diff --git a/src/modify.cpp b/src/modify.cpp
index e0e72730d46482289624eb747ab684aa1f41d3c8..5c611885b95a36f431c15d3634116f6c48f82a66 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -44,6 +44,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
n_pre_exchange = n_pre_neighbor = 0;
n_pre_force = n_pre_reverse = n_post_force = 0;
n_final_integrate = n_end_of_step = n_thermo_energy = 0;
+ n_thermo_energy_atom = 0;
n_initial_integrate_respa = n_post_integrate_respa = 0;
n_pre_force_respa = n_post_force_respa = n_final_integrate_respa = 0;
n_min_pre_exchange = n_min_pre_force = n_min_post_force = n_min_energy = 0;
@@ -54,7 +55,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
list_pre_exchange = list_pre_neighbor = NULL;
list_pre_force = list_pre_reverse = list_post_force = NULL;
list_final_integrate = list_end_of_step = NULL;
- list_thermo_energy = NULL;
+ list_thermo_energy = list_thermo_energy_atom = NULL;
list_initial_integrate_respa = list_post_integrate_respa = NULL;
list_pre_force_respa = list_post_force_respa = NULL;
list_final_integrate_respa = NULL;
@@ -124,6 +125,7 @@ Modify::~Modify()
delete [] list_final_integrate;
delete [] list_end_of_step;
delete [] list_thermo_energy;
+ delete [] list_thermo_energy_atom;
delete [] list_initial_integrate_respa;
delete [] list_post_integrate_respa;
delete [] list_pre_force_respa;
@@ -168,6 +170,7 @@ void Modify::init()
list_init(FINAL_INTEGRATE,n_final_integrate,list_final_integrate);
list_init_end_of_step(END_OF_STEP,n_end_of_step,list_end_of_step);
list_init_thermo_energy(THERMO_ENERGY,n_thermo_energy,list_thermo_energy);
+ list_init_thermo_energy_atom(n_thermo_energy_atom,list_thermo_energy_atom);
list_init(INITIAL_INTEGRATE_RESPA,
n_initial_integrate_respa,list_initial_integrate_respa);
@@ -440,6 +443,23 @@ double Modify::thermo_energy()
return energy;
}
+/* ----------------------------------------------------------------------
+ per-atom thermo energy call, only for relevant fixes
+ called by compute pe/atom
+------------------------------------------------------------------------- */
+
+void Modify::thermo_energy_atom(int nlocal, double *energy)
+{
+ int i,j;
+ double *eatom;
+
+ for (i = 0; i < n_thermo_energy_atom; i++) {
+ eatom = fix[list_thermo_energy_atom[i]]->eatom;
+ if (!eatom) continue;
+ for (j = 0; j < nlocal; j++) energy[j] += eatom[j];
+ }
+}
+
/* ----------------------------------------------------------------------
post_run call
------------------------------------------------------------------------- */
@@ -697,7 +717,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
// MUST change NEXCEPT above when add new fix to this list
const char *exceptions[NEXCEPT] =
- {"GPU","OMP","INTEL","property/atom","cmap","cmap2","rx"};
+ {"GPU","OMP","INTEL","property/atom","cmap","cmap3","rx"};
if (domain->box_exist == 0) {
int m;
@@ -1275,7 +1295,7 @@ void Modify::list_init_end_of_step(int mask, int &n, int *&list)
/* ----------------------------------------------------------------------
create list of fix indices for thermo energy fixes
- only added to list if fix has THERMO_ENERGY mask
+ only added to list if fix has THERMO_ENERGY mask set,
and its thermo_energy flag was set via fix_modify
------------------------------------------------------------------------- */
@@ -1293,6 +1313,26 @@ void Modify::list_init_thermo_energy(int mask, int &n, int *&list)
if (fmask[i] & mask && fix[i]->thermo_energy) list[n++] = i;
}
+/* ----------------------------------------------------------------------
+ create list of fix indices for peratom thermo energy fixes
+ only added to list if fix has its peatom_flag set,
+ and its thermo_energy flag was set via fix_modify
+------------------------------------------------------------------------- */
+
+void Modify::list_init_thermo_energy_atom(int &n, int *&list)
+{
+ delete [] list;
+
+ n = 0;
+ for (int i = 0; i < nfix; i++)
+ if (fix[i]->peatom_flag && fix[i]->thermo_energy) n++;
+ list = new int[n];
+
+ n = 0;
+ for (int i = 0; i < nfix; i++)
+ if (fix[i]->peatom_flag && fix[i]->thermo_energy) list[n++] = i;
+}
+
/* ----------------------------------------------------------------------
create list of compute indices for computes which store invocation times
------------------------------------------------------------------------- */
diff --git a/src/modify.h b/src/modify.h
index 5ca70428103338dc9c1adcd7307948d92f0bdf71..92d82347949bbd51bfe4843c26eaf152b9e0f3f0 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -30,7 +30,7 @@ class Modify : protected Pointers {
int nfix,maxfix;
int n_initial_integrate,n_post_integrate,n_pre_exchange,n_pre_neighbor;
int n_pre_force,n_pre_reverse,n_post_force;
- int n_final_integrate,n_end_of_step,n_thermo_energy;
+ int n_final_integrate,n_end_of_step,n_thermo_energy,n_thermo_energy_atom;
int n_initial_integrate_respa,n_post_integrate_respa;
int n_pre_force_respa,n_post_force_respa,n_final_integrate_respa;
int n_min_pre_exchange,n_min_pre_neighbor;
@@ -63,6 +63,7 @@ class Modify : protected Pointers {
virtual void final_integrate();
virtual void end_of_step();
virtual double thermo_energy();
+ virtual void thermo_energy_atom(int, double *);
virtual void post_run();
virtual void create_attribute(int);
@@ -117,6 +118,7 @@ class Modify : protected Pointers {
int *list_pre_exchange,*list_pre_neighbor;
int *list_pre_force,*list_pre_reverse,*list_post_force;
int *list_final_integrate,*list_end_of_step,*list_thermo_energy;
+ int *list_thermo_energy_atom;
int *list_initial_integrate_respa,*list_post_integrate_respa;
int *list_pre_force_respa,*list_post_force_respa;
int *list_final_integrate_respa;
@@ -142,6 +144,7 @@ class Modify : protected Pointers {
void list_init(int, int &, int *&);
void list_init_end_of_step(int, int &, int *&);
void list_init_thermo_energy(int, int &, int *&);
+ void list_init_thermo_energy_atom(int &, int *&);
void list_init_dofflag(int &, int *&);
void list_init_compute();