Arh3Writer.cc 24.5 KB
Newer Older
Siqi Ling's avatar
Siqi Ling committed
1
2
3
#include <fstream>
#include <stdint.h>
#include <iostream>
4
#include <streambuf>
Siqi Ling's avatar
Siqi Ling committed
5
6
7
8
9
10
11
12

#include "Arh3Writer.h"
#include "Mesh.h"
#include "MeshStructure.h"
#include "Traverse.h"
#include "DOFVector.h"
#include "../Arh3Reader.h"

Siqi Ling's avatar
Siqi Ling committed
13
#include <boost/iostreams/filtering_stream.hpp>
Siqi Ling's avatar
Siqi Ling committed
14
#include <boost/iostreams/filtering_streambuf.hpp>
Siqi Ling's avatar
Siqi Ling committed
15
#include <boost/iostreams/device/file_descriptor.hpp>
Siqi Ling's avatar
Siqi Ling committed
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
#include <boost/iostreams/copy.hpp>
#ifdef HAVE_COMPRESSION
#include <boost/iostreams/filter/zlib.hpp>
#include <boost/iostreams/filter/bzip2.hpp>
#endif

namespace AMDiS { namespace io {
  
  using namespace std;

  namespace Arh3Writer
  {
    namespace detail
    {
      void write(string filename, 
  			DOFVector<double>* vec0, 
  			DOFVector<double>* vec1,
  			DOFVector<double>* vec2,
			bool writeParallel,
			Cpsformat cps,
			string dataformat,
37
			bool writeMacro)
Siqi Ling's avatar
Siqi Ling committed
38
39
40
41
42
43
44
45
46
      {
        vector<DOFVector<double>*> vecs(0);
        if (vec0 != NULL)
          vecs.push_back(vec0);
        if (vec1 != NULL)
          vecs.push_back(vec1);
        if (vec2 != NULL)
          vecs.push_back(vec2);

47
        write(filename, NULL, vecs, writeParallel, cps, dataformat, writeMacro);
Siqi Ling's avatar
Siqi Ling committed
48
      }
Siqi Ling's avatar
Siqi Ling committed
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
      
      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);
      }
Siqi Ling's avatar
Siqi Ling committed
98
99
  
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS  
100
      void writeParallelFile(string filename, Mesh* mesh, bool createSubDir, bool writeMacro)
Siqi Ling's avatar
Siqi Ling committed
101
102
103
104
      {
	ofstream file;
        file.open(filename.c_str(), ios::out | ios::binary | ios::trunc);
	
105
	string typeId = "parh", macroFilename = "", perFilename = "";
Siqi Ling's avatar
Siqi Ling committed
106
	string baseDir = createSubDir ?  "./data/" : "./";
107
108
	string macroData = "", periodicData = "";
	uint32_t baseDirLen = baseDir.length();
Siqi Ling's avatar
Siqi Ling committed
109
	Parameters::get(mesh->getName() + "->macro file name", macroFilename);
110
111
	Parameters::get(mesh->getName() + "->periodic file", perFilename);
	
Siqi Ling's avatar
Siqi Ling committed
112
113
	int major = AMDiS::io::Arh3Reader::PARH_MAJOR; 
        int minor = AMDiS::io::Arh3Reader::PARH_MINOR;
Siqi Ling's avatar
Siqi Ling committed
114
	uint32_t nFiles = MPI::COMM_WORLD.Get_size();
115
	uint32_t macroFile_nl = 0;
Siqi Ling's avatar
Siqi Ling committed
116
117
	map<int, int> partitionMap = 
	  Parallel::MeshDistributor::globalMeshDistributor->getPartitionMap();
118
119
120
121
122
123
124
125
126
127
128
129
130
	uint32_t nMacros = partitionMap.size();
	
	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);
	}
	else
	  ERROR_EXIT("Should not happen.\n");
	
	file.write(typeId.c_str(), 16);
	file.write(reinterpret_cast<char*>(&baseDirLen), 4);
	file.write(baseDir.c_str(), baseDirLen);
Siqi Ling's avatar
Siqi Ling committed
131
	file.write(reinterpret_cast<char*>(&nFiles), 4);
132
133
134
135
136
137
138
139
140
141
	
	if (writeMacro && macroFilename.length()) {
	  macroFile_nl = 13;
	  readFileToString(macroFilename, macroData);
	  
	  if (perFilename.length()) {
	    macroFile_nl = 27;
	    readFileToString(perFilename, periodicData);
	  }
	}
Siqi Ling's avatar
Siqi Ling committed
142
	file.write(reinterpret_cast<char*>(&macroFile_nl), 4);
143
	file.write(reinterpret_cast<char*>(&nMacros), 4);
Siqi Ling's avatar
Siqi Ling committed
144
145
146
147
148
149
150
	
	map<int, int>::const_iterator it = partitionMap.begin();
	uint32_t rank = 0;
	for (;it != partitionMap.end(); it++) {
	  rank = it->second;
	  file.write(reinterpret_cast<char*>(&rank), 4);
	}
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
	
	// write macro and periodic file
	if (writeMacro && macroFilename.length()) {
	  file.seekp(0, ios_base::end);
	  long macroPos = file.tellp(), perPos = 0;
	  file.write(macroData.c_str(), macroData.length());
	  
	  if (perFilename.length()) {
	    perPos = file.tellp();
	    file.write(periodicData.c_str(), periodicData.length());
	  }
	  
	  // update macroFile_nl
	  int offset = 16 +		//typeId
		       4 +		//baseDirLen
		       baseDirLen +	//baseDir
		       4 +		//nFiles
		       4;		//macroFile_nl
	  file.seekp(offset);
	  file << "this:" << macroPos;
	  if (perFilename.length())
	    file << ";this:" << perPos;
	}
Siqi Ling's avatar
Siqi Ling committed
174
175
176
177
178
179
180
181
182
      }
#endif

      void write(string filename, 
		 Mesh* mesh, 
		 vector<DOFVector<double>*> vecs,
		 bool writeParallel,
		 Cpsformat cps,
		 string dataformat,
183
		 bool writeMacro)
Siqi Ling's avatar
Siqi Ling committed
184
185
186
187
188
189
      {
	FUNCNAME("Arh3Writer::detail::write()");
	
	map<string,Valformat>::const_iterator it = dataformatMap.find(dataformat);
	TEST_EXIT(it != dataformatMap.end())("Wrong data format.\n");
	
190
191
192
193
194
	std::set<Mesh*> meshset;
	std::set<string> nameset;
	if (mesh)
	  meshset.insert(mesh);
	for (size_t i = 0; i < vecs.size(); i++) {
Siqi Ling's avatar
Siqi Ling committed
195
	  TEST_EXIT(vecs[i] != NULL)("Vecs[%i] is NULL. Please check.\n", i);
196
197
198
	  meshset.insert(vecs[i]->getFeSpace()->getMesh());
	  nameset.insert(vecs[i]->getName());
	}
Siqi Ling's avatar
Siqi Ling committed
199
	  
200
201
202
	if (meshset.size() == 0) {
	  WARNING("There is nothing to be writen.\n");
	  return;
Siqi Ling's avatar
Siqi Ling committed
203
	}
204
205
206
207
208
209
	
	TEST_EXIT(nameset.size() == vecs.size())
	  ("DOFVectors in vecs cannot have idential name. Please check.\n");
	
	bool multiMesh = meshset.size() > 1;
	
Siqi Ling's avatar
Siqi Ling committed
210
	//if mesh exists, the meshes in vecs should be the same.
211
212
	if (mesh) {
	  for (size_t i = 0; i < vecs.size(); i++)
Siqi Ling's avatar
Siqi Ling committed
213
	    TEST_EXIT(mesh == vecs[i]->getFeSpace()->getMesh())
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
	      ("The mesh of DOFVector %i in vecs is not equal to the second parameter.\n", i);
	  writeAux(filename, mesh, vecs, writeParallel, cps, dataformat, writeMacro); 
	} else {
	  if (!multiMesh)
	    writeAux(filename, vecs[0]->getFeSpace()->getMesh(), vecs, writeParallel, cps, dataformat, writeMacro); 
	  else {
	    vector<bool> visited(vecs.size(), false);
	    vector<DOFVector<double>*> splitedVecs(0);
	    Mesh* tmpMesh = NULL;
	  
	    for(size_t i = 0; i < vecs.size(); i++) {
	      if(!visited[i]) {
		splitedVecs.clear();
		splitedVecs.push_back(vecs[i]);
		visited[i] = true;
		tmpMesh = vecs[i]->getFeSpace()->getMesh();
		for(size_t j = i + 1; j < vecs.size(); j++)
		  if(vecs[j]->getFeSpace()->getMesh() == tmpMesh)
		  {
		    splitedVecs.push_back(vecs[j]);
		    visited[j] = true;
		  }
Siqi Ling's avatar
Siqi Ling committed
236
237
	      }
	      string newfilename = filename;
238
239
240
241
242
243
244
245
246
247
248
249
250
	      if(filename.length() > 4 && filename.substr(filename.length()- 4, filename.length()) == ".arh")
		newfilename = filename.substr(0, filename.length() - 4) +
		  "." + tmpMesh->getName() + filename.substr(filename.length()-4 , filename.length());
	      else
		newfilename = filename + "." + tmpMesh->getName() + ".arh";
		
	      writeAux(newfilename, 
		       splitedVecs[0]->getFeSpace()->getMesh(), 
		       splitedVecs, 
		       writeParallel, 
		       cps, 
		       dataformat,
		       writeMacro); 
Siqi Ling's avatar
Siqi Ling committed
251
252
253
254
255
256
257
258
259
260
261
262
263
	    }
	  }
        }        
      }
  
      int writeHeader(ofstream& file,
                               Mesh *mesh,
                               vector<DOFVector<double>*> vecs,
                               map<const FiniteElemSpace*, vector<int> >& feSpaces,
			       Cpsformat cps,
			       string dataformat)
      {
        FUNCNAME("Arh3Writer::detail::writeHeader()");
264
// 	int nbits = boost::lexical_cast<int>(dataformat.substr(2, 2));
Siqi Ling's avatar
Siqi Ling committed
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
        TEST_EXIT(file.is_open())("the file is not open. should not happen.\n");
	
	map<const FiniteElemSpace*, string> AFEDfileName;
	
        uint32_t valueNamesLen = 0, fileNamesLen = 0;
        for (size_t i = 0; i < vecs.size(); i++)
          valueNamesLen += vecs[i]->getName().length();
	
	map<const FiniteElemSpace*, vector<int> >::iterator feSpaceIt;
	for (feSpaceIt = feSpaces.begin(); feSpaceIt != feSpaces.end(); feSpaceIt++)
	  AFEDfileName.insert(make_pair(feSpaceIt->first, string()));
    
        uint32_t nValueVectors = vecs.size();
        uint32_t nFeSpaces = feSpaces.size();
	uint32_t nMacroElements = mesh->getNumberOfMacros();
	
	uint32_t nMacro = 0;
	TraverseStack st;
	ElInfo *el = st.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
	while (el) {
	  nMacro++;
	  el = st.traverseNext(el);
	}
	
        uint32_t dow = mesh->getGeo(WORLD);
        uint32_t dim = mesh->getDim();
        uint32_t headerLen = 34 +                         //fixed part of header 
			     nMacroElements * 12 + 12 +   //macroElemnts table
			     fileNamesLen +		  //feSpaces table
			     nFeSpaces * 20 + 	          //feSpaces table
			     valueNamesLen + 	          //value vector table
296
297
			     nValueVectors * 12 +         //also value vector table
			     4;				  //macroFile_nl
Siqi Ling's avatar
Siqi Ling committed
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
        string typeId = "sarh";
#ifndef HAVE_COMPRESSION
	cps = NONE;
#endif
        uint8_t *major = const_cast<uint8_t*>(&(AMDiS::io::Arh3Reader::MAJOR)); 
        uint8_t *minor = const_cast<uint8_t*>(&(AMDiS::io::Arh3Reader::MINOR));
	int cpsflag = static_cast<int>(cps);
	uint32_t minus1 = -1;
        
	//fixed header
        file.write(typeId.c_str(), 4);
        file.write(reinterpret_cast<char*>(major), 1);
        file.write(reinterpret_cast<char*>(minor), 1);
        file.write(reinterpret_cast<char*>(&headerLen), 4);
        file.write(reinterpret_cast<char*>(&dow), 4);
        file.write(reinterpret_cast<char*>(&dim), 4);
        file.write(reinterpret_cast<char*>(&nFeSpaces), 4);
        file.write(reinterpret_cast<char*>(&nValueVectors), 4);
        file.write(reinterpret_cast<char*>(&nMacroElements), 4);
	file.write(reinterpret_cast<char*>(&cpsflag), 4);
	//macro table
	deque<MacroElement*>::const_iterator macroIter = mesh->firstMacroElement();
	
	while(macroIter != mesh->endOfMacroElements())
	{
	  uint32_t macroIndex = (*macroIter)->getIndex();
	  file.write(reinterpret_cast<char*>(&macroIndex), 4);
	  file.write(reinterpret_cast<char*>(&minus1), 4);
	  file.write(reinterpret_cast<char*>(&minus1), 4);
	  macroIter++;
	}
	file.write(reinterpret_cast<char*>(&minus1), 4);
	file.write(reinterpret_cast<char*>(&minus1), 4);
	file.write(reinterpret_cast<char*>(&minus1), 4);
	
	vector<int> feSpaceNumOfVecs(vecs.size());
	uint32_t posDOFs = 0, nameStrLen = 0;
	string nameStr("");
	size_t i = 0;
	
	//feSpace table
	for(feSpaceIt = feSpaces.begin(); feSpaceIt != feSpaces.end(); feSpaceIt++, i++)
	{
	  nameStr = AFEDfileName[feSpaceIt->first];
	  nameStrLen = nameStr.length();
	  file.write(reinterpret_cast<char*>(&nameStrLen), 4);
	  file.write(nameStr.c_str(), nameStrLen);
	  DimVec<int>* nDOF = feSpaceIt->first->getBasisFcts()->getNumberOfDofs();
	  //
347
	  for(int j = 1; j < nDOF->getSize(); j++) {
Siqi Ling's avatar
Siqi Ling committed
348
349
350
            posDOFs = (*nDOF)[j];
            file.write(reinterpret_cast<char*>(&posDOFs), 4);
          }
351
          for(int j = nDOF->getSize(); j < 4 ; j++) {
Siqi Ling's avatar
Siqi Ling committed
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
            posDOFs = 0;
            file.write(reinterpret_cast<char*>(&posDOFs), 4);
          }
          posDOFs = (*nDOF)[0];
	  file.write(reinterpret_cast<char*>(&posDOFs), 4);
	  //
          for(size_t j = 0; j < feSpaceIt->second.size(); j++)
	    feSpaceNumOfVecs[feSpaceIt->second[j]] = i;
	}
	
	//vector table
        for(i = 0; i < vecs.size(); i++)
        {
          nameStr = vecs[i]->getName();
          nameStrLen = nameStr.length();
          file.write(reinterpret_cast<char*>(&nameStrLen), 4);
          file.write(nameStr.c_str(), nameStrLen);
	  file.write(reinterpret_cast<char*>(&feSpaceNumOfVecs[i]), 4);
	  file.write(dataformat.c_str(), 4);
        }
372
373
374
        
        uint32_t macroFile_nl = 0;
        file.write(reinterpret_cast<char*>(&macroFile_nl), 4);
Siqi Ling's avatar
Siqi Ling committed
375
376
377
378
379
380
381
        return headerLen;
      }
 
      void writeAux(string filename, Mesh *mesh,
                        vector<DOFVector<double>*> vecs,
                        bool writeParallel,
			Cpsformat cps,
382
383
			string dataformat,
			bool writeMacro)
Siqi Ling's avatar
Siqi Ling committed
384
385
386
      {
        FUNCNAME("Arh3Writer::detail::writeAux()");
	
387
388
	TEST_EXIT(mesh)("empty mesh.\n");
	
Siqi Ling's avatar
Siqi Ling committed
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
        //initialization
        ofstream file;
        file.open(filename.c_str(), ios::out | ios::binary | ios::trunc);

        map<const FiniteElemSpace*, vector<int> > sortedFeSpaces;
	map<const FiniteElemSpace*, vector<int> >::iterator feSpaceIt;
        vector<pair<int, int> > macroSize; // (uncompressed size, compressed size)
        
        DegreeOfFreedom globalDof;  
        size_t i = 0, j = 0;
    
        for(i = 0; i < vecs.size(); i++)
	{
          sortedFeSpaces[vecs[i]->getFeSpace()].push_back(i);
	}
	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);
    
        //macro elements information
        MeshStructure elementStructure;
        vector<vector<double> > values(vecs.size());
        int32_t macroElIndex = -1;
    
        TraverseStack stack;
        ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
        while (elInfo) {
          if (elInfo->getLevel() == 0) {
            if (macroElIndex != -1) {
              elementStructure.commit();
	      macroSize.push_back(writeMacroElement(file, elementStructure, values, sortedFeSpaces, cps, dataformat));
            }
	    elementStructure.clear();
 	
	    macroElIndex = elInfo->getElement()->getIndex();
	    
	    for (j = 0; j < vecs.size(); j++)
	      values[j].clear();
	    
            for (j = 0; j < sortedFeSpaces.size(); j++)
              visited[j].clear();
          }
          elementStructure.insertElement(elInfo->getElement()->isLeaf());
      
          if (elInfo->getElement()->isLeaf()) 
          {
            int valuePos = 0;
            for(feSpaceIt = sortedFeSpaces.begin(), i = 0; feSpaceIt != sortedFeSpaces.end(); feSpaceIt++, i++)
            {
              DOFAdmin* admin = feSpaceIt->first->getAdmin();
              TEST_EXIT(admin)("the DOFAdmin of DOFVector is null, this should not happen.\n");       
  
              int n0, nd, nd0;

              if ((nd = admin->getNumberOfDofs(VERTEX)))  {                                                      
                int vertices = mesh->getGeo(VERTEX);
                nd0 = admin->getNumberOfPreDofs(VERTEX);                                                         
                n0 = mesh->getNode(VERTEX); //                                                          
                for (int n = 0; n < vertices; n++)
                  for(int d = 0; d < nd; d++)
                  {
                    globalDof = elInfo->getElement()->getDof(n0 + n, nd0 + d);
                    ret = visited[i].insert(globalDof);
                    if(ret.second)
                    {
                      for(j = 0 ; j < feSpaceIt->second.size(); j++)
                      {
                        values[valuePos + j].push_back((*vecs[feSpaceIt->second[j]])[globalDof]);
                      }
                    }
                  }
              }
              if (mesh->getDim() > 1) {
                if ((nd = admin->getNumberOfDofs(EDGE)))  {                                                      
                  int edges = mesh->getGeo(EDGE); 
                  nd0 = admin->getNumberOfPreDofs(EDGE);                                                         
                  n0 = mesh->getNode(EDGE);                                                          
                  for (int n = 0; n < edges; n++)
                  for(int d = 0; d < nd; d++)
                  {
                    globalDof = elInfo->getElement()->getDof(n0 + n, nd0 + d);
                    ret = visited[i].insert(globalDof);
                    if(ret.second)
                    {
                      for(j = 0 ; j < feSpaceIt->second.size(); j++)
                      {
                        values[valuePos + j].push_back((*vecs[feSpaceIt->second[j]])[globalDof]);
                      }
                    }
                  }
                }
              }
              if (mesh->getDim() == 3) {
                if ((nd = admin->getNumberOfDofs(FACE)))  {                                                      
                  int faces = mesh->getGeo(FACE);
                  nd0 = admin->getNumberOfPreDofs(FACE);                                                         
                  n0 = mesh->getNode(FACE);                                                          
                  for (int n = 0; n < faces; n++)
                  for(int d = 0; d < nd; d++)
                  {
                    globalDof = elInfo->getElement()->getDof(n0 + n, nd0 + d);
                    ret = visited[i].insert(globalDof);
                    if(ret.second)
                    {
                      for(j = 0 ; j < feSpaceIt->second.size(); j++)
                      {
                        values[valuePos + j].push_back((*vecs[feSpaceIt->second[j]])[globalDof]);
                      }
                    }
                  }
                }
              }                                   
              if ((nd = admin->getNumberOfDofs(CENTER)))  {                                                      
                nd0 = admin->getNumberOfPreDofs(CENTER);                                                         
                n0 = mesh->getNode(CENTER);      
                for(int d = 0; d < nd; d++)
                {
                  globalDof = elInfo->getElement()->getDof(n0, nd0 + d);
                  ret = visited[i].insert(globalDof);
                    if(ret.second)
                    {
                      for(j = 0 ; j < feSpaceIt->second.size(); j++)
                      {
                        values[valuePos + j].push_back((*vecs[feSpaceIt->second[j]])[globalDof]);
                      }
                    }
                }
              }
              valuePos += feSpaceIt->second.size();
            }//feSpace loop
          }//isLeaf

          elInfo = stack.traverseNext(elInfo);
        }
        // And write the last macro element to file.
        TEST_EXIT_DBG(macroElIndex != -1)("Should not happen!\n");
        elementStructure.commit();
	macroSize.push_back(writeMacroElement(file, elementStructure, values, sortedFeSpaces, cps, dataformat));
	TEST_EXIT(macroSize.size() == (unsigned)mesh->getNumberOfMacros())("Should not happen.\n");
	//reset the macro positions in file
	setMacrosPos(file, headerLen, macroSize);
531
532
	if (writeMacro)
	  setMacroFile(file, headerLen, mesh);
Siqi Ling's avatar
Siqi Ling committed
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
        file.close();
        MSG("ARH file written to: %s\n", filename.c_str());
      }
      
      void setMacrosPos(ofstream& file, int headerLen,
	                    vector<pair<int, int> >& macroSize)
      {
	file.seekp(34);
	long pos = 0;
	int startPos = headerLen;
	for(size_t i = 0; i < macroSize.size(); i++)
	{
	  pos = file.tellp();
	  file.seekp(pos + 4);
	  file.write(reinterpret_cast<char*>(&startPos), 4);
	  file.write(reinterpret_cast<char*>(&macroSize[i].first), 4);
	  startPos += macroSize[i].second;
	}
	pos = file.tellp();
	file.seekp(pos + 4);
	file.write(reinterpret_cast<char*>(&startPos), 4);
      }
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
      
      void setMacroFile(std::ofstream& file, int headerLen, Mesh* mesh)
      {
	string macroFilename = "", perFilename = "";
	string macroData = "", periodicData = "";
	
	Parameters::get(mesh->getName() + "->macro file name", macroFilename);
	Parameters::get(mesh->getName() + "->periodic file", perFilename);
	
	if (!macroFilename.length()) {
	  WARNING("macro file not found.\n");
	  return;
	}
	
	// write macro file to the end
	readFileToString(macroFilename, macroData);
	file.seekp(0, ios_base::end);
	long macroPos = file.tellp(), perPos = 0;
	file.write(macroData.c_str(), macroData.length());
	
	// write periodic file to the end
	if (perFilename.length()) {
	  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*>(&macroFile_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);
      }
      
      void readFileToString(std::string filename, std::string& data)
      {
	ifstream file(filename.c_str());
	file.seekg(0, std::ios::end);
	data.reserve(file.tellg());
	file.seekg(0, std::ios::beg);
	data.assign((istreambuf_iterator<char>(file)), istreambuf_iterator<char>());
      }
Siqi Ling's avatar
Siqi Ling committed
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
  
      pair<int, int> writeMacroElement(ofstream &file, 
				    MeshStructure &code,
				    vector<vector<double> >& values,
                                    map<const FiniteElemSpace*, vector<int> >& feSpaces,
				    Cpsformat cps,
				    string dataformat)
      {
	stringstream dataStream(ios::out | ios::in | ios::binary);
    
        uint32_t nStructureCodes = code.getCode().size();
        dataStream.write(reinterpret_cast<char*>(&nStructureCodes), 4);
    
        uint32_t codeSize = code.getNumElements();
        dataStream.write(reinterpret_cast<char*>(&codeSize), 4);

        dataStream.write(reinterpret_cast<char*>(&(const_cast<vector<uint64_t>&>(code.getCode())[0])), 
	       8 * nStructureCodes);
	
        if (values.size() > 0) {
	  int moreSize = 0, valuePos = 0;
          map<const FiniteElemSpace*, vector<int> >::iterator it; 
          for(it = feSpaces.begin(); it != feSpaces.end(); it++)
          {
            uint32_t nValuesPerVector = values[valuePos].size();
            dataStream.write(reinterpret_cast<char*>(&nValuesPerVector), 4);
	    moreSize += 4;
	    
            for (size_t i = 0; i < it->second.size(); i++)
	      moreSize += writeValues(dataStream, dataformat, values[valuePos + i]);
	    
            valuePos += it->second.size();
          }
        }
	stringstream tmp(ios::out | ios::in | ios::binary);
        boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
#ifdef HAVE_COMPRESSION
	switch(cps)
	{
	  case ZLIB: 
	    in.push(boost::iostreams::zlib_compressor());
	    break;
	  case BZIP2:
	    in.push(boost::iostreams::bzip2_compressor());
	    break;
	  case NONE:
	    break;
	  default:
	    MSG("NOT correct compression flag.\n");
	}
#endif
	in.push(dataStream);
	boost::iostreams::copy(in, tmp);
	file << tmp.rdbuf();
        return make_pair(dataStream.str().length(), tmp.str().length());
      }
      
      template<typename T>
      int writeValues(stringstream& file, vector<double>& values)
      {
664
665
	size_t size = values.size();
	T* data = new T[size];
Siqi Ling's avatar
Siqi Ling committed
666
667
668
669
	for (size_t i = 0; i < size; i++)
	  data[i] = static_cast<T>(values[i]);
	
	file.write(reinterpret_cast<char*>(&data[0]), sizeof(T) * size);
670
	delete [] data;
Siqi Ling's avatar
Siqi Ling committed
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
	return sizeof(T) * size;
      }
      
      int writeValues(stringstream& file,
		       string dataformat, 
		       vector<double>& values)
      {
	FUNCNAME("Arh3Writer::detail::writeValues()");
	int newsize = 0;
	std::map<string,Valformat>::const_iterator it = dataformatMap.find(dataformat);
	
	TEST_EXIT(it != dataformatMap.end())("Wrong data format.\n");
	
	switch(it->second) {
	  case SI08:
	    newsize = writeValues<int8_t>(file, values);
	    break;
	  case SI16:
	    newsize = writeValues<int16_t>(file, values);
	    break;
	  case SI32:
	    newsize = writeValues<int32_t>(file, values);
	    break;	    
	  case SI64:
	    newsize = writeValues<int64_t>(file, values);
	    break;	
	  case UI08:
	    newsize = writeValues<uint8_t>(file, values);
	    break;	  
	  case UI16:
	    newsize = writeValues<uint16_t>(file, values);
	    break;
	  case UI32:
	    newsize = writeValues<uint32_t>(file, values);
	    break;	  
	  case UI64:
	    newsize = writeValues<uint64_t>(file, values);
	    break;
	  case SF32:
	    newsize = writeValues<float>(file, values);
	    break;	
	  case SF64:
	    newsize = writeValues<double>(file, values);
	    break;
	  default:
	    ERROR_EXIT("Wrong data format.\n");
	}
	return newsize;
      }
    }//end namespace detail
  } // end namespace Arh3Writer
} } // end namespace io, AMDiS