void Master::treeInterfaceNodeBounds(int id, double lb, double ub)
{
if (VbcLog_ == NoVbc) return;
//char string[256];
ostringstream info;
if (isInfinity(fabs(lb))) {
if (isInfinity(fabs(ub)))
info << "I " << id << " \\iLower Bound: ---\\nUpper Bound: ---\\i";
else
info << "I " << id << " \\iLower Bound: ---\\nUpper Bound: "
<< std::ios::fixed << std::setprecision(2) << std::setw(6) << ub << "\\i";
}
else {
if (isInfinity(fabs(ub)))
info << "I " << id << " \\iLower Bound: "
<< std::ios::fixed << std::setprecision(2) << std::setw(6) << lb
<< "\\nUpper Bound: ---\\i";
else
info << "I " << id << " \\iLower Bound: "
<< std::ios::fixed << std::setprecision(2) << std::setw(6) << lb
<< "\\nUpper Bound: "
<< std::ios::fixed << std::setprecision(2) << std::setw(6) << ub
<< "\\i";
}
writeTreeInterface(info.str());
}
void
Coordinator::processInit(Simulator* simulator)
{
Time tn = simulator->init(m_currentTime);
if (not isInfinity(tn)) {
m_eventTable.addInternal(simulator, tn);
}
}
InternalEvent * Simulator::buildInternalEvent(const Time& currentTime)
{
Time time(timeAdvance());
if (not isInfinity(time)) {
return new InternalEvent(currentTime + time, this);
} else {
return 0;
}
}
InternalEvent* Simulator::init(const Time& currentTime)
{
Time time(m_dynamics->init(currentTime));
if (not isInfinity(time)) {
return new InternalEvent(currentTime + time, this);
} else {
return 0;
}
}
unsigned int
floatToUint (float f)
{
if (isNegative (f) || isNan (f))
return 0;
if (isInfinity (f) || f > UINT_MAX)
return UINT_MAX;
return (unsigned int) f;
}
string Cost::toString(CostType costType) const
{
if (!isInfinity() && costType == CompressionCost)
{
return SpritePack::toString((double)value / 1000.0, 1) + "ms";
}
else
{
return Number::toString();
}
}
void NominalEventMonitor::stopMonitor() {
stopped = true;
if (running) {
running = false;
if (isInfinity(expectedSleepTime) || paused) {
unlockConditionSatisfied();
} else {
wakeUp();
}
}
}
bool
RootCoordinator::run()
{
m_currentTime = m_coordinator->getCurrentTime();
if (isInfinity(m_currentTime))
return false;
if ((m_end - m_currentTime) < 0)
return false;
m_coordinator->run();
return true;
}
void NominalEventMonitor::prepareNptTransitionsEvents() {
AttributionEvent* event;
set<double>* transValues;
set<double>::iterator i;
executionObject->prepareTransitionEvents(
ContentAnchor::CAT_NPT,
timeBaseProvider->getCurrentTimeValue(timeBaseId));
transValues = executionObject->getTransitionsValues(
ContentAnchor::CAT_NPT);
if (transValues == NULL || transValues->empty()) {
cout << "NominalEventMonitor::prepareNptTransitionsEvents ";
cout << "nothing to do (2)." << endl;
return;
}
executionObject->updateTransitionTable(
timeBaseProvider->getCurrentTimeValue(timeBaseId),
NULL,
ContentAnchor::CAT_NPT);
i = transValues->begin();
while (i != transValues->end()) {
if (!isInfinity(*i)) {
/*cout << "NominalEventMonitor::prepareNptTransitionsEvents ";
cout << "add listener contentId '" << timeBaseId;
cout << "' for value '" << *i;
cout << "' (current time = '";
cout << timeBaseProvider->getCurrentTimeValue(timeBaseId);
cout << "')" << endl;*/
timeBaseProvider->addTimeListener(timeBaseId, *i, this);
}
++i;
}
delete transValues;
event = (AttributionEvent*)(executionObject->getEventFromAnchorId(
"contentId"));
if (event != NULL) {
adapter->setPropertyValue(event, itos(timeBaseId), NULL);
event->stop();
}
}
void NominalEventMonitor::stopMonitor() {
stopped = true;
if (timeBaseProvider != NULL) {
timeBaseProvider->removeTimeListener(timeBaseId, this);
timeBaseProvider->removeIdListener(this);
}
if (running) {
running = false;
if (isInfinity(expectedSleepTime) || paused) {
unlockConditionSatisfied();
} else {
wakeUp();
}
}
}
string FlexibleTimeMeasurement::toString() {
return (
"expected value: "
+ itos(expectedValue)
+ "; actual value: "
+ (isNaN(actualValue) ? "UNDEFINED" :
"" + itos(actualValue))) + (
"; minimum value: "
+ itos(minimumValue)
+ "; maximum value : "
+ (isInfinity(maximumValue) ?
"INFINITY" : ""
+ itos(maximumValue))
+ "; computed value: "
+ (isNaN(computedValue) ? "UNDEFINED"
: "" + itos(computedValue)));
}
std::string DecimalDecNumber::toStringAllowScientific(uint32 decimalPlaces) const
{
if (!isZero() && !isInfinity() && !decNumberIsNaN(&m_value))
{
static const int BUFFER_SIZE = 256;
char buffer[BUFFER_SIZE];
{
DecimalDecNumber rounded(*this);
rounded.round(decimalPlaces, RoundingMode::ROUND_TO_ZERO);
decNumberToString(&rounded.m_value, buffer);
}
char * e = buffer + strlen(buffer);
char * f = std::find(buffer, e, '+');
if (f != e)
return buffer;
}
return toString(decimalPlaces);
}
string LinearCostFunctionDuration::toString() {
return (
(
"expected value: "
+ itos(expectedValue)
+ "; actual value: "
+ (!isNaN(actualValue) ? "UNDEFINED" :
"" + itos(actualValue))) +
("; minimum value: "
+ itos(minimumValue)
+ "; maximum value : "
+ (isInfinity(maximumValue) ?
"INFINITY" : "" + itos(maximumValue))
+ "; computed value: "
+ (!isNaN(computedValue) ? "UNDEFINED"
: "" + itos(computedValue)))
+ "; shrinking cost rate: "
+ itos(getShrinkingCostRate())
+ "; stretching cost rate: "
+ itos(getStretchingCostRate()));
}
int ss_func( const gsl_vector* x, void* params, gsl_vector* f )
{
struct reac_info* ri = (struct reac_info *)params;
// Stoich* s = reinterpret_cast< Stoich* >( ri->stoich.eref().data() );
int num_consv = ri->num_mols - ri->rank;
for ( unsigned int i = 0; i < ri->num_mols; ++i ) {
double temp = op( gsl_vector_get( x, i ) );
if ( isNaN( temp ) || isInfinity( temp ) ) {
return GSL_ERANGE;
} else {
ri->nVec[i] = temp;
}
}
vector< double > vels;
ri->pool->updateReacVelocities( &ri->nVec[0], vels );
assert( vels.size() == static_cast< unsigned int >( ri->num_reacs ) );
// y = Nr . v
// Note that Nr is row-echelon: diagonal and above.
for ( int i = 0; i < ri->rank; ++i ) {
double temp = 0;
for ( int j = i; j < ri->num_reacs; ++j )
temp += gsl_matrix_get( ri->Nr, i, j ) * vels[j];
gsl_vector_set( f, i, temp );
}
// dT = gamma.S - T
for ( int i = 0; i < num_consv; ++i ) {
double dT = - ri->T[i];
for ( unsigned int j = 0; j < ri->num_mols; ++j )
dT += gsl_matrix_get( ri->gamma, i, j) *
op( gsl_vector_get( x, j ) );
gsl_vector_set( f, i + ri->rank, dT );
}
return GSL_SUCCESS;
}
void
Coordinator::run()
{
Bag& bag = m_eventTable.getCurrentBag();
if (not bag.dynamics.empty() or not bag.executives.empty())
m_currentTime = m_eventTable.getCurrentTime();
else
vDbg(m_context, "Coordinator::run bag is empty...\n");
vDbg(m_context, _("-------- BAG [%f] --------\n"), m_currentTime);
//
// Call output functions for all executives and dynamics models then
// dispatches external events for all executives and dynamics.
//
const std::size_t nb_dynamics = bag.dynamics.size();
const std::size_t nb_executive = bag.executives.size();
if (nb_dynamics > 0) {
for (std::size_t i = 0; i != nb_dynamics; ++i)
bag.dynamics[i]->output(m_currentTime);
dispatchExternalEvent(bag.dynamics, nb_dynamics);
}
if (nb_executive > 0) {
for (std::size_t i = 0; i != nb_executive; ++i)
bag.executives[i]->output(m_currentTime);
dispatchExternalEvent(bag.executives, nb_executive);
}
//
// First we sort executives models according to the depth of the executive
// model into the structure of the models.
//
if (not bag.executives.empty()) {
std::sort(bag.executives.begin(),
bag.executives.end(),
[](const Simulator* lhs, const Simulator* rhs) {
return ::depth(lhs->dynamics()) <
::depth(rhs->dynamics());
});
}
//
// Compute internal, confluent or external transition for dynamics models.
// If parallelization is available, use it otherwise, compute transition
// linearly.
//
if (m_simulators_thread_pool.parallelize()) {
m_simulators_thread_pool.for_each(bag.dynamics, m_currentTime);
} else {
for (auto& elem : bag.dynamics) {
if (elem->haveInternalEvent()) {
if (not elem->haveExternalEvents())
elem->internalTransition(m_currentTime);
else
elem->confluentTransitions(m_currentTime);
} else {
elem->externalTransition(m_currentTime);
}
}
}
for (auto& elem : bag.dynamics) {
auto tn = elem->getTn();
if (not isInfinity(tn))
m_eventTable.addInternal(elem, tn);
}
for (auto& elem : bag.executives) {
if (elem->haveInternalEvent()) {
if (not elem->haveExternalEvents())
elem->internalTransition(m_currentTime);
else
elem->confluentTransitions(m_currentTime);
} else {
elem->externalTransition(m_currentTime);
}
}
for (auto& elem : bag.executives) {
auto tn = elem->getTn();
if (not isInfinity(tn))
m_eventTable.addInternal(elem, tn);
}
//
// Finally, we go through simulators and executive to get all observation
// and dispatch to output plug-in.
//
for (auto& elem : bag.dynamics) {
auto& observations = elem->getObservations();
for (auto& obs : observations)
obs.view->run(elem->dynamics().get(),
m_currentTime,
obs.portname,
std::move(obs.value));
observations.clear();
}
for (auto& elem : bag.executives) {
auto& observations = elem->getObservations();
for (auto& obs : observations)
obs.view->run(elem->dynamics().get(),
m_currentTime,
obs.portname,
std::move(obs.value));
observations.clear();
}
//
// Process observation event if the next bag is scheduled for a different
// date than \e m_currentTime.
//
auto next = m_eventTable.getNextTime();
if (next > m_currentTime) {
//
// Scheduler is empty. We eat all timed view until the duration time
//
auto eatuntil = std::min(next, m_durationTime);
while (m_timed_observation_scheduler.haveObservationAtTime(eatuntil)) {
auto obs =
m_timed_observation_scheduler.getObservationAtTime(eatuntil);
if (not obs.empty()) {
m_currentTime = obs.back().mTime;
for (auto& elem : obs) {
elem.run();
elem.update();
if (not isInfinity(elem.mTime))
m_timed_observation_scheduler.add(
elem.mView, elem.mTime, elem.mTimestep);
}
}
}
if (isInfinity(next) or next > m_durationTime) {
//
// For all Timed view, process a final observation and clear the
// scheduler.
//
m_currentTime = m_durationTime;
m_timed_observation_scheduler.finalize(m_currentTime);
}
}
//
// Finally, we destroy model and simulator if one executive delete a model
//
if (not m_delete_model.empty())
dynamic_deletion();
m_eventTable.makeNextBag();
m_currentTime = m_eventTable.getCurrentTime();
}
void NominalEventMonitor::resumeMonitor() {
if (!isInfinity(expectedSleepTime) && paused) {
paused = false;
unlockConditionSatisfied();
}
}
bool IntervalAnchor::isObjectDuration(double value) {
return isInfinity(value);
}
void NominalEventMonitor::run() {
lock();
EventTransition* nextTransition;
double time;
double mediaTime = 0;
double nextEntryTime;
nextTransition = NULL;
/*cout << "====== Anchor Monitor Activated for '";
cout << executionObject->getId().c_str() << "' (";
cout << this << " ======" << endl;*/
while (running) {
if (deleting) {
break;
}
if (paused) {
waitForUnlockCondition();
} else {
if (executionObject != NULL) {
nextTransition = executionObject->getNextTransition();
} else {
nextTransition = NULL;
running = false;
}
if (nextTransition == NULL) {
running = false;
} else {
nextEntryTime = nextTransition->getTime();
if (isInfinity(nextEntryTime)) {
expectedSleepTime = infinity();
} else {
mediaTime = (adapter->getPlayer()->getMediaTime()
* 1000);
expectedSleepTime = nextEntryTime - mediaTime;
}
/*cout << "ANCHORMONITOR NEXTTRANSITIONTIME = '";
cout << nextEntryTime << "' MEDIATIME = '" << mediaTime;
cout << "' EXPECTEDSLEEPTIME = '" << expectedSleepTime;
cout << "' (" << this << ")" << endl;*/
if (running && !deleting) {
if (isInfinity(expectedSleepTime)) {
waitForUnlockCondition();
} else {
Thread::usleep((int)(expectedSleepTime));
}
if (running && !deleting) {
if (executionObject == NULL || adapter == NULL) {
unlock();
return;
}
mediaTime = (adapter->getPlayer()->getMediaTime()
* 1000);
time = nextEntryTime - mediaTime;
if (time < 0) {
time = 0;
}
if (!paused && time <= DEFAULT_ERROR) {
// efetua a transicao no estado do evento
executionObject->updateTransitionTable(
mediaTime + DEFAULT_ERROR,
adapter->getPlayer(),
ContentAnchor::CAT_TIME);
}
}
}
}
}
}
if (!stopped && adapter != NULL && !deleting) {
adapter->getPlayer()->forceNaturalEnd();
}
unlock();
}
void NominalEventMonitor::pauseMonitor() {
if (!isInfinity(expectedSleepTime)) {
wakeUp();
paused = true;
}
}
// Lalit: toString should "truncate" values rather than round
std::string DecimalDecNumber::toString(uint32 decimalPlaces) const
{
// Remove these statics if we ever get a short string optimisation in place (gcc 4.1)
static const std::string zero = "0.0";
static const std::string posinf = "+INF";
static const std::string neginf = "-INF";
static const std::string nan = "NaN";
if (isZero())
return zero;
else if (isInfinity())
{
return isNegative() ? neginf : posinf;
}
else if (decNumberIsNaN(&m_value))
{
// TODO: is it possible to have positive/negative nans?
return nan;
}
static const int BUFFER_SIZE = 256;
char buffer[BUFFER_SIZE];
{
DecimalDecNumber rounded(*this);
rounded.round(decimalPlaces, RoundingMode::ROUND_TO_ZERO);
decNumberToString(&rounded.m_value, buffer);
}
// printf("after round: %s\n", buffer);
char * b = buffer;
char * e = buffer + strlen(buffer);
unpackScientificFormat(b, e, BUFFER_SIZE, decimalPlaces);
if ((e-b) == 3 && strcmp(buffer, "NaN") == 0)
{
return buffer;
}
else if (std::find(b, e, '.') == e)
{
strcpy(e, ".0");
return buffer;
}
{
// This code makes the unit tests pass (which were based on the old Decimal implementation)
// Ensure that there are no trailing zeros, except when the value is an integer, in which case there should be one trailing zero.
char * lastNonZeroDigitAfterDecimal = e - 1;
while (*lastNonZeroDigitAfterDecimal == '0')
{
--lastNonZeroDigitAfterDecimal;
}
if (*lastNonZeroDigitAfterDecimal == '.')
{
*(++lastNonZeroDigitAfterDecimal) = '0';
}
*(lastNonZeroDigitAfterDecimal + 1) = 0;
}
// printf("last return\n");
return buffer;
}