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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13937 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-08-28 20:00:56 +00:00
parent 962dd0da74
commit ce59e32d1c
189 changed files with 1526 additions and 587 deletions
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37
src/verlet.cpp
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@ -231,8 +231,10 @@ void Verlet::run(int n)
// initial time integration
timer->stamp();
modify->initial_integrate(vflag);
if (n_post_integrate) modify->post_integrate();
timer->stamp(Timer::MODIFY);
// regular communication vs neighbor list rebuild
@ -241,9 +243,13 @@ void Verlet::run(int n)
if (nflag == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(TIME_COMM);
timer->stamp(Timer::COMM);
} else {
if (n_pre_exchange) modify->pre_exchange();
if (n_pre_exchange) {
timer->stamp();
modify->pre_exchange();
timer->stamp(Timer::MODIFY);
}
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
@ -256,10 +262,13 @@ void Verlet::run(int n)
if (sortflag && ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(TIME_COMM);
if (n_pre_neighbor) modify->pre_neighbor();
timer->stamp(Timer::COMM);
if (n_pre_neighbor) {
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
neighbor->build();
timer->stamp(TIME_NEIGHBOR);
timer->stamp(Timer::NEIGH);
}
// force computations
@ -268,13 +277,17 @@ void Verlet::run(int n)
// and Pair:ev_tally() needs to be called before any tallying
force_clear();
if (n_pre_force) modify->pre_force(vflag);
timer->stamp();
if (n_pre_force) {
modify->pre_force(vflag);
timer->stamp(Timer::MODIFY);
}
if (pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(TIME_PAIR);
timer->stamp(Timer::PAIR);
}
if (atom->molecular) {
@ -282,19 +295,19 @@ void Verlet::run(int n)
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
timer->stamp(TIME_BOND);
timer->stamp(Timer::BOND);
}
if (kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_KSPACE);
timer->stamp(Timer::KSPACE);
}
// reverse communication of forces
if (force->newton) {
comm->reverse_comm();
timer->stamp(TIME_COMM);
timer->stamp(Timer::COMM);
}
// force modifications, final time integration, diagnostics
@ -302,13 +315,14 @@ void Verlet::run(int n)
if (n_post_force) modify->post_force(vflag);
modify->final_integrate();
if (n_end_of_step) modify->end_of_step();
timer->stamp(Timer::MODIFY);
// all output
if (ntimestep == output->next) {
timer->stamp();
output->write(ntimestep);
timer->stamp(TIME_OUTPUT);
timer->stamp(Timer::OUTPUT);
}
}
}
@ -329,7 +343,6 @@ void Verlet::cleanup()
void Verlet::force_clear()
{
int i;
size_t nbytes;
if (external_force_clear) return;