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// Copyright 2007 Nanorex, Inc. See LICENSE file for details.
#include <stdlib.h>
#include <stdio.h>
#include <signal.h>
#include <time.h>
#include <string>
#include "Nanorex/HDF5_SimResults.h"
using namespace Nanorex;
unsigned int renderHelper(HDF5_SimResults* hdf5_SimResults,
const unsigned int& frameIndex,
bool justFrameCount);
void printScene(unsigned int frameIndex, unsigned int frameCount);
void set_timespec(struct timespec *tmr, unsigned long long ustime) {
tmr->tv_sec = (time_t) (ustime / 1000000ULL);
tmr->tv_nsec = (long) (1000ULL * (ustime % 1000000ULL));
}
HDF5_SimResults* simResults = 0;
unsigned int frameIndex = 0;
void render(int dummy) {
int frameCount = renderHelper(simResults, frameIndex, false);
if (frameIndex < frameCount)
frameIndex++;
}
/* FUNCTION: main */
int main(int argc, char* argv[]) {
simResults = new HDF5_SimResults();
std::string message;
int status;
if (argc > 1)
status = simResults->openDataStore(argv[1], message);
else
status = simResults->openDataStore("Testing/shared", message);
if (status) {
printf("Couldn't open %s: %s\n", "Testing/shared", message.c_str());
exit(1);
}
int frameCount, frameIndex = 0;
// Set up a repeating timer and start it
timer_t timerid;
struct sigaction sigact;
struct sigevent sigev;
sigact.sa_handler = render;
sigemptyset(&(sigact.sa_mask));
sigact.sa_flags = 0;
if (sigaction(SIGUSR1, &sigact, (struct sigaction *)NULL) == -1) {
printf("sigaction failed");
exit(1);
}
sigev.sigev_notify = SIGEV_SIGNAL;
sigev.sigev_signo = SIGUSR1;
if (timer_create(CLOCK_REALTIME, &sigev, &timerid) == -1) {
printf("timer_create failed");
exit(1);
}
struct itimerspec tmr;
set_timespec(&tmr.it_value, 100 * 1000); // 100 milliseconds
set_timespec(&tmr.it_interval, 100 * 1000);
if (timer_settime(timerid, 0, &tmr, (struct itimerspec *)NULL) == -1) {
printf("timer_create failed");
exit(1);
}
while (true) {
pause();
//sleep(1);
}
return 0;
}
/* Variables needed by renderHelper() and printScene(). */
unsigned int atomIdCount, bondIdCount;
int* atomicNumbers, *aIds, *bIds;
float zoom;
float* xCoords, *yCoords, *zCoords;
/* FUNCTION: renderHelper */
unsigned int renderHelper(HDF5_SimResults* hdf5_SimResults,
const unsigned int& frameIndex,
bool justFrameCount) {
int status, frameCount;
std::string message;
hdf5_SimResults->synchronize();
// Setup atom arrays (once), assumes the number of atoms in the system is
// constant.
static bool InitializeAtoms = true;
if (InitializeAtoms) {
hdf5_SimResults->getFrameAtomIdsCount("frame-set-1", atomIdCount);
if (atomIdCount > 0) {
xCoords = (float*)malloc(atomIdCount*sizeof(float));
yCoords = (float*)malloc(atomIdCount*sizeof(float));
zCoords = (float*)malloc(atomIdCount*sizeof(float));
atomicNumbers = (int*)malloc(atomIdCount*sizeof(int));
InitializeAtoms = false;
}
}
// Check bond counts and memory allocation.
// Note: The zero in the following makes assumptions that need to be
// generalized later. Plus, this assumes that bonds never change.
static bool InitializeBonds = true;
if (InitializeBonds) {
hdf5_SimResults->getFrameBondsCount("frame-set-1", 0, bondIdCount);
if (bondIdCount > 0) {
aIds = (int*)malloc(bondIdCount*sizeof(int));
bIds = (int*)malloc(bondIdCount*sizeof(int));
InitializeBonds = false;
}
}
// Get time dimension count
hdf5_SimResults->getFrameCount("frame-set-1", frameCount);
if ((frameIndex < frameCount) && !justFrameCount) {
// Atoms
//
float* positions = (float*)malloc(atomIdCount*3*sizeof(float));
status =
hdf5_SimResults->getFrameAtomPositions("frame-set-1",
frameIndex, atomIdCount,
positions, message);
// Collect the atom positions. Center the molecule and assign atomic
// numbers the first time it is displayed.
static bool InitializeMolecule = true;
static float xShift = 0.0, yShift = 0.0, zShift = 0.0;
float maxX, minX, maxY, minY, maxZ, minZ;
for (unsigned int atomIdIndex = 0;
atomIdIndex < atomIdCount;
atomIdIndex++) {
xCoords[atomIdIndex] = positions[atomIdIndex*3 + 0] * 10 + xShift;
yCoords[atomIdIndex] = positions[atomIdIndex*3 + 1] * 10 + yShift;
zCoords[atomIdIndex] = positions[atomIdIndex*3 + 2] * 10 + zShift;
if (InitializeMolecule) {
if (atomIdIndex == 0) {
maxX = minX = xCoords[atomIdIndex];
maxY = minY = yCoords[atomIdIndex];
maxZ = minZ = zCoords[atomIdIndex];
} else {
if (xCoords[atomIdIndex] > maxX)
maxX = xCoords[atomIdIndex];
else if (xCoords[atomIdIndex] < minX)
minX = xCoords[atomIdIndex];
if (yCoords[atomIdIndex] > maxY)
maxY = yCoords[atomIdIndex];
else if (yCoords[atomIdIndex] < minY)
minY = yCoords[atomIdIndex];
if (zCoords[atomIdIndex] > maxZ)
maxZ = zCoords[atomIdIndex];
else if (zCoords[atomIdIndex] < minZ)
minZ = zCoords[atomIdIndex];
}
}
}
free(positions);
if (InitializeMolecule) {
xShift = (minX + maxX) / -2.0;
yShift = (minY + maxY) / -2.0;
zShift = (minZ + maxZ) / -2.0;
// Determine initial zoom
float maxVector = maxX - minX;
if (maxY - minY > maxVector) maxVector = maxY - minY;
if (maxZ - minZ > maxVector) maxVector = maxZ - minZ;
zoom = maxVector * -1.28;
unsigned int* _atomicNumbers =
(unsigned int*)malloc(atomIdCount*3*sizeof(unsigned int));
status =
hdf5_SimResults->getFrameAtomicNumbers("frame-set-1",
_atomicNumbers, message);
for (unsigned int atomIdIndex = 0;
atomIdIndex < atomIdCount;
atomIdIndex++) {
xCoords[atomIdIndex] += xShift;
yCoords[atomIdIndex] += yShift;
zCoords[atomIdIndex] += zShift;
atomicNumbers[atomIdIndex] = _atomicNumbers[atomIdIndex];
}
free(_atomicNumbers);
InitializeMolecule = false;
}
// Bonds
//
static bool InitializeBonds2 = true;
if (InitializeBonds2) {
SimResultsBond* bonds =
(SimResultsBond*)malloc
(bondIdCount*sizeof(SimResultsBond));
status =
hdf5_SimResults->getFrameBonds("frame-set-1", 0,
bonds, message);
for (unsigned int bondIdIndex = 0;
bondIdIndex < bondIdCount;
bondIdIndex++) {
aIds[bondIdIndex] = bonds[bondIdIndex].atomId_1;
bIds[bondIdIndex] = bonds[bondIdIndex].atomId_2;
}
free(bonds);
InitializeBonds2 = false;
}
// Redraw scene
//Refresh(FALSE);
printScene(frameIndex, frameCount);
}
return frameCount;
}
/* FUNCTION: printScene */
void printScene(unsigned int frameIndex, unsigned int frameCount) {
printf("\n==========================\n");
printf("atoms:%d bonds:%d frame:%d/%d\n",
atomIdCount, bondIdCount, frameIndex+1, frameCount);
}
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