/* set current vmdcon log level */
void vmdcon_set_loglvl(int lvl)
{
wkf_mutex_lock(&vmdcon_status_lock);
vmdcon_loglvl=lvl;
wkf_mutex_unlock(&vmdcon_status_lock);
}
extern "C" void * bondsearchthread(void *voidparms) {
int i, j, aindex;
int paircount = 0;
bondsearchthrparms *parms = (bondsearchthrparms *) voidparms;
const int threadid = parms->threadid;
const int threadcount = parms->threadcount;
wkf_mutex_t *pairlistmutex = parms->pairlistmutex;
const float *pos = parms->pos;
const float *radii = parms->radii;
const int totb = parms->totb;
const int **boxatom = (const int **) parms->boxatom;
const int *numinbox = parms->numinbox;
const int **nbrlist = (const int **) parms->nbrlist;
const int maxpairs = parms->maxpairs;
const float pairdist = parms->pairdist;
ResizeArray<int> *pairs = new ResizeArray<int>;
float sqdist = pairdist * pairdist;
wkfmsgtimer *msgt = wkf_msg_timer_create(5);
for (aindex = threadid; (aindex < totb) && (paircount < maxpairs); aindex+=threadcount) {
const int *tmpbox, *nbr;
tmpbox = boxatom[aindex];
int anbox = numinbox[aindex];
if (((aindex & 255) == 0) && wkf_msg_timer_timeout(msgt)) {
char tmpbuf[128];
sprintf(tmpbuf, "%6.2f", (100.0f * aindex) / (float) totb);
// XXX: we have to use printf here as msgInfo is not thread-safe.
// msgInfo << "vmd_gridsearch_bonds (thread " << threadid << "): "
// << tmpbuf << "% complete" << sendmsg;
printf("vmd_gridsearch_bonds (thread %d): %s %% complete\n",
threadid, tmpbuf);
}
for (nbr = nbrlist[aindex]; (*nbr != -1) && (paircount < maxpairs); nbr++) {
int nnbr=*nbr;
const int *nbrbox = boxatom[nnbr];
int nbox=numinbox[nnbr];
int self = (aindex == nnbr) ? 1 : 0;
for (i=0; (i<anbox) && (paircount < maxpairs); i++) {
int ind1 = tmpbox[i];
const float *p1 = pos + 3L*ind1;
// skip over self and already-tested atoms
int startj = (self) ? i+1 : 0;
for (j=startj; (j<nbox) && (paircount < maxpairs); j++) {
int ind2 = nbrbox[j];
const float *p2 = pos + 3L*ind2;
float dx = p1[0] - p2[0];
float dy = p1[1] - p2[1];
float dz = p1[2] - p2[2];
float ds2 = dx*dx + dy*dy + dz*dz;
// perform distance test, but ignore pairs between atoms
// with nearly identical coords
if ((ds2 > sqdist) || (ds2 < 0.001))
continue;
if (radii) { // Do atom-specific distance check
float cut = 0.6f * (radii[ind1] + radii[ind2]);
if (ds2 > cut*cut)
continue;
}
pairs->append(ind1);
pairs->append(ind2);
paircount++;
}
}
}
}
// setup results pairlist node
GridSearchPairlist *head;
head = (GridSearchPairlist *) malloc(sizeof(GridSearchPairlist));
head->next = NULL;
head->pairlist = pairs;
wkf_mutex_lock(pairlistmutex); // lock pairlist before update
parms->head = head;
wkf_mutex_unlock(pairlistmutex); // unlock pairlist after update
wkf_msg_timer_destroy(msgt);
return NULL;
}
