diff --git a/AMDiS/src/io/ArhReader.cc b/AMDiS/src/io/ArhReader.cc
index 9642cb4ed725d8a99f91efe6d024778d8544b7d5..6747b1b2c5ffbcd9412753ff38a32d7426af5a56 100644
--- a/AMDiS/src/io/ArhReader.cc
+++ b/AMDiS/src/io/ArhReader.cc
@@ -1,7 +1,7 @@
//
// Software License for AMDiS
//
-// Copyright (c) 2010 Dresden University of Technology
+// Copyright (c) 2010 Dresden University of Technology
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
@@ -20,12 +20,12 @@
#include "DOFVector.h"
namespace AMDiS {
-
+
using namespace std;
void ArhReader::read(string filename, Mesh *mesh,
- DOFVector<double>* vec0,
+ DOFVector<double>* vec0,
DOFVector<double>* vec1,
DOFVector<double>* vec2,
bool writeParallel,
@@ -41,12 +41,12 @@ namespace AMDiS {
vecs.push_back(vec2);
for (size_t i = 3; i < nValueVectors; i++)
vecs.push_back(NULL);
-
+
ArhReader::read(filename, mesh, vecs, writeParallel, nProcs);
}
- void ArhReader::read(string filename, Mesh *mesh,
+ void ArhReader::read(string filename, Mesh *mesh,
vector<DOFVector<double>*> vecs,
bool writeParallel,
int nProcs)
@@ -57,9 +57,9 @@ namespace AMDiS {
using boost::lexical_cast;
int sPos = filename.find(".arh");
TEST_EXIT(sPos >= 0)("Failed to find file postfix!\n");
- string name = filename.substr(0, sPos);
+ string name = filename.substr(0, sPos);
- if (nProcs == -1) {
+ if (nProcs == -1) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
string procFilename = name + "-p" + lexical_cast<string>(MPI::COMM_WORLD.Get_rank()) + "-.arh";
readFile(procFilename, mesh, vecs);
@@ -78,8 +78,8 @@ namespace AMDiS {
MSG("ARH file read from: %s\n", filename.c_str());
}
-
- void ArhReader::readFile(string filename,
+
+ void ArhReader::readFile(string filename,
Mesh *mesh,
vector<DOFVector<double>*> vecs)
{
@@ -90,7 +90,7 @@ namespace AMDiS {
for (std::deque<MacroElement*>::iterator it = mesh->getMacroElements().begin();
it != mesh->getMacroElements().end(); ++it)
macroInMesh.insert((*it)->getIndex());
-
+
RefinementManager *refManager = NULL;
switch (mesh->getDim()) {
@@ -121,7 +121,7 @@ namespace AMDiS {
file.read(reinterpret_cast<char*>(&nAllValues), 4);
TEST_EXIT(nValueVectors == vecs.size())
- ("File %s has %d vectors, but %d DOFVectors are provided!\n",
+ ("File %s has %d vectors, but %d DOFVectors are provided!\n",
filename.c_str(), nValueVectors, vecs.size());
for (unsigned int i = 0; i < nMacroElements; i++) {
@@ -141,15 +141,17 @@ namespace AMDiS {
if (macroInMesh.count(elIndex) == 1)
elementStructure.fitMeshToStructure(mesh, refManager, false, elIndex);
- uint32_t nValuesPerVector = 0;
- file.read(reinterpret_cast<char*>(&nValuesPerVector), 4);
+ if(nValueVectors > 0){
+ uint32_t nValuesPerVector = 0;
+ file.read(reinterpret_cast<char*>(&nValuesPerVector), 4);
- for (unsigned int j = 0; j < nValueVectors; j++) {
- vector<double> values(nValuesPerVector);
- file.read(reinterpret_cast<char*>(&(values[0])), 8 * nValuesPerVector);
- if (vecs[j] != NULL) {
- if (macroInMesh.count(elIndex) == 1)
- setDofValues(elIndex, mesh, values, vecs[j]);
+ for (unsigned int j = 0; j < nValueVectors; j++) {
+ vector<double> values(nValuesPerVector);
+ file.read(reinterpret_cast<char*>(&(values[0])), 8 * nValuesPerVector);
+ if (vecs[j] != NULL) {
+ if (macroInMesh.count(elIndex) == 1)
+ setDofValues(elIndex, mesh, values, vecs[j]);
+ }
}
}
}
@@ -174,7 +176,7 @@ namespace AMDiS {
if (!macroElement) {
Element *mEl = elInfo->getMacroElement()->getElement();
for (int i = 0; i < mesh->getGeo(VERTEX); i++)
- (*vec)[mEl->getDof(i, 0)] = values[valuePos++];
+ (*vec)[mEl->getDof(i, 0)] = values[valuePos++];
macroElement = true;
}
@@ -185,4 +187,130 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
}
+
+
+ //the following three functions are identical to read/readfile except that they read from
+ //a block of memory instead of from a file
+ void ArhReader::readFromMemoryBlock(vector<char> &data, Mesh *mesh,
+ DOFVector<double>* vec0,
+ DOFVector<double>* vec1,
+ DOFVector<double>* vec2,
+ bool writeParallel,
+ int nProcs)
+ {
+ uint32_t nValueVectors;
+ memcpy(reinterpret_cast<char*>(&nValueVectors), &data[8], 4);
+ vector<DOFVector<double>*> vecs(0);
+ if (nValueVectors > 0)
+ vecs.push_back(vec0);
+ if (nValueVectors > 1)
+ vecs.push_back(vec1);
+ if (nValueVectors > 2)
+ vecs.push_back(vec2);
+ for (uint32_t i = 3; i < nValueVectors; i++)
+ vecs.push_back(NULL);
+
+ readFromMemoryBlock(data, mesh, vecs, writeParallel, nProcs);
+ }
+
+
+ void ArhReader::readFromMemoryBlock(vector<char> &data, Mesh *mesh,
+ vector<DOFVector<double>*> vecs,
+ bool writeParallel,
+ int nProcs)
+ {
+ FUNCNAME("ArhReader::readFromMemoryBlock()");
+
+ if (writeParallel) {
+ ERROR_EXIT("Reading a hierarchy from several memory blocks is not implemented yet!\n");
+ } else {
+ readBlock(data, mesh, vecs);
+ }
+ }
+
+
+ void ArhReader::readBlock(vector<char> &data,
+ Mesh *mesh,
+ vector<DOFVector<double>*> vecs)
+ {
+ FUNCNAME("ArhReader::readBlock()");
+
+ // === Get set of all macro elements in mesh. ===
+ std::set<int> macroInMesh;
+ for (std::deque<MacroElement*>::iterator it = mesh->getMacroElements().begin();
+ it != mesh->getMacroElements().end(); ++it)
+ macroInMesh.insert((*it)->getIndex());
+
+
+ RefinementManager *refManager = NULL;
+ switch (mesh->getDim()) {
+ case 2:
+ refManager = new RefinementManager2d();
+ break;
+ case 3:
+ refManager = new RefinementManager3d();
+ break;
+ default:
+ ERROR_EXIT("Should not happen!\n");
+ }
+
+ string typeId = "";
+ uint32_t nMacroElements = 0;
+ uint32_t nValueVectors = 0;
+ uint32_t nAllValues = 0;
+ uint32_t mem_index = 0;
+
+ memcpy(const_cast<char*>(typeId.data()), &data[mem_index], 4);
+ mem_index += 4;
+ memcpy(reinterpret_cast<char*>(&nMacroElements), &data[mem_index], 4);
+ mem_index += 4;
+ memcpy(reinterpret_cast<char*>(&nValueVectors), &data[mem_index], 4);
+ mem_index += 4;
+ memcpy(reinterpret_cast<char*>(&nAllValues), &data[mem_index], 4);
+ mem_index += 4;
+
+ TEST_EXIT(nValueVectors == vecs.size())
+ ("data has %d vectors, but %d DOFVectors are provided!\n", nValueVectors, vecs.size());
+
+ for (unsigned int i = 0; i < nMacroElements; i++) {
+ uint32_t elIndex = 0;
+ uint32_t nStructureCodes = 0;
+ uint32_t codeSize = 0;
+
+ memcpy(reinterpret_cast<char*>(&elIndex), &data[mem_index], 4);
+ mem_index += 4;
+ memcpy(reinterpret_cast<char*>(&nStructureCodes), &data[mem_index], 4);
+ mem_index += 4;
+ memcpy(reinterpret_cast<char*>(&codeSize), &data[mem_index], 4);
+ mem_index += 4;
+
+ vector<uint64_t> structureCode(nStructureCodes);
+ memcpy(reinterpret_cast<char*>(&structureCode[0]), &data[mem_index], 8 * nStructureCodes);
+ mem_index += 8 * nStructureCodes;
+
+ MeshStructure elementStructure;
+ elementStructure.init(structureCode, codeSize);
+ if (macroInMesh.count(elIndex) == 1)
+ elementStructure.fitMeshToStructure(mesh, refManager, false, elIndex);
+
+ if(nValueVectors > 0){
+ uint32_t nValuesPerVector = 0;
+ memcpy(reinterpret_cast<char*>(&nValuesPerVector), &data[mem_index], 4);
+ mem_index += 4;
+
+ for (unsigned int j = 0; j < nValueVectors; j++) {
+ vector<double> values(nValuesPerVector);
+ memcpy(reinterpret_cast<char*>(&values[0]), &data[mem_index], 8 * nValuesPerVector);
+ mem_index += 8 * nValuesPerVector;
+ if (vecs[j] != NULL) {
+ if (macroInMesh.count(elIndex) == 1)
+ setDofValues(elIndex, mesh, values, vecs[j]);
+ }
+ }
+ }
+ }
+
+ delete refManager;
+ }
+
}
diff --git a/AMDiS/src/io/ArhReader.h b/AMDiS/src/io/ArhReader.h
index 800564ef1ae49781cc56c1b38c8d21afa184e71c..5614d2b913f5a1a295d062bb6070194922dd9d12 100644
--- a/AMDiS/src/io/ArhReader.h
+++ b/AMDiS/src/io/ArhReader.h
@@ -8,7 +8,7 @@
//
// Software License for AMDiS
//
-// Copyright (c) 2010 Dresden University of Technology
+// Copyright (c) 2010 Dresden University of Technology
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
@@ -33,9 +33,9 @@ namespace AMDiS {
{
public:
static void read(string filename, Mesh *mesh,
- DOFVector<double>* vec0 = NULL,
+ DOFVector<double>* vec0 = NULL,
DOFVector<double>* vec1 = NULL,
- DOFVector<double>* vec2 = NULL,
+ DOFVector<double>* vec2 = NULL,
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
bool writeParallel = true,
#else
@@ -43,7 +43,7 @@ namespace AMDiS {
#endif
int nProcs = -1);
- static void read(string filename, Mesh *mesh,
+ static void read(string filename, Mesh *mesh,
vector<DOFVector<double>*> vecs,
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
bool writeParallel = true,
@@ -52,34 +52,59 @@ namespace AMDiS {
#endif
int nProcs = -1);
+ static void readFromMemoryBlock(vector<char> &data, Mesh *mesh,
+ DOFVector<double>* vec0 = NULL,
+ DOFVector<double>* vec1 = NULL,
+ DOFVector<double>* vec2 = NULL,
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ bool writeParallel = true,
+#else
+ bool writeParallel = false,
+#endif
+ int nProcs = -1);
+
+ static void readFromMemoryBlock(vector<char> &data, Mesh *mesh,
+ vector<DOFVector<double>*> vecs,
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ bool writeParallel = true,
+#else
+ bool writeParallel = false,
+#endif
+ int nProcs = -1);
+
static int getNumValueVectors(string filename)
- {
+ {
ifstream file;
file.open(filename.c_str(), ios::in | ios::binary);
string typeId = "";
uint32_t nMacroElements = 0;
uint32_t nValueVectors = 0;
- uint32_t nAllValues = 0;
+ //uint32_t 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);
+ //file.read(reinterpret_cast<char*>(&nAllValues), 4);
file.close();
-
+
return nValueVectors;
}
-
+
private:
- static void readFile(string filename,
+ static void readFile(string filename,
Mesh *mesh,
vector<DOFVector<double>*> vecs);
- static void setDofValues(int macroElIndex, Mesh *mesh,
+ static void setDofValues(int macroElIndex, Mesh *mesh,
vector<double>& values, DOFVector<double>* vec);
+
+ static void readBlock(vector<char> &data,
+ Mesh *mesh,
+ vector<DOFVector<double>*> vecs);
+
};
}
diff --git a/AMDiS/src/io/ArhWriter.cc b/AMDiS/src/io/ArhWriter.cc
index c06406f7beb9009ecc0601c374d28eda7a2f9bf3..b16c5f46233cd811a4f7f85747fe589b83665690 100644
--- a/AMDiS/src/io/ArhWriter.cc
+++ b/AMDiS/src/io/ArhWriter.cc
@@ -140,11 +140,13 @@ namespace AMDiS {
file.write(reinterpret_cast<char*>(&(const_cast<vector<uint64_t>&>(code.getCode())[0])),
8 * nStructureCodes);
- uint32_t nValuesPerVector = (values.size() > 0 ? values[0].size() : 0);
- file.write(reinterpret_cast<char*>(&nValuesPerVector), 4);
+ if(values.size() > 0){
+ uint32_t nValuesPerVector = values[0].size();
+ file.write(reinterpret_cast<char*>(&nValuesPerVector), 4);
- for (unsigned int i = 0; i < values.size(); i++)
- file.write(reinterpret_cast<char*>(&(values[i][0])), 8 * nValuesPerVector);
+ for (unsigned int i = 0; i < values.size(); i++)
+ file.write(reinterpret_cast<char*>(&(values[i][0])), 8 * nValuesPerVector);
+ }
}
}