Indentations fixed. Identifiers fixed in .h files.

diff --git a/TravelingWaves/IntegrateSystem.h b/TravelingWaves/IntegrateSystem.h
index 1078293f4faa9a66c04342942905d970c4d30829..ec714940b58d87f19d9237aebfdcb60805e36ce7 100644 (file)
--- a/TravelingWaves/IntegrateSystem.h
+++ b/TravelingWaves/IntegrateSystem.h
@@ -1,4 +1,3 @@
-
 #ifndef INTEGRATE_SYSTEM
 #define INTEGRATE_SYSTEM
 

diff --git a/TravelingWaves/Parameters.cc b/TravelingWaves/Parameters.cc
index ed55a0a7ff9249b012ec7f309229b8ace5dff29b..4222601c659162749633e0feb285a8878fa32ecf 100644 (file)
--- a/TravelingWaves/Parameters.cc
+++ b/TravelingWaves/Parameters.cc
@@ -7,13 +7,13 @@ namespace TravelingWave
   Problem::Problem() 
     : ParameterAcceptor("Problem")
   {
-         add_parameter("delta", delta = 0.01); 
-       add_parameter("epsilon", epsilon = 0.1);            
-       add_parameter("Prandtl number", Pr = 0.75);        
-       add_parameter("Lewis number", Le = 1.0);      
-       add_parameter("Constant of reaction rate", k = 1.0);
-       add_parameter("Activation energy", theta = 1.65);
-       add_parameter("Heat release", q = 1.7);
+    add_parameter("delta", delta = 0.01); 
+    add_parameter("epsilon", epsilon = 0.1);            
+    add_parameter("Prandtl number", Pr = 0.75);        
+    add_parameter("Lewis number", Le = 1.0);      
+    add_parameter("Constant of reaction rate", k = 1.0);
+    add_parameter("Activation energy", theta = 1.65);
+    add_parameter("Heat release", q = 1.7);
     add_parameter("Ignition Temperature", T_ign = 1.0);
     add_parameter("Type of the wave (deflagration / detonation)", wave_type = 1);   // 0 for "deflagration"; 1 for "detonation".
 
@@ -35,12 +35,12 @@ namespace TravelingWave
   }
 
   Mesh::Mesh()
-         : ParameterAcceptor("Mesh")
+    : ParameterAcceptor("Mesh")
   {
-         add_parameter("Interval left boundary", interval_left = -50.0);  
-       add_parameter("Interval right boundary", interval_right = 20.0);
-       add_parameter<unsigned int>("Refinements number", refinements_number = 10);
-       add_parameter("Adaptive mesh refinement", adaptive = 1);    // 1 for adaptive; 0 for global.
+    add_parameter("Interval left boundary", interval_left = -50.0);  
+    add_parameter("Interval right boundary", interval_right = 20.0);
+    add_parameter<unsigned int>("Refinements number", refinements_number = 10);
+    add_parameter("Adaptive mesh refinement", adaptive = 1);    // 1 for adaptive; 0 for global.
   }
 
   Solver::Solver()

diff --git a/TravelingWaves/Parameters.h b/TravelingWaves/Parameters.h
index 2dd02c65514d385849a125ba56be7e3f8a1baa76..554a5109a882408bbc2d1433d221eb008b1e118a 100644 (file)
--- a/TravelingWaves/Parameters.h
+++ b/TravelingWaves/Parameters.h
@@ -25,7 +25,7 @@ namespace TravelingWave
 
   struct FiniteElements : ParameterAcceptor
   {
-         FiniteElements();
+    FiniteElements();
 
     unsigned int poly_degree;
     unsigned int quadrature_points_number;
@@ -35,25 +35,25 @@ namespace TravelingWave
   {
     Mesh();
     
-    double interval_left;
-    double interval_right;
-    unsigned int refinements_number;
-    int adaptive;
+    double        interval_left;
+    double        interval_right;
+    unsigned int  refinements_number;
+    int           adaptive;
   };
 
   struct Solver : ParameterAcceptor
   {
     Solver();
 
-    double       tol;
+    double tol;
   };
 
   struct Parameters
   {
     Problem           problem;
-    FiniteElements             fe;
-    Mesh                                     mesh;
-    Solver                   solver;
+    FiniteElements    fe;
+    Mesh              mesh;
+    Solver            solver;
   };
 
 } // namespace TravelingWave

diff --git a/TravelingWaves/Solution.cc b/TravelingWaves/Solution.cc
index 8087337fe8738e976de57a8b64faf2a4347f133d..962334b5fb82c2f1f0537364423ae7f18329c6bc 100644 (file)
--- a/TravelingWaves/Solution.cc
+++ b/TravelingWaves/Solution.cc
@@ -7,7 +7,7 @@ namespace TravelingWave
   
   SolutionStruct::SolutionStruct() {}
   SolutionStruct::SolutionStruct(const std::vector<double> &ix, const std::vector<double> &iu, 
-                      const std::vector<double> &iT, const std::vector<double> &ilambda, double iwave_speed)
+                                  const std::vector<double> &iT, const std::vector<double> &ilambda, double iwave_speed)
     : x(ix)
     , u(iu)
     , T(iT)
@@ -15,7 +15,7 @@ namespace TravelingWave
     , wave_speed(iwave_speed)
   {}
   SolutionStruct::SolutionStruct(const std::vector<double> &ix, const std::vector<double> &iu, 
-                      const std::vector<double> &iT, const std::vector<double> &ilambda)
+                                  const std::vector<double> &iT, const std::vector<double> &ilambda)
     : SolutionStruct(ix, iu, iT, ilambda, 0.)
   {}
 
@@ -59,7 +59,7 @@ namespace TravelingWave
 
   double Interpolant::value(const Point<1> &p, const unsigned int component) const
   {
-    double x = p[0];
+    double x   = p[0];
     double res = interpolant.value(x);
 
     return res;
@@ -78,9 +78,9 @@ namespace TravelingWave
   double SolutionVectorFunction<InterpolantType>::value(const Point<1> &p, const unsigned int component) const
   {
     double res = 0.;
-    if (component == 0)                        {       res = u_interpolant.value(p); }
-    else if (component == 1)   { res = T_interpolant.value(p); }
-    else if (component == 2)   {       res = lambda_interpolant.value(p);      }
+    if      (component == 0)  { res = u_interpolant.value(p); }
+    else if (component == 1)  { res = T_interpolant.value(p); }
+    else if (component == 2)  { res = lambda_interpolant.value(p); }
 
     return res;
   }

diff --git a/TravelingWaves/Solution.h b/TravelingWaves/Solution.h
index 2de6619af1ce8c7228886897490d6e4cdf30f745..4bddad2277c5fb7b160b42af804b96eaee6fe06a 100644 (file)
--- a/TravelingWaves/Solution.h
+++ b/TravelingWaves/Solution.h
@@ -1,5 +1,5 @@
-#ifndef SOLUTION_STRUCT
-#define SOLUTION_STRUCT
+#ifndef SOLUTION
+#define SOLUTION
 
 #include <deal.II/base/function.h>
 
@@ -21,20 +21,20 @@ namespace TravelingWave
   {
     SolutionStruct();
     SolutionStruct(const std::vector<double> &ix, const std::vector<double> &iu, 
-              const std::vector<double> &iT, const std::vector<double> &ilambda, const double iwave_speed);
+                    const std::vector<double> &iT, const std::vector<double> &ilambda, const double iwave_speed);
     SolutionStruct(const std::vector<double> &ix, const std::vector<double> &iu, 
-              const std::vector<double> &iT, const std::vector<double> &ilambda);
+                    const std::vector<double> &iT, const std::vector<double> &ilambda);
 
     void reinit(const unsigned int number_of_elements);
     
     void save_to_file(std::string filename) const;
 
-    std::vector<double> x;                             // mesh coordinates (must be an increasing sequence)
-    std::vector<double> u;                             // array of u components
-    std::vector<double> T;                             // array of T components
-    std::vector<double> lambda;                // array of lambda components
+    std::vector<double> x;        // mesh coordinates (must be an increasing sequence)
+    std::vector<double> u;        // array of u components
+    std::vector<double> T;        // array of T components
+    std::vector<double> lambda;   // array of lambda components
 
-    double wave_speed;                                         // speed of the wave
+    double wave_speed;            // speed of the wave
   };
 
   // Interpolation class

diff --git a/TravelingWaves/TravelingWaveSolver.cc b/TravelingWaves/TravelingWaveSolver.cc
index 09b67eaaa7350387ef8e132e942e31499864a215..cb5fd1d4c8b96c2bf5f675c87f39dbe9ab818852 100644 (file)
--- a/TravelingWaves/TravelingWaveSolver.cc
+++ b/TravelingWaves/TravelingWaveSolver.cc
@@ -12,7 +12,7 @@ namespace TravelingWave
     , triangulation_uploaded(false)
     , fe(FE_Q<1>(params.fe.poly_degree), 1, 
           FE_Q<1>(params.fe.poly_degree), 1,
-          FE_Q<1>(params.fe.poly_degree), 1)    // 3 fe basis sets, corresponding to du, dT, dlambda
+          FE_Q<1>(params.fe.poly_degree), 1)   // 3 fe basis sets, corresponding to du, dT, dlambda
     , dof_handler(triangulation)
     , current_wave_speed(0.)
     , initial_guess(initial_guess_input)

diff --git a/TravelingWaves/TravelingWaveSolver.h b/TravelingWaves/TravelingWaveSolver.h
index b031567994d1207d582b38cda8cc1e9aeb99b61f..56b0187cf26bcb3b48fae0bb22e63521d024249f 100644 (file)
--- a/TravelingWaves/TravelingWaveSolver.h
+++ b/TravelingWaves/TravelingWaveSolver.h
@@ -1,5 +1,5 @@
-#ifndef WAVE_CONSTRUCTOR
-#define WAVE_CONSTRUCTOR
+#ifndef TRAVELING_WAVE_SOLVER
+#define TRAVELING_WAVE_SOLVER
 
 #include <deal.II/base/timer.h>
 #include <deal.II/base/function.h>
@@ -46,9 +46,9 @@ namespace TravelingWave
   {
   public:
     TravelingWaveSolver(const Parameters &parameters, const SolutionStruct &initial_guess_input);
-    
+
     void set_triangulation(const Triangulation<1> &itriangulation);
-    
+
     void run(const std::string filename="solution", const bool save_solution_to_file=true);
     void get_solution(SolutionStruct &solution) const;
     void get_triangulation(Triangulation<1> &otriangulation) const;
@@ -61,7 +61,7 @@ namespace TravelingWave
     void set_initial_guess();
 
     double Heaviside_func(double x) const;
-    
+
     void compute_and_factorize_jacobian(const Vector<double> &evaluation_point_extended);
     double compute_residual(const Vector<double> &evaluation_point_extended, Vector<double> &residual);
     void split_extended_solution_vector();
@@ -77,37 +77,37 @@ namespace TravelingWave
     std::map<std::string, unsigned int> boundary_and_centering_dof_numbers;
 
     // Parameters of the problem, taken from a .prm file.
-    const Parameters &params;
-    const Problem               &problem; // Reference variable, just for convenience.
+    const Parameters  &params;
+    const Problem     &problem;    // Reference variable, just for convenience.
 
     unsigned int number_of_quadrature_points;
 
     Triangulation<1> triangulation;
     // The flag indicating whether the triangulation was uploaded externally or created within the <code> run </code> member function.
-    bool                                                triangulation_uploaded;
-    FESystem<1>      fe;
-    DoFHandler<1>    dof_handler;
+    bool            triangulation_uploaded;
+    FESystem<1>     fe;
+    DoFHandler<1>   dof_handler;
 
     // Constraints for Dirichlet boundary conditions.
     AffineConstraints<double> zero_boundary_constraints;       
 
-    SparsityPattern                                                                                    sparsity_pattern_extended;
-    SparseMatrix<double>                                                               jacobian_matrix_extended;
-    std::unique_ptr<SparseDirectUMFPACK>       jacobian_matrix_extended_factorization;
+    SparsityPattern                       sparsity_pattern_extended;
+    SparseMatrix<double>                  jacobian_matrix_extended;
+    std::unique_ptr<SparseDirectUMFPACK>  jacobian_matrix_extended_factorization;
 
     // Finite element solution of the problem.
-    Vector<double>     current_solution;
+    Vector<double>  current_solution;
 
     // Value of the wave speed $c$.
-    double                                     current_wave_speed;
+    double          current_wave_speed;
 
     // Solution with an additional term, corresponding to the variable wave_speed.
-    Vector<double>     current_solution_extended;
+    Vector<double>  current_solution_extended;
 
     // Initial guess for Newton's iterations.
-    SolutionStruct initial_guess;
+    SolutionStruct  initial_guess;
 
-    TimerOutput computing_timer;
+    TimerOutput     computing_timer;
   };
 
 } // namespace TravelingWave

diff --git a/TravelingWaves/calculate_profile.cc b/TravelingWaves/calculate_profile.cc
index a6a9e2ea2d583fef38b3a304fdd7b618a7e818ea..21be543147814ae2cc422aaf6247e85d312a3045 100644 (file)
--- a/TravelingWaves/calculate_profile.cc
+++ b/TravelingWaves/calculate_profile.cc
@@ -254,10 +254,10 @@ namespace TravelingWave
     // Error estimation.
     {
       unsigned int sol_length = sol.x.size();
-      double u_r = sol.u[sol_length-1];                        // Dirichlet boundary condition
-      double T_r = sol.T[sol_length-1];                        // Dirichlet condition only for detonation case
+      double u_r = sol.u[sol_length-1];     // Dirichlet boundary condition
+      double T_r = sol.T[sol_length-1];     // Dirichlet condition only for detonation case
       double u_l = sol.u[0];
-      double T_l = sol.T[0];                                                           // Dirichlet boundary condition
+      double T_l = sol.T[0];                // Dirichlet boundary condition
       double wave_speed = sol.wave_speed;
 
       std::cout << "Error estimates:" << std::endl;

diff --git a/TravelingWaves/calculate_profile.h b/TravelingWaves/calculate_profile.h
index ff5761d63e1783adc8483066499406798f0b2748..8194f9933c5677bcaa1230ee0f511b766bf80e7d 100644 (file)
--- a/TravelingWaves/calculate_profile.h
+++ b/TravelingWaves/calculate_profile.h
@@ -1,5 +1,5 @@
-#ifndef INITIAL_GUESS
-#define INITIAL_GUESS
+#ifndef CALCULATE_PROFILE
+#define CALCULATE_PROFILE
 
 #include "Parameters.h"
 #include "Solution.h"
@@ -21,9 +21,9 @@ namespace TravelingWave
        void compute_initial_guess_deflagration(const Parameters &params, SolutionStruct &initial_guess);
 
   void calculate_profile(Parameters& parameters,
-                                                                                                                                       const bool continuation_for_delta=false /* Compute with the continuation. */, 
-                                                                                                                                       const double delta_start=0.01 /* The starting value of delta for the continuation method. */, 
-                                                                                                                                       const unsigned int number_of_continuation_points=10);
+                          const bool continuation_for_delta=false /* Compute with the continuation. */, 
+                          const double delta_start=0.01 /* The starting value of delta for the continuation method. */, 
+                          const unsigned int number_of_continuation_points=10);
 
 } // namespace TravelingWave