8 +358,9 @@ void FixNPTSphere::final_integrate()
 	      factor_rotate;
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
 	for (i = 0; i < nlocal; i++) {
+	  double tmp = temperature->compute_scalar();
 	  if (mask[i] & groupbit) {
 	    itype = type[i];
 	    temperature->remove_bias(i,v[i]);
@@ -388,7 +402,8 @@ void FixNPTSphere::final_integrate()
 	      factor_rotate;
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    itype = type[i];
@@ -430,7 +445,8 @@ void FixNPTSphere::final_integrate()
 	      factor_rotate;
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    itype = type[i];

src/fix_nve.cpp

@@ -64,6 +64,8 @@ void FixNVE::initial_integrate(int vflag)
 {
   double dtfm;
 
+  // update v and x of atoms in group
+
   double **x = atom->x;
   double **v = atom->v;
   double **f = atom->f;
@@ -108,6 +110,8 @@ void FixNVE::final_integrate()
 {
   double dtfm;
 
+  // update v of atoms in group
+
   double **v = atom->v;
   double **f = atom->f;
   double *mass = atom->mass;

src/fix_nvt.cpp

@@ -200,7 +200,11 @@ void FixNVT::initial_integrate(int vflag)
 
   factor = exp(-dthalf*eta_dot);
 
-  // update v and x of only atoms in group
+  // update v and x of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
 
   double **x = atom->x;
   double **v = atom->v;
@@ -223,7 +227,8 @@ void FixNVT::initial_integrate(int vflag)
 	  x[i][2] += dtv * v[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -252,7 +257,8 @@ void FixNVT::initial_integrate(int vflag)
 	  x[i][2] += dtv * v[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -284,7 +290,11 @@ void FixNVT::final_integrate()
 {
   double dtfm;
 
-  // update v of only atoms in group
+  // update v of atoms in group
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
 
   double **v = atom->v;
   double **f = atom->f;
@@ -307,7 +317,8 @@ void FixNVT::final_integrate()
 	  v[i][2] = v[i][2]*factor + dtfm*f[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -330,7 +341,8 @@ void FixNVT::final_integrate()
 	  v[i][2] = v[i][2]*factor + dtfm*f[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -369,19 +381,20 @@ void FixNVT::final_integrate()
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    dtfm = dtf / mass[type[i]];
-	    v[i][0] = v[i][0] * factor;
+	    v[i][0] *= factor;
-	    v[i][1] = v[i][1] * factor;
+	    v[i][1] *= factor;
-	    v[i][2] = v[i][2] * factor;
+	    v[i][2] *= factor;
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    temperature->remove_bias(i,v[i]);
 	    dtfm = dtf / mass[type[i]];
-	    v[i][0] = v[i][0] * factor;
+	    v[i][0] *= factor;
-	    v[i][1] = v[i][1] * factor;
+	    v[i][1] *= factor;
-	    v[i][2] = v[i][2] * factor;
+	    v[i][2] *= factor;
 	    temperature->restore_bias(i,v[i]);
 	  }
 	}
@@ -392,19 +405,20 @@ void FixNVT::final_integrate()
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    dtfm = dtf / mass[type[i]];
-	    v[i][0] = v[i][0] * factor;
+	    v[i][0] *= factor;
-	    v[i][1] = v[i][1] * factor;
+	    v[i][1] *= factor;
-	    v[i][2] = v[i][2] * factor;
+	    v[i][2] *= factor;
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    temperature->remove_bias(i,v[i]);
 	    dtfm = dtf / mass[type[i]];
-	    v[i][0] = v[i][0] * factor;
+	    v[i][0] *= factor;
-	    v[i][1] = v[i][1] * factor;
+	    v[i][1] *= factor;
-	    v[i][2] = v[i][2] * factor;
+	    v[i][2] *= factor;
 	    temperature->restore_bias(i,v[i]);
 	  }
 	}
@@ -492,7 +506,8 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
 	  v[i][2] = v[i][2]*factor + dtfm*f[i][2];
 	}
       }
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);
@@ -516,7 +531,8 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
 	}
       }
 
-    } else if (which == BIAS) {
+    } else {
+      double tmp = temperature->compute_scalar();
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
 	  temperature->remove_bias(i,v[i]);

src/fix_nvt_sllod.cpp

@@ -35,7 +35,6 @@
 using namespace LAMMPS_NS;
 
 enum{NO_REMAP,X_REMAP,V_REMAP};                   // same as fix_deform.cpp
-enum{NOBIAS,BIAS};
 
 /* ---------------------------------------------------------------------- */
 
@@ -51,13 +50,17 @@ void FixNVTSlodd::init()
   if (!temperature->tempbias)
     error->all("Temperature for fix nvt/sllod does not have a bias");
 
+  nondeformbias = 0;
+  if (strcmp(temperature->style,"temp/deform") != 0) nondeformbias = 1;
+
   // check fix deform remap settings
 
   int i;
   for (i = 0; i < modify->nfix; i++)
     if (strcmp(modify->fix[i]->style,"deform") == 0) {
       if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
-	error->all("Using fix nvt/sllod with inconsistent fix deform remap option");
+	error->all("Using fix nvt/sllod with inconsistent fix deform "
+		   "remap option");
       break;
     }
   if (i == modify->nfix)
@@ -82,10 +85,15 @@ void FixNVTSlodd::initial_integrate(int vflag)
   eta += dtv*eta_dot;
   factor = exp(-dthalf*eta_dot);
 
-  // update v and x of only atoms in group
+  // update v and x of atoms in group
   // remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
   // thermostat thermal velocity only
   // vdelu = SLLOD correction = Hrate*Hinv*vthermal
+  // for non temp/deform BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+
+  if (nondeformbias) double tmp = temperature->compute_scalar();
 
   double **x = atom->x;
   double **v = atom->v;
@@ -124,10 +132,16 @@ void FixNVTSlodd::final_integrate()
 {
   double dtfm;
 
-  // update v of only atoms in group
+  // update v of atoms in group
   // remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
   // thermostat thermal velocity only
   // vdelu = SLLOD correction = Hrate*Hinv*vthermal
+  // for non temp/deform BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
+
+  if (nondeformbias) double tmp = temperature->compute_scalar();
 
   double **v = atom->v;
   double **f = atom->f;
@@ -207,7 +221,9 @@ void FixNVTSlodd::initial_integrate_respa(int vflag, int ilevel, int flag)
     factor = exp(-dthalf*eta_dot);
   } else factor = 1.0;
 
-  // update v of only atoms in group
+  // update v of atoms in group
+
+  if (nondeformbias) double tmp = temperature->compute_scalar();
 
   double h_two[6],vdelu[3];
   MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);

src/fix_nvt_sllod.h

@@ -25,6 +25,9 @@ class FixNVTSlodd : public FixNVT {
   void initial_integrate(int);
   void final_integrate();
   void initial_integrate_respa(int, int, int);
+
+ private:
+  int nondeformbias;
 };
 
 }

src/fix_nvt_sphere.cpp

@@ -125,9 +125,13 @@ void FixNVTSphere::initial_integrate(int vflag)
 
   double dtfrotate = dtf / INERTIA;
 
-  // update v,x,omega for all particles
+  // update v,x,omega of atoms in group
   // d_omega/dt = torque / inertia
   // 8 cases depending on radius vs shape, rmass vs mass, bias vs nobias
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
 
   if (radius) {
     if (rmass) {
@@ -148,7 +152,8 @@ void FixNVTSphere::initial_integrate(int vflag)
 	    omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    temperature->remove_bias(i,v[i]);
@@ -188,7 +193,8 @@ void FixNVTSphere::initial_integrate(int vflag)
 	    omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    itype = type[i];
@@ -231,7 +237,8 @@ void FixNVTSphere::initial_integrate(int vflag)
 	    omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    itype = type[i];
@@ -273,7 +280,8 @@ void FixNVTSphere::initial_integrate(int vflag)
 	    omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];
 	  }
 	}
-      } else if (which == BIAS) {
+      } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    itype = type[i];
@@ -306,7 +314,13 @@ void FixNVTSphere::final_integrate()
   int itype;
   double dtfm,dtirotate;
 
-  // update v of only atoms in group
+  // update v,omega of atoms in group
+  // d_omega/dt = torque / inertia
+  // 8 cases depending on radius vs shape, rmass vs mass, bias vs nobias
+  // for BIAS:
+  //   calculate temperature since some computes require temp
+  //   computed on current nlocal atoms to remove bias
+  //   OK to not test returned v = 0, since factor is multiplied by v
 
   double **v = atom->v;
   double **f = atom->f;
@@ -325,10 +339,6 @@ void FixNVTSphere::final_integrate()
 
   double dtfrotate = dtf / INERTIA;
 
-  // update v,omega for all particles
-  // d_omega/dt = torque / inertia
-  // 8 cases depending on radius vs shape, rmass vs mass, bias vs nobias
-
   if (radius) {
     if (rmass) {
       if (which == NOBIAS) {
@@ -346,6 +356,7 @@ void FixNVTSphere::final_integrate()
 	  }
 	}
       } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    temperature->remove_bias(i,v[i]);
@@ -380,6 +391,7 @@ void FixNVTSphere::final_integrate()
 	  }
 	}
       } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    itype = type[i];
@@ -417,6 +429,7 @@ void FixNVTSphere::final_integrate()
 	  }
 	}
       } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    itype = type[i];
@@ -453,6 +466,7 @@ void FixNVTSphere::final_integrate()
 	  }
 	}
       } else {
+	double tmp = temperature->compute_scalar();
 	for (int i = 0; i < nlocal; i++) {
 	  if (mask[i] & groupbit) {
 	    itype = type[i];

src/fix_temp_berendsen.cpp

@@ -109,6 +109,9 @@ void FixTempBerendsen::end_of_step()
   t_target = t_start + delta * (t_stop-t_start);
 
   // rescale velocities by lamda
+  // for BIAS:
+  //   temperature is current, so do not need to re-compute
+  //   OK to not test returned v = 0, since lamda is multiplied by v
 
   double lamda = sqrt(1.0 + update->dt/t_period*(t_target/t_current - 1.0));
 
@@ -124,7 +127,7 @@ void FixTempBerendsen::end_of_step()
 	v[i][2] *= lamda;
       }
     }
-  } else if (which == BIAS) {
+  } else {
     for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
 	temperature->remove_bias(i,v[i]);

src/fix_temp_rescale.cpp

@@ -114,6 +114,9 @@ void FixTempRescale::end_of_step()
   double t_target = t_start + delta * (t_stop-t_start);
 
   // rescale velocity of appropriate atoms if outside window
+  // for BIAS:
+  //   temperature is current, so do not need to re-compute
+  //   OK to not test returned v = 0, since factor is multiplied by v
 
   if (fabs(t_current-t_target) > t_window) {
     t_target = t_current - fraction*(t_current-t_target);
@@ -133,8 +136,7 @@ void FixTempRescale::end_of_step()
 	  v[i][2] *= factor;
 	}
       }
-
+    } else {
-    } else if (which == BIAS) {
       energy += (t_current-t_target) * efactor;
       for (int i = 0; i < nlocal; i++) {
 	if (mask[i] & groupbit) {
@@ -178,7 +180,6 @@ int FixTempRescale::modify_param(int narg, char **arg)
   return 0;
 }
 
-
 /* ---------------------------------------------------------------------- */
 
 void FixTempRescale::reset_target(double t_new)

src/lammps.cpp

@@ -41,6 +41,7 @@ using namespace LAMMPS_NS;
 
 LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
 {
+  printf("AAA\n");
   memory = new Memory(this);
   error = new Error(this);
   universe = new Universe(this,communicator);