git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11935 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/compute_temp_asphere.cpp

@@ -25,7 +25,6 @@
 #include "force.h"
 #include "domain.h"
 #include "modify.h"
-#include "fix.h"
 #include "group.h"
 #include "memory.h"
 #include "error.h"
@@ -128,9 +127,7 @@ void ComputeTempAsphere::init()
 
 void ComputeTempAsphere::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -138,6 +135,8 @@ void ComputeTempAsphere::setup()
 
 void ComputeTempAsphere::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
+
   // 6 dof for 3d, 3 dof for 2d
   // which dof are included also depends on mode
   // assume full rotation of extended particles

src/USER-EFF/compute_temp_eff.cpp

@@ -23,8 +23,6 @@
 #include "update.h"
 #include "force.h"
 #include "domain.h"
-#include "modify.h"
-#include "fix.h"
 #include "group.h"
 #include "error.h"
 
@@ -58,9 +56,7 @@ ComputeTempEff::~ComputeTempEff()
 
 void ComputeTempEff::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -68,6 +64,7 @@ void ComputeTempEff::setup()
 
 void ComputeTempEff::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
   double natoms = group->count(igroup);
   dof = domain->dimension * natoms;
   dof -= extra_dof + fix_dof;

src/USER-MISC/compute_temp_rotate.cpp

@@ -23,8 +23,6 @@
 #include "update.h"
 #include "force.h"
 #include "group.h"
-#include "modify.h"
-#include "fix.h"
 #include "domain.h"
 #include "lattice.h"
 #include "error.h"
@@ -70,9 +68,7 @@ void ComputeTempRotate::init()
 
 void ComputeTempRotate::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -80,6 +76,7 @@ void ComputeTempRotate::setup()
 
 void ComputeTempRotate::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
   double natoms = group->count(igroup);
   int nper = domain->dimension;
   dof = nper * natoms;

src/atom.cpp

@@ -330,7 +330,7 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
   // create instance of AtomVec
   // use grow() to initialize atom-based arrays to length 1
   //   so that x[0][0] can always be referenced even if proc has no atoms
-  // but reset nmax = 0
+  // but reset nmax = 0 in both Atom and AtomVec
   //   so 2d arrays like bond_type will later be allocated correctly
   //   since currently, 2nd dimension bond_per_atom = 0
 

src/compute.cpp

@@ -21,6 +21,8 @@
 #include "domain.h"
 #include "comm.h"
 #include "group.h"
+#include "modify.h"
+#include "fix.h"
 #include "atom_masks.h"
 #include "memory.h"
 #include "error.h"
@@ -131,6 +133,17 @@ void Compute::modify_params(int narg, char **arg)
   }
 }
 
+/* ----------------------------------------------------------------------
+   calculate adjustment in DOF due to fixes
+------------------------------------------------------------------------- */
+
+void Compute::adjust_dof_fix()
+{
+  fix_dof = 0;
+  for (int i = 0; i < modify->nfix; i++)
+    fix_dof += modify->fix[i]->dof(igroup);
+}
+
 /* ----------------------------------------------------------------------
    reset extra_dof to its default value
 ------------------------------------------------------------------------- */

src/compute.h

@@ -86,6 +86,7 @@ class Compute : protected Pointers {
   Compute(class LAMMPS *, int, char **);
   virtual ~Compute();
   void modify_params(int, char **);
+  void adjust_dof_fix();
   void reset_extra_dof();
 
   virtual void init() = 0;
@@ -122,6 +123,7 @@ class Compute : protected Pointers {
 
  protected:
   int extra_dof;               // extra DOF for temperature computes
+  int fix_dof;                 // DOF due to fixes
   int dynamic;                 // recount atoms for temperature computes
   int thermoflag;              // 1 if include fix PE for PE computes
 

src/compute_temp.cpp

@@ -52,9 +52,7 @@ ComputeTemp::~ComputeTemp()
 
 void ComputeTemp::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -62,6 +60,7 @@ void ComputeTemp::setup()
 
 void ComputeTemp::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
   double natoms = group->count(igroup);
   dof = domain->dimension * natoms;
   dof -= extra_dof + fix_dof;

src/compute_temp.h

@@ -34,7 +34,6 @@ class ComputeTemp : public Compute {
   void compute_vector();
 
  protected:
-  int fix_dof;
   double tfactor;
 
   virtual void dof_compute();

src/compute_temp_com.cpp

@@ -19,8 +19,6 @@
 #include "update.h"
 #include "force.h"
 #include "group.h"
-#include "modify.h"
-#include "fix.h"
 #include "domain.h"
 #include "lattice.h"
 #include "error.h"
@@ -62,9 +60,7 @@ void ComputeTempCOM::init()
 
 void ComputeTempCOM::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -72,6 +68,7 @@ void ComputeTempCOM::setup()
 
 void ComputeTempCOM::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
   double natoms = group->count(igroup);
   int nper = domain->dimension;
   dof = nper * natoms;

src/compute_temp_deform.cpp

@@ -86,9 +86,7 @@ void ComputeTempDeform::init()
 
 void ComputeTempDeform::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -96,6 +94,7 @@ void ComputeTempDeform::setup()
 
 void ComputeTempDeform::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
   double natoms = group->count(igroup);
   dof = domain->dimension * natoms;
   dof -= extra_dof + fix_dof;

src/compute_temp_partial.cpp

@@ -18,8 +18,6 @@
 #include "update.h"
 #include "force.h"
 #include "domain.h"
-#include "modify.h"
-#include "fix.h"
 #include "group.h"
 #include "memory.h"
 #include "error.h"
@@ -63,9 +61,7 @@ ComputeTempPartial::~ComputeTempPartial()
 
 void ComputeTempPartial::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -76,6 +72,7 @@ void ComputeTempPartial::setup()
 
 void ComputeTempPartial::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
   double natoms = group->count(igroup);
   int nper = xflag+yflag+zflag;
   dof = nper * natoms;

src/compute_temp_profile.cpp

@@ -161,9 +161,7 @@ ComputeTempProfile::~ComputeTempProfile()
 
 void ComputeTempProfile::init()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 
   // ptrs to domain data
@@ -189,9 +187,7 @@ void ComputeTempProfile::init()
 
 void ComputeTempProfile::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -199,6 +195,7 @@ void ComputeTempProfile::setup()
 
 void ComputeTempProfile::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
   double natoms = group->count(igroup);
   int nper = domain->dimension;
   dof = nper * natoms;

src/compute_temp_ramp.cpp

@@ -117,9 +117,7 @@ ComputeTempRamp::~ComputeTempRamp()
 
 void ComputeTempRamp::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -127,6 +125,7 @@ void ComputeTempRamp::setup()
 
 void ComputeTempRamp::dof_compute()
 {
+  if (fix_dof) adjust_dof_fix();
   double natoms = group->count(igroup);
   int nper = domain->dimension;
   dof = nper * natoms;

src/compute_temp_region.cpp

@@ -17,7 +17,6 @@
 #include "atom.h"
 #include "update.h"
 #include "force.h"
-#include "modify.h"
 #include "domain.h"
 #include "region.h"
 #include "memory.h"

src/compute_temp_sphere.cpp

@@ -20,7 +20,6 @@
 #include "force.h"
 #include "domain.h"
 #include "modify.h"
-#include "fix.h"
 #include "group.h"
 #include "error.h"
 
@@ -109,9 +108,7 @@ void ComputeTempSphere::init()
 
 void ComputeTempSphere::setup()
 {
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  fix_dof = -1;
   dof_compute();
 }
 
@@ -121,6 +118,8 @@ void ComputeTempSphere::dof_compute()
 {
   int count,count_all;
 
+  if (fix_dof) adjust_dof_fix();
+
   // 6 or 3 dof for extended/point particles for 3d
   // 3 or 2 dof for extended/point particles for 2d
   // which dof are included also depends on mode

src/modify.cpp

@@ -271,7 +271,7 @@ void Modify::init()
 void Modify::setup(int vflag)
 {
   // compute setup needs to come before fix setup
-  // b/c NH fixes need use DOF of temperature computes
+  // b/c NH fixes need DOF of temperature computes
 
   for (int i = 0; i < ncompute; i++) compute[i]->setup();