Use static type metadata

demo/analytic_continuum/src/continuum_model.h

@@ -26,7 +26,6 @@ namespace bdm {
 class AnalyticContinuum final : public ScalarField {
  public:
   AnalyticContinuum() = default;
-  explicit AnalyticContinuum(const TRootIOCtor *) {}
   ~AnalyticContinuum() final = default;
 
   void Initialize() final {}
@@ -58,8 +57,6 @@ class AnalyticContinuum final : public ScalarField {
     return {0, 0, 0};
   };
 
-  BDM_CLASS_DEF_OVERRIDE(AnalyticContinuum, 1);  // NOLINT
-
  private:
   real_t time_ = 0.0;
 };

demo/analytic_continuum/src/my_agent.h

@@ -23,7 +23,7 @@ namespace bdm {
 /// A simple agent that can sense the continuum value and stores the value in
 /// a member variable.
 class ContinuumRetrieverAgent : public SphericalAgent {
-  BDM_AGENT_HEADER(ContinuumRetrieverAgent, SphericalAgent, 1);
+  BDM_AGENT_HEADER(ContinuumRetrieverAgent, SphericalAgent);
 
  public:
   ContinuumRetrieverAgent() {}

demo/analytic_continuum/src/my_behavior.h

@@ -24,7 +24,7 @@ namespace bdm {
 /// Behavior that allows agents to sense the continuum value and stores the
 /// value in its member variable.
 struct RetrieveContinuumValue : public Behavior {
-  BDM_BEHAVIOR_HEADER(RetrieveContinuumValue, Behavior, 1);
+  BDM_BEHAVIOR_HEADER(RetrieveContinuumValue, Behavior);
 
   RetrieveContinuumValue() {}
   virtual ~RetrieveContinuumValue() {}

demo/cell_division_enhanced/src/cell_division_enhanced.h

@@ -33,7 +33,7 @@ inline int signum(const T& x) {
 namespace bdm {
 
 class MyCell : public Cell {
-  BDM_AGENT_HEADER(MyCell, Cell, 1);
+  BDM_AGENT_HEADER(MyCell, Cell);
 
  public:
   MyCell() : Cell() { UpdateVolume(); }

demo/flocking/src/boid.h

@@ -50,7 +50,7 @@ real_t FluctuateCoefficient(real_t coefficient, real_t fluctuation_strength,
 ////////////////////////////////////////////////////////////////////////////////
 
 class Boid : public Agent {
-  BDM_AGENT_HEADER(Boid, Agent, 1);
+  BDM_AGENT_HEADER(Boid, Agent);
 
  public:
   Boid() {}
@@ -171,13 +171,13 @@ class Boid : public Agent {
 ////////////////////////////////////////////////////////////////////////////////
 
 struct Flocking : public Behavior {
-  BDM_BEHAVIOR_HEADER(Flocking, Behavior, 1);
+  BDM_BEHAVIOR_HEADER(Flocking, Behavior);
 
   void Run(Agent* agent) override;
 };
 
 struct RandomPerturbation : public Behavior {
-  BDM_BEHAVIOR_HEADER(RandomPerturbation, Behavior, 1);
+  BDM_BEHAVIOR_HEADER(RandomPerturbation, Behavior);
 
  public:
   RandomPerturbation(real_t v = 1) : velocity_(v) { AlwaysCopyToNew(); }

demo/mars/src/CelestialObjects.h

@@ -22,7 +22,7 @@ namespace astrophysics {
 // creating the custom agent that
 // defines celestial objects
 class CelestialObject : public Cell {
-  BDM_AGENT_HEADER(CelestialObject, Cell, 1);
+  BDM_AGENT_HEADER(CelestialObject, Cell);
 
  public:
   // constructors
@@ -51,7 +51,7 @@ class CelestialObject : public Cell {
 
 // Planet subclass
 class Planet : public CelestialObject {
-  BDM_AGENT_HEADER(Planet, CelestialObject, 1);
+  BDM_AGENT_HEADER(Planet, CelestialObject);
 
  public:
   Planet() : CelestialObject() {}
@@ -65,7 +65,7 @@ class Planet : public CelestialObject {
 
 // Satellite subclass
 class Satellite : public CelestialObject {
-  BDM_AGENT_HEADER(Satellite, CelestialObject, 1);
+  BDM_AGENT_HEADER(Satellite, CelestialObject);
 
  public:
   Satellite() : CelestialObject() {}

demo/monolayer_growth/src/behaviours.h

@@ -24,7 +24,7 @@ namespace bdm {
 
 // Define growth behaviour
 struct GrowthAndCellCycle : public Behavior {
-  BDM_BEHAVIOR_HEADER(GrowthAndCellCycle, Behavior, 1);
+  BDM_BEHAVIOR_HEADER(GrowthAndCellCycle, Behavior);
 
   GrowthAndCellCycle() { AlwaysCopyToNew(); }
   virtual ~GrowthAndCellCycle() {}

demo/monolayer_growth/src/cell_cell_force.cc

@@ -17,6 +17,10 @@
 
 namespace bdm {
 
+namespace {
+constexpr real_t kCoincidentCenterTolerance = 1e-8;
+}  // namespace
+
 /// Custom force. Changed adhesive and repulsive parameters compared to standard
 /// force to achieve quick separation of mother and daughter cells after
 /// division.
@@ -52,7 +56,7 @@ Real4 CellCellForce::Calculate(const Agent* lhs, const Agent* rhs) const {
   }
   // to avoid a division by 0 if the centers are (almost) at the same
   //  location
-  if (center_distance < 0.00000001) {
+  if (center_distance < kCoincidentCenterTolerance) {
     auto* random = Simulation::GetActive()->GetRandom();
     auto force2on1 = random->template UniformArray<3>(-3.0, 3.0);
     return {force2on1[0], force2on1[1], force2on1[2], 0};

demo/monolayer_growth/src/cycling_cell.h

@@ -25,7 +25,7 @@ enum CellState { kG1, kS, kG2, kM };
 
 class CyclingCell : public Cell {  // our object extends the Cell object
                                    // create the header with our new data member
-  BDM_AGENT_HEADER(CyclingCell, Cell, 1);
+  BDM_AGENT_HEADER(CyclingCell, Cell);
 
  public:
   CyclingCell() {}

demo/monolayer_growth/src/evaluate.h

@@ -15,16 +15,13 @@
 #ifndef EVALUATE_H_
 #define EVALUATE_H_
 
-#include <TAxis.h>
-#include <TLegend.h>
-#include <TMultiGraph.h>
 #include <cmath>
+#include <fstream>
+#include <string>
 #include <vector>
 #include "biodynamo.h"
 #include "sim_param.h"
 
-using namespace bdm::experimental;
-
 namespace bdm {
 
 inline void SetupResultCollection(Simulation* sim) {
@@ -56,46 +53,27 @@ inline void SetupResultCollection(Simulation* sim) {
   ts->AddCollector("env_dims", get_env_dims, get_time);
 }
 
-inline void ExportResults(const bool plot_legend = true,
-                          const std::string& filename = "result") {
-  // Prerequisites
+inline void ExportResults(const std::string& filename = "result.csv") {
   const std::string folder = Simulation::GetActive()->GetOutputDir();
   auto* ts = Simulation::GetActive()->GetTimeSeries();
-  TimeSeries allts;
-  std::vector<real_t> times, sizes;
-
-  // Add simulated data
-  allts.Add(*ts, Concat("i", 0));
-  times = ts->GetXValues("env_dims");
-  sizes = ts->GetYValues("env_dims");
-
-  // Add experimental data from Figure 1 from Drasdo and Hoehme (2005)
-  allts.Add("experimental_data",
-            {336 / 24., 386 / 24., 408 / 24., 481 / 24., 506 / 24., 646 / 24.},
-            {1140, 1400, 1590, 2040, 2250, 3040});
-
-  // Initialize line graph
-  LineGraph lg(&allts, "", "Time [days]", "2D Monolayer size (um)", plot_legend,
-               nullptr, 350, 250);
-
-  // Add simulated data
-  lg.Add(Concat("env_dims-i", 0), "Sim data ", "LP", kBlue, 0.2, kSolid, 2,
-         kBlue, 0.7, kFullCircle, 0.5);
-
-  // Add style for exp data
-  lg.Add("experimental_data", "Exp data ", "LP", kBlack, 0.2, kSolid, 2, kBlack,
-         0.7, kFullCircle, 0.5);
-
-  // Add legend
-  if (plot_legend) {
-    lg.SetLegendPosNDC(0.1, 0.7, 0.3, 0.9);
+  const auto& times = ts->GetXValues("env_dims");
+  const auto& sizes = ts->GetYValues("env_dims");
+  std::ofstream output(Concat(folder, "/", filename));
+  output << "source,time_days,size_um\n";
+  for (size_t i = 0; i < times.size(); ++i) {
+    output << "simulation," << times[i] << ',' << sizes[i] << '\n';
   }
 
-  // Save plot
-  lg.SaveAs(Concat(folder, "/", filename), {".svg", ".png"});
-
-  // Save data
-  ts->SaveJson(Concat(folder, "/monolayer_growth.json"));
+  constexpr real_t kHoursPerDay = 24.0;
+  const std::vector<real_t> experimental_times = {
+      336 / kHoursPerDay, 386 / kHoursPerDay, 408 / kHoursPerDay,
+      481 / kHoursPerDay, 506 / kHoursPerDay, 646 / kHoursPerDay};
+  const std::vector<real_t> experimental_sizes = {1140, 1400, 1590,
+                                                  2040, 2250, 3040};
+  for (size_t i = 0; i < experimental_times.size(); ++i) {
+    output << "experiment," << experimental_times[i] << ','
+           << experimental_sizes[i] << '\n';
+  }
 }
 
 }  // namespace bdm

demo/newtons_law_test/src/CelestialObjects.h

@@ -22,7 +22,7 @@ namespace astrophysics {
 // creating the custom agent that
 // defines celestial objects
 class CelestialObject : public Cell {
-  BDM_AGENT_HEADER(CelestialObject, Cell, 1);
+  BDM_AGENT_HEADER(CelestialObject, Cell);
 
  public:
   // constructors

demo/parameters/src/parameters.h

@@ -24,6 +24,13 @@ struct SimParam : public ParamGroup {
 
   real_t foo = 3.14;
   int bar = -42;
+
+ protected:
+  void AssignFromConfig(
+      const std::shared_ptr<cpptoml::table>& config) override {
+    BDM_ASSIGN_CONFIG_VALUE(foo, "parameters.foo");
+    BDM_ASSIGN_CONFIG_VALUE(bar, "parameters.bar");
+  }
 };
 
 inline int Simulate(int argc, const char** argv) {

demo/pyramidal_cell/src/pyramidal_cell.h

@@ -24,7 +24,7 @@ namespace bdm {
 enum Substances { kApical, kBasal };
 
 struct ApicalDendriteGrowth : public Behavior {
-  BDM_BEHAVIOR_HEADER(ApicalDendriteGrowth, Behavior, 1);
+  BDM_BEHAVIOR_HEADER(ApicalDendriteGrowth, Behavior);
   ApicalDendriteGrowth() { AlwaysCopyToNew(); }
   virtual ~ApicalDendriteGrowth() {}
 
@@ -83,7 +83,7 @@ struct ApicalDendriteGrowth : public Behavior {
 };
 
 struct BasalDendriteGrowth : public Behavior {
-  BDM_BEHAVIOR_HEADER(BasalDendriteGrowth, Behavior, 1);
+  BDM_BEHAVIOR_HEADER(BasalDendriteGrowth, Behavior);
   BasalDendriteGrowth() { AlwaysCopyToNew(); }
   virtual ~BasalDendriteGrowth() {}
 

demo/regulatory_networks/src/bdm_ex1.h

@@ -22,7 +22,6 @@ namespace bdm {
 
 enum Substances { kProtein };
 
-#ifndef __ROOTCLING__
 struct ODE_system {
   const std::map<std::string, DiffusionGrid*>& mdg;
   const std::vector<real_t> param;
@@ -80,8 +79,6 @@ struct ODE_output {
     std::clog << std::endl;
   }
 };
-#endif
-
 namespace ex1 {
 
 inline int Simulate(int argc, const char** argv) {
@@ -136,15 +133,12 @@ inline int Simulate(int argc, const char** argv) {
     c->SetAdherence(0.4);
     c->SetMass(1.0);
     c->SetPosition(xyz);
-#ifndef __ROOTCLING__
     c->AddBehavior(new RegulatoryNetwork(
         dt_RN, 1000, {1., 5., 7.},
         // ODE_solver::Euler,
         // ODE_solver::Rosenbrock,
         ODE_solver::RungeKutta, ODE_system(dg_map, {0.2, 0.1, 3.0}),
         ODE_jacobian(dg_map, {0.2, 0.1, 3.0}), ODE_output()));
-#endif
-
     sim.GetExecutionContext()->AddAgent(c);
   }
 

demo/regulatory_networks/src/bdm_ex2.h

@@ -22,7 +22,7 @@
 namespace bdm {
 
 class MyCell : public Cell {
-  BDM_AGENT_HEADER(MyCell, Cell, 1);
+  BDM_AGENT_HEADER(MyCell, Cell);
 
  public:
   MyCell() {}
@@ -42,12 +42,20 @@ class MyCell : public Cell {
   real_t GetTrail() const { return trail_; }
   void SetTrail(real_t t) { trail_ += t; }
 
+  bool GetVisualizationData(const std::string& name,
+                            VisualizationData* values) const override {
+    if (name == "trail_") {
+      *values = std::vector<real_t>{trail_};
+      return true;
+    }
+    return Base::GetVisualizationData(name, values);
+  }
+
  private:
   /// keep track of the trail of the agent
   real_t trail_;
 };
 
-#ifndef __ROOTCLING__
 struct Lorenz_rhs_ {
   void operator()(const b_vector_t& x, b_vector_t& dxdt, double t,
                   Agent* agent) const {
@@ -91,18 +99,14 @@ struct Lorenz_out_ {
     std::clog << std::endl;
   }
 };
-#endif
-
 class Trajectory : public RegulatoryNetwork {
-  BDM_BEHAVIOR_HEADER(Trajectory, RegulatoryNetwork, 1);
+  BDM_BEHAVIOR_HEADER(Trajectory, RegulatoryNetwork);
 
  public:
   Trajectory() { AlwaysCopyToNew(); }
-#ifndef __ROOTCLING__
   Trajectory(real_t dt, int n_dt, const std::vector<real_t>& x)
       : RegulatoryNetwork(dt, n_dt, x, ODE_solver::Rosenbrock, Lorenz_rhs_(),
                           Lorenz_jac_(), Lorenz_out_()) {}
-#endif
   virtual ~Trajectory() = default;
 
   void Initialize(const NewAgentEvent& event) override {
@@ -112,7 +116,6 @@ class Trajectory : public RegulatoryNetwork {
   void Run(Agent* agent) override {
     Base::Run(agent);
 
-#ifndef __ROOTCLING__
     Real3 xyz;
     for (int i = 0; i < 3; i++)
       xyz[i] = this->GetSpecie(i);
@@ -126,7 +129,6 @@ class Trajectory : public RegulatoryNetwork {
     } else {
       Log::Fatal("Trajectory::Run", "agent is not of 'MyCell' type");
     }
-#endif
   }
 };
 
@@ -164,11 +166,7 @@ inline int Simulate(int argc, const char** argv) {
     MyCell* c = new MyCell();
     c->SetDiameter(1.0);
     c->SetPosition(xyz);
-#ifndef __ROOTCLING__
     c->AddBehavior(new Trajectory(dt_RN, 222, {xyz[0], xyz[1], xyz[2]}));
-#else
-    c->AddBehavior(new Trajectory());
-#endif
 
     sim.GetExecutionContext()->AddAgent(c);
   }