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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11766 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-04-10 20:21:07 +00:00
parent e6edae3916
commit 0343052dc9
9 changed files with 81 additions and 74 deletions
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5
src/USER-REAXC/fix_qeq_reax.cpp
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@ -322,13 +322,14 @@ void FixQEqReax::init()
error->all(FLERR,"Must use pair_style reax/c with fix qeq/reax");
// need a half neighbor list w/ Newton off and ghost neighbors
// built whenever re-neighboring occurs
// make it occasional if QeQ not performed every timestep
int irequest = neighbor->request(this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->newton = 2;
neighbor->requests[irequest]->ghost = 1;
if (nevery) neighbor->requests[irequest]->occasional = 1;
init_shielding();
init_taper();
@ -523,12 +524,14 @@ void FixQEqReax::compute_H()
tagint *tag = atom->tag;
x = atom->x;
if (nevery > 1) neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// fill in the H matrix
m_fill = 0;
r_sqr = 0;
for( ii = 0; ii < inum; ii++ ) {

6
src/delete_atoms.cpp
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@ -266,8 +266,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
error->all(FLERR,"Delete_atoms cutoff > neighbor cutoff");
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor list based on earlier request
// acquire ghosts and build standard neighbor lists
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@ -277,6 +276,9 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
// build neighbor list this command needs based on earlier request
NeighList *list = neighbor->lists[irequest];
neighbor->build_one(irequest);

4
src/neigh_full.cpp
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@ -247,7 +247,7 @@ void Neighbor::full_bin(NeighList *list)
// bin owned & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -355,7 +355,7 @@ void Neighbor::full_bin_ghost(NeighList *list)
// bin owned & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;

8
src/neigh_half_bin.cpp
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@ -38,7 +38,7 @@ void Neighbor::half_bin_no_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -151,7 +151,7 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -291,7 +291,7 @@ void Neighbor::half_bin_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -433,7 +433,7 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;

2
src/neigh_list.cpp
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@ -42,6 +42,8 @@ NeighList::NeighList(LAMMPS *lmp) :
dnum = 0;
last_build = -1;
iskip = NULL;
ijskip = NULL;

2
src/neigh_list.h
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@ -45,6 +45,8 @@ class NeighList : protected Pointers {
MyPage<int> *ipage; // pages of neighbor indices
MyPage<double> *dpage; // pages of neighbor doubles, if dnum > 0
bigint last_build; // timestep of last build for occasional lists
// atom types to skip when building list
// iskip,ijskip are just ptrs to corresponding request

6
src/neigh_respa.cpp
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@ -378,7 +378,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -548,7 +548,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -765,7 +765,7 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;

117
src/neighbor.cpp
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@ -83,6 +83,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
binsizeflag = 0;
build_once = 0;
cluster_check = 0;
binatomflag = 1;
cutneighsq = NULL;
cutneighghostsq = NULL;
@ -508,27 +509,6 @@ void Neighbor::init()
// detect lists that are connected to other lists
// if-then-else sequence and processed flag is important
// since don't want to re-process skip or copy lists further down
// skip list needs to have granhistory or respa info added
// copy: point this list at request->otherlist, could be a skip list
// skip: point this list at request->otherlist, copy skip info from request
// also set granular and respa info if applicable
// half_from_full: point this list at preceeding full list
// granhistory: set preceeding list's listgranhistory to this list
// also set preceeding list's ptr to FixShearHistory
// respaouter: point this list at preceeding 1/2 inner/middle lists
// 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:
// whether request is occasional or not doesn't matter
// if request = half and non-skip pair half/respaouter exists,
// become copy of that list if cudable flag matches
// if request = full and non-skip pair full exists,
// become copy of that list if cudable flag matches
// if request = half and non-skip pair full exists,
// become half_from_full of that list if cudable flag matches
// if no matches, do nothing, fix/compute list will be built directly
// ok if parent is copy list
int processed;
@ -536,20 +516,32 @@ void Neighbor::init()
if (!lists[i]) continue;
processed = 0;
// copy: point this list at request->otherlist, could be a skip list
if (requests[i]->copy) {
lists[i]->listcopy = lists[requests[i]->otherlist];
processed = 1;
// skip: point this list at request->otherlist,
// copy skip info from request
// skip list still needs to have granhistory or respa info added below
} else if (requests[i]->skip) {
lists[i]->listskip = lists[requests[i]->otherlist];
lists[i]->copy_skip_info(requests[i]->iskip,requests[i]->ijskip);
processed = 1;
// half_from_full: point this list at full list that comes right before
// will only be case if pair style requested one after other
} else if (requests[i]->half_from_full) {
lists[i]->listfull = lists[i-1];
processed = 1;
}
// granhistory: set preceeding list's listgranhistory to this list
// also set preceeding list's ptr to FixShearHistory
if (requests[i]->granhistory) {
lists[i-1]->listgranhistory = lists[i];
for (int ifix = 0; ifix < modify->nfix; ifix++)
@ -557,6 +549,8 @@ void Neighbor::init()
lists[i-1]->fix_history = (FixShearHistory *) modify->fix[ifix];
processed = 1;
// respaouter: point this list at preceeding 1/2 inner/middle lists
} else if (requests[i]->respaouter) {
if (requests[i-1]->respainner) {
lists[i]->respamiddle = 0;
@ -571,6 +565,10 @@ void Neighbor::init()
if (processed) continue;
// 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
if (requests[i]->pair && requests[i]->half) {
for (j = 0; j < nrequest; j++) {
if (!lists[j]) continue;
@ -583,6 +581,18 @@ void Neighbor::init()
lists[i]->listfull = lists[j];
}
// fix/compute requests:
// whether request is occasional or not doesn't matter
// if request = half and non-skip pair half/respaouter exists,
// become copy of that list if cudable flag matches
// if request = full and non-skip pair full exists,
// become copy of that list if cudable flag matches
// if request = half and non-skip pair full exists,
// become half_from_full of that list if cudable flag matches
// if no matches, do nothing
// fix/compute list will be built independently as needed
// ok if parent is itself a copy list
} else if (requests[i]->fix || requests[i]->compute) {
for (j = 0; j < nrequest; j++) {
if (!lists[j]) continue;
@ -1349,8 +1359,8 @@ int Neighbor::check_distance()
}
/* ----------------------------------------------------------------------
build all perpetual neighbor lists every few timesteps
pairwise & topology lists are created as needed
build perpetuals neighbor lists
called at setup and every few timesteps during run or minimization
topology lists only built if topoflag = 1, USER-CUDA calls with topoflag = 0
------------------------------------------------------------------------- */
@ -1419,12 +1429,12 @@ void Neighbor::build(int topoflag)
memory->create(bins,maxbin,"bins");
}
// check that neighbor list with special bond flags will not overflow
// check that using special bond flags will not overflow neigh lists
if (atom->nlocal+atom->nghost > NEIGHMASK)
error->one(FLERR,"Too many local+ghost atoms for neighbor list");
// invoke building of pair and molecular neighbor lists
// invoke building of pair and molecular topology neighbor lists
// only for pairwise lists with buildflag set
// blist is for standard neigh lists, otherwise is a Kokkos list
@ -1455,9 +1465,22 @@ void Neighbor::build_topology()
called by other classes
------------------------------------------------------------------------- */
void Neighbor::build_one(int i)
void Neighbor::build_one(int i, int preflag)
{
// update stencils and grow atom arrays and bins as needed
// no need to build if already built since last re-neighbor
// preflag is set by fix bond/create and fix bond/swap
// b/c they invoke build_one() on same step neigh list is re-built,
// but before re-build, so need to use ">" instead of ">="
if (preflag) {
if (lists[i]->last_build > lastcall) return;
} else {
if (lists[i]->last_build >= lastcall) return;
}
lists[i]->last_build = update->ntimestep;
// update stencils and grow atom arrays as needed
// only for relevant settings of stencilflag and growflag
// grow atom array for this list to current size of perpetual lists
@ -1468,42 +1491,14 @@ void Neighbor::build_one(int i)
if (lists[i]->growflag) lists[i]->grow(maxatom);
// extend atom bin list if necessary
if (style != NSQ && atom->nmax > maxbin) {
maxbin = atom->nmax;
memory->destroy(bins);
memory->create(bins,maxbin,"bins");
}
// check that neighbor list with special bond flags will not overflow
if (atom->nlocal+atom->nghost > NEIGHMASK)
error->one(FLERR,"Too many local+ghost atoms for neighbor list");
// when occasional list built, LAMMPS can crash if atoms have moved too far
// why is this? maybe b/c this list is derived from some now out-of-date list?
// give warning if this is the case
// no easy workaround b/c all neighbor lists really need to be rebuilt
// solution is for input script to check more often for rebuild
// only check_distance if running a simulation, not between simulations
// comment out for now
// is sometimes giving warning when there is no issue
// e.g. when a variable uses a fix with an occasional neigh list
// at the beginning of a timestep (e.g. fix move) where
// all neigh lists are about to be re-built anyway
/*
int flag = 0;
if (dist_check && update->whichflag) flag = check_distance();
if (flag && me == 0) {
printf("BUILD ONE ERROR: %ld\n",update->ntimestep);
error->warning(FLERR,"Building an occasional neighbor list when "
"atoms may have moved too far");
}
*/
// build list I, turning off atom binning
// binning results from last re-neighbor should be used instead
// if re-bin now, atoms may have moved outside of proc domain & bin extent,
// leading to errors or even a crash
binatomflag = 0;
(this->*pair_build[i])(lists[i]);
binatomflag = 1;
}
/* ----------------------------------------------------------------------

5
src/neighbor.h
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@ -75,7 +75,7 @@ class Neighbor : protected Pointers {
void setup_bins(); // setup bins based on box and cutoff
virtual void build(int topoflag=1); // create all neighbor lists (pair,bond)
virtual void build_topology(); // create all topology neighbor lists
void build_one(int); // create a single neighbor list
void build_one(int, int preflag=0); // create a single neighbor list
void set(int, char **); // set neighbor style and skin distance
void modify_params(int, char**); // modify parameters that control builds
bigint memory_usage();
@ -107,6 +107,9 @@ class Neighbor : protected Pointers {
double boxlo_hold[3],boxhi_hold[3]; // box size at last neighbor build
double corners_hold[8][3]; // box corners at last neighbor build
int binatomflag; // bin atoms or not when build neigh list
// turned off by build_one()
int nbinx,nbiny,nbinz; // # of global bins
int *bins; // ptr to next atom in each bin
int maxbin; // size of bins array