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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11283 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-21 15:43:45 +00:00
parent b26cc714c2
commit f709b5d63a
9 changed files with 120 additions and 126 deletions
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171
src/USER-MISC/fix_imd.cpp
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@ -47,10 +47,6 @@ negotiate an appropriate license for such distribution."
Justin Gullingsrud, and James Phillips, (TCBG, Beckman Institute, UIUC)
------------------------------------------------------------------------- */
#ifdef LAMMPS_BIGBIG
#error LAMMPS_BIGBIG not supported by this file
#endif
#include "fix_imd.h"
#include "atom.h"
#include "comm.h"
@ -83,48 +79,51 @@ negotiate an appropriate license for such distribution."
#include <errno.h>
using namespace LAMMPS_NS;
using namespace FixConst;
/* re-usable integer hash table code with static linkage. */
/** hash table top level data structure */
typedef struct inthash_t {
struct inthash_node_t **bucket; /* array of hash nodes */
int size; /* size of the array */
int entries; /* number of entries in table */
int downshift; /* shift cound, used in hash function */
int mask; /* used to select bits for hashing */
} inthash_t;
typedef struct taginthash_t {
struct taginthash_node_t **bucket; /* array of hash nodes */
tagint size; /* size of the array */
tagint entries; /* number of entries in table */
tagint downshift; /* shift count, used in hash function */
tagint mask; /* used to select bits for hashing */
} taginthash_t;
/** hash table node data structure */
typedef struct inthash_node_t {
int data; /* data in hash node */
int key; /* key for hash lookup */
struct inthash_node_t *next; /* next node in hash chain */
} inthash_node_t;
typedef struct taginthash_node_t {
tagint data; /* data in hash node */
tagint key; /* key for hash lookup */
struct taginthash_node_t *next; /* next node in hash chain */
} taginthash_node_t;
#define HASH_FAIL -1
#define HASH_LIMIT 0.5
/* initialize new hash table */
static void inthash_init(inthash_t *tptr, int buckets);
static void taginthash_init(taginthash_t *tptr, tagint buckets);
/* lookup entry in hash table */
static int inthash_lookup(const inthash_t *tptr, int key);
static tagint taginthash_lookup(const taginthash_t *tptr, tagint key);
/* generate list of keys for reverse lookups. */
static int *inthash_keys(inthash_t *tptr);
/* insert an entry into hash table. */
static int inthash_insert(inthash_t *tptr, int key, int data);
static tagint *taginthash_keys(taginthash_t *tptr);
/* insert an entry taginto hash table. */
static tagint taginthash_insert(taginthash_t *tptr, tagint key, tagint data);
/* delete the hash table */
static void inthash_destroy(inthash_t *tptr);
static void taginthash_destroy(taginthash_t *tptr);
/* adapted sort for in-place sorting of map indices. */
static void id_sort(int *idmap, int left, int right);
static void id_sort(tagint *idmap, tagint left, tagint right);
/************************************************************************
* integer hash code:
************************************************************************/
/* inthash() - Hash function returns a hash number for a given key.
/* taginthash() - Hash function returns a hash number for a given key.
* tptr: Pointer to a hash table, key: The key to create a hash number for */
static int inthash(const inthash_t *tptr, int key) {
int hashvalue;
static tagint taginthash(const taginthash_t *tptr, tagint key) {
tagint hashvalue;
hashvalue = (((key*1103515249)>>tptr->downshift) & tptr->mask);
if (hashvalue < 0) {
@ -135,25 +134,25 @@ static int inthash(const inthash_t *tptr, int key) {
}
/*
* rebuild_table_int() - Create new hash table when old one fills up.
* rebuild_table_tagint() - Create new hash table when old one fills up.
*
* tptr: Pointer to a hash table
*/
static void rebuild_table_int(inthash_t *tptr) {
inthash_node_t **old_bucket, *old_hash, *tmp;
int old_size, h, i;
static void rebuild_table_tagint(taginthash_t *tptr) {
taginthash_node_t **old_bucket, *old_hash, *tmp;
tagint old_size, h, i;
old_bucket=tptr->bucket;
old_size=tptr->size;
/* create a new table and rehash old buckets */
inthash_init(tptr, old_size<<1);
taginthash_init(tptr, old_size<<1);
for (i=0; i<old_size; i++) {
old_hash=old_bucket[i];
while(old_hash) {
tmp=old_hash;
old_hash=old_hash->next;
h=inthash(tptr, tmp->key);
h=taginthash(tptr, tmp->key);
tmp->next=tptr->bucket[h];
tptr->bucket[h]=tmp;
tptr->entries++;
@ -167,12 +166,12 @@ static void rebuild_table_int(inthash_t *tptr) {
}
/*
* inthash_init() - Initialize a new hash table.
* taginthash_init() - Initialize a new hash table.
*
* tptr: Pointer to the hash table to initialize
* buckets: The number of initial buckets to create
*/
void inthash_init(inthash_t *tptr, int buckets) {
void taginthash_init(taginthash_t *tptr, tagint buckets) {
/* make sure we allocate something */
if (buckets==0)
@ -192,25 +191,25 @@ void inthash_init(inthash_t *tptr, int buckets) {
} /* while */
/* allocate memory for table */
tptr->bucket=(inthash_node_t **) calloc(tptr->size, sizeof(inthash_node_t *));
tptr->bucket=(taginthash_node_t **) calloc(tptr->size, sizeof(taginthash_node_t *));
return;
}
/*
* inthash_lookup() - Lookup an entry in the hash table and return a pointer to
* taginthash_lookup() - Lookup an entry in the hash table and return a pointer to
* it or HASH_FAIL if it wasn't found.
*
* tptr: Pointer to the hash table
* key: The key to lookup
*/
int inthash_lookup(const inthash_t *tptr, int key) {
int h;
inthash_node_t *node;
tagint taginthash_lookup(const taginthash_t *tptr, tagint key) {
tagint h;
taginthash_node_t *node;
/* find the entry in the hash table */
h=inthash(tptr, key);
h=taginthash(tptr, key);
for (node=tptr->bucket[h]; node!=NULL; node=node->next) {
if (node->key == key)
break;
@ -222,17 +221,17 @@ int inthash_lookup(const inthash_t *tptr, int key) {
/*
* inthash_keys() - Return a list of keys.
* taginthash_keys() - Return a list of keys.
* NOTE: the returned list must be freed with free(3).
*/
int *inthash_keys(inthash_t *tptr) {
tagint *taginthash_keys(taginthash_t *tptr) {
int *keys;
inthash_node_t *node;
tagint *keys;
taginthash_node_t *node;
keys = (int *)calloc(tptr->entries, sizeof(int));
keys = (tagint *)calloc(tptr->entries, sizeof(tagint));
for (int i=0; i < tptr->size; ++i) {
for (tagint i=0; i < tptr->size; ++i) {
for (node=tptr->bucket[i]; node != NULL; node=node->next) {
keys[node->data] = node->key;
}
@ -242,29 +241,29 @@ int *inthash_keys(inthash_t *tptr) {
}
/*
* inthash_insert() - Insert an entry into the hash table. If the entry already
* taginthash_insert() - Insert an entry into the hash table. If the entry already
* exists return a pointer to it, otherwise return HASH_FAIL.
*
* tptr: A pointer to the hash table
* key: The key to insert into the hash table
* data: A pointer to the data to insert into the hash table
*/
int inthash_insert(inthash_t *tptr, int key, int data) {
int tmp;
inthash_node_t *node;
int h;
tagint taginthash_insert(taginthash_t *tptr, tagint key, tagint data) {
tagint tmp;
taginthash_node_t *node;
tagint h;
/* check to see if the entry exists */
if ((tmp=inthash_lookup(tptr, key)) != HASH_FAIL)
if ((tmp=taginthash_lookup(tptr, key)) != HASH_FAIL)
return(tmp);
/* expand the table if needed */
while (tptr->entries>=HASH_LIMIT*tptr->size)
rebuild_table_int(tptr);
rebuild_table_tagint(tptr);
/* insert the new entry */
h=inthash(tptr, key);
node=(struct inthash_node_t *) malloc(sizeof(inthash_node_t));
h=taginthash(tptr, key);
node=(struct taginthash_node_t *) malloc(sizeof(taginthash_node_t));
node->data=data;
node->key=key;
node->next=tptr->bucket[h];
@ -275,12 +274,12 @@ int inthash_insert(inthash_t *tptr, int key, int data) {
}
/*
* inthash_destroy() - Delete the entire table, and all remaining entries.
* taginthash_destroy() - Delete the entire table, and all remaining entries.
*
*/
void inthash_destroy(inthash_t *tptr) {
inthash_node_t *node, *last;
int i;
void taginthash_destroy(taginthash_t *tptr) {
taginthash_node_t *node, *last;
tagint i;
for (i=0; i<tptr->size; i++) {
node = tptr->bucket[i];
@ -294,18 +293,18 @@ void inthash_destroy(inthash_t *tptr) {
/* free the entire array of buckets */
if (tptr->bucket != NULL) {
free(tptr->bucket);
memset(tptr, 0, sizeof(inthash_t));
memset(tptr, 0, sizeof(taginthash_t));
}
}
/************************************************************************
* integer list sort code:
* taginteger list sort code:
************************************************************************/
/* sort for integer map. initial call id_sort(idmap, 0, natoms - 1); */
static void id_sort(int *idmap, int left, int right)
/* sort for taginteger map. initial call id_sort(idmap, 0, natoms - 1); */
static void id_sort(tagint *idmap, tagint left, tagint right)
{
int pivot, l_hold, r_hold;
tagint pivot, l_hold, r_hold;
l_hold = left;
r_hold = right;
@ -433,12 +432,9 @@ static void imdsock_destroy(void *);
* The implementation follows at the end of the file. *
***************************************************************/
using namespace LAMMPS_NS;
using namespace FixConst;
/* struct for packed data communication of coordinates and forces. */
struct commdata {
int tag;
tagint tag;
float x,y,z;
};
@ -580,10 +576,10 @@ FixIMD::~FixIMD()
}
#endif
inthash_t *hashtable = (inthash_t *)idmap;
taginthash_t *hashtable = (taginthash_t *)idmap;
memory->destroy(comm_buf);
memory->destroy(force_buf);
inthash_destroy(hashtable);
taginthash_destroy(hashtable);
delete hashtable;
free(rev_idmap);
// close sockets
@ -626,12 +622,13 @@ int FixIMD::reconnect()
if (me == 0) {
if (clientsock) return 1;
if (screen && connect_msg)
if (nowait_flag)
if (screen && connect_msg) {
if (nowait_flag) {
fprintf(screen,"Listening for IMD connection on port %d. Transfer rate %d.\n",imd_port, imd_trate);
else
} else {
fprintf(screen,"Waiting for IMD connection on port %d. Transfer rate %d.\n",imd_port, imd_trate);
}
}
connect_msg = 0;
clientsock = NULL;
if (nowait_flag) {
@ -693,7 +690,7 @@ void FixIMD::setup(int)
int i,j;
int nmax,nme,nlocal;
int *mask = atom->mask;
int *tag = atom->tag;
tagint *tag = atom->tag;
nlocal = atom->nlocal;
nme=0;
for (i=0; i < nlocal; ++i)
@ -712,8 +709,8 @@ void FixIMD::setup(int)
error->all(FLERR,"LAMMPS terminated on error in setting up IMD connection.");
/* initialize and build hashtable. */
inthash_t *hashtable=new inthash_t;
inthash_init(hashtable, num_coords);
taginthash_t *hashtable=new taginthash_t;
taginthash_init(hashtable, num_coords);
idmap = (void *)hashtable;
MPI_Status status;
@ -722,7 +719,7 @@ void FixIMD::setup(int)
struct commdata *buf = static_cast<struct commdata *>(comm_buf);
if (me == 0) {
int *taglist = new int[num_coords];
tagint *taglist = new tagint[num_coords];
int numtag=0; /* counter to map atom tags to a 0-based consecutive index list */
for (i=0; i < nlocal; ++i) {
@ -750,13 +747,13 @@ void FixIMD::setup(int)
* same list when running in parallel and build hash table. */
id_sort(taglist, 0, num_coords-1);
for (i=0; i < num_coords; ++i) {
inthash_insert(hashtable, taglist[i], i);
taginthash_insert(hashtable, taglist[i], i);
}
delete[] taglist;
/* generate reverse index-to-tag map for communicating
* IMD forces back to the proper atoms */
rev_idmap=inthash_keys(hashtable);
rev_idmap=taginthash_keys(hashtable);
} else {
nme=0;
for (i=0; i < nlocal; ++i) {
@ -827,7 +824,7 @@ void FixIMD::post_force(int vflag)
return; /* IMD client has detached and not yet come back. do nothing. */
}
int *tag = atom->tag;
tagint *tag = atom->tag;
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
@ -1040,8 +1037,8 @@ void FixIMD::post_force(int vflag)
for (i=0; i<nlocal; ++i) {
if (mask[i] & groupbit) {
const int j = 3*inthash_lookup((inthash_t *)idmap, tag[i]);
if (j != HASH_FAIL) {
const tagint j = 3*taginthash_lookup((taginthash_t *)idmap, tag[i]);
if (j != 3*HASH_FAIL) {
int ix = (image[i] & IMGMASK) - IMGMAX;
int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int iz = (image[i] >> IMG2BITS) - IMGMAX;
@ -1061,8 +1058,8 @@ void FixIMD::post_force(int vflag)
} else {
for (i=0; i<nlocal; ++i) {
if (mask[i] & groupbit) {
const int j = 3*inthash_lookup((inthash_t *)idmap, tag[i]);
if (j != HASH_FAIL) {
const tagint j = 3*taginthash_lookup((taginthash_t *)idmap, tag[i]);
if (j != 3*HASH_FAIL) {
recvcoord[j] = x[i][0];
recvcoord[j+1] = x[i][1];
recvcoord[j+2] = x[i][2];
@ -1080,8 +1077,8 @@ void FixIMD::post_force(int vflag)
ndata /= size_one;
for (k=0; k<ndata; ++k) {
const int j = 3*inthash_lookup((inthash_t *)idmap, buf[k].tag);
if (j != HASH_FAIL) {
const tagint j = 3*taginthash_lookup((taginthash_t *)idmap, buf[k].tag);
if (j != 3*HASH_FAIL) {
recvcoord[j] = buf[k].x;
recvcoord[j+1] = buf[k].y;
recvcoord[j+2] = buf[k].z;