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

This commit is contained in:
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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@ -44,4 +44,4 @@ The person who created this package is Axel Kohlmeyer at Temple U
--------------------------------- ---------------------------------
Version: 2013-06-27 Version: 2013-12-16

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@ -1,7 +1,3 @@
#ifdef LAMMPS_BIGBIG
#error LAMMPS_BIGBIG not supported by this file
#endif
#include "mpi.h" #include "mpi.h"
#include "lammps.h" #include "lammps.h"
#include "atom.h" #include "atom.h"

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@ -443,6 +443,11 @@ void FixColvars::one_time_init()
if (screen) fputs("colvars: Creating proxy instance\n",screen); if (screen) fputs("colvars: Creating proxy instance\n",screen);
if (logfile) fputs("colvars: Creating proxy instance\n",logfile); if (logfile) fputs("colvars: Creating proxy instance\n",logfile);
#ifdef LAMMPS_BIGBIG
if (screen) fputs("colvars: cannot handle atom ids > 2147483647\n",screen);
if (logfile) fputs("colvars: cannot handle atom ids > 2147483647\n",logfile);
#endif
if (inp_name) { if (inp_name) {
if (strcmp(inp_name,"NULL") == 0) { if (strcmp(inp_name,"NULL") == 0) {
memory->sfree(inp_name); memory->sfree(inp_name);
@ -490,14 +495,14 @@ void FixColvars::one_time_init()
inthash_insert(hashtable, tl[i], i); inthash_insert(hashtable, tl[i], i);
} }
} }
MPI_Bcast(taglist, num_coords, MPI_INT, 0, world); MPI_Bcast(taglist, num_coords, MPI_LMP_TAGINT, 0, world);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixColvars::setup(int vflag) void FixColvars::setup(int vflag)
{ {
const int * const tag = atom->tag; const tagint * const tag = atom->tag;
const int * const type = atom->type; const int * const type = atom->type;
int i,nme,tmp,ndata; int i,nme,tmp,ndata;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
@ -510,7 +515,7 @@ void FixColvars::setup(int vflag)
// determine size of comm buffer // determine size of comm buffer
nme=0; nme=0;
for (i=0; i < num_coords; ++i) { for (i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) if ((k >= 0) && (k < nlocal))
++nme; ++nme;
} }
@ -536,7 +541,7 @@ void FixColvars::setup(int vflag)
// store coordinate data in holding array, clear old forces // store coordinate data in holding array, clear old forces
for (i=0; i<num_coords; ++i) { for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) { if ((k >= 0) && (k < nlocal)) {
of[i].tag = cd[i].tag = tag[k]; of[i].tag = cd[i].tag = tag[k];
@ -593,7 +598,7 @@ void FixColvars::setup(int vflag)
nme = 0; nme = 0;
for (i=0; i<num_coords; ++i) { for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) { if ((k >= 0) && (k < nlocal)) {
comm_buf[nme].tag = tag[k]; comm_buf[nme].tag = tag[k];
@ -665,7 +670,7 @@ void FixColvars::post_force(int vflag)
} }
} }
const int * const tag = atom->tag; const tagint * const tag = atom->tag;
const double * const * const x = atom->x; const double * const * const x = atom->x;
double * const * const f = atom->f; double * const * const f = atom->f;
const imageint * const image = atom->image; const imageint * const image = atom->image;
@ -681,7 +686,7 @@ void FixColvars::post_force(int vflag)
/* check and potentially grow local communication buffers. */ /* check and potentially grow local communication buffers. */
int i,nmax_new,nme=0; int i,nmax_new,nme=0;
for (i=0; i < num_coords; ++i) { for (i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) if ((k >= 0) && (k < nlocal))
++nme; ++nme;
} }
@ -702,7 +707,7 @@ void FixColvars::post_force(int vflag)
// store coordinate data // store coordinate data
for (i=0; i<num_coords; ++i) { for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) { if ((k >= 0) && (k < nlocal)) {
if (unwrap_flag) { if (unwrap_flag) {
@ -744,7 +749,7 @@ void FixColvars::post_force(int vflag)
/* copy coordinate data into communication buffer */ /* copy coordinate data into communication buffer */
nme = 0; nme = 0;
for (i=0; i<num_coords; ++i) { for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) { if ((k >= 0) && (k < nlocal)) {
comm_buf[nme].tag = tag[k]; comm_buf[nme].tag = tag[k];
@ -796,7 +801,7 @@ void FixColvars::post_force(int vflag)
MPI_Bcast(force_buf, 3*num_coords, MPI_DOUBLE, 0, world); MPI_Bcast(force_buf, 3*num_coords, MPI_DOUBLE, 0, world);
for (int i=0; i < num_coords; ++i) { for (int i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) { if ((k >= 0) && (k < nlocal)) {
f[k][0] += force_buf[3*i+0]; f[k][0] += force_buf[3*i+0];
f[k][1] += force_buf[3*i+1]; f[k][1] += force_buf[3*i+1];
@ -824,14 +829,14 @@ void FixColvars::end_of_step()
{ {
if (store_forces) { if (store_forces) {
const int * const tag = atom->tag; const tagint * const tag = atom->tag;
double * const * const f = atom->f; double * const * const f = atom->f;
const int nlocal = atom->nlocal; const int nlocal = atom->nlocal;
/* check and potentially grow local communication buffers. */ /* check and potentially grow local communication buffers. */
int i,nmax_new,nme=0; int i,nmax_new,nme=0;
for (i=0; i < num_coords; ++i) { for (i=0; i < num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) if ((k >= 0) && (k < nlocal))
++nme; ++nme;
} }
@ -852,7 +857,7 @@ void FixColvars::end_of_step()
std::vector<struct commdata> &of = *oforce; std::vector<struct commdata> &of = *oforce;
for (i=0; i<num_coords; ++i) { for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) { if ((k >= 0) && (k < nlocal)) {
const int j = inthash_lookup(idmap, tag[k]); const int j = inthash_lookup(idmap, tag[k]);
@ -887,7 +892,7 @@ void FixColvars::end_of_step()
/* copy total force data into communication buffer */ /* copy total force data into communication buffer */
nme = 0; nme = 0;
for (i=0; i<num_coords; ++i) { for (i=0; i<num_coords; ++i) {
const int k = atom->map(taglist[i]); const tagint k = atom->map(taglist[i]);
if ((k >= 0) && (k < nlocal)) { if ((k >= 0) && (k < nlocal)) {
comm_buf[nme].tag = tag[k]; comm_buf[nme].tag = tag[k];
comm_buf[nme].x = f[k][0]; comm_buf[nme].x = f[k][0];

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@ -65,7 +65,7 @@ class FixColvars : public Fix {
int me; // my MPI rank in this "world". int me; // my MPI rank in this "world".
int num_coords; // total number of atoms controlled by this fix int num_coords; // total number of atoms controlled by this fix
int *taglist; // list of all atom IDs referenced by colvars. tagint *taglist; // list of all atom IDs referenced by colvars.
std::vector<struct commdata> *coords; // coordinates of colvar atoms std::vector<struct commdata> *coords; // coordinates of colvar atoms
std::vector<struct commdata> *forces; // received forces of colvar atoms std::vector<struct commdata> *forces; // received forces of colvar atoms
std::vector<struct commdata> *oforce; // old total forces of colvar atoms std::vector<struct commdata> *oforce; // old total forces of colvar atoms

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@ -30,10 +30,10 @@ using namespace LAMMPS_NS;
helper function. integer comparison for qsort() helper function. integer comparison for qsort()
---------------------------------------------------------------------- */ ---------------------------------------------------------------------- */
static int cmpint(const void *p1, const void *p2) static int cmptagint(const void *p1, const void *p2)
{ {
const int i1 = * static_cast<const int *>(p1); const tagint i1 = * static_cast<const tagint *>(p1);
const int i2 = * static_cast<const int *>(p2); const tagint i2 = * static_cast<const tagint *>(p2);
if (i1 == i2) return 0; if (i1 == i2) return 0;
else { else {
if (i1 < i2) return -1; if (i1 < i2) return -1;
@ -49,7 +49,7 @@ static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
int np, MPI_Comm world, FILE *screen, FILE *logfile) int np, MPI_Comm world, FILE *screen, FILE *logfile)
{ {
char fmt[8]; char fmt[8];
int *sendlist, *recvlist; tagint *sendlist, *recvlist;
bigint num = group->count(gid); bigint num = group->count(gid);
int lnum, cols; int lnum, cols;
@ -77,13 +77,13 @@ static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
if (num > 0) { if (num > 0) {
const int * const mask = atom->mask; const int * const mask = atom->mask;
const int * const tag = atom->tag; const tagint * const tag = atom->tag;
const int groupbit = group->bitmask[gid]; const int groupbit = group->bitmask[gid];
const int nlocal = atom->nlocal; const int nlocal = atom->nlocal;
int i,j; int i,j;
sendlist = new int[nlocal]; sendlist = new tagint[nlocal];
recvlist = new int[num]; recvlist = new tagint[num];
lnum = 0; lnum = 0;
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) sendlist[lnum++] = tag[i]; if (mask[i] & groupbit) sendlist[lnum++] = tag[i];
@ -97,18 +97,18 @@ static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
allrecv = lnum; allrecv = lnum;
for (int i=1; i < np; ++i) { for (int i=1; i < np; ++i) {
MPI_Irecv(recvlist+allrecv,num-allrecv,MPI_INT,i,0, world,&request); MPI_Irecv(recvlist+allrecv,num-allrecv,MPI_LMP_TAGINT,i,0, world,&request);
MPI_Send(&nrecv,0,MPI_INT,i,0,world); MPI_Send(&nrecv,0,MPI_INT,i,0,world);
MPI_Wait(&request,&status); MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&nrecv); MPI_Get_count(&status,MPI_LMP_TAGINT,&nrecv);
allrecv += nrecv; allrecv += nrecv;
} }
// sort received list // sort received list
qsort((void *)recvlist, num, sizeof(int), cmpint); qsort((void *)recvlist, num, sizeof(tagint), cmptagint);
} else { } else {
MPI_Recv(&nrecv,0,MPI_INT,0,0,world,&status); MPI_Recv(&nrecv,0,MPI_INT,0,0,world,&status);
MPI_Rsend(sendlist,lnum,MPI_INT,0,0,world); MPI_Rsend(sendlist,lnum,MPI_LMP_TAGINT,0,0,world);
} }
delete [] sendlist; delete [] sendlist;
} }

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

View File

@ -82,7 +82,7 @@ class FixIMD : public Fix {
int maxbuf; // size of atom communication buffer. int maxbuf; // size of atom communication buffer.
void *comm_buf; // communication buffer void *comm_buf; // communication buffer
void *idmap; // hash for mapping atom indices to consistent order. void *idmap; // hash for mapping atom indices to consistent order.
int *rev_idmap; // list of the hash keys for reverse mapping. tagint *rev_idmap; // list of the hash keys for reverse mapping.
int imd_forces; // number of forces communicated via IMD. int imd_forces; // number of forces communicated via IMD.
void *force_buf; // force data buffer void *force_buf; // force data buffer

View File

@ -15,10 +15,6 @@
Contributing author: Axel Kohlmeyer (Temple U) Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#ifdef LAMMPS_BIGBIG
#error LAMMPS_BIGBIG not supported by this file
#endif
#include <stdio.h> #include <stdio.h>
#include <string.h> #include <string.h>
#include <math.h> #include <math.h>
@ -305,11 +301,11 @@ void DumpMolfile::openfile()
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void DumpMolfile::pack(int *ids) void DumpMolfile::pack(tagint *ids)
{ {
int m,n; int m,n;
int *tag = atom->tag; tagint *tag = atom->tag;
int *type = atom->type; int *type = atom->type;
double **x = atom->x; double **x = atom->x;
imageint *image = atom->image; imageint *image = atom->image;

View File

@ -49,7 +49,7 @@ class DumpMolfile : public Dump {
virtual void init_style(); virtual void init_style();
virtual int modify_param(int, char **); virtual int modify_param(int, char **);
virtual void write_header(bigint) {}; virtual void write_header(bigint) {};
virtual void pack(int *); virtual void pack(tagint *);
virtual void write_data(int, double *); virtual void write_data(int, double *);
virtual bigint memory_usage(); virtual bigint memory_usage();
virtual void openfile(); virtual void openfile();