/* initialize vmdcon */
void vmdcon_init(void)
{
wkf_mutex_init(&vmdcon_status_lock);
wkf_mutex_init(&vmdcon_output_lock);
vmdcon_set_status(VMDCON_NONE, NULL);
}
// setup and launch bond search threads
int vmd_bondsearch_thr(const float *pos, const float *radii,
GridSearchPairlist * head,
int totb, int **boxatom,
int *numinbox, int **nbrlist, int maxpairs,
float pairdist) {
int i;
bondsearchthrparms *parms;
wkf_thread_t * threads;
wkf_mutex_t pairlistmutex; ///< guards pairlist
wkf_mutex_init(&pairlistmutex); // init mutex before use
int numprocs = wkf_thread_numprocessors();
/* allocate array of threads */
threads = (wkf_thread_t *) calloc(numprocs * sizeof(wkf_thread_t), 1);
/* allocate and initialize array of thread parameters */
parms = (bondsearchthrparms *) malloc(numprocs * sizeof(bondsearchthrparms));
for (i=0; i<numprocs; i++) {
parms[i].threadid = i;
parms[i].threadcount = numprocs;
parms[i].pairlistmutex = &pairlistmutex;
parms[i].head = NULL;
parms[i].pos = (float *) pos;
parms[i].radii = (float *) radii;
parms[i].totb = totb;
parms[i].boxatom = boxatom;
parms[i].numinbox = numinbox;
parms[i].nbrlist = nbrlist;
parms[i].maxpairs = maxpairs;
parms[i].pairdist = pairdist;
}
#if defined(VMDTHREADS)
/* spawn child threads to do the work */
for (i=0; i<numprocs; i++) {
wkf_thread_create(&threads[i], bondsearchthread, &parms[i]);
}
/* join the threads after work is done */
for (i=0; i<numprocs; i++) {
wkf_thread_join(threads[i], NULL);
}
#else
bondsearchthread(&parms[0]); // single-threaded code
#endif
// assemble final pairlist from sublists
for (i=0; i<numprocs; i++) {
if (parms[i].head != NULL) {
GridSearchPairlist *tmp = head->next;
head->next = parms[i].head;
parms[i].head->next = tmp;
}
}
wkf_mutex_destroy(&pairlistmutex); // destroy mutex when finished
/* free thread parms */
free(parms);
free(threads);
return 0;
}