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refactoring of neighbor history

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This commit is contained in:
Steve Plimpton
2017-10-10 16:53:51 -06:00
parent 93c9a92743
commit 01051e4cb1
26 changed files with 523 additions and 964 deletions
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45
src/modify.cpp
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@ -42,7 +42,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
{
nfix = maxfix = 0;
n_initial_integrate = n_post_integrate = 0;
n_pre_exchange = n_pre_neighbor = 0;
n_pre_exchange = n_pre_neighbor = n_post_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;
@ -54,14 +54,14 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
fix = NULL;
fmask = NULL;
list_initial_integrate = list_post_integrate = NULL;
list_pre_exchange = list_pre_neighbor = NULL;
list_pre_exchange = list_pre_neighbor = list_post_neighbor = NULL;
list_pre_force = list_pre_reverse = list_post_force = NULL;
list_final_integrate = list_end_of_step = 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;
list_min_pre_exchange = list_min_pre_neighbor = NULL;
list_min_pre_exchange = list_min_pre_neighbor = list_min_post_neighbor = NULL;
list_min_pre_force = list_min_pre_reverse = list_min_post_force = NULL;
list_min_energy = NULL;
@ -123,6 +123,7 @@ Modify::~Modify()
delete [] list_post_integrate;
delete [] list_pre_exchange;
delete [] list_pre_neighbor;
delete [] list_post_neighbor;
delete [] list_pre_force;
delete [] list_pre_reverse;
delete [] list_post_force;
@ -137,6 +138,7 @@ Modify::~Modify()
delete [] list_final_integrate_respa;
delete [] list_min_pre_exchange;
delete [] list_min_pre_neighbor;
delete [] list_min_post_neighbor;
delete [] list_min_pre_force;
delete [] list_min_pre_reverse;
delete [] list_min_post_force;
@ -169,6 +171,7 @@ void Modify::init()
list_init(POST_INTEGRATE,n_post_integrate,list_post_integrate);
list_init(PRE_EXCHANGE,n_pre_exchange,list_pre_exchange);
list_init(PRE_NEIGHBOR,n_pre_neighbor,list_pre_neighbor);
list_init(POST_NEIGHBOR,n_post_neighbor,list_post_neighbor);
list_init(PRE_FORCE,n_pre_force,list_pre_force);
list_init(PRE_REVERSE,n_pre_reverse,list_pre_reverse);
list_init(POST_FORCE,n_post_force,list_post_force);
@ -190,6 +193,7 @@ void Modify::init()
list_init(MIN_PRE_EXCHANGE,n_min_pre_exchange,list_min_pre_exchange);
list_init(MIN_PRE_NEIGHBOR,n_min_pre_neighbor,list_min_pre_neighbor);
list_init(MIN_POST_NEIGHBOR,n_min_post_neighbor,list_min_post_neighbor);
list_init(MIN_PRE_FORCE,n_min_pre_force,list_min_pre_force);
list_init(MIN_PRE_REVERSE,n_min_pre_reverse,list_min_pre_reverse);
list_init(MIN_POST_FORCE,n_min_post_force,list_min_post_force);
@ -329,6 +333,21 @@ void Modify::setup_pre_neighbor()
fix[list_min_pre_neighbor[i]]->setup_pre_neighbor();
}
/* ----------------------------------------------------------------------
setup post_neighbor call, only for fixes that define post_neighbor
called from Verlet, RESPA
------------------------------------------------------------------------- */
void Modify::setup_post_neighbor()
{
if (update->whichflag == 1)
for (int i = 0; i < n_post_neighbor; i++)
fix[list_post_neighbor[i]]->setup_post_neighbor();
else if (update->whichflag == 2)
for (int i = 0; i < n_min_post_neighbor; i++)
fix[list_min_post_neighbor[i]]->setup_post_neighbor();
}
/* ----------------------------------------------------------------------
setup pre_force call, only for fixes that define pre_force
called from Verlet, RESPA, Min
@ -399,6 +418,16 @@ void Modify::pre_neighbor()
fix[list_pre_neighbor[i]]->pre_neighbor();
}
/* ----------------------------------------------------------------------
post_neighbor call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::post_neighbor()
{
for (int i = 0; i < n_post_neighbor; i++)
fix[list_post_neighbor[i]]->post_neighbor();
}
/* ----------------------------------------------------------------------
pre_force call, only for relevant fixes
------------------------------------------------------------------------- */
@ -589,6 +618,16 @@ void Modify::min_pre_neighbor()
fix[list_min_pre_neighbor[i]]->min_pre_neighbor();
}
/* ----------------------------------------------------------------------
minimizer post-neighbor call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_post_neighbor()
{
for (int i = 0; i < n_min_post_neighbor; i++)
fix[list_min_post_neighbor[i]]->min_post_neighbor();
}
/* ----------------------------------------------------------------------
minimizer pre-force call, only for relevant fixes
------------------------------------------------------------------------- */