Serialization is working

At least I can load the StandardMale0s state, run for 2 mins, and I match BasicStandard

cdm/cpp/system/physiology/SEBloodChemistrySystem.cpp

@@ -272,10 +272,10 @@ void SEBloodChemistrySystem::Serialize(const SEBloodChemistrySystem& src, cdm::B
     dst.set_allocated_pulmonaryarterialcarbondioxidepressure(SEScalarPressure::Unload(*src.m_PulmonaryArterialCarbonDioxidePressure));
   if (src.HasPulmonaryArterialOxygenPressure())
     dst.set_allocated_pulmonaryarterialoxygenpressure(SEScalarPressure::Unload(*src.m_PulmonaryArterialOxygenPressure));
-  if (src.HasPulmonaryVenousOxygenPressure())
-    dst.set_allocated_pulmonaryvenouscarbondioxidepressure(SEScalarPressure::Unload(*src.m_PulmonaryVenousOxygenPressure));
   if (src.HasPulmonaryVenousCarbonDioxidePressure())
-    dst.set_allocated_pulmonaryvenousoxygenpressure(SEScalarPressure::Unload(*src.m_PulmonaryVenousCarbonDioxidePressure));
+    dst.set_allocated_pulmonaryvenouscarbondioxidepressure(SEScalarPressure::Unload(*src.m_PulmonaryVenousCarbonDioxidePressure));
+  if (src.HasPulmonaryVenousOxygenPressure())
+    dst.set_allocated_pulmonaryvenousoxygenpressure(SEScalarPressure::Unload(*src.m_PulmonaryVenousOxygenPressure));
   if (src.HasVenousCarbonDioxidePressure())
     dst.set_allocated_venouscarbondioxidepressure(SEScalarPressure::Unload(*src.m_VenousCarbonDioxidePressure));
   if (src.HasVenousOxygenPressure())

engine/cpp/Controller/Engine.cpp

@@ -497,13 +497,18 @@ bool PulseEngine::ProcessAction(const SEAction& action)
     if (serialize->GetType() == cdm::SerializeStateData_eSerializationType_Save)
     {
       if (serialize->HasFilename())
+      {
         SaveState(serialize->GetFilename());
+      }
       else
       {
         std::stringstream ss;
         MKDIR("./states");
         ss << "./states/" << m_Patient->GetName() << "@" << GetSimulationTime(TimeUnit::s) << "s.pba";
         SaveState(ss.str());
+        // Debug code to make sure things are consistent
+        //LoadStateFile(ss.str());
+        //SaveState("./states/AfterSave.pba");
       }     
     }
     else

engine/cpp/Systems/Cardiovascular.cpp

@@ -1582,7 +1582,7 @@ void Cardiovascular::TuneCircuit()
       m_circuitCalculator.Process(*m_CirculatoryCircuit, m_dT_s);
       CalculateVitalSigns();
       m_circuitCalculator.PostProcess(*m_CirculatoryCircuit);
-      return; //Skip stabelization for debugging
+      //return; //Skip stabelization for debugging
 
       map_mmHg = GetMeanArterialPressure(PressureUnit::mmHg);
       systolic_mmHg = GetSystolicArterialPressure(PressureUnit::mmHg);

engine/cpp/Systems/Gastrointestinal.cpp

@@ -99,6 +99,9 @@ void Gastrointestinal::Initialize()
   m_InitialSubstanceMasses_ug[m_SmallIntestineChymeCalcium]    = m_SmallIntestineChymeCalcium->GetMass(MassUnit::ug);
   m_InitialSubstanceMasses_ug[m_SmallIntestineChymeSodium]     = m_SmallIntestineChymeSodium->GetMass(MassUnit::ug);
   m_InitialSubstanceMasses_ug[m_SmallIntestineChymeUrea]       = m_SmallIntestineChymeUrea->GetMass(MassUnit::ug);
+
+  m_ConsumeRate = false;
+  m_DecrementNutrients = false;
 }
 
 void Gastrointestinal::Load(const pulse::GastrointestinalSystemData& src, Gastrointestinal& dst)
@@ -126,16 +129,13 @@ void Gastrointestinal::Serialize(const Gastrointestinal& src, pulse::Gastrointes
 
 void Gastrointestinal::SetUp()
 {
-  m_ConsumeRate = false;
-  m_DecrementNutrients = false;
-
   m_WaterDigestionRate.SetValue(m_data.GetConfiguration().GetWaterDigestionRate(VolumePerTimeUnit::mL_Per_s), VolumePerTimeUnit::mL_Per_s);
   m_CalciumDigestionRate.SetValue(m_data.GetConfiguration().GetCalciumDigestionRate(MassPerTimeUnit::g_Per_s), MassPerTimeUnit::g_Per_s);
 
-  m_GItoCVPath = m_data.GetCircuits().GetActiveCardiovascularCircuit().GetPath(pulse::ChymePath::SmallIntestineC1ToSmallIntestine1);
-  m_GutT1ToGroundPath = m_data.GetCircuits().GetActiveCardiovascularCircuit().GetPath(pulse::ChymePath::GutT1ToGround);
+  m_GItoCVPath                    = m_data.GetCircuits().GetActiveCardiovascularCircuit().GetPath(pulse::ChymePath::SmallIntestineC1ToSmallIntestine1);
+  m_GutT1ToGroundPath             = m_data.GetCircuits().GetActiveCardiovascularCircuit().GetPath(pulse::ChymePath::GutT1ToGround);
 
-  m_SmallIntestineChyme = m_data.GetCompartments().GetLiquidCompartment(pulse::ChymeCompartment::SmallIntestine);
+  m_SmallIntestineChyme           = m_data.GetCompartments().GetLiquidCompartment(pulse::ChymeCompartment::SmallIntestine);
   m_SmallIntestineChymeGlucose    = m_SmallIntestineChyme->GetSubstanceQuantity(m_data.GetSubstances().GetGlucose());
   m_SmallIntestineChymeTristearin = m_SmallIntestineChyme->GetSubstanceQuantity(m_data.GetSubstances().GetTristearin());
   m_SmallIntestineChymeCalcium    = m_SmallIntestineChyme->GetSubstanceQuantity(m_data.GetSubstances().GetCalcium());

engine/cpp/Systems/Nervous.cpp

@@ -64,6 +64,10 @@ void Nervous::Initialize()
   GetLeftEyePupillaryResponse().GetReactivityModifier().SetValue(0);
   GetRightEyePupillaryResponse().GetSizeModifier().SetValue(0);
   GetRightEyePupillaryResponse().GetReactivityModifier().SetValue(0);
+
+  // Set when feedback is turned on
+  m_ArterialOxygenSetPoint_mmHg = 0;
+  m_ArterialCarbonDioxideSetPoint_mmHg = 0;
 }
 
 void Nervous::Load(const pulse::NervousSystemData& src, Nervous& dst)
@@ -112,10 +116,6 @@ void Nervous::SetUp()
   m_normalizedAlphaCompliance = m_data.GetConfiguration().GetNormalizedComplianceParasympatheticSlope();
   m_normalizedAlphaResistance = m_data.GetConfiguration().GetNormalizedResistanceSympatheticSlope();
   m_normalizedBetaHeartRate   = m_data.GetConfiguration().GetNormalizedHeartRateParasympatheticSlope();
-
-  // Set when feedback is turned on
-  m_ArterialOxygenSetPoint_mmHg = 0;
-  m_ArterialCarbonDioxideSetPoint_mmHg = 0;
 }
 
 void Nervous::AtSteadyState()