git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12693 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/compute_temp_asphere.cpp

@@ -127,6 +127,8 @@ void ComputeTempAsphere::init()
 
 void ComputeTempAsphere::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/USER-CUDA/compute_temp_cuda.cpp

@@ -89,6 +89,9 @@ ComputeTempCuda::~ComputeTempCuda()
 
 void ComputeTempCuda::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
+
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);

src/USER-CUDA/compute_temp_partial_cuda.cpp

@@ -103,6 +103,9 @@ ComputeTempPartialCuda::~ComputeTempPartialCuda()
 
 void ComputeTempPartialCuda::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
+
   fix_dof = 0;
   for (int i = 0; i < modify->nfix; i++)
     fix_dof += modify->fix[i]->dof(igroup);

src/USER-EFF/compute_temp_deform_eff.cpp

@@ -70,15 +70,9 @@ ComputeTempDeformEff::~ComputeTempDeformEff()
 
 void ComputeTempDeformEff::init()
 {
-  int i;
-
-  fix_dof = 0;
-  for (i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
-  dof_compute();
-
   // 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 == X_REMAP &&
@@ -88,7 +82,18 @@ void ComputeTempDeformEff::init()
       break;
     }
   if (i == modify->nfix && comm->me == 0)
-    error->warning(FLERR,"Using compute temp/deform/eff with no fix deform defined");
+    error->warning(FLERR,
+                   "Using compute temp/deform/eff with no fix deform defined");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeTempDeformEff::setup()
+{
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
+  fix_dof = -1;
+  dof_compute();
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-EFF/compute_temp_eff.cpp

@@ -56,6 +56,8 @@ ComputeTempEff::~ComputeTempEff()
 
 void ComputeTempEff::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/USER-EFF/compute_temp_region_eff.cpp

@@ -83,6 +83,8 @@ void ComputeTempRegionEff::init()
 
 void ComputeTempRegionEff::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   dof = 0.0;
 }
 

src/USER-MISC/compute_temp_rotate.cpp

@@ -68,6 +68,8 @@ void ComputeTempRotate::init()
 
 void ComputeTempRotate::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/compute.cpp

@@ -70,6 +70,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
 
   timeflag = 0;
   comm_forward = comm_reverse = 0;
+  dynamic = 0;
   dynamic_group_allow = 1;
   cudable = 0;
 
@@ -80,7 +81,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   // set modify defaults
 
   extra_dof = domain->dimension;
-  dynamic = 0;
+  dynamic_user = 0;
 
   // setup list of timesteps
 
@@ -120,8 +121,8 @@ void Compute::modify_params(int narg, char **arg)
       iarg += 2;
     } else if (strcmp(arg[iarg],"dynamic") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");
-      if (strcmp(arg[iarg+1],"no") == 0) dynamic = 0;
-      else if (strcmp(arg[iarg+1],"yes") == 0) dynamic = 1;
+      if (strcmp(arg[iarg+1],"no") == 0) dynamic_user = 0;
+      else if (strcmp(arg[iarg+1],"yes") == 0) dynamic_user = 1;
       else error->all(FLERR,"Illegal compute_modify command");
       iarg += 2;
     } else if (strcmp(arg[iarg],"thermo") == 0) {

src/compute.h

@@ -125,6 +125,7 @@ class Compute : protected Pointers {
   int extra_dof;               // extra DOF for temperature computes
   int fix_dof;                 // DOF due to fixes
   int dynamic;                 // recount atoms for temperature computes
+  int dynamic_user;            // user request for temp compute to be dynamic
   int thermoflag;              // 1 if include fix PE for PE computes
 
   double vbias[3];             // stored velocity bias for one atom

src/compute_temp.cpp

@@ -50,6 +50,8 @@ ComputeTemp::~ComputeTemp()
 
 void ComputeTemp::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/compute_temp_com.cpp

@@ -60,6 +60,8 @@ void ComputeTempCOM::init()
 
 void ComputeTempCOM::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/compute_temp_deform.cpp

@@ -86,6 +86,8 @@ void ComputeTempDeform::init()
 
 void ComputeTempDeform::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/compute_temp_partial.cpp

@@ -61,6 +61,8 @@ ComputeTempPartial::~ComputeTempPartial()
 
 void ComputeTempPartial::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/compute_temp_profile.cpp

@@ -187,6 +187,8 @@ void ComputeTempProfile::init()
 
 void ComputeTempProfile::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/compute_temp_ramp.cpp

@@ -117,6 +117,8 @@ ComputeTempRamp::~ComputeTempRamp()
 
 void ComputeTempRamp::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/compute_temp_sphere.cpp

@@ -108,6 +108,8 @@ void ComputeTempSphere::init()
 
 void ComputeTempSphere::setup()
 {
+  dynamic = 0;
+  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
   fix_dof = -1;
   dof_compute();
 }

src/fix_nh.cpp

@@ -131,7 +131,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
       pcouple = XYZ;
       p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
       p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
-      p_period[0] = p_period[1] = p_period[2] = force->numeric(FLERR,arg[iarg+3]);
+      p_period[0] = p_period[1] = p_period[2] = 
+        force->numeric(FLERR,arg[iarg+3]);
       p_flag[0] = p_flag[1] = p_flag[2] = 1;
       if (dimension == 2) {
         p_start[2] = p_stop[2] = p_period[2] = 0.0;
@@ -143,7 +144,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
       pcouple = NONE;
       p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
       p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
-      p_period[0] = p_period[1] = p_period[2] = force->numeric(FLERR,arg[iarg+3]);
+      p_period[0] = p_period[1] = p_period[2] = 
+        force->numeric(FLERR,arg[iarg+3]);
       p_flag[0] = p_flag[1] = p_flag[2] = 1;
       if (dimension == 2) {
         p_start[2] = p_stop[2] = p_period[2] = 0.0;
@@ -156,11 +158,13 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
       scalexy = scalexz = scaleyz = 0;
       p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
       p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
-      p_period[0] = p_period[1] = p_period[2] = force->numeric(FLERR,arg[iarg+3]);
+      p_period[0] = p_period[1] = p_period[2] = 
+        force->numeric(FLERR,arg[iarg+3]);
       p_flag[0] = p_flag[1] = p_flag[2] = 1;
       p_start[3] = p_start[4] = p_start[5] = 0.0;
       p_stop[3] = p_stop[4] = p_stop[5] = 0.0;
-      p_period[3] = p_period[4] = p_period[5] = force->numeric(FLERR,arg[iarg+3]);
+      p_period[3] = p_period[4] = p_period[5] = 
+        force->numeric(FLERR,arg[iarg+3]);
       p_flag[3] = p_flag[4] = p_flag[5] = 1;
       if (dimension == 2) {
         p_start[2] = p_stop[2] = p_period[2] = 0.0;
@@ -692,10 +696,6 @@ void FixNH::init()
 
 void FixNH::setup(int vflag)
 {
-  // initialize some quantities that were not available earlier
-
-  tdof = temperature->dof;
-
   // t_target is needed by NPH and NPT in compute_scalar()
   // If no thermostat or using fix nphug,
   // t_target must be defined by other means.
@@ -723,6 +723,8 @@ void FixNH::setup(int vflag)
   if (pstat_flag) compute_press_target();
 
   t_current = temperature->compute_scalar();
+  tdof = temperature->dof;
+
   if (pstat_flag) {
     if (pstyle == ISO) pressure->compute_scalar();
     else pressure->compute_vector();
@@ -851,6 +853,8 @@ void FixNH::final_integrate()
   // compute appropriately coupled elements of mvv_current
 
   t_current = temperature->compute_scalar();
+  tdof = temperature->dof;
+
   if (pstat_flag) {
     if (pstyle == ISO) pressure->compute_scalar();
     else pressure->compute_vector();
@@ -903,7 +907,7 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
         temperature->compute_scalar();
         pressure->compute_scalar();
       } else {
-               temperature->compute_vector();
+        temperature->compute_vector();
         pressure->compute_vector();
       }
       couple();

src/fix_temp_berendsen.cpp

@@ -135,6 +135,8 @@ void FixTempBerendsen::init()
 void FixTempBerendsen::end_of_step()
 {
   double t_current = temperature->compute_scalar();
+  double tdof = temperature->dof;
+
   if (t_current == 0.0)
     error->all(FLERR,
                "Computed temperature for fix temp/berendsen cannot be 0.0");
@@ -162,7 +164,7 @@ void FixTempBerendsen::end_of_step()
   //   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));
-  double efactor = 0.5 * force->boltz * temperature->dof;
+  double efactor = 0.5 * force->boltz * tdof;
   energy += t_current * (1.0-lamda*lamda) * efactor;
 
   double **v = atom->v;

src/modify.cpp

@@ -271,7 +271,12 @@ void Modify::init()
 void Modify::setup(int vflag)
 {
   // compute setup needs to come before fix setup
-  // b/c NH fixes need DOF of temperature computes
+  //   b/c NH fixes need DOF of temperature computes
+  // fix group setup() is special case since populates a dynamic group
+  //   needs to be done before temperature compute setup
+
+  for (int i = 0; i < nfix; i++)
+    if (strcmp(fix[i]->style,"GROUP") == 0) fix[i]->setup(vflag);
 
   for (int i = 0; i < ncompute; i++) compute[i]->setup();