Fix CeresFE

diff --git a/CeresFE/src/ceres.cc b/CeresFE/src/ceres.cc
index d47a70e5ba75118bd09df09168e4b4eb95f03f01..914cc4e9e0bd98dc96d40ea18b78318670d54c2a 100644 (file)
--- a/CeresFE/src/ceres.cc
+++ b/CeresFE/src/ceres.cc
@@ -185,7 +185,7 @@ private:
        BlockVector<double> solution;
        BlockVector<double> system_rhs;
 
-       std_cxx1x::shared_ptr<typename InnerPreconditioner<dim>::type> A_preconditioner;
+       std::shared_ptr<typename InnerPreconditioner<dim>::type> A_preconditioner;
 
        ellipsoid_fit<dim>   ellipsoid;
 };
@@ -228,6 +228,10 @@ class RightHandSide: public Function<dim> {
 public:
        RightHandSide () : Function<dim>(dim+1) {}
 
+    using Function<dim>::value;
+    using Function<dim>::vector_value;
+    using Function<dim>::vector_value_list;
+
        virtual double value(const Point<dim> &p, const unsigned int component,
                        A_Grav_namespace::AnalyticGravity<dim> *aGrav) const;
 
@@ -352,8 +356,8 @@ void SchurComplement<Preconditioner>::vmult(Vector<double> &dst,
 template<int dim>
 StokesProblem<dim>::StokesProblem(const unsigned int degree) :
                degree(degree),
-               mapping(),
                triangulation(Triangulation<dim>::maximum_smoothing),
+        mapping(),
                fe(FE_Q<dim>(degree + 1), dim, FE_Q<dim>(degree), 1),
                dof_handler(triangulation),
                quadrature_formula(degree + 2),
@@ -384,7 +388,7 @@ void StokesProblem<dim>::setup_dofs() {
                                BoundaryValuesP<dim>(), constraints, component_maskP);
        }
        {
-               std::set<unsigned char> no_normal_flux_boundaries;
+               std::set<types::boundary_id> no_normal_flux_boundaries;
                no_normal_flux_boundaries.insert(99);
                VectorTools::compute_no_normal_flux_constraints(dof_handler, 0,
                                no_normal_flux_boundaries, constraints);
@@ -392,7 +396,7 @@ void StokesProblem<dim>::setup_dofs() {
 
        constraints.close();
 
-       std::vector<unsigned int> dofs_per_block(2);
+       std::vector<types::global_dof_index> dofs_per_block(2);
        DoFTools::count_dofs_per_block(dof_handler, dofs_per_block,
                        block_component);
        n_u = dofs_per_block[0];
@@ -404,7 +408,7 @@ void StokesProblem<dim>::setup_dofs() {
                        << std::endl;
 
        {
-               BlockCompressedSimpleSparsityPattern csp(2, 2);
+               BlockDynamicSparsityPattern csp(2, 2);
 
                csp.block(0, 0).reinit(n_u, n_u);
                csp.block(1, 0).reinit(n_p, n_u);
@@ -464,7 +468,6 @@ double Rheology<dim>::get_eta(double &r, double &z)
        double ecc = system_parameters::q_axes[0] / system_parameters::p_axes[0];
        double Rminusr = system_parameters::q_axes[0] - system_parameters::p_axes[0];
        double approx_a = std::sqrt(r * r + z * z * ecc * ecc);
-       double approx_b = approx_a / ecc;
        double group1 = r * r + z * z - Rminusr * Rminusr;
 
                double a0 = approx_a;
@@ -600,7 +603,6 @@ void StokesProblem<dim>::initialize_eta_and_G() {
 
                        //defines local viscosity
                        double local_viscosity = 0;
-                       unsigned int m_id = cell->material_id();
 
                        local_viscosity = rheology.get_eta(r_value, z_value);
 
@@ -639,7 +641,7 @@ void StokesProblem<dim>::assemble_system() {
        FullMatrix<double> local_matrix(dofs_per_cell, dofs_per_cell);
        Vector<double> local_rhs(dofs_per_cell);
 
-       std::vector<unsigned int> local_dof_indices(dofs_per_cell);
+       std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
 
        // runs the gravity script function
        const RightHandSide<dim> right_hand_side;
@@ -741,7 +743,6 @@ void StokesProblem<dim>::assemble_system() {
                                double &local_old_phiphi_stress =
                                                local_quadrature_points_history[q].old_phiphi_stress;
                                double r_value = fe_values.quadrature_point(q)[0];
-                               double z_value = fe_values.quadrature_point(q)[1];
 
                                // get local density based on mat id
                                double local_density = system_parameters::rho[m_id];
@@ -836,7 +837,6 @@ void StokesProblem<dim>::assemble_system() {
                                double &local_old_phiphi_stress =
                                                local_quadrature_points_history[q].old_phiphi_stress;
                                double r_value = fe_values.quadrature_point(q)[0];
-                               double z_value = fe_values.quadrature_point(q)[1];
 
                 double local_density = system_parameters::rho[m_id];
 
@@ -930,7 +930,7 @@ void StokesProblem<dim>::assemble_system() {
 
        std::cout << "   Computing preconditioner..." << std::endl << std::flush;
 
-       A_preconditioner = std_cxx1x::shared_ptr<
+       A_preconditioner = std::shared_ptr<
                        typename InnerPreconditioner<dim>::type>(
                        new typename InnerPreconditioner<dim>::type());
        A_preconditioner->initialize(system_matrix.block(0, 0),
@@ -1239,7 +1239,6 @@ void StokesProblem<dim>::solution_stesses() {
                }
 
                // Finds adjusted effective viscosity
-               double cell_effective_viscosity = 0;
                if (system_parameters::plasticity_on)
                {
                        if(system_parameters::failure_criterion == 0) //Apply Byerlee's rule
@@ -1433,7 +1432,7 @@ void StokesProblem<dim>::smooth_eta_field(std::vector<bool> failing_cells)
                        std::vector<bool> cell_touched(triangulation.n_active_cells(), false);
                        std::vector< TriaIterator< CellAccessor<dim> > > neighbor_cells;
                        std::vector<int> neighbor_indices;
-                       int start_cell = 0; // Which cell in the neighbor_cells vector to start from
+                       unsigned int start_cell = 0; // Which cell in the neighbor_cells vector to start from
                        int new_cells_found = 0;
                        neighbor_cells.push_back(cell);
                        neighbor_indices.push_back(cell_no);
@@ -1441,7 +1440,7 @@ void StokesProblem<dim>::smooth_eta_field(std::vector<bool> failing_cells)
                        while(find_more_cells)
                        {
                                new_cells_found = 0;
-                               for(int i = start_cell; i<neighbor_cells.size(); i++)
+                               for(unsigned int i = start_cell; i<neighbor_cells.size(); i++)
                                {
                                        for (unsigned int f = 0; f < GeometryInfo<dim>::faces_per_cell; ++f)
                                        {
@@ -1741,7 +1740,7 @@ void StokesProblem<dim>::write_vertices(unsigned char boundary_that_we_need) {
                        triangulation.begin_active(); cell != triangulation.end(); ++cell)
                for (unsigned int f = 0; f < GeometryInfo<dim>::faces_per_cell; ++f)
                {
-                       unsigned char boundary_ids = cell->face(f)->boundary_indicator();
+                       unsigned char boundary_ids = cell->face(f)->boundary_id();
                        if(boundary_ids == boundary_that_we_need)
                                {
                                for (unsigned int v=0; v<GeometryInfo<dim>::vertices_per_face; ++v)
@@ -1834,9 +1833,9 @@ void StokesProblem<dim>::setup_initial_mesh() {
                                                if (fabs(cell->face(f)->center()[i]) > zero_tolerance)
                                            how_many++;
                                if (how_many==dim)
-                                       cell->face(f)->set_all_boundary_indicators(0); // if face center coordinates > zero_tol, set bnry indicators to 0
+                                       cell->face(f)->set_all_boundary_ids(0); // if face center coordinates > zero_tol, set bnry indicators to 0
                                else
-                                   cell->face(f)->set_all_boundary_indicators(99);
+                                   cell->face(f)->set_all_boundary_ids(99);
                        }
                }
        }

diff --git a/CeresFE/support_code/ellipsoid_fit.h b/CeresFE/support_code/ellipsoid_fit.h
index d47f3e3a45d7a9d9e2027bb5d096812e86623d83..c99458b5e08417316fe9583a5119ba3fa048a8bd 100644 (file)
--- a/CeresFE/support_code/ellipsoid_fit.h
+++ b/CeresFE/support_code/ellipsoid_fit.h
@@ -11,7 +11,6 @@
 #include <deal.II/lac/vector.h>
 #include <deal.II/lac/full_matrix.h>
 #include <deal.II/lac/sparse_matrix.h>
-#include <deal.II/lac/compressed_sparsity_pattern.h>
 #include <deal.II/lac/solver_cg.h>
 #include <deal.II/lac/precondition.h>
 #include <deal.II/grid/tria.h>
@@ -80,14 +79,13 @@ void ellipsoid_fit<dim>::compute_fit(std::vector<double> &ell, unsigned char bou
     std::vector<unsigned int> ind_bnry_col;
 
        // assemble the sensitivity matrix and r.h.s.
-    double zero_tolerance = 1e-3;
        for (; cell != endc; ++cell) {
                if (boundary_that_we_need != 0)
                        cell->set_manifold_id(cell->material_id());
                for (unsigned int f = 0; f < GeometryInfo<dim>::faces_per_cell; ++f) {
                        if (boundary_that_we_need == 0) //if this is the outer surface, then look for boundary ID 0; otherwise look for material ID change.
                                        {
-                               boundary_ids = cell->face(f)->boundary_indicator();
+                               boundary_ids = cell->face(f)->boundary_id();
                                if (boundary_ids == boundary_that_we_need) {
                                        for (unsigned int v = 0;
                                                        v < GeometryInfo<dim>::vertices_per_face; ++v)

diff --git a/CeresFE/support_code/local_math.h b/CeresFE/support_code/local_math.h
index 2dcc5a9c2c04a55ded7d5327e8f84682555a928f..cbece34b793143361256b4ba0c29c23310a2cbc4 100644 (file)
--- a/CeresFE/support_code/local_math.h
+++ b/CeresFE/support_code/local_math.h
@@ -11,8 +11,6 @@
 #define PI 3.14159265358979323846
 #define TWOPI 6.283185307179586476925287
 #define SECSINYEAR 3.155692608e+07
-#define MAX(x,y) ((x) > (y)) ? (x) : (y)
-#define MIN(x,y) ((x) < (y)) ? (x) : (y)
 //#define ABS(a) ((a) < 0 ? -(a) : (a))
 
 //double factorial(int n)