change virial_atom to virial_peratom

src/compute_stress_atom.cpp

@@ -222,7 +222,7 @@ void ComputeStressAtom::compute_peratom()
     Fix **fix = modify->fix;
     int nfix = modify->nfix;
     for (int ifix = 0; ifix < nfix; ifix++)
-      if (fix[i]->virial_atom_flag && fix[ifix]->virial_flag) {
+      if (fix[i]->virial_peratom_flag && fix[ifix]->virial_flag) {
         double **vatom = modify->fix[ifix]->vatom;
         if (vatom)
           for (i = 0; i < nlocal; i++)

src/fix.cpp

@@ -63,8 +63,8 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
   box_change = NO_BOX_CHANGE;
   thermo_energy = 0;
   thermo_virial = 0;
-  energy_global_flag = energy_atom_flag = 0;
-  virial_global_flag = virial_atom_flag = 0;
+  energy_global_flag = energy_peratom_flag = 0;
+  virial_global_flag = virial_peratom_flag = 0;
   ecouple_flag = 0;
   rigid_flag = 0;
   peatom_flag = 0;

src/fix.h

@@ -44,7 +44,7 @@ class Fix : protected Pointers {
   int thermo_energy;             // 1 if fix_modify energy enabled, 0 if not
   int thermo_virial;             // 1 if fix_modify virial enabled, 0 if not
   int energy_global_flag;        // 1 if contributes to global eng
-  int energy_atom_flag;          // 1 if contributes to peratom eng
+  int energy_peratom_flag;       // 1 if contributes to peratom eng
   int virial_global_flag;        // 1 if contributes to global virial
   int virial_peratom_flag;       // 1 if contributes to peratom virial
   int ecouple_flag;              // 1 if thermostat fix outputs cumulative

src/fix_addforce.cpp

@@ -49,7 +49,7 @@ FixAddForce::FixAddForce(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 1;
   extvector = 1;
   energy_global_flag = 1;
-  virial_global_flag = virial_atom_flag = 1;
+  virial_global_flag = virial_peratom_flag = 1;
   respa_level_support = 1;
   ilevel_respa = 0;
 

src/fix_external.cpp

@@ -36,8 +36,8 @@ FixExternal::FixExternal(LAMMPS *lmp, int narg, char **arg) :
   scalar_flag = 1;
   global_freq = 1;
   extscalar = 1;
-  energy_global_flag = energy_atom_flag = 1;
-  virial_global_flag = virial_atom_flag = 1;
+  energy_global_flag = energy_peratom_flag = 1;
+  virial_global_flag = virial_peratom_flag = 1;
   thermo_energy = thermo_virial = 1;
 
   if (strcmp(arg[3],"pf/callback") == 0) {

src/fix_wall.cpp

@@ -42,7 +42,7 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 1;
   extvector = 1;
   energy_global_flag = 1;
-  virial_global_flag = virial_atom_flag = 1;
+  virial_global_flag = virial_peratom_flag = 1;
   respa_level_support = 1;
   ilevel_respa = 0;
 

src/fix_wall_region.cpp

@@ -45,7 +45,7 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 1;
   extvector = 1;
   energy_global_flag = 1;
-  virial_global_flag = virial_atom_flag = 1;
+  virial_global_flag = virial_peratom_flag = 1;
   respa_level_support = 1;
   ilevel_respa = 0;
 

src/modify.cpp

@@ -1666,25 +1666,6 @@ void Modify::list_init_energy_couple(int &n, int *&list)
     if (fix[i]->ecouple_flag) list[n++] = i;
 }
 
-/* ----------------------------------------------------------------------
-   create list of fix indices for fixes that compute peratom energy
-   only added to list if fix has energy_atom_flag and thermo_energy set
-------------------------------------------------------------------------- */
-
-void Modify::list_init_energy_atom(int &n, int *&list)
-{
-  delete [] list;
-
-  n = 0;
-  for (int i = 0; i < nfix; i++)
-    if (fix[i]->energy_atom_flag && fix[i]->thermo_energy) n++;
-  list = new int[n];
-
-  n = 0;
-  for (int i = 0; i < nfix; i++)
-    if (fix[i]->energy_atom_flag && fix[i]->thermo_energy) list[n++] = i;
-}
-
 /* ----------------------------------------------------------------------
    create list of fix indices for fixes that compute global energy
    only added to list if fix has energy_global_flag and thermo_energy set
@@ -1706,7 +1687,7 @@ void Modify::list_init_energy_global(int &n, int *&list)
 
 /* ----------------------------------------------------------------------
    create list of fix indices for fixes that compute peratom energy
-   only added to list if fix has energy_atom_flag and thermo_energy set
+   only added to list if fix has energy_peratom_flag and thermo_energy set
 ------------------------------------------------------------------------- */
 
 void Modify::list_init_energy_atom(int &n, int *&list)
@@ -1715,12 +1696,12 @@ void Modify::list_init_energy_atom(int &n, int *&list)
 
   n = 0;
   for (int i = 0; i < nfix; i++)
-    if (fix[i]->energy_atom_flag && fix[i]->thermo_energy) n++;
+    if (fix[i]->energy_peratom_flag && fix[i]->thermo_energy) n++;
   list = new int[n];
 
   n = 0;
   for (int i = 0; i < nfix; i++)
-    if (fix[i]->energy_atom_flag && fix[i]->thermo_energy) list[n++] = i;
+    if (fix[i]->energy_peratom_flag && fix[i]->thermo_energy) list[n++] = i;
 }
 
 /* ----------------------------------------------------------------------