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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8391 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-25 16:42:20 +00:00
parent bee842bed7
commit e8ff810ee7
78 changed files with 396 additions and 474 deletions
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255
src/atom.cpp
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@ -129,21 +129,17 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
nextra_store = 0;
extra = NULL;
// default mapping values and hash table primes
// default mapping values
tag_enable = 1;
map_style = 0;
map_tag_max = 0;
map_nhash = 0;
nprimes = 38;
primes = new int[nprimes];
int plist[] = {5041,10007,20011,30011,40009,50021,60013,70001,80021,
90001,100003,110017,120011,130003,140009,150001,160001,
170003,180001,190027,200003,210011,220009,230003,240007,
250007,260003,270001,280001,290011,300007,310019,320009,
330017,340007,350003,362881,3628801};
for (int i = 0; i < nprimes; i++) primes[i] = plist[i];
sametag = NULL;
map_array = NULL;
map_bucket = NULL;
map_hash = NULL;
// default atom style = atomic
@ -236,7 +232,6 @@ Atom::~Atom()
// delete mapping data structures
map_delete();
delete [] primes;
}
/* ----------------------------------------------------------------------
@ -431,243 +426,6 @@ void Atom::modify_params(int narg, char **arg)
}
}
/* ----------------------------------------------------------------------
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
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
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;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
MPI_Allreduce(&max,&map_tag_max,1,MPI_INT,MPI_MAX,world);
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;
} else {
// map_nhash = max of atoms/proc or total atoms, times 2, at least 1000
int nper = static_cast<int> (natoms/comm->nprocs);
map_nhash = MAX(nper,nmax);
if (map_nhash > natoms) map_nhash = static_cast<int> (natoms);
if (comm->nprocs > 1) map_nhash *= 2;
map_nhash = MAX(map_nhash,1000);
// map_nbucket = prime just larger than map_nhash
int n = map_nhash/10000;
n = MIN(n,nprimes-1);
map_nbucket = primes[n];
if (map_nbucket < map_nhash && n < nprimes-1) map_nbucket = primes[n+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;
}
}
/* ----------------------------------------------------------------------
clear global -> local map for all of my own and ghost atoms
for hash table option:
global ID may not be in table if image atom was already cleared
------------------------------------------------------------------------- */
void Atom::map_clear()
{
if (map_style == 1) {
int nall = nlocal + nghost;
for (int i = 0; i < nall; i++) map_array[tag[i]] = -1;
} else {
int previous,global,ibucket,index;
int nall = nlocal + nghost;
for (int i = 0; i < nall; i++) {
// search for key
// if don't find it, done
previous = -1;
global = tag[i];
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index == -1) continue;
// delete the hash entry and add it to free list
// special logic if entry is 1st in the bucket
if (previous == -1) map_bucket[ibucket] = map_hash[index].next;
else map_hash[previous].next = map_hash[index].next;
map_hash[index].next = map_free;
map_free = index;
map_nused--;
}
}
}
/* ----------------------------------------------------------------------
set global -> local map for all of my own and ghost atoms
loop in reverse order so that nearby images take precedence over far ones
and owned atoms take precedence over images
this enables valid lookups of bond topology atoms
for hash table option:
if hash table too small, re-init
global ID may already be in table if image atom was set
------------------------------------------------------------------------- */
void Atom::map_set()
{
if (map_style == 1) {
int nall = nlocal + nghost;
for (int i = nall-1; i >= 0 ; i--) map_array[tag[i]] = i;
} else {
int previous,global,ibucket,index;
int nall = nlocal + nghost;
if (nall > map_nhash) map_init();
for (int i = nall-1; i >= 0 ; i--) {
// search for key
// if found it, just overwrite local value with index
previous = -1;
global = tag[i];
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index > -1) {
map_hash[index].local = i;
continue;
}
// take one entry from free list
// add the new global/local pair as entry at end of bucket list
// special logic if this entry is 1st in bucket
index = map_free;
map_free = map_hash[map_free].next;
if (previous == -1) map_bucket[ibucket] = index;
else map_hash[previous].next = index;
map_hash[index].global = global;
map_hash[index].local = i;
map_hash[index].next = -1;
map_nused++;
}
}
}
/* ----------------------------------------------------------------------
set global to local map for one atom
for hash table option:
global ID may already be in table if atom was already set
------------------------------------------------------------------------- */
void Atom::map_one(int global, int local)
{
if (map_style == 1) map_array[global] = local;
else {
// search for key
// if found it, just overwrite local value with index
int previous = -1;
int ibucket = global % map_nbucket;
int index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index > -1) {
map_hash[index].local = local;
return;
}
// take one entry from free list
// add the new global/local pair as entry at end of bucket list
// special logic if this entry is 1st in bucket
index = map_free;
map_free = map_hash[map_free].next;
if (previous == -1) map_bucket[ibucket] = index;
else map_hash[previous].next = index;
map_hash[index].global = global;
map_hash[index].local = local;
map_hash[index].next = -1;
map_nused++;
}
}
/* ----------------------------------------------------------------------
free the array or hash table for global to local mapping
------------------------------------------------------------------------- */
void Atom::map_delete()
{
if (map_style == 1) {
if (map_tag_max) memory->destroy(map_array);
} else {
if (map_nhash) {
delete [] map_bucket;
delete [] map_hash;
}
map_nhash = 0;
}
map_tag_max = 0;
}
/* ----------------------------------------------------------------------
lookup global ID in hash table, return local index
------------------------------------------------------------------------- */
int Atom::map_find_hash(int global)
{
int local = -1;
int index = map_bucket[global % map_nbucket];
while (index > -1) {
if (map_hash[index].global == global) {
local = map_hash[index].local;
break;
}
index = map_hash[index].next;
}
return local;
}
/* ----------------------------------------------------------------------
add unique tags to any atoms with tag = 0
new tags are grouped by proc and start after max current tag
@ -1644,6 +1402,7 @@ bigint Atom::memory_usage()
bigint bytes = avec->memory_usage();
memory->destroy(memstr);
bytes += smax*sizeof(int);
if (map_style == 1)
bytes += memory->usage(map_array,map_tag_max+1);
else if (map_style == 2) {