From 1641e7938e55776b48bedf19745900024d971f69 Mon Sep 17 00:00:00 2001
From: Siqi Ling <lsq0473@gmail.com>
Date: Wed, 21 Oct 2015 12:13:45 +0000
Subject: [PATCH] change in arh, parh file. update with meshconv
---
AMDiS/src/io/Arh3Writer.h | 28 +++----
AMDiS/src/io/detail/Arh3Reader.cc | 38 ++++-----
AMDiS/src/io/detail/Arh3Writer.cc | 134 +++++++++++++++++++-----------
AMDiS/src/io/detail/Arh3Writer.h | 48 +++++++----
4 files changed, 152 insertions(+), 96 deletions(-)
diff --git a/AMDiS/src/io/Arh3Writer.h b/AMDiS/src/io/Arh3Writer.h
index 4312209b..9f286e87 100644
--- a/AMDiS/src/io/Arh3Writer.h
+++ b/AMDiS/src/io/Arh3Writer.h
@@ -6,9 +6,9 @@
#include "detail/Arh3Writer.h"
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-#define WRITE_MACRO false
+#define WRITE_MACRO Macroformat::NONE
#else
-#define WRITE_MACRO true
+#define WRITE_MACRO Macroformat::PT_MACROFILE
#endif
namespace AMDiS { namespace io {
@@ -50,9 +50,9 @@ namespace AMDiS { namespace io {
inline void writeFile(SystemVector *sysVec,
std::string filename,
bool writeParallel = true,
- Cpsformat cps = NONE,
+ Cpsformat::Value cps = Cpsformat::NONE,
std::string dataformat = "SF64",
- bool writeMacro = WRITE_MACRO)
+ Macroformat::Value writeMacro = WRITE_MACRO)
{
std::vector<DOFVector<double>*> vecs;
for (int i = 0; i < sysVec->getSize(); i++)
@@ -63,9 +63,9 @@ namespace AMDiS { namespace io {
inline void writeFile(SystemVector &sysVec,
std::string filename,
bool writeParallel = true,
- Cpsformat cps = NONE,
+ Cpsformat::Value cps = Cpsformat::NONE,
std::string dataformat = "SF64",
- bool writeMacro = WRITE_MACRO)
+ Macroformat::Value writeMacro = WRITE_MACRO)
{
writeFile(&sysVec, filename, writeParallel, cps, dataformat, writeMacro);
}
@@ -75,9 +75,9 @@ namespace AMDiS { namespace io {
inline void writeFile(DOFVector<double>* vec0,
std::string filename,
bool writeParallel = true,
- Cpsformat cps = NONE,
+ Cpsformat::Value cps = Cpsformat::NONE,
std::string dataformat = "SF64",
- bool writeMacro = WRITE_MACRO)
+ Macroformat::Value writeMacro = WRITE_MACRO)
{
std::vector<DOFVector<double>*> vecs;
vecs.push_back(vec0);
@@ -89,9 +89,9 @@ namespace AMDiS { namespace io {
inline void writeFile(DOFVector<double>& vec0,
std::string filename,
bool writeParallel = true,
- Cpsformat cps = NONE,
+ Cpsformat::Value cps = Cpsformat::NONE,
std::string dataformat = "SF64",
- bool writeMacro = WRITE_MACRO)
+ Macroformat::Value writeMacro = WRITE_MACRO)
{
writeFile(&vec0, filename, writeParallel, cps, dataformat, writeMacro);
}
@@ -101,9 +101,9 @@ namespace AMDiS { namespace io {
inline void writeFile(std::vector<DOFVector<double>*> vecs,
std::string filename,
bool writeParallel = true,
- Cpsformat cps = NONE,
+ Cpsformat::Value cps = Cpsformat::NONE,
std::string dataformat = "SF64",
- bool writeMacro = WRITE_MACRO)
+ Macroformat::Value writeMacro = WRITE_MACRO)
{
detail::write(filename, NULL, vecs, writeParallel, cps, dataformat, writeMacro);
}
@@ -112,9 +112,9 @@ namespace AMDiS { namespace io {
inline void writeFile(Mesh *mesh,
std::string filename,
bool writeParallel = true,
- Cpsformat cps = NONE,
+ Cpsformat::Value cps = Cpsformat::NONE,
std::string dataformat = "SF64",
- bool writeMacro = WRITE_MACRO)
+ Macroformat::Value writeMacro = WRITE_MACRO)
{
std::vector<DOFVector<double>*> vecs;
detail::write(filename, mesh, vecs, writeParallel, cps, dataformat, writeMacro);
diff --git a/AMDiS/src/io/detail/Arh3Reader.cc b/AMDiS/src/io/detail/Arh3Reader.cc
index 38285fdb..99958000 100644
--- a/AMDiS/src/io/detail/Arh3Reader.cc
+++ b/AMDiS/src/io/detail/Arh3Reader.cc
@@ -228,7 +228,7 @@ namespace AMDiS { namespace io {
TEST_EXIT(file.is_open())
("Cannot open file %s\n", filename.c_str());
- Cpsformat cps = NONE;
+ Cpsformat::Value cps = Cpsformat::NONE;
uint32_t headerLen = 0;
uint32_t nMacroElements = 0;
uint32_t nValueVectors = 0;
@@ -246,15 +246,15 @@ namespace AMDiS { namespace io {
file.read(reinterpret_cast<char*>(&nValueVectors), 4);
file.read(reinterpret_cast<char*>(&nMacroElements), 4);
file.read(reinterpret_cast<char*>(&cpsflag), 4);
- cps = static_cast<Cpsformat>(cpsflag);
+ cps = static_cast<Cpsformat::Value>(cpsflag);
#ifdef HAVE_COMPRESSION
- TEST_EXIT(cps == ZLIB ||
- cps == BZIP2 ||
- cps == NONE)
+ TEST_EXIT(cps == Cpsformat::ZLIB ||
+ cps == Cpsformat::BZIP2 ||
+ cps == Cpsformat::NONE)
("Cannot read Arh2 file. Currently only support zlib and bzip2 compression.\n");
#else
- TEST_EXIT(cps == NONE)
+ TEST_EXIT(cps == Cpsformat::NONE)
("HAVE_COMPRESSION OFF. Cannot read compressed Arh2 file.\n");
#endif
@@ -323,7 +323,7 @@ namespace AMDiS { namespace io {
dataformat.push_back(tmpString);
}
- // Read macroFile_nl
+ // Read macroFile_nl //TODO
uint32_t macroFile_nl = 0;
file.read(reinterpret_cast<char*>(¯oFile_nl), 4);
if (macroFile_nl > 0) {
@@ -412,13 +412,13 @@ namespace AMDiS { namespace io {
boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
switch(cps)
{
- case ZLIB:
+ case Cpsformat::ZLIB:
in.push(boost::iostreams::zlib_decompressor());
break;
- case BZIP2:
+ case Cpsformat::BZIP2:
in.push(boost::iostreams::bzip2_decompressor());
break;
- case NONE:
+ case Cpsformat::NONE:
break;
default:
MSG("NOT correct compression flag.\n");
@@ -662,7 +662,7 @@ namespace AMDiS { namespace io {
uint32_t nValueVectors = 0;
uint32_t nFeSpaces = 0;
int cpsflag = 0, fileSize = 0;
- Cpsformat cps = NONE;
+ Cpsformat::Value cps = Cpsformat::NONE;
firstRead(file, "sarh", MAJOR, MINOR);
@@ -673,12 +673,12 @@ namespace AMDiS { namespace io {
file.read(reinterpret_cast<char*>(&nValueVectors), 4);
file.read(reinterpret_cast<char*>(&nMacroElements), 4);
file.read(reinterpret_cast<char*>(&cpsflag), 4);
- cps = static_cast<Cpsformat>(cpsflag);
+ cps = static_cast<Cpsformat::Value>(cpsflag);
#ifdef HAVE_COMPRESSION
- TEST_EXIT(cps == ZLIB ||
- cps == BZIP2 ||
- cps == NONE)
+ TEST_EXIT(cps == Cpsformat::ZLIB ||
+ cps == Cpsformat::BZIP2 ||
+ cps == Cpsformat::NONE)
("Cannot read Arh2 file. Currently only support zlib and bzip2 compression.\n");
#else
TEST_EXIT(cps == NONE)
@@ -746,13 +746,13 @@ namespace AMDiS { namespace io {
boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
switch(cps)
{
- case ZLIB:
+ case Cpsformat::ZLIB:
in.push(boost::iostreams::zlib_decompressor());
break;
- case BZIP2:
+ case Cpsformat::BZIP2:
in.push(boost::iostreams::bzip2_decompressor());
break;
- case NONE:
+ case Cpsformat::NONE:
break;
default:
MSG("NOT correct compression flag.\n");
@@ -857,7 +857,7 @@ namespace AMDiS { namespace io {
file.read(const_cast<char*>(baseDir.data()), baseDirLen);
file.read(reinterpret_cast<char*>(&nFiles), 4);
file.read(reinterpret_cast<char*>(¯oFile_nl), 4);
- if (macroFile_nl > 0) {
+ if (macroFile_nl > 0) { //TODO
macroFilename.resize(macroFile_nl, ' ');
file.read(const_cast<char*>(macroFilename.data()), macroFile_nl);
}
diff --git a/AMDiS/src/io/detail/Arh3Writer.cc b/AMDiS/src/io/detail/Arh3Writer.cc
index 1ba137c4..e3675fc3 100644
--- a/AMDiS/src/io/detail/Arh3Writer.cc
+++ b/AMDiS/src/io/detail/Arh3Writer.cc
@@ -32,9 +32,9 @@ namespace AMDiS { namespace io {
DOFVector<double>* vec1,
DOFVector<double>* vec2,
bool writeParallel,
- Cpsformat cps,
+ Cpsformat::Value cps,
string dataformat,
- bool writeMacro)
+ Macroformat::Value writeMacro)
{
vector<DOFVector<double>*> vecs(0);
if (vec0 != NULL)
@@ -97,22 +97,24 @@ namespace AMDiS { namespace io {
}
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- void writeParallelFile(string filename, Mesh* mesh, bool createSubDir, bool writeMacro)
+ void writeParallelFile(string filename, Mesh* mesh, bool createSubDir, Macroformat::Value writeMacro)
{
ofstream file;
file.open(filename.c_str(), ios::out | ios::binary | ios::trunc);
string typeId = "parh", macroFilename = "", perFilename = "";
string baseDir = createSubDir ? "./data/" : "./";
+ string macroFile = "";
+ uint32_t macroFile_nl = 0;
string macroData = "", periodicData = "";
uint32_t baseDirLen = baseDir.length();
Parameters::get(mesh->getName() + "->macro file name", macroFilename);
Parameters::get(mesh->getName() + "->periodic file", perFilename);
+ bool hasPeriodic = perFilename.length();
int major = AMDiS::io::Arh3Reader::PARH_MAJOR;
int minor = AMDiS::io::Arh3Reader::PARH_MINOR;
uint32_t nFiles = MPI::COMM_WORLD.Get_size();
- uint32_t macroFile_nl = 0;
map<int, int> partitionMap =
Parallel::MeshDistributor::globalMeshDistributor->getPartitionMap();
uint32_t nMacros = partitionMap.size();
@@ -130,16 +132,26 @@ namespace AMDiS { namespace io {
file.write(baseDir.c_str(), baseDirLen);
file.write(reinterpret_cast<char*>(&nFiles), 4);
- if (writeMacro && macroFilename.length()) {
- macroFile_nl = 13;
- readFileToString(macroFilename, macroData);
+ if (writeMacro != Macroformat::NONE && macroFilename.length()) {
- if (perFilename.length()) {
- macroFile_nl = 27;
- readFileToString(perFilename, periodicData);
+ if (writeMacro == Macroformat::PT_MACROFILE) {
+ macroFile = !hasPeriodic ? macroFilename :
+ macroFilename + ';' + perFilename;
+
+ macroFile_nl = macroFile.length();
+ } else if (writeMacro == Macroformat::THIS) {
+ macroFile_nl = 13;
+ readFileToString(macroFilename, macroData);
+
+ if (hasPeriodic) {
+ macroFile_nl = 27;
+ readFileToString(perFilename, periodicData);
+ }
+ macroFile.resize(macroFile_nl, ' ');
}
}
file.write(reinterpret_cast<char*>(¯oFile_nl), 4);
+ file.write(macroFile.c_str(), macroFile_nl);
file.write(reinterpret_cast<char*>(&nMacros), 4);
map<int, int>::const_iterator it = partitionMap.begin();
@@ -150,12 +162,12 @@ namespace AMDiS { namespace io {
}
// write macro and periodic file
- if (writeMacro && macroFilename.length()) {
+ if (writeMacro == Macroformat::THIS && macroFilename.length()) {
file.seekp(0, ios_base::end);
long macroPos = file.tellp(), perPos = 0;
file.write(macroData.c_str(), macroData.length());
- if (perFilename.length()) {
+ if (hasPeriodic) {
perPos = file.tellp();
file.write(periodicData.c_str(), periodicData.length());
}
@@ -167,9 +179,12 @@ namespace AMDiS { namespace io {
4 + //nFiles
4; //macroFile_nl
file.seekp(offset);
- file << "this:" << macroPos;
- if (perFilename.length())
- file << ";this:" << perPos;
+ file.write("this:", 5);
+ file.write(reinterpret_cast<char*>(¯oPos), 8);
+ if (hasPeriodic) {
+ file.write(";this:", 6);
+ file.write(reinterpret_cast<char*>(&perPos), 8);
+ }
}
}
#endif
@@ -178,9 +193,9 @@ namespace AMDiS { namespace io {
Mesh* mesh,
vector<DOFVector<double>*> vecs,
bool writeParallel,
- Cpsformat cps,
+ Cpsformat::Value cps,
string dataformat,
- bool writeMacro)
+ Macroformat::Value writeMacro)
{
FUNCNAME("Arh3Writer::detail::write()");
@@ -257,8 +272,9 @@ namespace AMDiS { namespace io {
Mesh *mesh,
vector<DOFVector<double>*> vecs,
map<const FiniteElemSpace*, vector<int> >& feSpaces,
- Cpsformat cps,
- string dataformat)
+ Cpsformat::Value cps,
+ string dataformat,
+ Macroformat::Value writeMacro)
{
FUNCNAME("Arh3Writer::detail::writeHeader()");
// int nbits = boost::lexical_cast<int>(dataformat.substr(2, 2));
@@ -286,7 +302,26 @@ namespace AMDiS { namespace io {
el = st.traverseNext(el);
}
- uint32_t dow = mesh->getGeo(WORLD);
+ string macroFilename = "", perFilename = "";
+ string macroFile = "";
+ uint32_t macroFile_nl = 0;
+ Parameters::get(mesh->getName() + "->macro file name", macroFilename);
+ Parameters::get(mesh->getName() + "->periodic file", perFilename);
+
+ if (writeMacro != Macroformat::NONE && macroFilename.length()) {
+
+ if (writeMacro == Macroformat::PT_MACROFILE) {
+ macroFile = !perFilename.length() ? macroFilename :
+ macroFilename + ';' + perFilename;
+
+ macroFile_nl = macroFile.length();
+ } else if (writeMacro == Macroformat::THIS) {
+ macroFile_nl = perFilename.length() ? 27 : 13;
+ macroFile.resize(macroFile_nl, ' ');
+ }
+ }
+
+ uint32_t dow = mesh->getGeo(WORLD);
uint32_t dim = mesh->getDim();
uint32_t headerLen = 34 + //fixed part of header
nMacroElements * 12 + 12 + //macroElemnts table
@@ -294,7 +329,8 @@ namespace AMDiS { namespace io {
nFeSpaces * 20 + //feSpaces table
valueNamesLen + //value vector table
nValueVectors * 12 + //also value vector table
- 4; //macroFile_nl
+ 4 + //macroFile_nl
+ macroFile_nl; //macroFile
string typeId = "sarh";
#ifndef HAVE_COMPRESSION
cps = NONE;
@@ -370,17 +406,17 @@ namespace AMDiS { namespace io {
file.write(dataformat.c_str(), 4);
}
- uint32_t macroFile_nl = 0;
file.write(reinterpret_cast<char*>(¯oFile_nl), 4);
+ file.write(macroFile.c_str(), macroFile_nl);
return headerLen;
}
void writeAux(string filename, Mesh *mesh,
vector<DOFVector<double>*> vecs,
bool writeParallel,
- Cpsformat cps,
+ Cpsformat::Value cps,
string dataformat,
- bool writeMacro)
+ Macroformat::Value writeMacro)
{
FUNCNAME("Arh3Writer::detail::writeAux()");
@@ -404,7 +440,7 @@ namespace AMDiS { namespace io {
vector<std::set<DegreeOfFreedom> > visited(sortedFeSpaces.size());
pair<std::set<DegreeOfFreedom>::iterator,bool> ret;
//file header information
- int headerLen = writeHeader(file, mesh, vecs, sortedFeSpaces, cps, dataformat);
+ int headerLen = writeHeader(file, mesh, vecs, sortedFeSpaces, cps, dataformat, writeMacro);
//macro elements information
MeshStructure elementStructure;
@@ -528,8 +564,10 @@ namespace AMDiS { namespace io {
TEST_EXIT(macroSize.size() == (unsigned)mesh->getNumberOfMacros())("Should not happen.\n");
//reset the macro positions in file
setMacrosPos(file, headerLen, macroSize);
- if (writeMacro)
- setMacroFile(file, headerLen, mesh);
+
+ if (writeMacro == Macroformat::THIS)
+ setMacroFile(file, headerLen, mesh, writeMacro);
+
file.close();
MSG("ARH file written to: %s\n", filename.c_str());
}
@@ -553,18 +591,22 @@ namespace AMDiS { namespace io {
file.write(reinterpret_cast<char*>(&startPos), 4);
}
- void setMacroFile(std::ofstream& file, int headerLen, Mesh* mesh)
+ void setMacroFile(std::ofstream& file, int headerLen, Mesh* mesh, Macroformat::Value writeMacro)
{
+ FUNCNAME("setMacroFile()");
+
+ TEST_EXIT(writeMacro == Macroformat::THIS)
+ ("This function should only be called under Macroformat::THIS.\n");
+
string macroFilename = "", perFilename = "";
string macroData = "", periodicData = "";
Parameters::get(mesh->getName() + "->macro file name", macroFilename);
Parameters::get(mesh->getName() + "->periodic file", perFilename);
+ bool hasPeriodic = perFilename.length();
- if (!macroFilename.length()) {
- WARNING("macro file not found.\n");
+ if (!macroFilename.length())
return;
- }
// write macro file to the end
readFileToString(macroFilename, macroData);
@@ -573,24 +615,22 @@ namespace AMDiS { namespace io {
file.write(macroData.c_str(), macroData.length());
// write periodic file to the end
- if (perFilename.length()) {
+ if (hasPeriodic) {
readFileToString(perFilename, periodicData);
perPos = file.tellp();
file.write(periodicData.c_str(), periodicData.length());
}
// update macroFile_nl
- uint32_t macroFile_nl = perFilename.length() ? 27 : 13;
- file.seekp(headerLen - 4);
- file.write(reinterpret_cast<char*>(¯oFile_nl), 4);
- file << "this:" << macroPos;
- if (perFilename.length())
- file << ";this:" << perPos;
-
- // update headerLen
- headerLen += macroFile_nl;
- file.seekp(6);
- file.write(reinterpret_cast<char*>(&headerLen), 4);
+ int offset = hasPeriodic ? 27 : 13;
+ file.seekp(headerLen - offset);
+
+ file.write("this:", 5);
+ file.write(reinterpret_cast<char*>(¯oPos), 8);
+ if (hasPeriodic) {
+ file.write(";this:", 6);
+ file.write(reinterpret_cast<char*>(&perPos), 8);
+ }
}
void readFileToString(std::string filename, std::string& data)
@@ -606,7 +646,7 @@ namespace AMDiS { namespace io {
MeshStructure &code,
vector<vector<double> >& values,
map<const FiniteElemSpace*, vector<int> >& feSpaces,
- Cpsformat cps,
+ Cpsformat::Value cps,
string dataformat)
{
stringstream dataStream(ios::out | ios::in | ios::binary);
@@ -640,13 +680,13 @@ namespace AMDiS { namespace io {
#ifdef HAVE_COMPRESSION
switch(cps)
{
- case ZLIB:
+ case Cpsformat::ZLIB:
in.push(boost::iostreams::zlib_compressor());
break;
- case BZIP2:
+ case Cpsformat::BZIP2:
in.push(boost::iostreams::bzip2_compressor());
break;
- case NONE:
+ case Cpsformat::NONE:
break;
default:
MSG("NOT correct compression flag.\n");
diff --git a/AMDiS/src/io/detail/Arh3Writer.h b/AMDiS/src/io/detail/Arh3Writer.h
index fdc36077..66f003e8 100644
--- a/AMDiS/src/io/detail/Arh3Writer.h
+++ b/AMDiS/src/io/detail/Arh3Writer.h
@@ -13,11 +13,23 @@ namespace AMDiS { namespace io {
namespace Arh3Writer
{
- typedef enum{
- NONE = 0,
- ZLIB = 1,
- BZIP2 = 2
- } Cpsformat;
+ namespace Cpsformat
+ {
+ typedef enum{
+ NONE = 0, // no compression
+ ZLIB = 1, // zlib compression
+ BZIP2 = 2 // bzip2 compression
+ } Value;
+ };
+
+ namespace Macroformat
+ {
+ typedef enum{
+ NONE = 0, // no macro
+ PT_MACROFILE = 1, // pointer to macro file
+ THIS = 2 // pointer to this file, at the end of this file
+ } Value;
+ };
typedef enum{SI08, SI16, SI32, SI64, UI08, UI16, UI32, UI64, SF32, SF64} Valformat;
@@ -42,9 +54,9 @@ namespace AMDiS { namespace io {
DOFVector<double>* vec1 = NULL,
DOFVector<double>* vec2 = NULL,
bool writeParallel = true,
- Cpsformat cps = NONE,
+ Cpsformat::Value cps = Cpsformat::NONE,
std::string dataformat = "SF64",
- bool writeMacro = false);
+ Macroformat::Value writeMacro = Macroformat::NONE);
/**
* \ingroup Output
@@ -70,15 +82,15 @@ namespace AMDiS { namespace io {
Mesh* mesh,
std::vector<DOFVector<double>*> vecs,
bool writeParallel = true,
- Cpsformat cps = NONE,
+ Cpsformat::Value cps = Cpsformat::NONE,
std::string dataformat = "SF64",
- bool writeMacro = false);
+ Macroformat::Value writeMacro = Macroformat::NONE);
void writeAux(std::string filename, Mesh *mesh,
std::vector<DOFVector<double>*> vecs,
- bool writeParallel, Cpsformat cps,
+ bool writeParallel, Cpsformat::Value cps,
std::string dataformat,
- bool writeMacro = false);
+ Macroformat::Value writeMacro = Macroformat::NONE);
///\return the size of the macro block in file
std::pair<int, int> writeMacroElement(std::ofstream &file,
@@ -86,7 +98,7 @@ namespace AMDiS { namespace io {
std::vector<std::vector<double> >& values,
std::map<const FiniteElemSpace*,
std::vector<int> >& feSpaces,
- Cpsformat cps, std::string dataformat);
+ Cpsformat::Value cps, std::string dataformat);
int writeValues(std::stringstream& file,
std::string dataformat,
@@ -100,15 +112,19 @@ namespace AMDiS { namespace io {
std::vector<DOFVector<double>*> vecs,
std::map<const FiniteElemSpace*,
std::vector<int> >& feSpaces,
- Cpsformat cps,
- std::string dataformat);
+ Cpsformat::Value cps,
+ std::string dataformat,
+ Macroformat::Value writeMacro);
///internal method, don't call
void setMacrosPos(std::ofstream& file, int headerLen,
std::vector<std::pair<int, int> >& macroSize);
///internal method, don't call
- void setMacroFile(std::ofstream& file, int headerLen, Mesh* mesh);
+ void setMacroFile(std::ofstream& file,
+ int headerLen,
+ Mesh* mesh,
+ Macroformat::Value writeMacro);
void readFileToString(std::string filename, std::string& data);
@@ -123,7 +139,7 @@ namespace AMDiS { namespace io {
void writeParallelFile(std::string filename,
Mesh* mesh,
bool createSubDir,
- bool writeMacro = true);
+ Macroformat::Value writeMacro = Macroformat::NONE);
#endif
}//end namespace detail
} // end namespace Arh3Writer
--
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