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Merge remote branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	doc/Manual.txt
	doc/pair_coeff.txt
	doc/pair_lj.txt
	doc/pair_style.txt
	src/respa.cpp
This commit is contained in:
Axel Kohlmeyer
2013-03-08 12:26:50 +01:00
parent 820f6002ef 10cdb7dc5e
commit 21e4a32e65
32 changed files with 959 additions and 134 deletions
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79
src/respa.cpp
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@ -47,7 +47,7 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
if (narg < 1) error->all(FLERR,"Illegal run_style respa command");
nlevels = atoi(arg[0]);
if (nlevels <= 1) error->all(FLERR,"Respa levels must be > 1");
if (nlevels < 1) error->all(FLERR,"Respa levels must be >= 1");
if (narg < nlevels) error->all(FLERR,"Illegal run_style respa command");
loop = new int[nlevels];
@ -367,14 +367,6 @@ void Respa::setup()
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
modify->setup_pre_force_respa(vflag,ilevel);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && pair_compute_flag)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && pair_compute_flag)
@ -383,6 +375,14 @@ void Respa::setup()
force->pair->compute_middle();
if (level_outer == ilevel && pair_compute_flag)
force->pair->compute_outer(eflag,vflag);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
@ -435,14 +435,6 @@ void Respa::setup_minimal(int flag)
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
modify->setup_pre_force_respa(vflag,ilevel);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && pair_compute_flag)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && pair_compute_flag)
@ -451,6 +443,14 @@ void Respa::setup_minimal(int flag)
force->pair->compute_middle();
if (level_outer == ilevel && pair_compute_flag)
force->pair->compute_outer(eflag,vflag);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
@ -562,6 +562,10 @@ void Respa::recurse(int ilevel)
}
neighbor->build();
timer->stamp(Timer::NEIGHBOR);
} else if (ilevel == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(Timer::COMM);
}
} else if (ilevel == 0) {
@ -570,6 +574,11 @@ void Respa::recurse(int ilevel)
timer->stamp(Timer::COMM);
}
// force computations
// important that ordering is same as Verlet
// so that any order dependencies are the same
// when potentials are invoked at same level
force_clear(newton[ilevel]);
if (modify->n_pre_force_respa) {
timer->stamp();
@ -578,22 +587,6 @@ void Respa::recurse(int ilevel)
}
timer->stamp();
if (level_bond == ilevel && force->bond) {
force->bond->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_angle == ilevel && force->angle) {
force->angle->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_dihedral == ilevel && force->dihedral) {
force->dihedral->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_improper == ilevel && force->improper) {
force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_pair == ilevel && pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
@ -610,6 +603,22 @@ void Respa::recurse(int ilevel)
force->pair->compute_outer(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (level_bond == ilevel && force->bond) {
force->bond->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_angle == ilevel && force->angle) {
force->angle->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_dihedral == ilevel && force->dihedral) {
force->dihedral->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_improper == ilevel && force->improper) {
force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_kspace == ilevel && kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
@ -637,10 +646,6 @@ void Respa::force_clear(int newtonflag)
{
if (external_force_clear) return;
int i;
if (external_force_clear) return;
// clear global force array
// nall includes ghosts only if newton flag is set