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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11250 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-17 18:43:09 +00:00
parent 961be6ee48
commit bad19033d0
172 changed files with 2523 additions and 2184 deletions
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140
src/atom_map.cpp
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@ -25,61 +25,100 @@ using namespace LAMMPS_NS;
allocate and initialize array or hash table for global -> local map
set map_tag_max = largest atom ID (may be larger than natoms)
for array option:
array length = 1 to largest tag of any atom
array length = 1 to map_tag_max
set entire array to -1 as initial values
for hash option:
map_nhash = length of hash table
map_nbucket = # of hash buckets, prime larger than map_nhash
map_nbucket = # of hash buckets, prime larger than map_nhash * 2
so buckets will only be filled with 0 or 1 atoms on average
------------------------------------------------------------------------- */
void Atom::map_init()
{
map_delete();
if (tag_enable == 0)
error->all(FLERR,"Cannot create an atom map unless atoms have IDs");
int max = 0;
int map_style_old = map_style;
// map_tag_max = max ID of any atom that will be in new map
tagint max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
MPI_Allreduce(&max,&map_tag_max,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&max,&map_tag_max,1,MPI_LMP_TAGINT,MPI_MAX,world);
memory->destroy(sametag);
smax = nlocal + nghost + EXTRA;
memory->create(sametag,smax,"atom:sametag");
// set map_style for new map
// if user-selected, use that setting
// else if map_tag_max > 1M, use hash
// else use array
if (map_user) map_style = map_user;
else if (map_tag_max > 1000000) map_style = 2;
else map_style = 1;
if (map_style == 1) {
memory->create(map_array,map_tag_max+1,"atom:map_array");
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
// recreate = 1 if must delete old map and create new map
// recreate = 0 if can re-use old map w/out realloc and just adjust settings
int recreate = 0;
if (map_style != map_style_old) recreate = 1;
else if (map_style == 1 && map_tag_max > max_array) recreate = 1;
else if (map_style == 2 && nlocal+nghost > map_nhash) recreate = 1;
// if not recreating:
// for array, just initialize current map_tag_max values
// for hash, set all buckets to empty, put all entries in free list
if (!recreate) {
if (map_style == 1) {
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
} else {
for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
map_nused = 0;
map_free = 0;
for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
map_hash[map_nhash-1].next = -1;
}
// delete old map and create new one for array or hash
} else {
map_delete();
// map_nhash = max # of atoms that can be hashed on this proc
// set to max of ave atoms/proc or atoms I can store
// multiply by 2, require at least 1000
// doubling means hash table will be re-init only rarely
if (map_style == 1) {
max_array = map_tag_max;
memory->create(map_array,max_array+1,"atom:map_array");
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
} else {
int nper = static_cast<int> (natoms/comm->nprocs);
map_nhash = MAX(nper,nmax);
map_nhash *= 2;
map_nhash = MAX(map_nhash,1000);
// map_nhash = max # of atoms that can be hashed on this proc
// set to max of ave atoms/proc or atoms I can store
// multiply by 2, require at least 1000
// doubling means hash table will need to be re-init only rarely
// map_nbucket = prime just larger than map_nhash
int nper = static_cast<int> (natoms/comm->nprocs);
map_nhash = MAX(nper,nmax);
map_nhash *= 2;
map_nhash = MAX(map_nhash,1000);
map_nbucket = next_prime(map_nhash);
// map_nbucket = prime just larger than map_nhash
// next_prime() should be fast enough,
// about 10% of odd integers are prime above 1M
// set all buckets to empty
// set hash to map_nhash in length
// put all hash entries in free list and point them to each other
map_nbucket = next_prime(map_nhash);
map_bucket = new int[map_nbucket];
for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
// set all buckets to empty
// set hash to map_nhash in length
// put all hash entries in free list and point them to each other
map_bucket = new int[map_nbucket];
for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
map_hash = new HashElem[map_nhash];
map_nused = 0;
map_free = 0;
for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
map_hash[map_nhash-1].next = -1;
map_hash = new HashElem[map_nhash];
map_nused = 0;
map_free = 0;
for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
map_hash[map_nhash-1].next = -1;
}
}
}
@ -99,7 +138,8 @@ void Atom::map_clear()
}
} else {
int previous,global,ibucket,index;
int previous,ibucket,index;
tagint global;
int nall = nlocal + nghost;
for (int i = 0; i < nall; i++) {
sametag[i] = -1;
@ -144,21 +184,37 @@ void Atom::map_clear()
void Atom::map_set()
{
int nall = nlocal + nghost;
if (nall > smax) {
smax = nall + EXTRA;
memory->destroy(sametag);
memory->create(sametag,smax,"atom:sametag");
}
if (map_style == 1) {
// possible reallocation of sametag must come before loop over atoms
// since loop sets sametag
if (nall > max_same) {
max_same = nall + EXTRA;
memory->destroy(sametag);
memory->create(sametag,max_same,"atom:sametag");
}
for (int i = nall-1; i >= 0 ; i--) {
sametag[i] = map_array[tag[i]];
map_array[tag[i]] = i;
}
} else {
int previous,global,ibucket,index;
// possible reallocation of sametag must come after map_init()
// since map_init() will invoke map_delete(), whacking sametag
if (nall > map_nhash) map_init();
if (nall > max_same) {
max_same = nall + EXTRA;
memory->destroy(sametag);
memory->create(sametag,max_same,"atom:sametag");
}
int previous,ibucket,index;
tagint global;
for (int i = nall-1; i >= 0 ; i--) {
sametag[i] = map_find_hash(tag[i]);
@ -203,7 +259,7 @@ void Atom::map_set()
called by Special class
------------------------------------------------------------------------- */
void Atom::map_one(int global, int local)
void Atom::map_one(tagint global, int local)
{
if (map_style == 1) map_array[global] = local;
else {
@ -246,6 +302,7 @@ void Atom::map_delete()
{
memory->destroy(sametag);
sametag = NULL;
max_same = 0;
if (map_style == 1) {
memory->destroy(map_array);
@ -259,7 +316,6 @@ void Atom::map_delete()
}
map_nhash = 0;
}
map_tag_max = 0;
}
/* ----------------------------------------------------------------------
@ -267,7 +323,7 @@ void Atom::map_delete()
called by map() in atom.h
------------------------------------------------------------------------- */
int Atom::map_find_hash(int global)
int Atom::map_find_hash(tagint global)
{
int local = -1;
int index = map_bucket[global % map_nbucket];