GridSearchPairlist *vmd_gridsearch_bonds(const float *pos, const float *radii,
int natoms, float pairdist, int maxpairs) {
float min[3], max[3];
int i, xb, yb, zb, xytotb, totb;
int **boxatom, *numinbox, *maxinbox, **nbrlist;
int numon = 0;
float sidelen[3], volume;
int paircount = 0;
// find bounding box for selected atoms, and number of atoms in selection.
#if 1
minmax_3fv_aligned(pos, natoms, min, max);
#else
find_minmax_all(pos, natoms, min, max);
#endif
// check for NaN coordinates propagating to the bounding box result
if (!(max[0] >= min[0] && max[1] >= min[1] && max[2] >= min[2])) {
msgErr << "vmd_gridsearch_bonds: NaN coordinates in bounds, aborting!" << sendmsg;
return NULL;
}
// do sanity checks and complain if we've got bogus atom coordinates,
// we shouldn't ever have density higher than 0.1 atom/A^3, but we'll
// be generous and allow much higher densities.
if (maxpairs != -1) {
vec_sub(sidelen, max, min);
// include estimate for atom radius (1 Angstrom) in volume determination
volume = fabsf((sidelen[0] + 2.0f) * (sidelen[1] + 2.0f) * (sidelen[2] + 2.0f));
if ((numon / volume) > 1.0) {
msgWarn << "vmd_gridsearch_bonds: insane atom density" << sendmsg;
}
}
// I don't want the grid to get too large, otherwise I could run out
// of memory. Octrees would be cool, but I'll just limit the grid size
// and let the performance degrade a little for pathological systems.
// Note that pairdist^2 is what gets used for the actual distance checks;
// from here on out pairdist is only used to set the grid size, so we
// can set it to anything larger than the original pairdist.
const int MAXBOXES = 4000000;
totb = MAXBOXES + 1;
float newpairdist = pairdist;
float xrange = max[0]-min[0];
float yrange = max[1]-min[1];
float zrange = max[2]-min[2];
do {
pairdist = newpairdist;
const float invpairdist = 1.0f / pairdist;
xb = ((int)(xrange*invpairdist))+1;
yb = ((int)(yrange*invpairdist))+1;
zb = ((int)(zrange*invpairdist))+1;
xytotb = yb * xb;
totb = xytotb * zb;
newpairdist = pairdist * 1.26f; // cbrt(2) is about 1.26
} while (totb > MAXBOXES || totb < 1); // check for integer wraparound too
// 2. Sort each atom into appropriate bins
boxatom = (int **) calloc(1, totb*sizeof(int *));
numinbox = (int *) calloc(1, totb*sizeof(int));
maxinbox = (int *) calloc(1, totb*sizeof(int));
if (boxatom == NULL || numinbox == NULL || maxinbox == NULL) {
if (boxatom != NULL)
free(boxatom);
if (numinbox != NULL)
free(numinbox);
if (maxinbox != NULL)
free(maxinbox);
msgErr << "Bondsearch memory allocation failed, bailing out" << sendmsg;
return NULL; // ran out of memory, bail out!
}
const float invpairdist = 1.0f / pairdist;
for (i=0; i<natoms; i++) {
int axb, ayb, azb, aindex, num;
// compute box index for new atom
const float *loc = pos + 3L*i;
axb = (int)((loc[0] - min[0])*invpairdist);
ayb = (int)((loc[1] - min[1])*invpairdist);
azb = (int)((loc[2] - min[2])*invpairdist);
// clamp box indices to valid range in case of FP error
if (axb >= xb) axb = xb-1;
if (ayb >= yb) ayb = yb-1;
if (azb >= zb) azb = zb-1;
aindex = azb * xytotb + ayb * xb + axb;
// grow box if necessary
if ((num = numinbox[aindex]) == maxinbox[aindex]) {
boxatom[aindex] = (int *) realloc(boxatom[aindex], (num+4)*sizeof(int));
maxinbox[aindex] += 4;
}
// store atom index in box
boxatom[aindex][num] = i;
numinbox[aindex]++;
}
free(maxinbox);
nbrlist = (int **) calloc(1, totb*sizeof(int *));
if (make_neighborlist(nbrlist, xb, yb, zb)) {
if (boxatom != NULL) {
for (i=0; i<totb; i++) {
if (boxatom[i] != NULL) free(boxatom[i]);
}
free(boxatom);
}
if (nbrlist != NULL) {
for (i=0; i<totb; i++) {
if (nbrlist[i] != NULL) free(nbrlist[i]);
}
free(nbrlist);
}
free(numinbox);
msgErr << "Bondsearch memory allocation failed, bailing out" << sendmsg;
return NULL; // ran out of memory, bail out!
}
// if maxpairs is "unlimited", set it to the biggest positive int
if (maxpairs < 0) {
maxpairs = 2147483647;
}
// setup head of pairlist
GridSearchPairlist *head, *cur;
head = (GridSearchPairlist *) malloc(sizeof(GridSearchPairlist));
head->next = NULL;
paircount = vmd_bondsearch_thr(pos, radii, head, totb,
boxatom, numinbox, nbrlist,
maxpairs, pairdist);
for (i=0; i<totb; i++) {
free(boxatom[i]);
free(nbrlist[i]);
}
free(boxatom);
free(nbrlist);
free(numinbox);
cur = head->next;
free(head);
if (paircount > maxpairs)
msgErr << "vmdgridsearch_bonds: exceeded pairlist sanity check, aborted" << sendmsg;
return cur;
}
int main() {
int i;
float minfv[3], maxfv[3];
float minf, maxf;
int isz = 100000000;
int sz = 3 * isz;
int *on = (int *) malloc(isz * sizeof(int));
float *fv = (float *) malloc(sz * sizeof(float));
for (i=0; i<sz; i++)
fv[i] = (float) i;
wkf_timerhandle timer = wkf_timer_create();
int j;
for (j=0; j<1; j++) {
memset(on, 0, isz*sizeof(int));
wkf_timer_start(timer);
minmax_1fv_aligned(fv, sz, &minf, &maxf);
wkf_timer_stop(timer);
printf("minmax_1fv_aligned: %f\n", wkf_timer_time(timer));
// printf("min: %f max: %f\n", minf, maxf);
wkf_timer_start(timer);
minmax_3fv_aligned(fv, sz/3, minfv, maxfv);
wkf_timer_stop(timer);
printf("minmax_3fv_aligned: %f\n", wkf_timer_time(timer));
for (i=0; i<3; i++) {
minf += minfv[i];
maxf += maxfv[i];
}
// set exactly one selected atom to measure perf of the
// fast first/last selection traversal loops
on[isz/2 + 7] = 1;
print_firstlast_selection(timer, isz, on);
print_analyze_selection(timer, isz, on);
#if 1
wkf_timer_start(timer);
minmax_selected_3fv_aligned(fv, on, isz, 0, isz-1, minfv, maxfv);
wkf_timer_stop(timer);
printf("minmax_selected_3fv_aligned( 0%%): %f\n", wkf_timer_time(timer));
for (i=0; i<(isz-7); i+=8) {
on[i+7] = 1;
}
print_analyze_selection(timer, isz, on);
wkf_timer_start(timer);
minmax_selected_3fv_aligned(fv, on, isz, 0, isz-1, minfv, maxfv);
wkf_timer_stop(timer);
printf("minmax_selected_3fv_aligned( 12%%): %f\n", wkf_timer_time(timer));
for (i=0; i<3; i++) {
minf += minfv[i];
maxf += maxfv[i];
}
for (i=0; i<(isz-7); i+=8) {
on[i+6] = 1;
}
print_analyze_selection(timer, isz, on);
wkf_timer_start(timer);
minmax_selected_3fv_aligned(fv, on, isz, 0, isz-1, minfv, maxfv);
wkf_timer_stop(timer);
printf("minmax_selected_3fv_aligned( 25%%): %f\n", wkf_timer_time(timer));
for (i=0; i<3; i++) {
minf += minfv[i];
maxf += maxfv[i];
}
for (i=0; i<(isz-7); i+=8) {
on[i+4] = 1;
on[i+5] = 1;
on[i+6] = 1;
on[i+7] = 1;
}
print_analyze_selection(timer, isz, on);
wkf_timer_start(timer);
minmax_selected_3fv_aligned(fv, on, isz, 0, isz-1, minfv, maxfv);
wkf_timer_stop(timer);
printf("minmax_selected_3fv_aligned( 50%%): %f\n", wkf_timer_time(timer));
for (i=0; i<3; i++) {
minf += minfv[i];
maxf += maxfv[i];
}
for (i=0; i<isz; i++)
on[i] = 1;
print_analyze_selection(timer, isz, on);
wkf_timer_start(timer);
minmax_selected_3fv_aligned(fv, on, isz, 0, isz-1, minfv, maxfv);
wkf_timer_stop(timer);
printf("minmax_selected_3fv_aligned(100%%): %f\n", wkf_timer_time(timer));
for (i=0; i<3; i++) {
minf += minfv[i];
maxf += maxfv[i];
}
#endif
msmparms mp;
setupmsm(mp);
wkf_timer_start(timer);
testmsm(mp);
wkf_timer_stop(timer);
printf("MSM testmsm(): %f\n", wkf_timer_time(timer));
finishmsm(mp);
printf("\n");
}
wkf_timer_destroy(timer);
printf("checking sum: %g\n", minf+maxf);
return 0;
}
