Skip to content
GitLab
Commit 733b3e73 authored by Thomas Witkowski's avatar Thomas Witkowski
Browse files

Added first support to read and write arh files.

parent 14739310
Hide whitespace changes
Inline Side-by-side
AMDiS/CMakeLists.txt
View file @ 733b3e73
......@@ -151,6 +151,8 @@ SET(AMDIS_SRC ${SOURCE_DIR}/DOFIndexed.cc
${SOURCE_DIR}/parallel/InteriorBoundary.cc
${SOURCE_DIR}/ElementDofIterator.cc
${SOURCE_DIR}/Debug.cc
${SOURCE_DIR}/ArhReader.cc
${SOURCE_DIR}/ArhWriter.cc
${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
${SOURCE_DIR}/time/RosenbrockStationary.cc
${SOURCE_DIR}/time/RosenbrockMethod.cc
......
AMDiS/bin/Makefile.am
View file @ 733b3e73
......@@ -226,6 +226,8 @@ $(SOURCE_DIR)/SolutionDataStorage.h $(SOURCE_DIR)/SolutionDataStorage.hh \
$(SOURCE_DIR)/ElementDofIteartor.h $(SOURCE_DIR)/ElementDofIterator.cc \
$(SOURCE_DIR)/parallel/InteriorBoundary.h $(SOURCE_DIR)/parallel/InteriorBoundary.cc \
$(SOURCE_DIR)/Debug.h $(SOURCE_DIR)/Debug.cc \
$(SOURCE_DIR)/ArhReader.h $(SOURCE_DIR)/ArhReader.cc \
$(SOURCE_DIR)/ArhWriter.h $(SOURCE_DIR)/ArhWriter.cc \
$(SOURCE_DIR)/time/RosenbrockAdaptInstationary.h $(SOURCE_DIR)/time/RosenbrockAdaptInstationary.cc \
$(SOURCE_DIR)/time/RosenbrockStationary.h $(SOURCE_DIR)/time/RosenbrockStationary.cc \
$(SOURCE_DIR)/time/RosenbrockMethod.h $(SOURCE_DIR)/time/RosenbrockMethod.cc
......
AMDiS/bin/Makefile.in
View file @ 733b3e73
This source diff could not be displayed because it is too large. You can view the blob instead.
AMDiS/libtool
View file @ 733b3e73
......@@ -128,7 +128,7 @@ old_postinstall_cmds="chmod 644 \$oldlib~\$RANLIB \$oldlib"
old_postuninstall_cmds=""
# A C compiler.
LTCC="gcc"
LTCC="/usr/lib64/mpi/gcc/openmpi//bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
......@@ -259,7 +259,7 @@ LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs~\$RANLIB \$oldlib"
# A language specific compiler.
CC="gcc"
CC="/usr/lib64/mpi/gcc/openmpi//bin/mpicc"
# Is the compiler the GNU compiler?
with_gcc=yes
......@@ -274,7 +274,7 @@ wl="-Wl,"
pic_flag=" -fPIC -DPIC"
# Compiler flag to prevent dynamic linking.
link_static_flag="-static"
link_static_flag=""
# Does compiler simultaneously support -c and -o options?
compiler_c_o="yes"
......@@ -8914,7 +8914,7 @@ LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs~\$RANLIB \$oldlib"
# A language specific compiler.
CC="g++"
CC="/usr/lib64/mpi/gcc/openmpi//bin/mpicxx"
# Is the compiler the GNU compiler?
with_gcc=yes
......@@ -8929,7 +8929,7 @@ wl="-Wl,"
pic_flag=" -fPIC -DPIC"
# Compiler flag to prevent dynamic linking.
link_static_flag="-static"
link_static_flag=""
# Does compiler simultaneously support -c and -o options?
compiler_c_o="yes"
......@@ -9039,17 +9039,17 @@ file_list_spec=""
hardcode_action=immediate
# The directories searched by this compiler when creating a shared library.
compiler_lib_search_dirs="/usr/lib64/gcc/x86_64-suse-linux/4.5 /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 /lib/../lib64 /usr/lib/../lib64 /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib /usr/lib64/gcc/x86_64-suse-linux/4.5/../../.."
compiler_lib_search_dirs="/usr/lib64/mpi/gcc/openmpi/lib64 /usr/lib64/gcc/x86_64-suse-linux/4.5 /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 /lib/../lib64 /usr/lib/../lib64 /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib /usr/lib64/gcc/x86_64-suse-linux/4.5/../../.."
# Dependencies to place before and after the objects being linked to
# create a shared library.
predep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.5/crtbeginS.o"
postdep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.5/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crtn.o"
predeps=""
postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
# The library search path used internally by the compiler when linking
# a shared library.
compiler_lib_search_path="-L/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../.."
compiler_lib_search_path="-L/usr/lib64/mpi/gcc/openmpi/lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../.."
# ### END LIBTOOL TAG CONFIG: CXX
AMDiS/src/AMDiS.h
View file @ 733b3e73
......@@ -5,6 +5,8 @@
#include "AdaptInfo.h"
#include "AdaptInstationary.h"
#include "AdaptStationary.h"
#include "ArhReader.h"
#include "ArhWriter.h"
#include "Assembler.h"
#include "BasisFunction.h"
#include "Boundary.h"
......
AMDiS/src/ArhReader.cc 0 → 100644
View file @ 733b3e73
#include <fstream>
#include "ArhReader.h"
#include "Mesh.h"
#include "MeshStructure.h"
namespace AMDiS {
using namespace std;
void ArhReader::read(string filename, Mesh *mesh)
{
FUNCNAME("ArhReader::read()");
RefinementManager *refManager;
switch (mesh->getDim()) {
case 2:
refManager = new RefinementManager2d();
break;
case 3:
refManager = new RefinementManager3d();
break;
default:
ERROR_EXIT("Should not happen!\n");
}
ifstream file;
file.open(filename.c_str(), ios::in | ios::binary);
string typeId = "";
long nMacroElements = 0;
long nValueVectors = 0;
long nAllValues = 0;
file.read(const_cast<char*>(typeId.data()), 4);
file.read(reinterpret_cast<char*>(&nMacroElements), 4);
file.read(reinterpret_cast<char*>(&nValueVectors), 4);
file.read(reinterpret_cast<char*>(&nAllValues), 4);
for (long i = 0; i < nMacroElements; i++) {
long elIndex = 0;
long nStructureCodes = 0;
long codeSize = 0;
file.read(reinterpret_cast<char*>(&elIndex), 4);
file.read(reinterpret_cast<char*>(&nStructureCodes), 4);
file.read(reinterpret_cast<char*>(&codeSize), 4);
vector<unsigned long> structureCode(nStructureCodes);
file.read(reinterpret_cast<char*>(&(structureCode[0])), 4 * nStructureCodes);
MeshStructure elementStructure;
elementStructure.init(structureCode, codeSize);
elementStructure.fitMeshToStructure(mesh, refManager, false, false, elIndex);
long nValuesPerVector = 0;
file.read(reinterpret_cast<char*>(&nValuesPerVector), 4);
for (long j = 0; j < nValuesPerVector * nValueVectors; j++) {
double value = 0.0;
file.read(reinterpret_cast<char*>(&value), 8);
}
}
file.close();
MSG("ARH file read from: %s\n", filename.c_str());
}
}
AMDiS/src/ArhReader.h 0 → 100644
View file @ 733b3e73
// ============================================================================
// == ==
// == Amdis - Adaptive multidimensional simulations ==
// == ==
// ============================================================================
// == ==
// == TU Dresden ==
// == ==
// == Institut für Wissenschaftliches Rechnen ==
// == Zellescher Weg 12-14 ==
// == 01069 Dresden ==
// == germany ==
// == ==
// ============================================================================
// == ==
// == https://gforge.zih.tu-dresden.de/projects/amdis/ ==
// == ==
// ============================================================================
/** \file ArhReader.h */
#ifndef AMDIS_ARH_READER_H
#define AMDIS_ARH_READER_H
#include "AMDiS_fwd.h"
namespace AMDiS {
class ArhReader
{
public:
static void read(std::string filename, Mesh *mesh);
};
}
#endif
AMDiS/src/ArhWriter.cc 0 → 100644
View file @ 733b3e73
#include <fstream>
#include "ArhWriter.h"
#include "Mesh.h"
#include "MeshStructure.h"
#include "Traverse.h"
namespace AMDiS {
using namespace std;
void ArhWriter::write(string filename, Mesh *mesh)
{
FUNCNAME("ArhWriter::write()");
ofstream file;
file.open(filename.c_str(), ios::out | ios::binary | ios::trunc);
string typeId = "arhS";
file.write(typeId.c_str(), 4);
long nMacroElements = 0;
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
while (elInfo) {
nMacroElements++;
elInfo = stack.traverseNext(elInfo);
}
file.write(reinterpret_cast<char*>(&nMacroElements), 4);
long nValueVectors = 0;
file.write(reinterpret_cast<char*>(&nValueVectors), 4);
long nAllValues = 0;
file.write(reinterpret_cast<char*>(&nAllValues), 4);
MeshStructure elementStructure;
long macroElIndex = -1;
elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
while (elInfo) {
if (elInfo->getLevel() == 0) {
if (macroElIndex != -1) {
elementStructure.commit();
writeMacroElement(file, elementStructure, macroElIndex);
}
elementStructure.clear();
macroElIndex = elInfo->getElement()->getIndex();
}
elementStructure.insertElement(elInfo->getElement()->isLeaf());
elInfo = stack.traverseNext(elInfo);
}
// And write the last macro element to file.
TEST_EXIT_DBG(macroElIndex != -1)("Should not happen!\n");
elementStructure.commit();
writeMacroElement(file, elementStructure, macroElIndex);
file.close();
MSG("ARH file written to: %s\n", filename.c_str());
}
void ArhWriter::writeMacroElement(std::ofstream &file,
MeshStructure &code,
long elIndex)
{
file.write(reinterpret_cast<char*>(&elIndex), 4);
long nStructureCodes = code.getCode().size();
file.write(reinterpret_cast<char*>(&nStructureCodes), 4);
long codeSize = code.getNumElements();
file.write(reinterpret_cast<char*>(&codeSize), 4);
file.write(reinterpret_cast<char*>(&(const_cast<vector<unsigned long int>&>(code.getCode())[0])),
4 * nStructureCodes);
long nValuesPerVector = 0;
file.write(reinterpret_cast<char*>(&nValuesPerVector), 4);
}
}
AMDiS/src/ArhWriter.h 0 → 100644
View file @ 733b3e73
// ============================================================================
// == ==
// == Amdis - Adaptive multidimensional simulations ==
// == ==
// ============================================================================
// == ==
// == TU Dresden ==
// == ==
// == Institut für Wissenschaftliches Rechnen ==
// == Zellescher Weg 12-14 ==
// == 01069 Dresden ==
// == germany ==
// == ==
// ============================================================================
// == ==
// == https://gforge.zih.tu-dresden.de/projects/amdis/ ==
// == ==
// ============================================================================
/** \file ArhWriter.h */
#ifndef AMDIS_ARH_WRITER_H
#define AMDIS_ARH_WRITER_H
#include <iostream>
#include <fstream>
#include "AMDiS_fwd.h"
namespace AMDiS {
class ArhWriter
{
public:
static void write(std::string filename, Mesh *mesh);
protected:
static void writeMacroElement(std::ofstream &file,
MeshStructure &code,
long elIndex);
};
}
#endif
AMDiS/src/MeshStructure.cc
View file @ 733b3e73
......@@ -347,99 +347,4 @@ namespace AMDiS {
{
return (other.getCode() == code);
}
void MeshStructure::writeMeshFile(Mesh *mesh, std::string filename)
{
FUNCNAME("MeshStructure::writeMeshFile()");
int nMacroElements = 0;
int macroElIndex = -1;
std::ofstream file;
file.open(filename.c_str(), std::ios::out | std::ios::binary | std::ios::trunc);
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
while (elInfo) {
nMacroElements++;
elInfo = stack.traverseNext(elInfo);
}
file.write(reinterpret_cast<char*>(&nMacroElements), sizeof(nMacroElements));
elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
while (elInfo) {
if (elInfo->getLevel() == 0) {
if (macroElIndex != -1) {
commit();
writeMacroElement(file, macroElIndex);
}
clear();
macroElIndex = elInfo->getElement()->getIndex();
}
insertElement(elInfo->getElement()->isLeaf());
elInfo = stack.traverseNext(elInfo);
}
// And write the last macro element to file.
TEST_EXIT_DBG(macroElIndex != -1)("Should not happen!\n");
commit();
writeMacroElement(file, macroElIndex);
file.close();
}
void MeshStructure::readMeshFile(Mesh *mesh,
RefinementManager *refManager,
std::string filename)
{
FUNCNAME("MeshStructure::readMeshFile()");
std::ifstream file;
file.open(filename.c_str(), std::ios::in | std::ios::binary);
int nMacroElements = -1;
file.read(reinterpret_cast<char*>(&nMacroElements), sizeof(nMacroElements));
for (int i = 0; i < nMacroElements; i++) {
int macroElIndex = -1;
int codeSize = 0;
code.clear();
file.read(reinterpret_cast<char*>(&macroElIndex), sizeof(macroElIndex));
file.read(reinterpret_cast<char*>(&nElements), sizeof(nElements));
file.read(reinterpret_cast<char*>(&codeSize), sizeof(codeSize));
for (int j = 0; j < codeSize; j++) {
unsigned long int readCode = 0;
file.read(reinterpret_cast<char*>(&readCode), sizeof(readCode));
code.push_back(readCode);
}
TEST_EXIT_DBG(macroElIndex >= 0)("Should not happen!\n");
reset();
fitMeshToStructure(mesh, refManager, false, false, macroElIndex);
}
file.close();
}
void MeshStructure::writeMacroElement(std::ofstream& file, int macroElIndex)
{
unsigned int size = code.size();
file.write(reinterpret_cast<char*>(&macroElIndex), sizeof(macroElIndex));
file.write(reinterpret_cast<char*>(&nElements), sizeof(nElements));
file.write(reinterpret_cast<char*>(&size), sizeof(size));
for (unsigned int i = 0; i < code.size(); i++)
file.write(reinterpret_cast<char*>(&(code[i])), sizeof(code[i]));
}
}
AMDiS/src/MeshStructure.h
View file @ 733b3e73
......@@ -140,10 +140,6 @@ namespace AMDiS {
/// Returns true, if the given mesh structure code is equal to this one.
bool compare(MeshStructure &other);
void writeMeshFile(Mesh *mesh, std::string filename);
void readMeshFile(Mesh *mesh, RefinementManager *refManager, std::string filename);
protected:
/// Insert a new element to the structure code. Is used by the init function.
void insertElement(bool isLeaf);
......@@ -155,8 +151,6 @@ namespace AMDiS {
MeshStructure *structure2,
MeshStructure *result);
void writeMacroElement(std::ofstream& file, int macroElIndex);
protected:
/// Mesh structure code.
std::vector<unsigned long int> code;
......@@ -175,6 +169,8 @@ namespace AMDiS {
bool debugMode;
static const int unsignedLongSize;
friend class ArhWriter;
};
}
......
AMDiS/src/RefinementManager.cc
View file @ 733b3e73
......@@ -93,6 +93,7 @@ namespace AMDiS {
Mesh::CALL_LEAF_EL | Mesh::FILL_NEIGH | Mesh::FILL_BOUND);
while (elInfo) {
if (elInfo->getElement() == el) {
MSG("REFINE EL IN HERE\n");
refineFunction(elInfo);
TEST_EXIT(!doMoreRecursiveRefine)("Okay, this will not work in that way!\n");
......
AMDiS/src/parallel/MeshDistributor.cc
View file @ 733b3e73
......@@ -516,7 +516,7 @@ namespace AMDiS {
// === Check the boundaries and adapt mesh if necessary. ===
MSG("TEST 1: %d\n", mesh->getDOFAdmin(0).getUsedSize());
#if (DEBUG != 0)
MSG("Run checkAndAdaptBoundary ...\n");
#endif
......@@ -534,6 +534,7 @@ namespace AMDiS {
#endif
} while (recvAllValues != 0);
MSG("TEST 2: %d\n", mesh->getDOFAdmin(0).getUsedSize());
#if (DEBUG != 0)
debug::writeMesh(feSpace, -1, "mesh");
......@@ -698,9 +699,7 @@ namespace AMDiS {
refineManager->setMesh(el->getMesh());
refineManager->setStack(&stack);
refineManager->refineFunction(elInfo);
MSG("A-NEW ELs %d %d\n", el->getChild(0)->getIndex(), el->getChild(1)->getIndex());
MSG("REFINE EL %d %d %d\n", elInfo->getElement()->getIndex(), el->getChild(0)->getIndex(), el->getChild(1)->getIndex());
meshChanged = true;
}
......@@ -779,6 +778,7 @@ namespace AMDiS {
refineManager->setMesh(el->getMesh());
refineManager->setStack(&stack);
refineManager->refineFunction(elInfo);
MSG("REFINE EL %d %d %d\n", elInfo->getElement()->getIndex(), el->getChild(0)->getIndex(), el->getChild(1)->getIndex());
meshChanged = true;
}
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment