Update Simbody to the most recent commit, revert StatesTrajectory changes, and update Manager documentation

Author: nickbianco

OpenSim/Simulation/Manager/Manager.cpp

@@ -39,7 +39,7 @@ using namespace OpenSim;
 //=============================================================================
 // CONSTRUCTOR(S)
 //=============================================================================
-Manager::Manager(Model& model) : _recordStatesTrajectory(false), 
+Manager::Manager(Model& model) : _recordStatesTrajectory(false),
         _performAnalyses(true), _writeToStorage(true), _model(&model) {
     _sessionName = _model->getName();
     _integ.reset(new SimTK::RungeKuttaMersonIntegrator(
@@ -135,7 +135,7 @@ Manager::IntegratorMethod Manager::getIntegratorMethod() const {
 
 void Manager::setIntegratorAccuracy(double accuracy) {
     OPENSIM_THROW_IF(!_integ->methodHasErrorControl(), Exception,
-        "Integrator method {} does not support error control.", 
+        "Integrator method {} does not support error control.",
         _integ->getMethodName());
 
     _integ->setAccuracy(accuracy);
@@ -198,7 +198,7 @@ void Manager::record(const SimTK::State& state, int step) {
         vec.setStates(state.getTime(), stateValues);
         _stateStore->append(vec);
         if (_model->isControlled()) {
-            _model->updControllerSet().storeControls(state, 
+            _model->updControllerSet().storeControls(state,
                     (step < 0) ? getStateStorage().getSize() : step);
         }
     }
@@ -217,9 +217,9 @@ void Manager::record(const SimTK::State& state, int step) {
     }
 
     if (_recordStatesTrajectory) {
-        if (_statesTraj->getSize() > 0 && 
-                _statesTraj->back().getTime() == state.getTime()) { 
-            return; 
+        if (_statesTraj->getSize() > 0 &&
+                _statesTraj->back().getTime() == state.getTime()) {
+            return;
         }
         _statesTraj->append(state);
     }
@@ -232,22 +232,21 @@ void Manager::initialize(const SimTK::State& s) {
 
     if (_recordStatesTrajectory || _writeToStorage || _performAnalyses) {
         _integ->setReturnEveryInternalStep(true);
-    } 
+    }
 
     // Initialize the time stepper.
     _timeStepper->setReportAllSignificantStates(true);
     _timeStepper->initialize(s);
-    
-    // TODO: find a better way to intialize capacity.
+
+    // Initialize the states trajectory.
     if (_recordStatesTrajectory) {
-        // Initialize the states trajectory.
         _statesTraj->clear();
-        _statesTraj->reserve(1024);
     }
-    
+
+    // Initialize the states storage.
     if (_writeToStorage) {
-        // Initialize the states storage.
-        _stateStore.reset(new Storage(1024, "states"));
+        _stateStore.reset(new Storage(512));
+        _stateStore->setName(_sessionName);
         Array<std::string> stateNames = _model->getStateVariableNames();
         Array<std::string> columnLabels;
         columnLabels.setSize(0);
@@ -292,7 +291,7 @@ const SimTK::State& Manager::integrate(double finalTime) {
     record(s, step++);
     double time = s.getTime();
     auto status = SimTK::Integrator::InvalidSuccessfulStepStatus;
-    while (time < finalTime) { 
+    while (time < finalTime) {
         status = _timeStepper->stepTo(finalTime);
         const SimTK::State& s = _integ->getState();
 
@@ -317,7 +316,7 @@ const SimTK::State& Manager::integrate(double finalTime) {
                     _integ->getTerminationReasonString(
                             _integ->getTerminationReason()));
                 return s;
-            } 
+            }
         }
         time = s.getTime();
     }
@@ -331,7 +330,7 @@ const SimTK::State& Manager::integrate(double finalTime) {
     log_info(" - ratio sim-to-real time: {:.3f}", simFinalTime / realTime);
     log_info(" - integrator method: {}", _integ->getMethodName());
     log_info(" - number of realizations: {}", _integ->getNumRealizations());
-    log_info(" - number of steps taken / attempted: {} / {}", 
+    log_info(" - number of steps taken / attempted: {} / {}",
             _integ->getNumStepsTaken(), _integ->getNumStepsAttempted());
     log_info(" - number of projections: {}", _integ->getNumProjections());
     log_info(" - number of iterations: {}", _integ->getNumIterations());