Apply clang-format to regulatory_networks demo sources

Author: sportokalidis

demo/regulatory_networks/src/bdm_ex1.h

@@ -74,9 +74,9 @@ struct ODE_jacobian {
 struct ODE_output {
   void operator()(const b_vector_t& x, real_t t, const Agent* agent) {
     auto& xyz = agent->GetPosition();
-    std::clog << agent->GetUid()
-              << ',' << xyz[0] << ',' << xyz[1] << ',' << xyz[2]
-              << ',' << t << ',' << x[0] << ',' << x[1] << ',' << x[2];
+    std::clog << agent->GetUid() << ',' << xyz[0] << ',' << xyz[1] << ','
+              << xyz[2] << ',' << t << ',' << x[0] << ',' << x[1] << ','
+              << x[2];
     std::clog << std::endl;
   }
 };
@@ -103,7 +103,8 @@ inline int Simulate(int argc, const char** argv) {
     param->visualize_agents["Cell"] = {"diameter_", "volume_"};
     param->statistics = false;
     param->simulation_time_step = 1.0;
-    param->visualize_diffusion = {Param::VisualizeDiffusion{"cytokine", true, true}};
+    param->visualize_diffusion = {
+        Param::VisualizeDiffusion{"cytokine", true, true}};
     param->calculate_gradients = false;
     param->diffusion_method = "euler";
   };
@@ -138,10 +139,8 @@ inline int Simulate(int argc, const char** argv) {
         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()));
+        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
     return c;
   };

demo/regulatory_networks/src/bdm_ex2.h

@@ -85,9 +85,9 @@ struct Lorenz_jac_ {
 struct Lorenz_out_ {
   void operator()(const b_vector_t& x, real_t t, const Agent* agent) {
     auto& xyz = agent->GetPosition();
-    std::clog << agent->GetUid()
-              << ',' << xyz[0] << ',' << xyz[1] << ',' << xyz[2]
-              << ',' << t << ',' << x[0] << ',' << x[1] << ',' << x[2];
+    std::clog << agent->GetUid() << ',' << xyz[0] << ',' << xyz[1] << ','
+              << xyz[2] << ',' << t << ',' << x[0] << ',' << x[1] << ','
+              << x[2];
     std::clog << std::endl;
   }
 };
@@ -100,8 +100,8 @@ class Trajectory : public RegulatoryNetwork {
   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_()) {}
+      : RegulatoryNetwork(dt, n_dt, x, ODE_solver::Rosenbrock, Lorenz_rhs_(),
+                          Lorenz_jac_(), Lorenz_out_()) {}
 #endif
   virtual ~Trajectory() = default;
 

demo/regulatory_networks/src/regulatory_networks.h

@@ -20,9 +20,9 @@
 
 #include "biodynamo.h"
 
-#include "sine.h"
 #include "lorenz.h"
 #include "oscillator.h"
+#include "sine.h"
 
 #include "bdm_ex1.h"
 #include "bdm_ex2.h"

demo/regulatory_networks/src/sine.h

@@ -65,8 +65,8 @@ inline int Simulate(int argc, const char** argv) {
   auto stepper = boost::numeric::odeint::make_dense_output<ode_int>(1e-6, 1e-6);
 
   // perform the time-integration
-  integrate_const(stepper, ODE_system(), x,
-                  0.0, 12.5663706144, 0.001, ODE_output());
+  integrate_const(stepper, ODE_system(), x, 0.0, 12.5663706144, 0.001,
+                  ODE_output());
 #endif
 
   // restore the original buffer of std::clog