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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@954 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-10-04 23:59:26 +00:00
parent 60da95b755
commit ed9ce73904
10 changed files with 404 additions and 156 deletions
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153
src/neighbor.cpp
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@ -54,6 +54,8 @@ using namespace LAMMPS_NS;
enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
// #define NEIGH_LIST_DEBUG 1
/* ---------------------------------------------------------------------- */
Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
@ -196,7 +198,11 @@ void Neighbor::init()
// set to 0 if cutforce = 0
// cutneighmin/max used for neighbor bin sizes
// cutghost determines comm distance = max of cutneigh & skin
// may need ghosts for bonds even if all cutneigh = 0 (pair = NULL)
// skin is only > cutneighmax when cutneighmax = 0.0 due to pair = NULL
// in this case, are running a bond-only simulation
// still need ghost atom communication for bonds and atom exchange
// triggered by atoms moving 1/2 skin distance, but no neigh lists formed
// user should set skin big enough to find all bonds
triggersq = 0.25*skin*skin;
@ -382,7 +388,9 @@ void Neighbor::init()
for (i = 0; i < nrequest; i++)
if (requests[i]->identical(old_requests[i]) == 0) same = 0;
printf("SAME %d\n",same);
#ifdef NEIGH_LIST_DEBUG
if (comm->me == 0) printf("SAME flag %d\n",same);
#endif
// if old and new are not the same, create new pairwise lists
@ -422,42 +430,47 @@ void Neighbor::init()
}
// detect lists that are connected to other lists
// if-the-else sequence is important
// since don't want to re-process skip or copy lists further down
// skip: point this list at request->otherlist, copy skip ptrs from request
// copy: point this list at request->otherlist
// half_from_full: point this list at preceeding full list
// granhistory: set preceeding list's listgranhistory to this list
// also set precedding list's ptr to FixShearHistory
// respaouter: point this list at preceeding 1/2 inner/middle lists
// pair and half and non-skip: if there is a pair full non-skip list,
// pair and half: if there is a full non-occasional non-skip list
// change this list to half_from_full and point at the full list
// parent could be copy list or pair or fix
// fix/compute requests:
// kind of request = half or full
// occasional or not doesn't matter
// if non-skip pair list of same kind exists, become copy of that list
// else if request is half and non-skip pair full exists,
// kind of request = half or full, occasional or not doesn't matter
// if request = half and non-skip pair half/respaouter exists,
// become copy of that list
// if request = full and non-skip pair full exists,
// become copy of that list
// if request = half and non-skip pair full exists,
// become half_from_full of that list
// else do nothing and the fix/compute list will be built directly
// if no matches, do nothing, fix/compute list will be built directly
// ok if parent is copy list
for (i = 0; i < nlist; i++) {
if (requests[i]->skip) {
lists[i]->listskip = lists[requests[i]->otherlist];
lists[i]->iskip = requests[i]->iskip;
lists[i]->ijskip = requests[i]->ijskip;
}
if (requests[i]->copy)
} else if (requests[i]->copy)
lists[i]->listcopy = lists[requests[i]->otherlist];
if (requests[i]->half_from_full) lists[i]->listfull = lists[i-1];
else if (requests[i]->half_from_full)
lists[i]->listfull = lists[i-1];
if (requests[i]->granhistory) {
else if (requests[i]->granhistory) {
lists[i-1]->listgranhistory = lists[i];
for (int ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"SHEAR_HISTORY") == 0)
lists[i-1]->fix_history = (FixShearHistory *) modify->fix[ifix];
}
if (requests[i]->respaouter) {
} else if (requests[i]->respaouter) {
if (requests[i-1]->respainner) {
lists[i]->respamiddle = 0;
lists[i]->listinner = lists[i-1];
@ -466,33 +479,33 @@ void Neighbor::init()
lists[i]->listmiddle = lists[i-1];
lists[i]->listinner = lists[i-2];
}
}
if (requests[i]->pair && requests[i]->half && requests[i]->skip == 0) {
} else if (requests[i]->pair && requests[i]->half) {
for (j = 0; j < nlist; j++)
if (requests[j]->pair && requests[j]->full &&
if (requests[j]->full && requests[j]->occasional == 0 &&
requests[j]->skip == 0) break;
if (j < nlist) {
requests[i]->half = 0;
requests[i]->half_from_full = 1;
lists[i]->listfull = lists[j];
}
}
if (requests[i]->fix || requests[i]->compute) {
} else if (requests[i]->fix || requests[i]->compute) {
for (j = 0; j < nlist; j++) {
if (requests[j]->pair && requests[j]->skip == 0 &&
requests[j]->half && requests[i]->half) break;
if (requests[j]->pair && requests[j]->skip == 0 &&
requests[j]->full && requests[i]->full) break;
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->half) break;
if (requests[i]->full && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->full) break;
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->respaouter) break;
}
if (j < nlist) {
requests[i]->copy = 1;
lists[i]->listcopy = lists[j];
} else {
for (j = 0; j < nlist; j++) {
if (requests[j]->pair && requests[j]->skip == 0 &&
requests[j]->full && requests[i]->half) break;
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->full) break;
}
if (j < nlist) {
requests[i]->half = 0;
@ -530,10 +543,10 @@ void Neighbor::init()
if (stencil_create[i] == NULL) lists[i]->stencilflag = 0;
}
// DEBUG: print list attributes
#ifdef NEIGH_LIST_DEBUG
for (i = 0; i < nlist; i++) lists[i]->print_attributes();
#endif
// allocate atom arrays and 1st pages of lists that store them
for (i = 0; i < nlist; i++)
@ -565,23 +578,13 @@ void Neighbor::init()
slist[nslist++] = i;
}
// DEBUG: print lists of lists
if (comm->me == 0) {
printf("Build lists = %d: ",nblist);
for (i = 0; i < nblist; i++) printf("%d ",blist[i]);
printf("\n");
printf("Grow lists = %d: ",nglist);
for (i = 0; i < nglist; i++) printf("%d ",glist[i]);
printf("\n");
printf("Stencil lists = %d: ",nslist);
for (i = 0; i < nslist; i++) printf("%d ",slist[i]);
printf("\n");
}
#ifdef NEIGH_LIST_DEBUG
print_lists_of_lists();
#endif
// reorder build vector if necessary
// relevant for lists that copy/skip/half-full from parent
// the derived lst must appear in blist after the parent list
// the derived list must appear in blist after the parent list
// no occasional lists are in build vector
// swap two lists within blist when dependency is mis-ordered
// done when entire pass thru blist results in no swaps
@ -608,19 +611,9 @@ void Neighbor::init()
}
}
// DEBUG: print lists of lists
if (comm->me == 0) {
printf("Build lists = %d: ",nblist);
for (i = 0; i < nblist; i++) printf("%d ",blist[i]);
printf("\n");
printf("Grow lists = %d: ",nglist);
for (i = 0; i < nglist; i++) printf("%d ",glist[i]);
printf("\n");
printf("Stencil lists = %d: ",nslist);
for (i = 0; i < nslist; i++) printf("%d ",slist[i]);
printf("\n");
}
#ifdef NEIGH_LIST_DEBUG
print_lists_of_lists();
#endif
}
// delete old requests
@ -750,11 +743,13 @@ int Neighbor::request(void *requestor)
return nrequest-1;
}
/* ----------------------------------------------------------------------
determine which pair_build function each neigh list needs
based on settings of neigh request
skip or copy -> single function
copy -> copy_from function
skip -> granular function if gran with granhistory
respa function if respaouter
skip_from function for everything else
half_from_full, half, full, gran, respaouter -> choose by newton and tri
style NSQ options = newton off, newton on
style BIN options = newton off, newton on and not tri, newton on and tri
@ -767,13 +762,17 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
{
PairPtr pb = NULL;
if (rq->skip) pb = &Neighbor::skip_from;
if (rq->copy) pb = &Neighbor::copy_from;
else if (rq->copy) pb = &Neighbor::copy_from;
else if (rq->skip) {
if (rq->gran && lists[index]->listgranhistory)
pb = &Neighbor::skip_from_granular;
else if (rq->respaouter) pb = &Neighbor::skip_from_respa;
else pb = &Neighbor::skip_from;
else if (rq->half_from_full) {
if (newton_pair == 0) pb = &Neighbor::half_full_no_newton;
else if (newton_pair == 1) pb = &Neighbor::half_full_newton;
} else if (rq->half_from_full) {
if (newton_pair == 0) pb = &Neighbor::half_from_full_no_newton;
else if (newton_pair == 1) pb = &Neighbor::half_from_full_newton;
} else if (rq->half) {
if (style == NSQ) {
@ -878,6 +877,23 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq)
/* ---------------------------------------------------------------------- */
void Neighbor::print_lists_of_lists()
{
if (comm->me == 0) {
printf("Build lists = %d: ",nblist);
for (int i = 0; i < nblist; i++) printf("%d ",blist[i]);
printf("\n");
printf("Grow lists = %d: ",nglist);
for (int i = 0; i < nglist; i++) printf("%d ",glist[i]);
printf("\n");
printf("Stencil lists = %d: ",nslist);
for (int i = 0; i < nslist; i++) printf("%d ",slist[i]);
printf("\n");
}
}
/* ---------------------------------------------------------------------- */
int Neighbor::decide()
{
if (must_check) {
@ -968,17 +984,6 @@ void Neighbor::build()
for (i = 0; i < nblist; i++)
(this->*pair_build[blist[i]])(lists[blist[i]]);
/*
if (comm->me == 0) {
for (int m = 0; m < nlist; m++) {
int num = 0;
for (i = 0; i < lists[m]->inum; i++)
num += lists[m]->numneigh[lists[m]->ilist[i]];
printf("List %d length = %d\n",m,num);
}
}
*/
if (atom->molecular) {
if (atom->nbonds) (this->*bond_build)();
if (atom->nangles) (this->*angle_build)();