CoorPluginData::~CoorPluginData() {
delete plugin;
plugin = NULL;
if (tm) {
wkf_timer_destroy(tm);
tm=NULL;
}
delete [] selection;
}
QuickSurf::~QuickSurf() {
#if defined(VMDCUDA)
if (cudaqs) {
delete cudaqs;
}
#endif
if (voltexmap != NULL)
free(voltexmap);
voltexmap = NULL;
wkf_timer_destroy(timer);
}
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;
}
/// destroy message timer
void wkf_msg_timer_destroy(wkfmsgtimer * mt) {
wkf_timer_destroy(mt->timer);
free(mt);
}
void DrawMolItem::draw_orbital(int density, int wavefnctype, int wavefncspin,
int wavefncexcitation, int orbid,
float isovalue,
int drawbox, int style,
float gridspacing, int stepsize, int thickness) {
if (!mol->numframes() || gridspacing <= 0.0f)
return;
// only recalculate the orbital grid if necessary
int regenorbital=0;
if (density != orbgridisdensity ||
wavefnctype != waveftype ||
wavefncspin != wavefspin ||
wavefncexcitation != wavefexcitation ||
orbid != gridorbid ||
gridspacing != orbgridspacing ||
orbvol == NULL ||
needRegenerate & MOL_REGEN ||
needRegenerate & SEL_REGEN) {
regenorbital=1;
}
double motime=0, voltime=0, gradtime=0;
wkf_timerhandle timer = wkf_timer_create();
wkf_timer_start(timer);
if (regenorbital) {
// XXX this needs to be fixed so that things like the
// draw multiple frames feature will work correctly for Orbitals
int frame = mol->frame(); // draw currently active frame
const Timestep *ts = mol->get_frame(frame);
if (!ts->qm_timestep || !mol->qm_data ||
!mol->qm_data->num_basis || orbid < 1) {
wkf_timer_destroy(timer);
return;
}
// Find the timestep independent wavefunction ID tag
// by comparing type, spin, and excitation with the
// signatures of existing wavefunctions.
int waveid = mol->qm_data->find_wavef_id_from_gui_specs(
wavefnctype, wavefncspin, wavefncexcitation);
// Translate the wavefunction ID into the index the
// wavefunction has in this timestep
int iwave = ts->qm_timestep->get_wavef_index(waveid);
if (iwave<0 ||
!ts->qm_timestep->get_wavecoeffs(iwave) ||
!ts->qm_timestep->get_num_orbitals(iwave) ||
orbid > ts->qm_timestep->get_num_orbitals(iwave)) {
wkf_timer_destroy(timer);
return;
}
// Get the orbital index for this timestep from the orbital ID.
int orbindex = ts->qm_timestep->get_orbital_index_from_id(iwave, orbid);
// Build an Orbital object and prepare to calculate a grid
Orbital *orbital = mol->qm_data->create_orbital(iwave, orbindex,
ts->pos, ts->qm_timestep);
// Set the bounding box of the atom coordinates as the grid dimensions
orbital->set_grid_to_bbox(ts->pos, 3.0, gridspacing);
// XXX needs more testing, can get stuck for certain orbitals
#if 0
// XXX for GPU, we need to only optimize to a stepsize of 4 or more, as
// otherwise doing this actually slows us down rather than speeding up
// orbital.find_optimal_grid(0.01, 4, 8);
//
// optimize: minstep 2, maxstep 8, threshold 0.01
orbital->find_optimal_grid(0.01, 2, 8);
#endif
// Calculate the molecular orbital
orbital->calculate_mo(mol, density);
motime = wkf_timer_timenow(timer);
// query orbital grid origin, dimensions, and axes
const int *numvoxels = orbital->get_numvoxels();
const float *origin = orbital->get_origin();
float xaxis[3], yaxis[3], zaxis[3];
orbital->get_grid_axes(xaxis, yaxis, zaxis);
// build a VolumetricData object for rendering
char dataname[64];
sprintf(dataname, "molecular orbital %i", orbid);
// update attributes of cached orbital grid
orbgridisdensity = density;
waveftype = wavefnctype;
wavefspin = wavefncspin;
wavefexcitation = wavefncexcitation;
gridorbid = orbid;
orbgridspacing = gridspacing;
delete orbvol;
orbvol = new VolumetricData(dataname, origin,
xaxis, yaxis, zaxis,
numvoxels[0], numvoxels[1], numvoxels[2],
orbital->get_grid_data());
delete orbital;
voltime = wkf_timer_timenow(timer);
orbvol->compute_volume_gradient(); // calc gradients: smooth vertex normals
gradtime = wkf_timer_timenow(timer);
} // regen the orbital grid...
// draw the newly created VolumetricData object
sprintf(commentBuffer, "MoleculeID: %d ReprID: %d Beginning Orbital",
mol->id(), repNumber);
cmdCommentX.putdata(commentBuffer, cmdList);
if (drawbox > 0) {
// don't texture the box if color by volume is active
if (atomColor->method() == AtomColor::VOLUME) {
append(DVOLTEXOFF);
}
// wireframe only? or solid?
if (style > 0 || drawbox == 2) {
draw_volume_box_lines(orbvol);
} else {
draw_volume_box_solid(orbvol);
}
if (atomColor->method() == AtomColor::VOLUME) {
append(DVOLTEXON);
}
}
if ((drawbox == 2) || (drawbox == 0)) {
switch (style) {
case 3:
// shaded points isosurface looping over X-axis, 1 point per voxel
draw_volume_isosurface_lit_points(orbvol, isovalue, stepsize, thickness);
break;
case 2:
// points isosurface looping over X-axis, max of 1 point per voxel
draw_volume_isosurface_points(orbvol, isovalue, stepsize, thickness);
break;
case 1:
// lines implementation, max of 18 line per voxel (3-per triangle)
draw_volume_isosurface_lines(orbvol, isovalue, stepsize, thickness);
break;
case 0:
default:
// trimesh polygonalized surface, max of 6 triangles per voxel
draw_volume_isosurface_trimesh(orbvol, isovalue, stepsize);
break;
}
}
if (regenorbital) {
double surftime = wkf_timer_timenow(timer);
if (surftime > 5) {
char strmsg[1024];
sprintf(strmsg, "Total MO rep time: %.3f [MO: %.3f vol: %.3f grad: %.3f surf: %.2f]",
surftime, motime, voltime - motime, gradtime - motime, surftime - gradtime);
msgInfo << strmsg << sendmsg;
}
}
wkf_timer_destroy(timer);
}