Merge branch 'fix/warnings-tests' into '3.x'

Fix warnings

See merge request !75

src/cpp/bind/CMakeLists.txt

@@ -93,3 +93,11 @@ add_library_ex(DataModelBindings
     protobuf::libprotobuf
   LIB_INSTALL_ONLY
 )
+
+if (MSVC)
+    target_compile_options(DataModelBindings PRIVATE  "/wd4100") # 'identifier' : unreferenced formal parameter
+    target_compile_options(DataModelBindings PRIVATE  "/wd4125") # decimal digit terminates octal escape sequence
+    target_compile_options(DataModelBindings PRIVATE  "/wd4127") # conditional expression is constant
+    target_compile_options(DataModelBindings PRIVATE  "/wd4244") # 'conversion' conversion from 'type1' to 'type2', possible loss of data
+    target_compile_options(DataModelBindings PRIVATE  "/wd4267") # 'var' : conversion from 'size_t' to 'type', possible loss of data
+endif()
\ No newline at end of file

src/cpp/cdm/CommonDataModel.h

@@ -36,6 +36,7 @@
   #define PUSH_PROTO_WARNINGS() \
     __pragma(pack(push)) \
     __pragma(warning(disable:4127)) \
+    __pragma(warning(disable:4244)) \
     __pragma(warning(disable:4267))
   #define POP_PROTO_WARNINGS() __pragma(pack(pop))
 #else

src/cpp/cdm/io/protobuf/PBBlackBox.cpp

@@ -2,8 +2,10 @@
    See accompanying NOTICE file for details.*/
 
 #include "stdafx.h"
+PUSH_PROTO_WARNINGS()
 #include "io/protobuf/PBBlackBox.h"
 #include "pulse/cdm/bind/BlackBox.pb.h"
+POP_PROTO_WARNINGS()
 #include "blackbox/SEBlackBox.h"
 
 const std::string& eBlackBox_Property_Type_Name(eBlackBox_Property_Type m)

src/cpp/cdm/test/AdvancedCircuitTest.cpp

@@ -323,8 +323,8 @@ void CommonDataModelTest::CombinedCircuitTest(const std::string& sTestDirectory)
   SEFluidCircuit* CombinedCircuit = &m_Circuits->CreateFluidCircuit("Combined");
   CombinedCircuit->AddCircuit(*MasterCircuit);
   CombinedCircuit->AddCircuit(*SlaveCircuit);
-  SEFluidCircuitPath& GroundPath = CombinedCircuit->CreatePath(MasterNode4, SlaveNode4, "GroundPath");
-  SEFluidCircuitPath& CombinedPath = CombinedCircuit->CreatePath(MasterNode3, SlaveNode3, "CombinedPath");
+  CombinedCircuit->CreatePath(MasterNode4, SlaveNode4, "GroundPath");
+  CombinedCircuit->CreatePath(MasterNode3, SlaveNode3, "CombinedPath");
   CombinedCircuit->RemovePath(SlavePath1);
   CombinedCircuit->StateChange();
 
@@ -379,7 +379,6 @@ void CommonDataModelTest::CircuitErrorTest(const std::string& sTestDirectory)
   std::cout << "CircuitErrorTest\n";
   //Setup a basic circuit
   m_Logger->SetLogFile(sTestDirectory + "/CombinedCircuitTest.log");
-  double timeStep_s = 1.0 / 165.0;
   SEFluidCircuitCalculator fluidCalculator(m_Logger);
   SEFluidCircuit* fluidCircuit = &m_Circuits->CreateFluidCircuit("Fluid");
   //-----------------------------------------------------------
@@ -487,9 +486,7 @@ void CommonDataModelTest::DynamicallyChangingCircuitTest(const std::string& sTes
       fluidCircuit->GetPath("Path4")->GetResistanceBaseline().SetValue(50, PressureTimePerVolumeUnit::Pa_s_Per_m3);
 
       //Add a new Path
-      SEFluidCircuitNode* Node2 = fluidCircuit->GetNode("Node2");
-      SEFluidCircuitNode* Node4 = fluidCircuit->GetNode("Node4");
-      SEFluidCircuitPath& Path5 = fluidCircuit->CreatePath(*Node2, *Node4, "Path5");
+      SEFluidCircuitPath& Path5 = fluidCircuit->CreatePath(Node2, Node4, "Path5");
       Path5.GetNextResistance().SetValue(25, PressureTimePerVolumeUnit::Pa_s_Per_m3);
       //Reset the baselines
       fluidCircuit->StateChange();
@@ -715,7 +712,6 @@ void CommonDataModelTest::PolarizedCapacitorTest(const std::string& sTestDirecto
   fluidCircuit->StateChange();
 
   bool serialized = false;
-  double sample = 0;
   while (currentTime_s < 150)
   {
     if (currentTime_s > 100)
@@ -871,7 +867,7 @@ void CommonDataModelTest::ComplianceVolumeChange(const std::string& sTestDirecto
   SEFluidCircuitPath* groundTonode2 = &fluidCircuit->CreatePath(*ground, *node2, "groundTonode2");
   groundTonode2->GetPressureSourceBaseline().SetValue(0.0, PressureUnit::cmH2O);
   SEFluidCircuitPath* node2Tonode3 = &fluidCircuit->CreatePath(*node2, *node3, "node2Tonode3");
-  SEFluidCircuitPath* node3Toground = &fluidCircuit->CreatePath(*node3, *ground, "node3Toground");
+  fluidCircuit->CreatePath(*node3, *ground, "node3Toground");
   node2Tonode3->GetComplianceBaseline().SetValue(1.0, VolumePerPressureUnit::L_Per_cmH2O);
   fluidCircuit->SetNextAndCurrentFromBaselines();
   fluidCircuit->StateChange();
@@ -962,7 +958,7 @@ void CommonDataModelTest::CircuitLockingTest(const std::string& sOutputDirectory
   flowSource.GetFlowSourceBaseline().SetValue(0.1, VolumePerTimeUnit::m3_Per_s);
   SEFluidCircuitPath& potentialSource = fluidCircuit->CreatePath(Node5, Node1, "Potential Source");
   potentialSource.GetPotentialSourceBaseline().SetValue(10, PressureUnit::Pa);
-  SEFluidCircuitPath& dummyPath = fluidCircuit->CreatePath(Node1, Node3, "Short");
+  fluidCircuit->CreatePath(Node1, Node3, "Short");
   
   fluidCircuit->SetNextAndCurrentFromBaselines();
   fluidCircuit->StateChange();

src/cpp/cdm/test/BasicCircuitTest.cpp

@@ -4138,7 +4138,6 @@ void CommonDataModelTest::TestPreProcess2(double dT, int i)
   //    Never change "current" values, only next.
 
   // ALL PRESSURE SOURCES MUST EXIST ON PATH 1 UNTIL THIS IS CHANGED TO BE MORE FLEXIBLE
-  double ONE = 1;
   bool FLOWSOURCE = false;
   bool SWITCHPRESENT = false;
   bool PRESSURESOURCE  = false;
@@ -4384,7 +4383,6 @@ void CommonDataModelTest::TestPreProcess4(double dT, int i)
   //    Never change "current" values, only next.
 
   // ALL PRESSURE SOURCES MUST EXIST ON PATH 1 UNTIL THIS IS CHANGED TO BE MORE FLEXIBLE
-  double ONE = 1;
   bool FLOWSOURCE = false;
   bool SWITCHPRESENT = false;
   bool PRESSURESOURCE  = false;
@@ -5252,7 +5250,6 @@ void CommonDataModelTest::RunTest(const std::string& outputDirectory, const std:
   fluidCircuit->SetNextAndCurrentFromBaselines();
   fluidCircuit->StateChange();
 
-  double sample = 0;
   bool serialized = false;
   double outputTime_s = 0;
   while (currentTime_s < 10) // Run for 10 secs

src/cpp/cdm/test/GasCompartmentTest.cpp

@@ -344,8 +344,6 @@ void CommonDataModelTest::TestGasHierarchy(SETestSuite& testSuite, SESubstanceMa
 
   double L2C3_mL = 12;
   double L2C3_mmHg = 12;
-  double L2C3_H20 = 0.5;
-  double L2C3_pH = 7.38;
   SEGasCompartment* L2C3 = &cmptMgr.CreateGasCompartment("L2C3");
   L2C3->GetVolume().SetValue(L2C3_mL, VolumeUnit::mL);
   L2C3->GetPressure().SetValue(L2C3_mmHg, PressureUnit::mmHg);

src/cpp/cdm/test/SubstanceTransport.cpp

@@ -187,24 +187,24 @@ void CommonDataModelTest::LiquidTransportTest(const std::string& rptDirectory)
   SEFluidCircuitPath& groundToNode6 = circuit.CreatePath(Ground,Node6,"GroundToNode6");
   groundToNode6.GetFlowSourceBaseline().SetValue(0.5, VolumePerTimeUnit::mL_Per_s);
 
-  SEFluidCircuitPath& Node1ToNode7 = circuit.CreatePath(Node1,Node7,"Node1ToNode7");
-  SEFluidCircuitPath& Node2ToNode7 = circuit.CreatePath(Node2,Node7,"Node2ToNode7");
-  SEFluidCircuitPath& Node3ToNode8 = circuit.CreatePath(Node3,Node8,"Node3ToNode8");
-  SEFluidCircuitPath& Node4ToNode8 = circuit.CreatePath(Node4,Node8,"Node4ToNode8");
-  SEFluidCircuitPath& Node5ToNode9 = circuit.CreatePath(Node5,Node9,"Node5ToNode9");
-  SEFluidCircuitPath& Node6ToNode9 = circuit.CreatePath(Node6,Node9,"Node6ToNode9");
-  SEFluidCircuitPath& Node7ToNode10 = circuit.CreatePath(Node7,Node10,"Node7ToNode10");
-  SEFluidCircuitPath& Node8ToNode10 = circuit.CreatePath(Node8,Node10,"Node8ToNode10");
-  SEFluidCircuitPath& Node9ToNode10 = circuit.CreatePath(Node9,Node10,"Node9ToNode10");
-  SEFluidCircuitPath& Node10ToNode11 = circuit.CreatePath(Node10,Node11,"Node10ToNode11");
-  SEFluidCircuitPath& Node10ToNode12 = circuit.CreatePath(Node10,Node12,"Node10ToNode12");
-  SEFluidCircuitPath& Node10ToNode13 = circuit.CreatePath(Node10,Node13,"Node10ToNode13");
-  SEFluidCircuitPath& Node11ToNode14 = circuit.CreatePath(Node11,Node14,"Node11ToNode14");
-  SEFluidCircuitPath& Node11ToNode15 = circuit.CreatePath(Node11,Node15,"Node11ToNode15");
-  SEFluidCircuitPath& Node12ToNode16 = circuit.CreatePath(Node12,Node16,"Node12ToNode16");
-  SEFluidCircuitPath& Node12ToNode17 = circuit.CreatePath(Node12,Node17,"Node12ToNode17");
-  SEFluidCircuitPath& Node13ToNode18 = circuit.CreatePath(Node13,Node18,"Node13ToNode18");
-  SEFluidCircuitPath& Node13ToNode19 = circuit.CreatePath(Node13,Node19,"Node13ToNode19");
+  circuit.CreatePath(Node1,Node7,"Node1ToNode7");
+  circuit.CreatePath(Node2,Node7,"Node2ToNode7");
+  circuit.CreatePath(Node3,Node8,"Node3ToNode8");
+  circuit.CreatePath(Node4,Node8,"Node4ToNode8");
+  circuit.CreatePath(Node5,Node9,"Node5ToNode9");
+  circuit.CreatePath(Node6,Node9,"Node6ToNode9");
+  circuit.CreatePath(Node7,Node10,"Node7ToNode10");
+  circuit.CreatePath(Node8,Node10,"Node8ToNode10");
+  circuit.CreatePath(Node9,Node10,"Node9ToNode10");
+  circuit.CreatePath(Node10,Node11,"Node10ToNode11");
+  circuit.CreatePath(Node10,Node12,"Node10ToNode12");
+  circuit.CreatePath(Node10,Node13,"Node10ToNode13");
+  circuit.CreatePath(Node11,Node14,"Node11ToNode14");
+  circuit.CreatePath(Node11,Node15,"Node11ToNode15");
+  circuit.CreatePath(Node12,Node16,"Node12ToNode16");
+  circuit.CreatePath(Node12,Node17,"Node12ToNode17");
+  circuit.CreatePath(Node13,Node18,"Node13ToNode18");
+  circuit.CreatePath(Node13,Node19,"Node13ToNode19");
 
   SEFluidCircuitPath& Node14ToGround = circuit.CreatePath(Node14,Ground,"Node14ToGround");
   Node14ToGround.GetFlowSourceBaseline().SetValue(0.5, VolumePerTimeUnit::mL_Per_s);
@@ -370,24 +370,24 @@ void CommonDataModelTest::GasTransportTest(const std::string& rptDirectory)
   SEFluidCircuitPath& groundToNode6 = circuit.CreatePath(Ground,Node6,"GroundToNode6");
   groundToNode6.GetFlowSourceBaseline().SetValue(0.5, VolumePerTimeUnit::mL_Per_s);
 
-  SEFluidCircuitPath& Node1ToNode7 = circuit.CreatePath(Node1,Node7,"Node1ToNode7");
-  SEFluidCircuitPath& Node2ToNode7 = circuit.CreatePath(Node2,Node7,"Node2ToNode7");
-  SEFluidCircuitPath& Node3ToNode8 = circuit.CreatePath(Node3,Node8,"Node3ToNode8");
-  SEFluidCircuitPath& Node4ToNode8 = circuit.CreatePath(Node4,Node8,"Node4ToNode8");
-  SEFluidCircuitPath& Node5ToNode9 = circuit.CreatePath(Node5,Node9,"Node5ToNode9");
-  SEFluidCircuitPath& Node6ToNode9 = circuit.CreatePath(Node6,Node9,"Node6ToNode9");
-  SEFluidCircuitPath& Node7ToNode10 = circuit.CreatePath(Node7,Node10,"Node7ToNode10");
-  SEFluidCircuitPath& Node8ToNode10 = circuit.CreatePath(Node8,Node10,"Node8ToNode10");
-  SEFluidCircuitPath& Node9ToNode10 = circuit.CreatePath(Node9,Node10,"Node9ToNode10");
-  SEFluidCircuitPath& Node10ToNode11 = circuit.CreatePath(Node10,Node11,"Node10ToNode11");
-  SEFluidCircuitPath& Node10ToNode12 = circuit.CreatePath(Node10,Node12,"Node10ToNode12");
-  SEFluidCircuitPath& Node10ToNode13 = circuit.CreatePath(Node10,Node13,"Node10ToNode13");
-  SEFluidCircuitPath& Node11ToNode14 = circuit.CreatePath(Node11,Node14,"Node11ToNode14");
-  SEFluidCircuitPath& Node11ToNode15 = circuit.CreatePath(Node11,Node15,"Node11ToNode15");
-  SEFluidCircuitPath& Node12ToNode16 = circuit.CreatePath(Node12,Node16,"Node12ToNode16");
-  SEFluidCircuitPath& Node12ToNode17 = circuit.CreatePath(Node12,Node17,"Node12ToNode17");
-  SEFluidCircuitPath& Node13ToNode18 = circuit.CreatePath(Node13,Node18,"Node13ToNode18");
-  SEFluidCircuitPath& Node13ToNode19 = circuit.CreatePath(Node13,Node19,"Node13ToNode19");
+  circuit.CreatePath(Node1,Node7,"Node1ToNode7");
+  circuit.CreatePath(Node2,Node7,"Node2ToNode7");
+  circuit.CreatePath(Node3,Node8,"Node3ToNode8");
+  circuit.CreatePath(Node4,Node8,"Node4ToNode8");
+  circuit.CreatePath(Node5,Node9,"Node5ToNode9");
+  circuit.CreatePath(Node6,Node9,"Node6ToNode9");
+  circuit.CreatePath(Node7,Node10,"Node7ToNode10");
+  circuit.CreatePath(Node8,Node10,"Node8ToNode10");
+  circuit.CreatePath(Node9,Node10,"Node9ToNode10");
+  circuit.CreatePath(Node10,Node11,"Node10ToNode11");
+  circuit.CreatePath(Node10,Node12,"Node10ToNode12");
+  circuit.CreatePath(Node10,Node13,"Node10ToNode13");
+  circuit.CreatePath(Node11,Node14,"Node11ToNode14");
+  circuit.CreatePath(Node11,Node15,"Node11ToNode15");
+  circuit.CreatePath(Node12,Node16,"Node12ToNode16");
+  circuit.CreatePath(Node12,Node17,"Node12ToNode17");
+  circuit.CreatePath(Node13,Node18,"Node13ToNode18");
+  circuit.CreatePath(Node13,Node19,"Node13ToNode19");
 
   SEFluidCircuitPath& Node14ToGround = circuit.CreatePath(Node14,Ground,"Node14ToGround");
   Node14ToGround.GetFlowSourceBaseline().SetValue(0.5, VolumePerTimeUnit::mL_Per_s);

src/cpp/cdm/test/ThermalCompartmentTest.cpp

@@ -294,8 +294,6 @@ void CommonDataModelTest::TestThermalHierarchy(SETestSuite& testSuite, SESubstan
   SETestCase& testCase = testSuite.CreateTestCase();
   testCase.SetName("HierarchyHeatTemperatureFlows");
 
-  SESubstance* N2 = subMgr.GetSubstance("Nitrogen");
-
   SEScalarTemperature partialTemperature;
 
   TimingProfile pTimer;

src/cpp/cdm/test/TissueCompartmentTest.cpp

@@ -52,14 +52,7 @@ void CommonDataModelTest::TissueCompartmentTest(const std::string& rptDirectory)
   double TissueToPlasmaAlbuminRatio = 1.0;
   double TissueToPlasmaAlphaAcidGlycoproteinRatio = 0.8;
   double TissueToPlasmaLipoproteinRatio = 0.54;
-  //double TotalMass_mg = 333;
-
-  double ec_pH = 7.14;
-  double ec_WaterVolumeFraction = 0.67;
-
-  double ic_pH = 7.42;
-  double ic_WaterVolumeFraction = 0.76;
-
+  
   SECompartmentManager cmptMgr(subMgr);
   SETissueCompartment* tissue = &cmptMgr.CreateTissueCompartment("Tissue");
   tissue->GetAcidicPhospohlipidConcentration().SetValue(AcidicPhospohlipidConcentration_mg_Per_g, MassPerMassUnit::mg_Per_g);

src/cpp/cpm/physiology/Saturation.cpp

@@ -105,7 +105,7 @@ public:
     // Huge penalty for negative numbers
     double negativePenaltyO2 = MIN(0.0, o2_mM);
     double negativePenaltyCO2 = (MIN(0.0, bicarb_mM) + MIN(0.0, co2_mM));
-    double pHpenalty = MAX((pH - 8.0), 0.0);
+    // unused: double pHpenalty = MAX((pH - 8.0), 0.0);
 
     fvec(0) = f0;
     fvec(1) = f1 - negativePenaltyCO2*100.0;
@@ -352,9 +352,7 @@ void SaturationCalculator::CalculateCarbonMonoxideSpeciesDistribution(SELiquidCo
   m_subCOQ->Balance(BalanceLiquidBy::PartialPressure);
 
   m_subHbCOQ->GetMolarity().SetValue(targetBoundCO_mM, AmountPerVolumeUnit::mmol_Per_L);
-  double check1 = m_subHbCOQ->GetMolarity().GetValue(AmountPerVolumeUnit::mmol_Per_L);
   m_subHbCOQ->Balance(BalanceLiquidBy::Molarity);
-  double check2 = m_subHbCOQ->GetMolarity().GetValue(AmountPerVolumeUnit::mmol_Per_L);
   // No need to balance everything. The sat method only uses moles, and it balances at the end. Just need to balance CO
 }
 
@@ -953,80 +951,80 @@ void SaturationCalculator::CalculateHemoglobinSaturations(double O2PartialPressu
     temperature_C += 4.6;
 
   // Currently fixed, but could be expanded to be variable
-  double DPG = 4.65e-3;          // standard 2; 3 - DPG concentration in RBCs; M
+  const double DPG = 4.65e-3;          // standard 2; 3 - DPG concentration in RBCs; M
 
                                           // Fixed parameters
-  double Wpl = 0.94;                      // fractional water space in plasma; unitless
-  double Wrbc = 0.65;                     // fractional water space in RBCs; unitless
-  double Rrbc = 0.69;                     // Gibbs - Donnan ratio across RBC membrane; unitless
-  double Hbrbc = 5.18e-3;                 // hemoglobin concentration in RBCs; M
-  double K2 = 2.95e-5;                    // CO2 + HbNH2 equilibrium constant; unitless
-  double K2dp = 1.0e-6;                   // HbNHCOOH dissociation constant; M
-  double K2p = K2 / K2dp;                 // kf2p / kb2p; 1 / M
-  double K3 = 2.51e-5;                    // CO2 + O2HbNH2 equilibrium constant; unitless
-  double K3dp = 1.0e-6;                   // O2HbNHCOOH dissociation constant; M
-  double K3p = K3 / K3dp;                 // kf3p / kb3p; 1 / M
-  double K5dp = 2.63e-8;                  // HbNH3 + dissociation constant; M
-  double K6dp = 1.91e-8;                  // O2HbNH3 + dissociation constant; M
-  double nhill = 2.7 - 1.1*CO_sat;        // Hill coefficient; unitless
-  double n0 = nhill - 1.0 - 0.2*CO_sat;   // Deviation term
-
-  double pO20 = 100.0;                    // standard O2 partial pressure in blood; mmHg
-  double pCO20 = 40.0;                    // standard CO2 partial pressure in blood; mmHg
-  double pH0 = 7.24;                      // standard pH in RBCs; unitless
-  double DPG0 = 4.65e-3;                  // standard 2; 3 - DPG concentration in RBCs; M
-  double Temp0 = 37.0;                    // standard temperature in blood; degC
-  double fact = 1.0e-6 / Wpl;             // a multiplicative factor; M / mmHg
-  double alphaO20 = fact*1.37;            // solubility of O2 in water at 37 C; M / mmHg
-  double alphaCO20 = fact*30.7;            // solubility of CO2 in water at 37 C; M / mmHg
-  double O20 = alphaO20*pO20;              // standard O2 concentration in RBCs; M
-  double CO20 = alphaCO20*pCO20;          // standard CO2 concentration in RBCs; M
-  double Hp0 = pow(10, (-pH0));           // standard H + concentration in RBCs; M
-  double pHpl0 = pH0 - log10(Rrbc);        // standard pH in plasma; unitless
-  double P500 = 26.8 - 20*CO_sat;         // standard pO2 at 50% SHbO2; mmHg
-  double C500 = alphaO20*P500;            // standard O2 concentration at 50 % SHbO2; M
-
-  double Wbl = (1 - hematocrit)*Wpl + hematocrit*Wrbc;
-  double pHpl = pH - log10(Rrbc);
-  double pHpldiff = pHpl - pHpl0;
-  double pHdiff = pH - pH0;
-  double pCO2diff = CO2PartialPressureGuess_mmHg - pCO20;
-  double DPGdiff = DPG - DPG0;
-  double Tempdiff = temperature_C - Temp0;
-  double alphaO2 = fact*(1.37 - 0.0137*Tempdiff + 0.00058*Tempdiff*Tempdiff);
-  double alphaCO2 = fact*(30.7 - 0.57*Tempdiff + 0.02*Tempdiff*Tempdiff);
-  double pK1 = 6.091 - 0.0434*pHpldiff + 0.0014*Tempdiff*pHpldiff;
-  double K1 = pow(10, -pK1);
-  double O2 = alphaO2*O2PartialPressureGuess_mmHg;
-  double CO2 = alphaCO2*CO2PartialPressureGuess_mmHg;
-  double Hp = pow(10, -pH);
-  double Hppl = pow(10, -pHpl);
-
-  double Term1 = K2p*(1 + K2dp / Hp);
-  double Term2 = K3p*(1 + K3dp / Hp);
-  double Term3 = (1 + Hp / K5dp);
-  double Term4 = (1 + Hp / K6dp);
-  double Term10 = K2p*(1 + K2dp / Hp0);
-  double Term20 = K3p*(1 + K3dp / Hp0);
-  double Term30 = (1 + Hp0 / K5dp);
-  double Term40 = (1 + Hp0 / K6dp);
-  double Kratio10 = (Term10*CO20 + Term30) / (Term20*CO20 + Term40);
-  double Kratio11 = (Term1*CO20 + Term3) / (Term2*CO20 + Term4);
-  double Kratio12 = (Term10*alphaCO20*CO2PartialPressureGuess_mmHg + Term30) / (Term20*alphaCO20*CO2PartialPressureGuess_mmHg + Term40);
-  double K4dp = Kratio10*pow(O20, n0) / pow(C500, nhill);
-  double K4tp = K4dp / pow(O20, n0);
-  double Kratio20 = Kratio10 / K4tp; // = C500^nhill
-  double Kratio21 = Kratio11 / K4tp;
-  double Kratio22 = Kratio12 / K4tp;
-
-  double P501 = 26.765 - 21.279*pHdiff + 8.872*pHdiff*pHdiff;
-  double P502 = 26.80 + 0.0428*pCO2diff + 3.64e-5*pCO2diff*pCO2diff;
-  double P503 = 26.78 + 795.633533*DPGdiff - 19660.8947*DPGdiff*DPGdiff;
-  double P504 = 26.75 + 1.4945*Tempdiff + 0.04335*Tempdiff*Tempdiff + 0.0007*Tempdiff*Tempdiff*Tempdiff;
-  double C501 = alphaO20*P501;
-  double C502 = alphaO20*P502;
-  double C503 = alphaO20*P503;
-  double C504 = alphaO2*P504;
+  const double Wpl = 0.94;                      // fractional water space in plasma; unitless
+  const double Wrbc = 0.65;                     // fractional water space in RBCs; unitless
+  const double Rrbc = 0.69;                     // Gibbs - Donnan ratio across RBC membrane; unitless
+  const double Hbrbc = 5.18e-3;                 // hemoglobin concentration in RBCs; M
+  const double K2 = 2.95e-5;                    // CO2 + HbNH2 equilibrium constant; unitless
+  const double K2dp = 1.0e-6;                   // HbNHCOOH dissociation constant; M
+  const double K2p = K2 / K2dp;                 // kf2p / kb2p; 1 / M
+  const double K3 = 2.51e-5;                    // CO2 + O2HbNH2 equilibrium constant; unitless
+  const double K3dp = 1.0e-6;                   // O2HbNHCOOH dissociation constant; M
+  const double K3p = K3 / K3dp;                 // kf3p / kb3p; 1 / M
+  const double K5dp = 2.63e-8;                  // HbNH3 + dissociation constant; M
+  const double K6dp = 1.91e-8;                  // O2HbNH3 + dissociation constant; M
+  const double nhill = 2.7 - 1.1*CO_sat;        // Hill coefficient; unitless
+  const double n0 = nhill - 1.0 - 0.2*CO_sat;   // Deviation term
+
+  const double pO20 = 100.0;                    // standard O2 partial pressure in blood; mmHg
+  const double pCO20 = 40.0;                    // standard CO2 partial pressure in blood; mmHg
+  const double pH0 = 7.24;                      // standard pH in RBCs; unitless
+  const double DPG0 = 4.65e-3;                  // standard 2; 3 - DPG concentration in RBCs; M
+  const double Temp0 = 37.0;                    // standard temperature in blood; degC
+  const double fact = 1.0e-6 / Wpl;             // a multiplicative factor; M / mmHg
+  const double alphaO20 = fact*1.37;            // solubility of O2 in water at 37 C; M / mmHg
+  const double alphaCO20 = fact*30.7;            // solubility of CO2 in water at 37 C; M / mmHg
+  const double O20 = alphaO20*pO20;              // standard O2 concentration in RBCs; M
+  const double CO20 = alphaCO20*pCO20;          // standard CO2 concentration in RBCs; M
+  const double Hp0 = pow(10, (-pH0));           // standard H + concentration in RBCs; M
+  const double pHpl0 = pH0 - log10(Rrbc);        // standard pH in plasma; unitless
+  const double P500 = 26.8 - 20*CO_sat;         // standard pO2 at 50% SHbO2; mmHg
+  const double C500 = alphaO20*P500;            // standard O2 concentration at 50 % SHbO2; M
+
+  const double Wbl = (1 - hematocrit)*Wpl + hematocrit*Wrbc;
+  const double pHpl = pH - log10(Rrbc);
+  const double pHpldiff = pHpl - pHpl0;
+  const double pHdiff = pH - pH0;
+  const double pCO2diff = CO2PartialPressureGuess_mmHg - pCO20;
+  const double DPGdiff = DPG - DPG0;
+  const double Tempdiff = temperature_C - Temp0;
+  const double alphaO2 = fact*(1.37 - 0.0137*Tempdiff + 0.00058*Tempdiff*Tempdiff);
+  const double alphaCO2 = fact*(30.7 - 0.57*Tempdiff + 0.02*Tempdiff*Tempdiff);
+  const double pK1 = 6.091 - 0.0434*pHpldiff + 0.0014*Tempdiff*pHpldiff;
+  const double K1 = pow(10, -pK1);
+  const double O2 = alphaO2*O2PartialPressureGuess_mmHg;
+  const double CO2 = alphaCO2*CO2PartialPressureGuess_mmHg;
+  const double Hp = pow(10, -pH);
+  const double Hppl = pow(10, -pHpl);
+
+  const double Term1 = K2p*(1 + K2dp / Hp);
+  const double Term2 = K3p*(1 + K3dp / Hp);
+  const double Term3 = (1 + Hp / K5dp);
+  const double Term4 = (1 + Hp / K6dp);
+  const double Term10 = K2p*(1 + K2dp / Hp0);
+  const double Term20 = K3p*(1 + K3dp / Hp0);
+  const double Term30 = (1 + Hp0 / K5dp);
+  const double Term40 = (1 + Hp0 / K6dp);
+  const double Kratio10 = (Term10*CO20 + Term30) / (Term20*CO20 + Term40);
+  const double Kratio11 = (Term1*CO20 + Term3) / (Term2*CO20 + Term4);
+  const double Kratio12 = (Term10*alphaCO20*CO2PartialPressureGuess_mmHg + Term30) / (Term20*alphaCO20*CO2PartialPressureGuess_mmHg + Term40);
+  const double K4dp = Kratio10*pow(O20, n0) / pow(C500, nhill);
+  const double K4tp = K4dp / pow(O20, n0);
+  const double Kratio20 = Kratio10 / K4tp; // = C500^nhill
+  const double Kratio21 = Kratio11 / K4tp;
+  const double Kratio22 = Kratio12 / K4tp;
+
+  const double P501 = 26.765 - 21.279*pHdiff + 8.872*pHdiff*pHdiff;
+  const double P502 = 26.80 + 0.0428*pCO2diff + 3.64e-5*pCO2diff*pCO2diff;
+  const double P503 = 26.78 + 795.633533*DPGdiff - 19660.8947*DPGdiff*DPGdiff;
+  const double P504 = 26.75 + 1.4945*Tempdiff + 0.04335*Tempdiff*Tempdiff + 0.0007*Tempdiff*Tempdiff*Tempdiff;
+  const double C501 = alphaO20*P501;
+  const double C502 = alphaO20*P502;
+  const double C503 = alphaO20*P503;
+  const double C504 = alphaO2*P504;
 
   double n1 = 1.0;
   double n2 = 1.0;

src/cpp/cpm/physiology/Tissue.cpp

@@ -616,22 +616,22 @@ void Tissue::CalculateMetabolicConsumptionAndProduction(double time_s)
 
   // The following fractions are used to compute the metabolic conversion of substances.
   // Stoichiometric ratios can be found in any physiology text, such as \cite guyton2006medical
-  double FractionOfO2CO2ToGlucose = 0.157894737;    // Ratio of o2/co2 required to produce ATP for glucose consumption. = 6.0 / 38.0 
-  double FractionOfO2ToLipid = 0.212239583;         // Ratio of o2 required to produce ATP for lipid consumption. = 163.0 / 768.0;
-  double FractionOfCO2ToLipid = 0.1484375;          // ratio of co2 required to produce ATP for lipid consumption. = 114.0 / 768.0;
+  const double FractionOfO2CO2ToGlucose = 0.157894737;    // Ratio of o2/co2 required to produce ATP for glucose consumption. = 6.0 / 38.0 
+  const double FractionOfO2ToLipid = 0.212239583;         // Ratio of o2 required to produce ATP for lipid consumption. = 163.0 / 768.0;
+  const double FractionOfCO2ToLipid = 0.1484375;          // ratio of co2 required to produce ATP for lipid consumption. = 114.0 / 768.0;
   SEScalarPressure ppO2;
   SEScalarMassPerVolume atConc;
   ppO2.SetValue(40.0, PressureUnit::mmHg);
   GeneralMath::CalculateHenrysLawConcentration(*m_O2, ppO2, atConc, m_Logger);
-  double anaerobicThresholdConcentration_mM = atConc.GetValue(MassPerVolumeUnit::g_Per_L) / m_O2->GetMolarMass(MassPerAmountUnit::g_Per_mmol);
-  double FractionOfGlucoseToATP = 0.026315789;      // Ratio of glucose required to ATP produced. = 1.0 / 38.0;
-  double FractionOfLactateToGlucose = 0.5;          // Ratio of glucose required to lactate produced during anaerobic metabolism. = 1.0 / 2.0;
-  double FractionOfAcetoacetateToATP = 0.041666667; // Ratio of acetoacetate required to ATP produced. = 1.0 / 24.0;
-  double FractionOfLactateToATP = 0.027777778;      // Ratio of lactate required to ATP produced. = 1.0 / 36.0;
-  double FractionOfLipidToATP = 0.002604167;        // Ratio of of lipid required to ATP produced. = 2.0 / 768.0;
-  double FractionLipidsAsTristearin = 0.256;        // This is an empirically determined value specific to the Pulse implementation
-
-  double exerciseTuningFactor = 1.0; // 2.036237;           // A tuning factor to adjust production and consumption during exercise
+  const double anaerobicThresholdConcentration_mM = atConc.GetValue(MassPerVolumeUnit::g_Per_L) / m_O2->GetMolarMass(MassPerAmountUnit::g_Per_mmol);
+  const double FractionOfGlucoseToATP = 0.026315789;      // Ratio of glucose required to ATP produced. = 1.0 / 38.0;
+  const double FractionOfLactateToGlucose = 0.5;          // Ratio of glucose required to lactate produced during anaerobic metabolism. = 1.0 / 2.0;
+  const double FractionOfAcetoacetateToATP = 0.041666667; // Ratio of acetoacetate required to ATP produced. = 1.0 / 24.0;
+  const double FractionOfLactateToATP = 0.027777778;      // Ratio of lactate required to ATP produced. = 1.0 / 36.0;
+  const double FractionOfLipidToATP = 0.002604167;        // Ratio of of lipid required to ATP produced. = 2.0 / 768.0;
+  const double FractionLipidsAsTristearin = 0.256;        // This is an empirically determined value specific to the Pulse implementation
+
+  const double exerciseTuningFactor = 1.0; // 2.036237;           // A tuning factor to adjust production and consumption during exercise
 
   double insulinConc_ug_Per_L = m_data.GetSubstances().GetInsulin().GetBloodConcentration(MassPerVolumeUnit::ug_Per_L);
 

src/cpp/cpm/test/AcidBaseTests.cpp

@@ -76,19 +76,19 @@ void PulseEngineTest::AcidBaseMathTest(const std::string& rptDirectory)
   SELiquidSubstanceQuantity* nHCO3 = cmpt.GetSubstanceQuantity(*HCO3);
   SELiquidSubstanceQuantity* nHbCO2 = cmpt.GetSubstanceQuantity(*HbCO2);
 
-  double cmptVolume_mL = 100.0;
-  double normalTotalO2_mM = 6.2;
-  double normalTotalCO2_mM = 28.86;
+  const double cmptVolume_mL = 100.0;
+  const double normalTotalO2_mM = 6.2;
+  const double normalTotalCO2_mM = 28.86;
   double currentTotalO2_mM;
   double currentTotalCO2_mM;
-  double normalDissolvedCO2_gPerL = 0.05526; // 0.05526;
-  double normalDissolvedO2_gPerL = 0.004287; // 0.004287;
-  double normalBicarbonate_gPerL = 0.026*61.0168;
-  double normalHgb_mM = 1.55;
-  double percentNothingBound = 0.01;
-  double percentO2OnlyBound = 0.73;
-  double percentO2CO2Bound = 0.25;
-  double percentCO2Bound = 0.01;
+  const double normalDissolvedCO2_gPerL = 0.05526; // 0.05526;
+  const double normalDissolvedO2_gPerL = 0.004287; // 0.004287;
+  const double normalBicarbonate_gPerL = 0.026*61.0168;
+  const double normalHgb_mM = 1.55;
+  const double percentNothingBound = 0.01;
+  const double percentO2OnlyBound = 0.73;
+  const double percentO2CO2Bound = 0.25;
+  const double percentCO2Bound = 0.01;
   //double O2ppGuess_mmHg = 100.0;
   //double CO2ppGuess_mmHg = 1000.0*normalDissolvedCO2_gPerL/(44.01*0.0314);
   //normalDissolvedCO2_gPerL = CO2ppGuess_mmHg*(44.01*0.0314) / 1000.0;
@@ -572,16 +572,16 @@ void PulseEngineTest::AcidBaseLimitsTest(const std::string& rptDirectory)
     c.CalculateBloodGasDistribution(cmpt);
 
     // Get and print results
-    double finalDissovledCO2_gPerL = nCO2->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L);
-    double finalDissovledCO2_mM = finalDissovledCO2_gPerL / CO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol);
-    double finalBicarb_gPerL = nHCO3->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L);
-    double finalBicarbCO2_mM = finalBicarb_gPerL / HCO3->GetMolarMass(MassPerAmountUnit::g_Per_mmol); // Yes this should be m_CO2_g_Per_mmol because 1 mol CO2 per mol bicarb
-    double finalBicarbCO2_gPerL = finalBicarbCO2_mM * CO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol);
-    double finalBoundCO2_mM = 4.0 * (nHbCO2->GetMass().GetValue(MassUnit::g) / cmpt.GetVolume(VolumeUnit::L) / HbCO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol) + nHbO2CO2->GetMass().GetValue(MassUnit::g) / cmpt.GetVolume(VolumeUnit::L) / HbO2CO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol)); //4 moles CO2 per mole Hb
-    double finalBoundCO2_gPerL = finalBoundCO2_mM * CO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol);
-    double finalTotalCO2_mM = finalDissovledCO2_mM + finalBicarbCO2_mM + finalBoundCO2_mM;
-    double finalTotalCO2_gPerL = finalDissovledCO2_gPerL + finalBicarbCO2_gPerL + finalBoundCO2_gPerL;
-    double finalTotalHemoglobin_gPerL = nHb->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L) +
+    finalDissovledCO2_gPerL = nCO2->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L);
+    finalDissovledCO2_mM = finalDissovledCO2_gPerL / CO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol);
+    finalBicarb_gPerL = nHCO3->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L);
+    finalBicarbCO2_mM = finalBicarb_gPerL / HCO3->GetMolarMass(MassPerAmountUnit::g_Per_mmol); // Yes this should be m_CO2_g_Per_mmol because 1 mol CO2 per mol bicarb
+    finalBicarbCO2_gPerL = finalBicarbCO2_mM * CO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol);
+    finalBoundCO2_mM = 4.0 * (nHbCO2->GetMass().GetValue(MassUnit::g) / cmpt.GetVolume(VolumeUnit::L) / HbCO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol) + nHbO2CO2->GetMass().GetValue(MassUnit::g) / cmpt.GetVolume(VolumeUnit::L) / HbO2CO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol)); //4 moles CO2 per mole Hb
+    finalBoundCO2_gPerL = finalBoundCO2_mM * CO2->GetMolarMass(MassPerAmountUnit::g_Per_mmol);
+    finalTotalCO2_mM = finalDissovledCO2_mM + finalBicarbCO2_mM + finalBoundCO2_mM;
+    finalTotalCO2_gPerL = finalDissovledCO2_gPerL + finalBicarbCO2_gPerL + finalBoundCO2_gPerL;
+    finalTotalHemoglobin_gPerL = nHb->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L) +
       nHbO2->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L) +
       nHbCO2->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L) +
       nHbO2CO2->GetConcentration().GetValue(MassPerVolumeUnit::g_Per_L);
@@ -896,7 +896,6 @@ void PulseEngineTest::AcidBaseBloodGasTest(PulseController& pc, bloodType bloodC
   double CO2sat_max = 0;         //Computed using Dash model
   double pH_min = 0;             //Leeuwen 
   double pH_max = 0;             //Leeuwen 
-  double percentTolerance = .02;
 
   double O2_sat = 0;
   double CO2_sat = 0;

src/cpp/cpm/test/AnesthesiaCircuit.cpp

@@ -122,7 +122,6 @@ void PulseEngineTest::AnesthesiaMachineCircuitAndTransportTest(RespiratoryConfig
   SEFluidCircuitPath* EnvironmentToVentilatorPath = amCircuit->GetPath(pulse::AnesthesiaMachinePath::EnvironmentToVentilator);
   SEFluidCircuitPath* EnvironmentToReliefValve = amCircuit->GetPath(pulse::AnesthesiaMachinePath::EnvironmentToReliefValve);
   SEFluidCircuitPath* GasSourceToGasInlet = amCircuit->GetPath(pulse::AnesthesiaMachinePath::GasSourceToGasInlet);
-  SEFluidCircuitPath* EnvironmentToGasSource = amCircuit->GetPath(pulse::AnesthesiaMachinePath::EnvironmentToGasSource);
 
   SEGasTransporter txpt(VolumePerTimeUnit::L_Per_s, VolumeUnit::L, VolumeUnit::L, pc.GetLogger());
   SEFluidCircuitCalculator calc(VolumePerPressureUnit::L_Per_cmH2O, VolumePerTimeUnit::L_Per_s, PressureTimeSquaredPerVolumeUnit::cmH2O_s2_Per_L, PressureUnit::cmH2O, VolumeUnit::L, PressureTimePerVolumeUnit::cmH2O_s_Per_L, pc.GetLogger());

src/cpp/cpm/test/CardiovascularCircuit.cpp

@@ -367,11 +367,6 @@ void PulseEngineTest::CardiovascularCircuitAndTransportTest(CardiovascularDriver
   SEFluidCircuitNode* VenaCava = cvCircuit.GetNode("VenaCava");
   SEFluidCircuitPath *RightCompliance = cvCircuit.GetPath(pulse::CardiovascularPath::RightHeart1ToRightHeart3);
   SEFluidCircuitPath *LeftCompliance = cvCircuit.GetPath(pulse::CardiovascularPath::LeftHeart1ToLeftHeart3);
-  SEFluidCircuitPath *HeartLeft = cvCircuit.GetPath(pulse::CardiovascularPath::LeftHeart1ToAorta2);
-
-  SELiquidSubstanceQuantity* venaCavaN2 = cvGraph.GetCompartment(pulse::VascularCompartment::VenaCava)->GetSubstanceQuantity(pc.GetSubstances().GetN2());
-  SELiquidSubstanceQuantity* leftPulmonaryCapillariesN2 = cvGraph.GetCompartment(pulse::VascularCompartment::LeftPulmonaryCapillaries)->GetSubstanceQuantity(pc.GetSubstances().GetN2());
-  SELiquidSubstanceQuantity* rightPulmonaryCapillariesN2 = cvGraph.GetCompartment(pulse::VascularCompartment::LeftPulmonaryCapillaries)->GetSubstanceQuantity(pc.GetSubstances().GetN2());
 
   SELiquidTransporter txpt(VolumePerTimeUnit::mL_Per_s, VolumeUnit::mL, MassUnit::ug, MassPerVolumeUnit::ug_Per_mL, pc.GetLogger());
   SEFluidCircuitCalculator calc(VolumePerPressureUnit::mL_Per_mmHg, VolumePerTimeUnit::mL_Per_s, PressureTimeSquaredPerVolumeUnit::mmHg_s2_Per_mL, PressureUnit::mmHg, VolumeUnit::mL, PressureTimePerVolumeUnit::mmHg_s_Per_mL, pc.GetLogger());
@@ -694,7 +689,7 @@ void PulseEngineTest::CardiovascularCircuitScaleTests(const std::string& sTestDi
   // Note: You could scale the amplitude/elastance of the driver if want (We didn't at the time I wrote it, but its possible!)
   double heartRate_bpm = 72;// Note, you should always pass in a bpm other than <=0 for a well named file
   ss << heartRate_bpm;
-  double comp = 1.0, res = 1.0, vol = 1, sysRes = 1, sysComp = 1, aortaRes = 0.7, aortaComp = 0.7, venaRes = 1, venaComp = 1;
+  const double comp = 1.0, res = 1.0, vol = 1, sysRes = 1, sysComp = 1, aortaRes = 0.7, aortaComp = 0.7, venaRes = 1, venaComp = 1;
 
   //for (double rFactor = 0.3; rFactor <= 1.7; rFactor += 0.1)
   //{

src/cpp/cpm/test/FourCompartmentTest.cpp

@@ -52,31 +52,31 @@ double TotalHbMols(SELiquidCompartmentGraph& Graph, SESubstance& Hb, SESubstance
   return totalHb_g / Hb_g_Per_mol + totalHbO2_g / HbO2_g_Per_mol + totalHbCO2_g / HbCO2_g_Per_mol + totalHBO2CO2_g / HbO2CO2_g_Per_mol;
 }
 
-void PulseEngineTest::FourCompartmentTest(bool usingAcidBase, bool usingProductionConsumption, bool usingDiffusion, const std::string& rptDirectory)
+void PulseEngineTest::FourCompartmentTest(bool localUsingAcidBase, bool localUsingProductionConsumption, bool localUsingDiffusion, const std::string& rptDirectory)
 {
   DataTrack trk;