src/hdf5/restart-io.hh

+#ifndef SRC_HDF_RESTART_HDF_HH
+#define SRC_HDF_RESTART_HDF_HH
+
+#include <dune/fufem/hdf5/file.hh>
+#include <dune/fufem/hdf5/sequenceio.hh>
+
+template <class ProgramState> class RestartIO {
+  using ScalarVector = typename ProgramState::ScalarVector;
+  using Vector = typename ProgramState::Vector;
+
+public:
+  RestartIO(HDF5::Grouplike &group, size_t vertexCount);
+
+  void write(ProgramState const &programState);
+
+  void read(size_t timeStep, ProgramState &programState);
+
+private:
+  HDF5::SequenceIO<2> displacementWriter_;
+  HDF5::SequenceIO<2> velocityWriter_;
+  HDF5::SequenceIO<2> accelerationWriter_;
+  HDF5::SequenceIO<1> stateWriter_;
+  HDF5::SequenceIO<1> weightedNormalStressWriter_;
+  HDF5::SequenceIO<0> relativeTimeWriter_;
+  HDF5::SequenceIO<0> relativeTimeIncrementWriter_;
+};
+#endif

src/hdf5/restart-io_tmpl.cc

+#include "../explicitvectors.hh"
+
+#include "../program_state.hh"
+
+using MyProgramState = ProgramState<Vector, ScalarVector>;
+
+template class RestartIO<MyProgramState>;

src/hdf5/restrict.hh

+#ifndef SRC_HDF5_RESTRICT_HH
+#define SRC_HDF5_RESTRICT_HH
+
+#include <cassert>
+
+#include <dune/common/bitsetvector.hh>
+
+#include "../tobool.hh"
+
+template <class Vector, class Patch>
+Vector restrictToSurface(Vector const &v1, Patch const &patch) {
+  auto const &vertices = *patch.getVertices();
+  assert(vertices.size() == v1.size());
+
+  Vector ret(vertices.count());
+  auto target = ret.begin();
+  for (size_t i = 0; i < v1.size(); ++i)
+    if (toBool(vertices[i]))
+      *(target++) = v1[i];
+  assert(target == ret.end());
+  return ret;
+}
+#endif

src/hdf5/surface-writer.cc

+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include "restrict.hh"
+#include "surface-writer.hh"
+
+template <class ProgramState, class GridView>
+SurfaceWriter<ProgramState, GridView>::SurfaceWriter(
+    HDF5::Grouplike &file, Vector const &vertexCoordinates, Patch const &surface)
+    : group_(file, "surface"),
+      surface_(surface),
+      surfaceDisplacementWriter_(group_, "displacement", surface.numVertices(),
+                                 Vector::block_type::dimension),
+      surfaceVelocityWriter_(group_, "velocity", surface.numVertices(),
+                             Vector::block_type::dimension) {
+  auto const surfaceCoordinates = restrictToSurface(vertexCoordinates, surface);
+  HDF5::SingletonWriter<2> surfaceCoordinateWriter(group_, "coordinates",
+                                                 surfaceCoordinates.size(),
+                                                 Vector::block_type::dimension);
+  setEntry(surfaceCoordinateWriter, surfaceCoordinates);
+}
+
+template <class ProgramState, class GridView>
+void SurfaceWriter<ProgramState, GridView>::write(
+    ProgramState const &programState) {
+  auto const surfaceDisplacements = restrictToSurface(programState.u, surface_);
+  addEntry(surfaceDisplacementWriter_, programState.timeStep,
+           surfaceDisplacements);
+
+  auto const surfaceVelocities = restrictToSurface(programState.v, surface_);
+  addEntry(surfaceVelocityWriter_, programState.timeStep, surfaceVelocities);
+}
+
+#include "surface-writer_tmpl.cc"

src/hdf5/surface-writer.hh

+#ifndef SRC_HDF_SURFACE_WRITER_HH
+#define SRC_HDF_SURFACE_WRITER_HH
+
+#include <dune/fufem/boundarypatch.hh>
+
+#include <dune/fufem/hdf5/sequenceio.hh>
+#include <dune/fufem/hdf5/singletonwriter.hh>
+
+template <class ProgramState, class GridView> class SurfaceWriter {
+  using Vector = typename ProgramState::Vector;
+  using Patch = BoundaryPatch<GridView>;
+
+public:
+  SurfaceWriter(HDF5::Grouplike &file, Vector const &vertexCoordinates,
+                Patch const &surface);
+
+  void write(ProgramState const &programState);
+
+private:
+  HDF5::Group group_;
+
+  Patch const &surface_;
+
+  HDF5::SequenceIO<2> surfaceDisplacementWriter_;
+  HDF5::SequenceIO<2> surfaceVelocityWriter_;
+};
+#endif

src/hdf5/surface-writer_tmpl.cc

+#include "../explicitvectors.hh"
+#include "../explicitgrid.hh"
+
+#include "../program_state.hh"
+
+using MyProgramState = ProgramState<Vector, ScalarVector>;
+
+template class SurfaceWriter<MyProgramState, GridView>;

src/hdf5/time-writer.cc

+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include "time-writer.hh"
+
+template <class ProgramState>
+TimeWriter<ProgramState>::TimeWriter(HDF5::Grouplike &file)
+    : file_(file),
+      relativeTimeWriter_(file_, "relativeTime"),
+      relativeTimeIncrementWriter_(file_, "relativeTimeIncrement") {}
+
+template <class ProgramState>
+void TimeWriter<ProgramState>::write(ProgramState const &programState) {
+  addEntry(relativeTimeWriter_, programState.timeStep,
+           programState.relativeTime);
+  addEntry(relativeTimeIncrementWriter_, programState.timeStep,
+           programState.relativeTau);
+}
+
+#include "time-writer_tmpl.cc"

src/hdf5/time-writer.hh

+#ifndef SRC_HDF_TIME_WRITER_HH
+#define SRC_HDF_TIME_WRITER_HH
+
+#include <dune/fufem/hdf5/file.hh>
+#include <dune/fufem/hdf5/sequenceio.hh>
+
+template <class ProgramState> class TimeWriter {
+public:
+  TimeWriter(HDF5::Grouplike &file);
+  void write(ProgramState const &programState);
+
+private:
+  HDF5::Grouplike &file_;
+  HDF5::SequenceIO<0> relativeTimeWriter_;
+  HDF5::SequenceIO<0> relativeTimeIncrementWriter_;
+};
+#endif

src/hdf5/time-writer_tmpl.cc

+#include "../explicitvectors.hh"
+
+#include "../program_state.hh"
+
+using MyProgramState = ProgramState<Vector, ScalarVector>;
+
+template class TimeWriter<MyProgramState>;

src/one-body-problem-data/bc.hh

+#ifndef SRC_ONE_BODY_PROBLEM_DATA_BC_HH
+#define SRC_ONE_BODY_PROBLEM_DATA_BC_HH
+
+class VelocityDirichletCondition
+    : public Dune::VirtualFunction<double, double> {
+  void evaluate(double const &relativeTime, double &y) const {
+    // Assumed to vanish at time zero
+    double const finalVelocity = -5e-5;
+    y = (relativeTime <= 0.1)
+            ? finalVelocity * (1.0 - std::cos(relativeTime * M_PI / 0.1)) / 2.0
+            : finalVelocity;
+  }
+};
+
+class NeumannCondition : public Dune::VirtualFunction<double, double> {
+  void evaluate(double const &relativeTime, double &y) const { y = 0.0; }
+};
+#endif

src/sand-wedge-data/mybody.hh → src/one-body-problem-data/mybody.hh

-#ifndef SRC_SAND_WEDGE_DATA_MYBODY_HH
-#define SRC_SAND_WEDGE_DATA_MYBODY_HH
+#ifndef SRC_ONE_BODY_PROBLEM_DATA_MYBODY_HH
+#define SRC_ONE_BODY_PROBLEM_DATA_MYBODY_HH
 
 #include <dune/common/fvector.hh>
 

src/sand-wedge-data/mygeometry.cc → src/one-body-problem-data/mygeometry.cc

@@ -12,13 +12,6 @@
 
 #include "mygeometry.hh"
 
-double MyGeometry::verticalProjection(LocalVector const &x) {
-  return zenith * x;
-}
-double MyGeometry::horizontalProjection(LocalVector const &x) {
-  return orthogonalZenith * x;
-}
-
 void MyGeometry::write() {
   std::fstream writer("geometry", std::fstream::out);
   writer << "A = " << A << std::endl;

src/sand-wedge-data/mygeometry.hh → src/one-body-problem-data/mygeometry.hh

@@ -11,24 +11,6 @@ namespace {
   using LocalMatrix2D = Dune::FieldMatrix<double, 2, 2>;
 
   using LocalVector = Dune::FieldVector<double, MY_DIM>;
-
-  // kludge because fieldvectors have no initialiser_list constructor, see
-  // https://dune-project.org/flyspray/index.php?do=details&task_id=1166
-  LocalVector2D createVector(double x, double y) {
-    LocalVector2D ret(0);
-    ret[0] = x;
-    ret[1] = y;
-    return ret;
-  }
-
-  LocalMatrix2D createMatrix(double a11, double a12, double a21, double a22) {
-    LocalMatrix2D ret(0);
-    ret[0][0] = a11;
-    ret[0][1] = a12;
-    ret[1][0] = a21;
-    ret[1][1] = a22;
-    return ret;
-  }
 }
 
 namespace reference {
@@ -42,34 +24,31 @@ namespace reference {
 
   double const zDistance = 0.35;
 
-  LocalVector2D const A = createVector(0, 0);
-  LocalVector2D const B = createVector(leftLeg, -rightLeg);
-  LocalVector2D const C = createVector(leftLeg, 0);
+  LocalVector2D const A = {0, 0};
+  LocalVector2D const B = {leftLeg, -rightLeg};
+  LocalVector2D const C = {leftLeg, 0};
 
-  LocalVector2D const Z = createVector(zDistance * s, 0);
-  LocalVector2D const Y =
-      createVector(zDistance * s, -zDistance *s / leftLeg * rightLeg);
-  LocalVector2D const X = createVector(Y[0] - weakLen * std::cos(leftAngle),
-                                       Y[1] + weakLen * std::sin(leftAngle));
+  LocalVector2D const Z = {zDistance * s, 0};
+  LocalVector2D const Y = {zDistance * s, -zDistance *s / leftLeg *rightLeg};
+  LocalVector2D const X = {Y[0] - weakLen * std::cos(leftAngle),
+                           Y[1] + weakLen *std::sin(leftAngle)};
 
-  LocalVector2D const U = createVector(X[0], 0);
+  LocalVector2D const U = {X[0], 0};
 
-  LocalVector2D const K =
-      createVector(B[0] - leftLeg * viscoHeight / rightLeg, B[1] + viscoHeight);
-  LocalVector2D const M = createVector(B[0], B[1] + viscoHeight);
+  LocalVector2D const K = {B[0] - leftLeg * viscoHeight / rightLeg,
+                           B[1] + viscoHeight};
+  LocalVector2D const M = {B[0], B[1] + viscoHeight};
 
   LocalVector2D const G = midPoint(A, X);
   LocalVector2D const H = midPoint(X, Y);
   LocalVector2D const J = midPoint(Y, B);
 
-  LocalVector2D const I = createVector(Y[0] + G[0], Y[1] + G[1]);
+  LocalVector2D const I = {Y[0] + G[0], Y[1] + G[1]};
 
-  LocalVector2D const zenith = createVector(0, 1);
-  LocalVector2D const orthogonalZenith = createVector(-1, 0);
+  LocalVector2D const zenith = {0, 1};
 
-  LocalMatrix2D const rotation =
-      createMatrix(std::cos(leftAngle), -std::sin(leftAngle),
-                   std::sin(leftAngle), std::cos(leftAngle));
+  LocalMatrix2D const rotation = {{std::cos(leftAngle), -std::sin(leftAngle)},
+                                  {std::sin(leftAngle), std::cos(leftAngle)}};
 }
 
 namespace {
@@ -102,10 +81,6 @@ LocalVector const Y = rotate(reference::Y);
 LocalVector const Z = rotate(reference::Z);
 
 LocalVector const zenith = rotate(reference::zenith);
-LocalVector const orthogonalZenith = rotate(reference::orthogonalZenith);
-
-double verticalProjection(LocalVector const &);
-double horizontalProjection(LocalVector const &);
 
 void write();
 

src/sand-wedge-data/myglobalfrictiondata.hh → src/one-body-problem-data/myglobalfrictiondata.hh

-#ifndef SRC_SAND_WEDGE_DATA_MYGLOBALFRICTIONDATA_HH
-#define SRC_SAND_WEDGE_DATA_MYGLOBALFRICTIONDATA_HH
+#ifndef SRC_ONE_BODY_PROBLEM_DATA_MYGLOBALFRICTIONDATA_HH
+#define SRC_ONE_BODY_PROBLEM_DATA_MYGLOBALFRICTIONDATA_HH
 
 #include <dune/common/function.hh>
 

src/sand-wedge-data/mygrid.cc → src/one-body-problem-data/mygrid.cc

@@ -2,9 +2,11 @@
 #include "config.h"
 #endif
 
+#include <dune/fufem/geometry/polyhedrondistance.hh>
+
 #include "mygrid.hh"
 #include "midpoint.hh"
-#include "../distances.hh"
+#include "../diameter.hh"
 
 #if MY_DIM == 3
 SimplexManager::SimplexManager(unsigned int shift) : shift_(shift) {}
@@ -199,11 +201,11 @@ void refine(Grid &grid, ConvexPolyhedron<LocalVector> const &weakPatch,
   bool needRefine = true;
   while (true) {
     needRefine = false;
-    for (auto it = grid.template leafbegin<0>();
-         it != grid.template leafend<0>(); ++it) {
-      auto const geometry = it->geometry();
+    for (auto &&e : elements(grid.leafGridView())) {
+      auto const geometry = e.geometry();
 
-      auto const weakeningRegionDistance = distance(geometry, weakPatch);
+      auto const weakeningRegionDistance =
+          distance(weakPatch, geometry, 1e-6 * MyGeometry::lengthScale);
       auto const admissibleDiameter =
           computeAdmissibleDiameter(weakeningRegionDistance, smallestDiameter);
 
@@ -211,7 +213,7 @@ void refine(Grid &grid, ConvexPolyhedron<LocalVector> const &weakPatch,
         continue;
 
       needRefine = true;
-      grid.mark(1, *it);
+      grid.mark(1, e);
     }
     if (!needRefine)
       break;

src/sand-wedge-data/mygrid.hh → src/one-body-problem-data/mygrid.hh

-#ifndef SRC_SAND_WEDGE_DATA_MYGRID_HH
-#define SRC_SAND_WEDGE_DATA_MYGRID_HH
-
-#include <boost/range/irange.hpp>
+#ifndef SRC_ONE_BODY_PROBLEM_DATA_MYGRID_HH
+#define SRC_ONE_BODY_PROBLEM_DATA_MYGRID_HH
 
 #include <dune/common/fmatrix.hh>
 #include <dune/grid/common/gridfactory.hh>
 
-#pragma clang diagnostic push
-#pragma clang diagnostic ignored "-Wdeprecated-declarations"
 #include <dune/fufem/boundarypatch.hh>
-#pragma clang diagnostic pop
-
-#include <dune/tectonic/convexpolyhedron.hh>
+#include <dune/fufem/geometry/convexpolyhedron.hh>
 
 #include "mygeometry.hh"