From 7acfe3ad94a386c0a5be06d6afbb76fba141a442 Mon Sep 17 00:00:00 2001
From: Siqi Ling <lsq0473@gmail.com>
Date: Tue, 20 Oct 2015 16:02:02 +0000
Subject: [PATCH] add write tarh
---
AMDiS/src/io/Arh3Reader.h | 4 +++
AMDiS/src/io/FileWriter.cc | 14 ++++++++
AMDiS/src/io/FileWriter.h | 11 ++++++
AMDiS/src/io/FileWriter.hh | 5 ++-
AMDiS/src/io/detail/Arh3Reader.cc | 7 ++--
AMDiS/src/io/detail/Arh3Writer.cc | 56 +++++++++++++++++++++++++++++--
AMDiS/src/io/detail/Arh3Writer.h | 8 +++++
7 files changed, 98 insertions(+), 7 deletions(-)
diff --git a/AMDiS/src/io/Arh3Reader.h b/AMDiS/src/io/Arh3Reader.h
index ae73d1df..f83e6f9d 100644
--- a/AMDiS/src/io/Arh3Reader.h
+++ b/AMDiS/src/io/Arh3Reader.h
@@ -25,6 +25,10 @@ namespace AMDiS { namespace io {
{
const uint8_t MAJOR = 3;
const uint8_t MINOR = 0;
+ const uint8_t PARH_MAJOR = 1;
+ const uint8_t PARH_MINOR = 0;
+ const uint8_t TARH_MAJOR = 1;
+ const uint8_t TARH_MINOR = 0;
/**
* \brief Read MeshStructure, refine the mesh and read dof values to sysVec by order.
diff --git a/AMDiS/src/io/FileWriter.cc b/AMDiS/src/io/FileWriter.cc
index c2b39ee4..77e25e6a 100644
--- a/AMDiS/src/io/FileWriter.cc
+++ b/AMDiS/src/io/FileWriter.cc
@@ -197,6 +197,20 @@ namespace AMDiS
filename + ".pvd");
}
}
+
+ if (writeArhAnimation) {
+#if HAVE_PARALLEL_DOMAIN_AMDIS
+ if (MPI::COMM_WORLD.Get_rank() == 0)
+#endif
+ {
+ Arh3Writer::detail::updateAnimationFile(adaptInfo,
+ &arhAnimationFrames,
+ createSubDir > 0,
+ indexLength,
+ indexDecimals,
+ filename + ".tarh");
+ }
+ }
if (writeDofFormat) {
diff --git a/AMDiS/src/io/FileWriter.h b/AMDiS/src/io/FileWriter.h
index 2341b46f..5d9f845d 100644
--- a/AMDiS/src/io/FileWriter.h
+++ b/AMDiS/src/io/FileWriter.h
@@ -83,6 +83,11 @@ namespace AMDiS {
{
return paraviewAnimationFrames;
}
+
+ std::vector<double>& getArhAnimationFrames()
+ {
+ return arhAnimationFrames;
+ }
bool getWriteParaViewFormat() const
{
@@ -177,6 +182,9 @@ namespace AMDiS {
/// write Arh2 version 3.0, prior to writeArhFormat
int writeArh3;
+
+ /// 0: Don't write Arh animation file; 1: Write Arh animation file.
+ int writeArhAnimation;
/// camera position for povray script files
std::string povrayCameraLocation;
@@ -191,6 +199,9 @@ namespace AMDiS {
/// Stores a set of std::pairs of timepoint and filename to write a ParaView
/// animation file.
std::vector<std::pair<double, std::string> > paraviewAnimationFrames;
+
+ /// Stores a set of timepoint to write a ParaView animation file.
+ std::vector<double> arhAnimationFrames;
///
int timestepNumber;
diff --git a/AMDiS/src/io/FileWriter.hh b/AMDiS/src/io/FileWriter.hh
index b060e9ca..74ef0743 100644
--- a/AMDiS/src/io/FileWriter.hh
+++ b/AMDiS/src/io/FileWriter.hh
@@ -142,9 +142,11 @@ namespace AMDiS
writeArh1 = 0;
writeArh2 = 0;
writeArh3 = 0;
+ writeArhAnimation = 0;
pngType = 0;
nTmpSolutions = 0;
- paraviewAnimationFrames.resize(0),
+ paraviewAnimationFrames.resize(0);
+ arhAnimationFrames.resize(0);
compression = NONE;
readParameters(name);
@@ -181,6 +183,7 @@ namespace AMDiS
Parameters::get(name + "->ARH1 format", writeArh1);
Parameters::get(name + "->ARH2 format", writeArh2);
Parameters::get(name + "->ARH3 format", writeArh3);
+ Parameters::get(name + "->Arh animation", writeArhAnimation);
std::string compressionStr = "";
Parameters::get(name + "->compression", compressionStr);
diff --git a/AMDiS/src/io/detail/Arh3Reader.cc b/AMDiS/src/io/detail/Arh3Reader.cc
index 3cbe5b6c..38285fdb 100644
--- a/AMDiS/src/io/detail/Arh3Reader.cc
+++ b/AMDiS/src/io/detail/Arh3Reader.cc
@@ -573,7 +573,7 @@ namespace AMDiS { namespace io {
sPos = file_onlyname.string().find(".arh");
string onlynameWithoutExt = file_onlyname.string().substr(0, sPos);
string parh = filenameWithoutExt + ".parh";
- string basedir = "";
+ string basedir = "./";
path file_path = file_name.remove_filename();
int nProcs_ = 0, nMacros_ = 0, nMacros = 0;
@@ -583,8 +583,7 @@ namespace AMDiS { namespace io {
if (parhExists)
basedir = readParallelFile(parh, partition, nProcs_, nMacros_);
- if (basedir != "")
- filenameWithoutExt = file_path.string() + '/' + basedir + onlynameWithoutExt;
+ filenameWithoutExt = file_path.string() + '/' + basedir + onlynameWithoutExt;
if (nProcs == -1) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
@@ -848,7 +847,7 @@ namespace AMDiS { namespace io {
string Id = fd.substr(0, 4);
int major = boost::lexical_cast<int>(fd.substr(5, 1));
int minor = boost::lexical_cast<int>(fd.substr(7, 1));
- firstRead(Id, major, minor, "parh", 1, 0);
+ firstRead(Id, major, minor, "parh", PARH_MAJOR, PARH_MINOR);
uint32_t baseDirLen = 0, macroFile_nl = 0;
string baseDir, macroFilename;
diff --git a/AMDiS/src/io/detail/Arh3Writer.cc b/AMDiS/src/io/detail/Arh3Writer.cc
index 6d010420..1ba137c4 100644
--- a/AMDiS/src/io/detail/Arh3Writer.cc
+++ b/AMDiS/src/io/detail/Arh3Writer.cc
@@ -10,7 +10,9 @@
#include "DOFVector.h"
#include "../Arh3Reader.h"
+#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filtering_streambuf.hpp>
+#include <boost/iostreams/device/file_descriptor.hpp>
#include <boost/iostreams/copy.hpp>
#ifdef HAVE_COMPRESSION
#include <boost/iostreams/filter/zlib.hpp>
@@ -44,6 +46,55 @@ namespace AMDiS { namespace io {
write(filename, NULL, vecs, writeParallel, cps, dataformat, writeMacro);
}
+
+ void updateAnimationFile(AdaptInfo *adaptInfo,
+ std::vector<double>* arhAnimationFrames,
+ bool createSubDir,
+ int indexLength,
+ int indexDecimals,
+ std::string animationFilename)
+ {
+ FUNCNAME("updateAnimationFile()");
+
+ arhAnimationFrames->push_back(adaptInfo->getTime());
+
+ boost::iostreams::filtering_ostream file;
+ {
+ ofstream swapfile(animationFilename.c_str(),
+ ios::out | ios::trunc | ios::binary);
+ TEST_EXIT(swapfile.is_open())
+ ("Cannot open file %s for writing!\n", animationFilename.c_str());
+ swapfile.close();
+ }
+ file.push(boost::iostreams::file_descriptor_sink(animationFilename,
+ ios::trunc | ios::binary));
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ string typeId = "tparh";
+#else
+ string typeId = "tarh";
+#endif
+ string baseDir = createSubDir ? "./data/" : "./";
+ uint32_t baseDirLen = baseDir.length();
+ int major = AMDiS::io::Arh3Reader::TARH_MAJOR;
+ int minor = AMDiS::io::Arh3Reader::TARH_MINOR;
+ typeId += '_' + boost::lexical_cast<string>(major) + '.' + boost::lexical_cast<string>(minor);
+ if (typeId.length() <= 16) { // 16 is the Id size
+ string rest(16 - typeId.length(), ' ');
+ typeId.append(rest);
+ }
+ uint32_t indexLength_ = indexLength;
+ uint32_t indexDecimals_ = indexDecimals;
+
+ file.write(typeId.c_str(), 16);
+ file.write(reinterpret_cast<char*>(&baseDirLen), 4);
+ file.write(baseDir.c_str(), baseDirLen);
+ file.write(reinterpret_cast<char*>(&indexLength_), 4);
+ file.write(reinterpret_cast<char*>(&indexDecimals_), 4);
+
+ for (size_t i = 0; i < arhAnimationFrames->size(); i++)
+ file.write(reinterpret_cast<char*>(&arhAnimationFrames[i]), 8);
+ }
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
void writeParallelFile(string filename, Mesh* mesh, bool createSubDir, bool writeMacro)
@@ -52,13 +103,14 @@ namespace AMDiS { namespace io {
file.open(filename.c_str(), ios::out | ios::binary | ios::trunc);
string typeId = "parh", macroFilename = "", perFilename = "";
- string baseDir = createSubDir ? "./data/" : "";
+ string baseDir = createSubDir ? "./data/" : "./";
string macroData = "", periodicData = "";
uint32_t baseDirLen = baseDir.length();
Parameters::get(mesh->getName() + "->macro file name", macroFilename);
Parameters::get(mesh->getName() + "->periodic file", perFilename);
- int major = 1, minor = 0;
+ 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 =
diff --git a/AMDiS/src/io/detail/Arh3Writer.h b/AMDiS/src/io/detail/Arh3Writer.h
index 6e46649d..fdc36077 100644
--- a/AMDiS/src/io/detail/Arh3Writer.h
+++ b/AMDiS/src/io/detail/Arh3Writer.h
@@ -6,6 +6,7 @@
#include "MeshStructure.h"
#include "DOFVector.h"
#include "SystemVector.h"
+#include "AdaptInfo.h"
#include "boost/assign.hpp"
namespace AMDiS { namespace io {
@@ -111,6 +112,13 @@ namespace AMDiS { namespace io {
void readFileToString(std::string filename, std::string& data);
+ void updateAnimationFile(AdaptInfo *adaptInfo,
+ std::vector<double>* arhAnimationFrames,
+ bool createSubDir,
+ int indexLength,
+ int indexDecimals,
+ std::string animationFilename);
+
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
void writeParallelFile(std::string filename,
Mesh* mesh,
--
GitLab