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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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53
src/neighbor.cpp
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@ -133,8 +133,6 @@ pairclass(NULL), pairnames(NULL), pairmasks(NULL)
old_pgsize = pgsize;
old_oneatom = oneatom;
zeroes = NULL;
binclass = NULL;
binnames = NULL;
binmasks = NULL;
@ -208,8 +206,6 @@ Neighbor::~Neighbor()
if (old_requests[i]) delete old_requests[i];
memory->sfree(old_requests);
delete [] zeroes;
delete [] binclass;
delete [] binnames;
delete [] binmasks;
@ -666,14 +662,12 @@ int Neighbor::init_pair()
// purpose is to avoid duplicate or inefficient builds
// may add new requests if a needed request to derive from does not exist
// methods:
// (1) other = point history and rRESPA lists at their partner lists
// (1) other = point rRESPA lists at their partner lists
// (2) skip = create any new non-skip lists needed by pair hybrid skip lists
// (3) granular = adjust parent and skip lists for granular onesided usage
// (4) h/f = pair up any matching half/full lists
// (5) copy = convert as many lists as possible to copy lists
// order of morph methods matters:
// (1) before (2), b/c (2) needs to know history partner pairings
// (2) after (1), b/c (2) may also need to create new history lists
// (3) after (2), b/c it adjusts lists created by (2)
// (4) after (2) and (3),
// b/c (2) may create new full lists, (3) may change them
@ -827,23 +821,14 @@ int Neighbor::init_pair()
}
// allocate initial pages for each list, except if copy flag set
// allocate dnum vector of zeroes if set
int dnummax = 0;
for (i = 0; i < nlist; i++) {
if (lists[i]->copy) continue;
lists[i]->setup_pages(pgsize,oneatom);
dnummax = MAX(dnummax,lists[i]->dnum);
}
if (dnummax) {
delete [] zeroes;
zeroes = new double[dnummax];
for (i = 0; i < dnummax; i++) zeroes[i] = 0.0;
}
// first-time allocation of per-atom data for lists that are built and store
// lists that are not built: granhistory, respa inner/middle (no neigh_pair)
// lists that are not built: respa inner/middle (no neigh_pair)
// lists that do not store: copy
// use atom->nmax for both grow() args
// i.e. grow first time to expanded size to avoid future reallocs
@ -923,7 +908,7 @@ int Neighbor::init_pair()
/* ----------------------------------------------------------------------
scan NeighRequests to set additional flags
only for history, respaouter, custom cutoff lists
only for respaouter, custom cutoff lists
------------------------------------------------------------------------- */
void Neighbor::morph_other()
@ -933,14 +918,6 @@ void Neighbor::morph_other()
for (int i = 0; i < nrequest; i++) {
irq = requests[i];
// if history, point this list and partner list at each other
if (irq->history) {
irq->historylist = i-1;
requests[i-1]->history_partner = 1;
requests[i-1]->historylist = i;
}
// if respaouter, point all associated rRESPA lists at each other
if (irq->respaouter) {
@ -987,7 +964,6 @@ void Neighbor::morph_skip()
// halffull list and its full parent may both skip,
// but are checked to insure matching skip info
if (irq->history) continue;
if (irq->respainner || irq->respamiddle) continue;
if (irq->halffull) continue;
if (irq->copy) continue;
@ -1022,11 +998,11 @@ void Neighbor::morph_skip()
// or their data structures are different
// this includes custom cutoff set by requestor
// no need to check respaouter b/c it stores same pairs
// no need to check dnum b/c only set for history
// NOTE: need check for 2 Kokkos flags?
if (irq->ghost != jrq->ghost) continue;
if (irq->size != jrq->size) continue;
if (irq->history != jrq->history) continue;
if (irq->bond != jrq->bond) continue;
if (irq->omp != jrq->omp) continue;
if (irq->intel != jrq->intel) continue;
@ -1045,8 +1021,8 @@ void Neighbor::morph_skip()
// else create a new identical list except non-skip
// for new list, set neigh = 1, skip = 0, no skip vec/array,
// copy unique flag (since copy_request() will not do it)
// note: parents of skip lists do not have associated history list
// b/c child skip lists store their own history info
// note: parents of skip lists do not have associated history
// b/c child skip lists have the associated history
if (j < nrequest) irq->skiplist = j;
else {
@ -1107,7 +1083,6 @@ void Neighbor::morph_granular()
if (onesided == 2) break;
}
// if onesided = 2, parent has children with both granonesided = 0/1
// force parent newton off (newton = 2) to enable onesided skip by child
// set parent granonesided = 0, so it stores all neighs in usual manner
@ -1159,7 +1134,6 @@ void Neighbor::morph_halffull()
// these lists are created other ways, no need for halffull
// do want to process skip lists
if (irq->history) continue;
if (irq->respainner || irq->respamiddle) continue;
if (irq->copy) continue;
@ -1180,10 +1154,10 @@ void Neighbor::morph_halffull()
// or their data structures are different
// this includes custom cutoff set by requestor
// no need to check respaouter b/c it stores same pairs
// no need to check dnum b/c only set for history
if (irq->ghost != jrq->ghost) continue;
if (irq->size != jrq->size) continue;
if (irq->history != jrq->history) continue;
if (irq->bond != jrq->bond) continue;
if (irq->omp != jrq->omp) continue;
if (irq->intel != jrq->intel) continue;
@ -1233,7 +1207,6 @@ void Neighbor::morph_copy()
// these lists are created other ways, no need to copy
// skip lists are eligible to become a copy list
if (irq->history) continue;
if (irq->respainner || irq->respamiddle) continue;
// check all other lists
@ -1272,9 +1245,8 @@ void Neighbor::morph_copy()
if (irq->ghost && !jrq->ghost) continue;
// do not copy from a history list or a respa middle/inner list
// do not copy from a respa middle/inner list
if (jrq->history) continue;
if (jrq->respamiddle) continue;
if (jrq->respainner) continue;
@ -1284,10 +1256,10 @@ void Neighbor::morph_copy()
// this includes custom cutoff set by requestor
// no need to check respaouter b/c it stores same pairs
// no need to check omp b/c it stores same pairs
// no need to check dnum b/c only set for history
// NOTE: need check for 2 Kokkos flags?
if (irq->size != jrq->size) continue;
if (irq->history != jrq->history) continue;
if (irq->bond != jrq->bond) continue;
if (irq->intel != jrq->intel) continue;
if (irq->kokkos_host != jrq->kokkos_host) continue;
@ -1535,9 +1507,7 @@ void Neighbor::print_pairwise_info()
// order these to get single output of most relevant
if (rq->history)
fprintf(out,", history for (%d)",rq->historylist+1);
else if (rq->copy)
if (rq->copy)
fprintf(out,", copy from (%d)",rq->copylist+1);
else if (rq->halffull)
fprintf(out,", half/full from (%d)",rq->halffulllist+1);
@ -1659,7 +1629,6 @@ int Neighbor::choose_bin(NeighRequest *rq)
if (style == NSQ) return 0;
if (rq->skip || rq->copy || rq->halffull) return 0;
if (rq->history) return 0;
if (rq->respainner || rq->respamiddle) return 0;
// use request settings to match exactly one NBin class mask
@ -1701,7 +1670,6 @@ int Neighbor::choose_stencil(NeighRequest *rq)
if (style == NSQ) return 0;
if (rq->skip || rq->copy || rq->halffull) return 0;
if (rq->history) return 0;
if (rq->respainner || rq->respamiddle) return 0;
// convert newton request to newtflag = on or off
@ -1795,7 +1763,6 @@ int Neighbor::choose_pair(NeighRequest *rq)
{
// no neighbor list build performed
if (rq->history) return 0;
if (rq->respainner || rq->respamiddle) return 0;
// error check for includegroup with ghost neighbor request