Real SimBox::calcAtomDistSquared(int a1, int a2, Real** aCoords, Real* bSize) {
Real dx = makePeriodic(aCoords[X_COORD][a2] - aCoords[X_COORD][a1], X_COORD, bSize);
Real dy = makePeriodic(aCoords[Y_COORD][a2] - aCoords[Y_COORD][a1], Y_COORD, bSize);
Real dz = makePeriodic(aCoords[Z_COORD][a2] - aCoords[Z_COORD][a1], Z_COORD, bSize);
return dx * dx + dy * dy + dz * dz;
}
void Thread::runThread()
{
char buffer[1024];
#if defined(_SYSTEM_WIN32_)
icl_core::os::snprintf(buffer, 1023, "%s, %lu", getDescription().c_str(), threadId());
#elif defined(_SYSTEM_DARWIN_)
icl_core::os::snprintf(buffer, 1023, "%s, %p", getDescription().c_str(), threadId().m_thread_id);
#else
icl_core::os::snprintf(buffer, 1023, "%s, %lu", getDescription().c_str(), threadId().m_thread_id);
#endif
m_thread_info = buffer;
LOGGING_TRACE_CO(IclCoreThread, Thread, threadInfo(), "Begin." << endl);
m_thread_mutex.lock();
m_execute = true;
m_starting = false;
m_finished = false;
// If this is actually a periodic thread, this call makes it periodic.
// It this is a "normal" thread, this call does nothing.
makePeriodic();
// Call the run loop.
run();
m_execute = false;
m_thread_mutex.unlock();
m_finished = true;
LOGGING_TRACE_CO(IclCoreThread, Thread, threadInfo(), "Done." << endl);
}
