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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15286 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-07-12 22:35:56 +00:00
parent 1df9db5091
commit 3f802d97c9
2 changed files with 47 additions and 4 deletions
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46
src/modify.cpp
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@ -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
------------------------------------------------------------------------- */