From 5b1fe7c8cb425d90a013f77fc0f6fd396e180850 Mon Sep 17 00:00:00 2001
From: Elias Pipping <elias.pipping@fu-berlin.de>
Date: Mon, 30 May 2016 17:07:21 +0200
Subject: [PATCH] [Extern] HDF5: moved to namespace and new headers
Prior to this change, dune-tectonic was incompatible with
dune-fufem releases/2.4-2 and later, thus also releases/2.5-1
Prior to this change, dune-tectonic is incompatible with
dune-fufem releases/2.4-1 and earlier
---
dune.module | 2 +-
src/CMakeLists.txt | 3 +--
src/hdf5-writer.hh | 6 +++---
src/hdf5/frictionalboundary-writer.cc | 6 ++++--
src/hdf5/frictionalboundary-writer.hh | 15 +++++++--------
src/hdf5/iteration-writer.cc | 2 +-
src/hdf5/iteration-writer.hh | 18 +++++++++---------
src/hdf5/patchinfo-writer.cc | 7 ++++---
src/hdf5/patchinfo-writer.hh | 9 ++++-----
src/hdf5/restart-io.cc | 2 +-
src/hdf5/restart-io.hh | 22 +++++++++++-----------
src/hdf5/surface-writer.cc | 4 ++--
src/hdf5/surface-writer.hh | 12 ++++++------
src/hdf5/time-writer.cc | 2 +-
src/hdf5/time-writer.hh | 12 ++++++------
src/one-body-problem.cc | 4 ++--
16 files changed, 63 insertions(+), 63 deletions(-)
diff --git a/dune.module b/dune.module
index 2ee4c409..df08e2c5 100644
--- a/dune.module
+++ b/dune.module
@@ -3,6 +3,6 @@
################################
Module: dune-tectonic
-Version: 2.4-1
+Version: 2.5-1
Maintainer: elias.pipping@fu-berlin.de
Depends: dune-common dune-fufem dune-geometry dune-grid dune-istl dune-solvers dune-tnnmg
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 44828564..ef471d7d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -35,8 +35,7 @@ foreach(_dim 2 3)
add_dune_ug_flags(${_sw_target})
add_dune_ug_flags(${_ugw_target})
- set_property(TARGET ${_sw_target} APPEND PROPERTY INCLUDE_DIRECTORIES ${HDF5_INCLUDE_DIR})
- target_link_libraries(${_sw_target} ${HDF5_LIBRARIES})
+ add_dune_hdf5_flags(${_sw_target})
set_property(TARGET ${_sw_target} APPEND PROPERTY COMPILE_DEFINITIONS "MY_DIM=${_dim}")
set_property(TARGET ${_ugw_target} APPEND PROPERTY COMPILE_DEFINITIONS "MY_DIM=${_dim}")
diff --git a/src/hdf5-writer.hh b/src/hdf5-writer.hh
index e4e5358e..02de2b27 100644
--- a/src/hdf5-writer.hh
+++ b/src/hdf5-writer.hh
@@ -3,7 +3,7 @@
#include <dune/fufem/functions/basisgridfunction.hh>
#include <dune/fufem/geometry/convexpolyhedron.hh>
-#include <dune/fufem/hdf5/hdf5file.hh>
+#include <dune/fufem/hdf5/file.hh>
#include "hdf5/frictionalboundary-writer.hh"
#include "hdf5/iteration-writer.hh"
@@ -21,7 +21,7 @@ class HDF5Writer {
using LocalVector = typename Vector::block_type;
public:
- HDF5Writer(HDF5Grouplike &file, Vector const &vertexCoordinates,
+ HDF5Writer(HDF5::Grouplike &file, Vector const &vertexCoordinates,
VertexBasis const &vertexBasis, Patch const &surface,
Patch const &frictionalBoundary,
ConvexPolyhedron<LocalVector> const &weakPatch)
@@ -58,7 +58,7 @@ class HDF5Writer {
}
private:
- HDF5Grouplike &file_;
+ HDF5::Grouplike &file_;
IterationWriter iterationWriter_;
TimeWriter<ProgramState> timeWriter_;
diff --git a/src/hdf5/frictionalboundary-writer.cc b/src/hdf5/frictionalboundary-writer.cc
index b98290df..e78b70f3 100644
--- a/src/hdf5/frictionalboundary-writer.cc
+++ b/src/hdf5/frictionalboundary-writer.cc
@@ -2,12 +2,14 @@
#include "config.h"
#endif
+#include <dune/fufem/hdf5/singletonwriter.hh>
+
#include "frictionalboundary-writer.hh"
#include "restrict.hh"
template <class ProgramState, class GridView>
FrictionalBoundaryWriter<ProgramState, GridView>::FrictionalBoundaryWriter(
- HDF5Grouplike &file, Vector const &vertexCoordinates,
+ HDF5::Grouplike &file, Vector const &vertexCoordinates,
Patch const &frictionalBoundary)
: group_(file, "frictionalBoundary"),
frictionalBoundary_(frictionalBoundary),
@@ -23,7 +25,7 @@ FrictionalBoundaryWriter<ProgramState, GridView>::FrictionalBoundaryWriter(
frictionalBoundary.numVertices()) {
auto const frictionalBoundaryCoordinates =
restrictToSurface(vertexCoordinates, frictionalBoundary);
- HDF5SingletonWriter<2> frictionalBoundaryCoordinateWriter(
+ HDF5::SingletonWriter<2> frictionalBoundaryCoordinateWriter(
group_, "coordinates", frictionalBoundaryCoordinates.size(),
Vector::block_type::dimension);
setEntry(frictionalBoundaryCoordinateWriter, frictionalBoundaryCoordinates);
diff --git a/src/hdf5/frictionalboundary-writer.hh b/src/hdf5/frictionalboundary-writer.hh
index 772b82df..705b7fb2 100644
--- a/src/hdf5/frictionalboundary-writer.hh
+++ b/src/hdf5/frictionalboundary-writer.hh
@@ -3,8 +3,7 @@
#include <dune/fufem/boundarypatch.hh>
-#include <dune/fufem/hdf5/hdf5-sequence-io.hh>
-#include <dune/fufem/hdf5/hdf5-singleton-writer.hh>
+#include <dune/fufem/hdf5/sequenceio.hh>
template <class ProgramState, class GridView> class FrictionalBoundaryWriter {
using ScalarVector = typename ProgramState::ScalarVector;
@@ -12,20 +11,20 @@ template <class ProgramState, class GridView> class FrictionalBoundaryWriter {
using Patch = BoundaryPatch<GridView>;
public:
- FrictionalBoundaryWriter(HDF5Grouplike &file, Vector const &vertexCoordinates,
+ FrictionalBoundaryWriter(HDF5::Grouplike &file, Vector const &vertexCoordinates,
Patch const &frictionalBoundary);
template <class Friction>
void write(ProgramState const &programState, Friction &friction);
private:
- HDF5Group group_;
+ HDF5::Group group_;
Patch const &frictionalBoundary_;
- HDF5SequenceIO<2> frictionalBoundaryDisplacementWriter_;
- HDF5SequenceIO<2> frictionalBoundaryVelocityWriter_;
- HDF5SequenceIO<1> frictionalBoundaryStateWriter_;
- HDF5SequenceIO<1> frictionalBoundaryCoefficientWriter_;
+ HDF5::SequenceIO<2> frictionalBoundaryDisplacementWriter_;
+ HDF5::SequenceIO<2> frictionalBoundaryVelocityWriter_;
+ HDF5::SequenceIO<1> frictionalBoundaryStateWriter_;
+ HDF5::SequenceIO<1> frictionalBoundaryCoefficientWriter_;
};
#endif
diff --git a/src/hdf5/iteration-writer.cc b/src/hdf5/iteration-writer.cc
index e48f091b..568c1cf5 100644
--- a/src/hdf5/iteration-writer.cc
+++ b/src/hdf5/iteration-writer.cc
@@ -4,7 +4,7 @@
#include "iteration-writer.hh"
-IterationWriter::IterationWriter(HDF5Grouplike &file)
+IterationWriter::IterationWriter(HDF5::Grouplike &file)
: group_(file, "iterations"),
fpiSubGroup_(group_, "fixedPoint"),
mgSubGroup_(group_, "multiGrid"),
diff --git a/src/hdf5/iteration-writer.hh b/src/hdf5/iteration-writer.hh
index 377ae749..f3cb6e06 100644
--- a/src/hdf5/iteration-writer.hh
+++ b/src/hdf5/iteration-writer.hh
@@ -1,24 +1,24 @@
#ifndef SRC_HDF_ITERATION_WRITER_HH
#define SRC_HDF_ITERATION_WRITER_HH
-#include <dune/fufem/hdf5/hdf5-sequence-io.hh>
+#include <dune/fufem/hdf5/sequenceio.hh>
#include "../time-stepping/adaptivetimestepper.hh"
class IterationWriter {
public:
- IterationWriter(HDF5Grouplike &file);
+ IterationWriter(HDF5::Grouplike &file);
void write(size_t timeStep, IterationRegister const &iterationCount);
private:
- HDF5Group group_;
- HDF5Group fpiSubGroup_;
- HDF5Group mgSubGroup_;
+ HDF5::Group group_;
+ HDF5::Group fpiSubGroup_;
+ HDF5::Group mgSubGroup_;
- HDF5SequenceIO<0, size_t> finalMGIterationWriter_;
- HDF5SequenceIO<0, size_t> finalFPIIterationWriter_;
- HDF5SequenceIO<0, size_t> totalMGIterationWriter_;
- HDF5SequenceIO<0, size_t> totalFPIIterationWriter_;
+ HDF5::SequenceIO<0, size_t> finalMGIterationWriter_;
+ HDF5::SequenceIO<0, size_t> finalFPIIterationWriter_;
+ HDF5::SequenceIO<0, size_t> totalMGIterationWriter_;
+ HDF5::SequenceIO<0, size_t> totalFPIIterationWriter_;
};
#endif
diff --git a/src/hdf5/patchinfo-writer.cc b/src/hdf5/patchinfo-writer.cc
index 253848c3..2df15c5f 100644
--- a/src/hdf5/patchinfo-writer.cc
+++ b/src/hdf5/patchinfo-writer.cc
@@ -3,6 +3,7 @@
#endif
#include <dune/fufem/grid/hierarchic-approximation.hh>
+#include <dune/fufem/hdf5/singletonwriter.hh>
#include "patchinfo-writer.hh"
@@ -65,7 +66,7 @@ GridEvaluator<LocalVector, GridView>::evaluate(Function const &f) const {
template <class ProgramState, class VertexBasis, class GridView>
PatchInfoWriter<ProgramState, VertexBasis, GridView>::PatchInfoWriter(
- HDF5Grouplike &file, VertexBasis const &vertexBasis,
+ HDF5::Grouplike &file, VertexBasis const &vertexBasis,
Patch const &frictionalBoundary,
ConvexPolyhedron<LocalVector> const &weakPatch)
: group_(file, "weakPatchGrid"),
@@ -74,11 +75,11 @@ PatchInfoWriter<ProgramState, VertexBasis, GridView>::PatchInfoWriter(
weakPatchGridVelocityWriter_(
group_, "velocity", gridEvaluator_.xCoordinates.size(),
gridEvaluator_.zCoordinates.size(), Vector::block_type::dimension) {
- HDF5SingletonWriter<1> weakPatchGridXCoordinateWriter(
+ HDF5::SingletonWriter<1> weakPatchGridXCoordinateWriter(
group_, "xCoordinates", gridEvaluator_.xCoordinates.size());
setEntry(weakPatchGridXCoordinateWriter, gridEvaluator_.xCoordinates);
- HDF5SingletonWriter<1> weakPatchGridZCoordinateWriter(
+ HDF5::SingletonWriter<1> weakPatchGridZCoordinateWriter(
group_, "zCoordinates", gridEvaluator_.zCoordinates.size());
setEntry(weakPatchGridZCoordinateWriter, gridEvaluator_.zCoordinates);
}
diff --git a/src/hdf5/patchinfo-writer.hh b/src/hdf5/patchinfo-writer.hh
index 23e988aa..82dea364 100644
--- a/src/hdf5/patchinfo-writer.hh
+++ b/src/hdf5/patchinfo-writer.hh
@@ -6,8 +6,7 @@
#include <dune/fufem/boundarypatch.hh>
#include <dune/fufem/functions/basisgridfunction.hh>
#include <dune/fufem/geometry/convexpolyhedron.hh>
-#include <dune/fufem/hdf5/hdf5-sequence-io.hh>
-#include <dune/fufem/hdf5/hdf5-singleton-writer.hh>
+#include <dune/fufem/hdf5/sequenceio.hh>
#include "../one-body-problem-data/mygeometry.hh"
@@ -35,18 +34,18 @@ class PatchInfoWriter {
using Patch = BoundaryPatch<GridView>;
public:
- PatchInfoWriter(HDF5Grouplike &file, VertexBasis const &vertexBasis,
+ PatchInfoWriter(HDF5::Grouplike &file, VertexBasis const &vertexBasis,
Patch const &frictionalBoundary,
ConvexPolyhedron<LocalVector> const &weakPatch);
void write(ProgramState const &programState);
private:
- HDF5Group group_;
+ HDF5::Group group_;
VertexBasis const &vertexBasis_;
GridEvaluator<LocalVector, GridView> const gridEvaluator_;
- HDF5SequenceIO<3> weakPatchGridVelocityWriter_;
+ HDF5::SequenceIO<3> weakPatchGridVelocityWriter_;
};
#endif
diff --git a/src/hdf5/restart-io.cc b/src/hdf5/restart-io.cc
index c7fc7422..8fe3c59a 100644
--- a/src/hdf5/restart-io.cc
+++ b/src/hdf5/restart-io.cc
@@ -5,7 +5,7 @@
#include "restart-io.hh"
template <class ProgramState>
-RestartIO<ProgramState>::RestartIO(HDF5Grouplike &file, size_t vertexCount)
+RestartIO<ProgramState>::RestartIO(HDF5::Grouplike &file, size_t vertexCount)
: group_(file, "restarts"),
displacementWriter_(group_, "displacement", vertexCount,
Vector::block_type::dimension),
diff --git a/src/hdf5/restart-io.hh b/src/hdf5/restart-io.hh
index c42b1022..94b60d67 100644
--- a/src/hdf5/restart-io.hh
+++ b/src/hdf5/restart-io.hh
@@ -1,29 +1,29 @@
#ifndef SRC_HDF_RESTART_HDF_HH
#define SRC_HDF_RESTART_HDF_HH
-#include <dune/fufem/hdf5/hdf5file.hh>
-#include <dune/fufem/hdf5/hdf5-sequence-io.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(HDF5Grouplike &file, size_t vertexCount);
+ RestartIO(HDF5::Grouplike &file, size_t vertexCount);
void write(ProgramState const &programState);
void read(size_t timeStep, ProgramState &programState);
private:
- HDF5Group group_;
+ HDF5::Group group_;
- HDF5SequenceIO<2> displacementWriter_;
- HDF5SequenceIO<2> velocityWriter_;
- HDF5SequenceIO<2> accelerationWriter_;
- HDF5SequenceIO<1> stateWriter_;
- HDF5SequenceIO<1> weightedNormalStressWriter_;
- HDF5SequenceIO<0> relativeTimeWriter_;
- HDF5SequenceIO<0> relativeTimeIncrementWriter_;
+ 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
diff --git a/src/hdf5/surface-writer.cc b/src/hdf5/surface-writer.cc
index 51b9508a..bdab1213 100644
--- a/src/hdf5/surface-writer.cc
+++ b/src/hdf5/surface-writer.cc
@@ -7,7 +7,7 @@
template <class ProgramState, class GridView>
SurfaceWriter<ProgramState, GridView>::SurfaceWriter(
- HDF5Grouplike &file, Vector const &vertexCoordinates, Patch const &surface)
+ HDF5::Grouplike &file, Vector const &vertexCoordinates, Patch const &surface)
: group_(file, "surface"),
surface_(surface),
surfaceDisplacementWriter_(group_, "displacement", surface.numVertices(),
@@ -15,7 +15,7 @@ SurfaceWriter<ProgramState, GridView>::SurfaceWriter(
surfaceVelocityWriter_(group_, "velocity", surface.numVertices(),
Vector::block_type::dimension) {
auto const surfaceCoordinates = restrictToSurface(vertexCoordinates, surface);
- HDF5SingletonWriter<2> surfaceCoordinateWriter(group_, "coordinates",
+ HDF5::SingletonWriter<2> surfaceCoordinateWriter(group_, "coordinates",
surfaceCoordinates.size(),
Vector::block_type::dimension);
setEntry(surfaceCoordinateWriter, surfaceCoordinates);
diff --git a/src/hdf5/surface-writer.hh b/src/hdf5/surface-writer.hh
index 7ac92a4c..e0ed4263 100644
--- a/src/hdf5/surface-writer.hh
+++ b/src/hdf5/surface-writer.hh
@@ -3,25 +3,25 @@
#include <dune/fufem/boundarypatch.hh>
-#include <dune/fufem/hdf5/hdf5-sequence-io.hh>
-#include <dune/fufem/hdf5/hdf5-singleton-writer.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(HDF5Grouplike &file, Vector const &vertexCoordinates,
+ SurfaceWriter(HDF5::Grouplike &file, Vector const &vertexCoordinates,
Patch const &surface);
void write(ProgramState const &programState);
private:
- HDF5Group group_;
+ HDF5::Group group_;
Patch const &surface_;
- HDF5SequenceIO<2> surfaceDisplacementWriter_;
- HDF5SequenceIO<2> surfaceVelocityWriter_;
+ HDF5::SequenceIO<2> surfaceDisplacementWriter_;
+ HDF5::SequenceIO<2> surfaceVelocityWriter_;
};
#endif
diff --git a/src/hdf5/time-writer.cc b/src/hdf5/time-writer.cc
index 1c141946..56e2c932 100644
--- a/src/hdf5/time-writer.cc
+++ b/src/hdf5/time-writer.cc
@@ -5,7 +5,7 @@
#include "time-writer.hh"
template <class ProgramState>
-TimeWriter<ProgramState>::TimeWriter(HDF5Grouplike &file)
+TimeWriter<ProgramState>::TimeWriter(HDF5::Grouplike &file)
: file_(file),
relativeTimeWriter_(file_, "relativeTime"),
relativeTimeIncrementWriter_(file_, "relativeTimeIncrement") {}
diff --git a/src/hdf5/time-writer.hh b/src/hdf5/time-writer.hh
index e8f72417..02c2c73b 100644
--- a/src/hdf5/time-writer.hh
+++ b/src/hdf5/time-writer.hh
@@ -1,17 +1,17 @@
#ifndef SRC_HDF_TIME_WRITER_HH
#define SRC_HDF_TIME_WRITER_HH
-#include <dune/fufem/hdf5/hdf5file.hh>
-#include <dune/fufem/hdf5/hdf5-sequence-io.hh>
+#include <dune/fufem/hdf5/file.hh>
+#include <dune/fufem/hdf5/sequenceio.hh>
template <class ProgramState> class TimeWriter {
public:
- TimeWriter(HDF5Grouplike &file);
+ TimeWriter(HDF5::Grouplike &file);
void write(ProgramState const &programState);
private:
- HDF5Grouplike &file_;
- HDF5SequenceIO<0> relativeTimeWriter_;
- HDF5SequenceIO<0> relativeTimeIncrementWriter_;
+ HDF5::Grouplike &file_;
+ HDF5::SequenceIO<0> relativeTimeWriter_;
+ HDF5::SequenceIO<0> relativeTimeIncrementWriter_;
};
#endif
diff --git a/src/one-body-problem.cc b/src/one-body-problem.cc
index e5da5529..2b7db539 100644
--- a/src/one-body-problem.cc
+++ b/src/one-body-problem.cc
@@ -35,7 +35,7 @@
#include <dune/tectonic/geocoordinate.hh>
#include <dune/tectonic/myblockproblem.hh>
#include <dune/tectonic/globalfriction.hh>
-#include <dune/fufem/hdf5/hdf5file.hh>
+#include <dune/fufem/hdf5/file.hh>
#include "assemblers.hh"
#include "diameter.hh"
@@ -174,7 +174,7 @@ int main(int argc, char *argv[]) {
auto const restartSpacing = parset.get<size_t>("restarts.spacing");
auto const restartTemplate = parset.get<std::string>("restarts.template");
- HDF5File ioFile("output.h5");
+ HDF5::File ioFile("output.h5");
if (firstRestart != 0)
RestartIO<ProgramState<Vector, ScalarVector>>(ioFile, leafVertexCount)
.read(firstRestart, programState);
--
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