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source: XIOS3/trunk/src/io/nc4_data_output.cpp @ 2384

Last change on this file since 2384 was 2384, checked in by jderouillat, 2 years ago
Replace OutputDomainName? by a CDomain pointer in the hash table which manage element names. Replace unordered_multimap by multimap
Property copyright set to Software name : XIOS (Xml I/O Server) http://forge.ipsl.jussieu.fr/ioserver Creation date : January 2009 Licence : CeCCIL version2 see license file in root directory : Licence_CeCILL_V2-en.txt or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement) CNRS/IPSL (Institut Pierre Simon Laplace) Project Manager : Yann Meurdesoif yann.meurdesoif@cea.fr Property svn:executable set to ``*
File size: 129.4 KB

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1	#include "nc4_data_output.hpp"
2
3	#include "attribute_template.hpp"
4	#include "group_template.hpp"
5
6	#include "file.hpp"
7	#include "calendar.hpp"
8	#include "context.hpp"
9	#include "context_server.hpp"
10	#include "netCdfException.hpp"
11	#include "exception.hpp"
12	#include "timer.hpp"
13	#include "uuid.hpp"
14	namespace xios
15	{
16	/// ////////////////////// Dfinitions ////////////////////// ///
17	CNc4DataOutput::CNc4DataOutput
18	(CFile* file, const StdString & filename, bool exist)
19	: SuperClass()
20	, SuperClassWriter(filename, exist)
21	, filename(filename)
22	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relElements_()
23	{
24	SuperClass::type = MULTI_FILE;
25	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
26	}
27
28	CNc4DataOutput::CNc4DataOutput
29	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
30	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
31	: SuperClass()
32	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
33	, comm_file(comm_file)
34	, filename(filename)
35	, isCollective(isCollective)
36	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relElements_()
37	{
38	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
39	if (file==NULL) compressionLevel = 0 ;
40	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
41	}
42
43	CNc4DataOutput::~CNc4DataOutput(void)
44	{ /* Ne rien faire de plus */ }
45
46	///--------------------------------------------------------------
47
48	const StdString & CNc4DataOutput::getFileName(void) const
49	{
50	return (this->filename);
51	}
52
53	//---------------------------------------------------------------
54
55	void CNc4DataOutput::writeDomain_(CDomain* domain)
56	TRY
57	{
58	StdString lonName,latName ;
59
60	if (domain->type == CDomain::type_attr::unstructured)
61	{
62	if (SuperClassWriter::useCFConvention)
63	writeUnstructuredDomain(domain) ;
64	else
65	writeUnstructuredDomainUgrid(domain) ;
66	return ;
67	}
68
69	CContext* context = CContext::getCurrent() ;
70	if (domain->IsWritten(this->filename)) return;
71	domain->checkAttributes();
72
73	if (domain->isEmpty())
74	if (SuperClass::type==MULTI_FILE) return;
75
76
77	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
78	if (!domain->lonvalue.isEmpty() )
79	{
80	int comm_file_rank(0);
81	MPI_Comm_rank( comm_file, &comm_file_rank );
82	int comm_file_size(1);
83	MPI_Comm_size( comm_file, &comm_file_size );
84
85	// Get element current FULL view
86	shared_ptr<CLocalView> srcView = domain->getLocalView(CElementView::FULL) ;
87	vector<shared_ptr<CLocalView>> srcViews;
88	srcViews.push_back( srcView );
89
90	// Compute a without redundancy element FULL view to enable a consistent hash computation
91	vector<shared_ptr<CLocalView>> remoteViews;
92	shared_ptr<CLocalView> remoteView;
93	// define the remote view without redundancy (naive distribution of the remote view)
94	int globalSize = domain->ni_glo.getValue()*domain->nj_glo.getValue();
95	int localSize = globalSize/comm_file_size;
96	if ( (comm_file_rank==comm_file_size-1) && (localSize*comm_file_size != globalSize ) )
97	localSize += globalSize-localSize*comm_file_size;
98	CArray<size_t,1> globalIndex( localSize );
99	CArray<int,1> index( localSize );
100	for (int iloc=0; iloc<localSize ; iloc++ )
101	{
102	globalIndex(iloc) = comm_file_rank*(globalSize/comm_file_size) + iloc;
103	index(iloc) = iloc;
104	}
105	shared_ptr<CLocalElement> localElement = make_shared<CLocalElement>(comm_file_rank, globalSize, globalIndex) ;
106	localElement->addView(CElementView::FULL, index) ;
107	remoteView = localElement->getView(CElementView::FULL) ;
108	remoteViews.push_back( remoteView );
109
110	// Compute the connector between current and without redundancy FULL views
111	shared_ptr<CGridTransformConnector> gridTransformConnector = make_shared<CGridTransformConnector>(srcViews, remoteViews, comm_file ) ;
112	gridTransformConnector->computeConnector(true) ; // eliminateRedondant = true
113	CArray<double,1> lon_distributedValue, lat_distributedValue ;
114	gridTransformConnector->transfer(domain->lonvalue, lon_distributedValue );
115	gridTransformConnector->transfer(domain->latvalue, lat_distributedValue );
116
117	// Compute the distributed hash (v0) of the element
118	// it will be associated to the default element name (= map key), and to the name really written
119	int localHash = 0;
120	for (int iloc=0; iloc<localSize ; iloc++ ) localHash+=globalIndex(iloc)lon_distributedValue(iloc)lat_distributedValue(iloc);
121	int globalHash(0);
122	globalHash = localHash;
123	MPI_Allreduce( &localHash, &globalHash, 1, MPI_INT, MPI_SUM, comm_file );
124
125	StdString defaultNameKey = domain->getDomainOutputName();
126	if ( !relDomains_.count ( defaultNameKey ) )
127	{
128	// if defaultNameKey not in the map, write the element such as it is defined
129	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) );
130	}
131	else // look if a hash associated this key is equal
132	{
133	bool elementIsInMap(false);
134	auto defaultNameKeyElements = relDomains_.equal_range( defaultNameKey );
135	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
136	{
137	if ( it->second.first == globalHash )
138	{
139	// if yes, associate the same ids to current element
140	domain->name = it->second.second->getDomainOutputName();
141	domain->lon_name = it->second.second->lon_name;
142	domain->lat_name = it->second.second->lat_name;
143	elementIsInMap = true;
144	}
145	}
146	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
147	if (!elementIsInMap) // ! in MAP
148	{
149	domain->name = domain->getId();
150	domain->lon_name = "lon_"+domain->getId();
151	domain->lat_name = "lat_"+domain->getId();
152	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) ) ;
153	}
154	}
155	}
156
157
158	std::vector<StdString> dim0, dim1;
159	StdString domid = domain->getDomainOutputName();
160	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
161	if (isWrittenDomain(domid)) return ;
162	else setWrittenDomain(domid);
163
164	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
165
166
167	StdString dimXid, dimYid ;
168
169	nc_type typePrec ;
170	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
171	else if (domain->prec==4) typePrec = NC_FLOAT ;
172	else if (domain->prec==8) typePrec = NC_DOUBLE ;
173
174	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
175	switch (domain->type)
176	{
177	case CDomain::type_attr::curvilinear :
178
179	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
180	else lonName = domain->lon_name;
181
182	if (domain->lat_name.isEmpty()) latName = "nav_lat";
183	else latName = domain->lat_name;
184
185	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
186	else dimXid=domain->dim_i_name.getValue() + appendDomid;
187
188	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
189	else dimYid=domain->dim_j_name.getValue() + appendDomid;
190
191	break ;
192
193	case CDomain::type_attr::rectilinear :
194
195	if (domain->lon_name.isEmpty())
196	{
197	if (domain->dim_i_name.isEmpty())
198	lonName = "lon";
199	else
200	lonName = domain->dim_i_name.getValue();
201	}
202	else lonName = domain->lon_name;
203
204	if (domain->lat_name.isEmpty())
205	{
206	if (domain->dim_j_name.isEmpty())
207	latName = "lat";
208	else
209	latName = domain->dim_j_name.getValue();
210	}
211	else latName = domain->lat_name;
212
213	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
214	else dimXid = domain->dim_i_name.getValue()+appendDomid;
215
216	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
217	else dimYid = domain->dim_j_name.getValue()+appendDomid;
218	break;
219	}
220
221	StdString dimVertId = StdString("nvertex").append(appendDomid);
222
223	string lonid,latid,bounds_lonid,bounds_latid ;
224	string areaId = "area" + appendDomid;
225
226	try
227	{
228	switch (SuperClass::type)
229	{
230	case (MULTI_FILE) :
231	{
232	switch (domain->type)
233	{
234	case CDomain::type_attr::curvilinear :
235	dim0.push_back(dimYid); dim0.push_back(dimXid);
236	lonid = lonName+appendDomid;
237	latid = latName+appendDomid;
238	break ;
239	case CDomain::type_attr::rectilinear :
240	lonid = lonName+appendDomid;
241	latid = latName+appendDomid;
242	dim0.push_back(dimYid);
243	dim1.push_back(dimXid);
244	break;
245	}
246	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
247	else bounds_lonid = "bounds_"+lonName+appendDomid;
248	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
249	else bounds_latid = "bounds_"+latName+appendDomid;
250
251	SuperClassWriter::addDimension(dimXid, domain->ni);
252	SuperClassWriter::addDimension(dimYid, domain->nj);
253
254	if (domain->hasBounds)
255	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
256
257	if (context->intraCommSize_ > 1)
258	{
259	this->writeLocalAttributes(domain->ibegin,
260	domain->ni,
261	domain->jbegin,
262	domain->nj,
263	appendDomid);
264
265	if (singleDomain)
266	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
267	domain->ibegin,
268	domain->ni,
269	domain->jbegin,
270	domain->nj,
271	domain->ni_glo,domain->nj_glo,
272	context->intraCommRank_,context->intraCommSize_);
273	}
274
275	if (domain->hasLonLat)
276	{
277	switch (domain->type)
278	{
279	case CDomain::type_attr::curvilinear :
280	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
281	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
282	break ;
283	case CDomain::type_attr::rectilinear :
284	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
285	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
286	break ;
287	}
288
289	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
290	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
291
292	if (domain->hasBounds)
293	{
294	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
295	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
296
297	dim0.clear();
298	dim0.push_back(dimYid);
299	dim0.push_back(dimXid);
300	dim0.push_back(dimVertId);
301	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
302	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
303	}
304	}
305
306	dim0.clear();
307	dim0.push_back(dimYid);
308	dim0.push_back(dimXid);
309
310	if (domain->hasArea)
311	{
312	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
313	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
314	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
315	}
316
317	SuperClassWriter::definition_end();
318
319	if (domain->hasLonLat)
320	{
321	switch (domain->type)
322	{
323	case CDomain::type_attr::curvilinear :
324	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
325	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
326	break;
327	case CDomain::type_attr::rectilinear :
328	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
329	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
330	CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
331	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
332	break;
333	}
334
335	if (domain->hasBounds)
336	{
337	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
338	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
339	}
340	}
341
342	if (domain->hasArea)
343	{
344	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
345	}
346
347	SuperClassWriter::definition_start();
348
349	break;
350	}
351	case (ONE_FILE) :
352	{
353	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
354	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
355
356	if (domain->hasBounds)
357	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
358
359	if (domain->hasLonLat)
360	{
361	switch (domain->type)
362	{
363	case CDomain::type_attr::curvilinear :
364	dim0.push_back(dimYid); dim0.push_back(dimXid);
365	lonid = lonName+appendDomid;
366	latid = latName+appendDomid;
367	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
368	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
369	break;
370
371	case CDomain::type_attr::rectilinear :
372	dim0.push_back(dimYid);
373	dim1.push_back(dimXid);
374	lonid = lonName+appendDomid;
375	latid = latName+appendDomid;
376	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
377	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
378	break;
379	}
380	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
381	else bounds_lonid = "bounds_"+lonName+appendDomid;
382	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
383	else bounds_latid = "bounds_"+latName+appendDomid;
384
385	this->writeAxisAttributes
386	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
387	this->writeAxisAttributes
388	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
389
390	if (domain->hasBounds)
391	{
392	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
393	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
394
395	dim0.clear();
396	dim0.push_back(dimYid);
397	dim0.push_back(dimXid);
398	dim0.push_back(dimVertId);
399	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
400	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
401	}
402	}
403
404	if (domain->hasArea)
405	{
406	dim0.clear();
407	dim0.push_back(dimYid); dim0.push_back(dimXid);
408	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
409	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
410	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
411	dim0.clear();
412	}
413
414	SuperClassWriter::definition_end();
415
416	switch (domain->type)
417	{
418	case CDomain::type_attr::curvilinear :
419	{
420	std::vector<StdSize> start(2) ;
421	std::vector<StdSize> count(2) ;
422	start[1]=domain->ibegin;
423	start[0]=domain->jbegin;
424	count[1]=domain->ni ; count[0]=domain->nj ;
425
426	if (domain->hasLonLat)
427	{
428	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
429	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
430	}
431	break;
432	}
433	case CDomain::type_attr::rectilinear :
434	{
435	if (domain->hasLonLat)
436	{
437	std::vector<StdSize> start(1) ;
438	std::vector<StdSize> count(1) ;
439
440	start[0]=domain->jbegin;
441	count[0]=domain->nj;
442	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni));
443	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
444
445	start[0]=domain->ibegin;
446	count[0]=domain->ni;
447	CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1));
448	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
449	}
450	break;
451	}
452	}
453
454	if (domain->hasBounds)
455	{
456	std::vector<StdSize> start(3);
457	std::vector<StdSize> count(3);
458	if (domain->isEmpty())
459	{
460	start[2] = start[1] = start[0] = 0;
461	count[2] = count[1] = count[0] = 0;
462	}
463	else
464	{
465	start[2] = 0;
466	start[1] = domain->ibegin;
467	start[0] = domain->jbegin;
468	count[2] = domain->nvertex;
469	count[1] = domain->ni;
470	count[0] = domain->nj;
471	}
472
473	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
474	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
475	}
476
477	if (domain->hasArea)
478	{
479	std::vector<StdSize> start(2);
480	std::vector<StdSize> count(2);
481
482	start[1] = domain->ibegin;
483	start[0] = domain->jbegin;
484	count[1] = domain->ni;
485	count[0] = domain->nj;
486
487	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
488	}
489
490	SuperClassWriter::definition_start();
491	break;
492	}
493	default :
494	ERROR("CNc4DataOutput::writeDomain(domain)",
495	<< "[ type = " << SuperClass::type << "]"
496	<< " not implemented yet !");
497	}
498	}
499	catch (CNetCdfException& e)
500	{
501	StdString msg("On writing the domain : ");
502	msg.append(domid); msg.append("\n");
503	msg.append("In the context : ");
504	msg.append(context->getId()); msg.append("\n");
505	msg.append(e.what());
506	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
507	}
508
509	domain->addRelFile(this->filename);
510	}
511	CATCH
512
513	//--------------------------------------------------------------
514
515	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
516	{
517	CContext* context = CContext::getCurrent() ;
518
519	if (domain->IsWritten(this->filename)) return;
520
521	StdString domid = domain->getDomainOutputName();
522
523	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
524	// Thus the entire mesh connectivity will be generated at once.
525	if (isWrittenDomain(domid)) return ;
526	else setWrittenDomain(domid);
527
528	domain->checkAttributes();
529	if (domain->isEmpty())
530	if (SuperClass::type==MULTI_FILE) return ;
531
532	nc_type typePrec ;
533	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
534	else if (domain->prec==4) typePrec = NC_FLOAT ;
535	else if (domain->prec==8) typePrec = NC_DOUBLE ;
536
537	std::vector<StdString> dim0;
538	StdString domainName = domain->name;
539	domain->assignMesh(domainName, domain->nvertex);
540	domain->mesh->createMeshEpsilon(context->intraComm_, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
541
542	StdString node_x = domainName + "_node_x";
543	StdString node_y = domainName + "_node_y";
544
545	StdString edge_x = domainName + "_edge_x";
546	StdString edge_y = domainName + "_edge_y";
547	StdString edge_nodes = domainName + "_edge_nodes";
548
549	StdString face_x = domainName + "_face_x";
550	StdString face_y = domainName + "_face_y";
551	StdString face_nodes = domainName + "_face_nodes";
552	StdString face_edges = domainName + "_face_edges";
553	StdString edge_faces = domainName + "_edge_face_links";
554	StdString face_faces = domainName + "_face_links";
555
556	StdString dimNode = "n" + domainName + "_node";
557	StdString dimEdge = "n" + domainName + "_edge";
558	StdString dimFace = "n" + domainName + "_face";
559	StdString dimVertex = "n" + domainName + "_vertex";
560	StdString dimTwo = "Two";
561
562	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
563	dim0.clear();
564	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
565	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
566	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
567	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
568	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
569
570	try
571	{
572	switch (SuperClass::type)
573	{
574	case (ONE_FILE) :
575	{
576	// Adding nodes
577	if (domain->nvertex == 1)
578	{
579	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
580	{
581	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
582	dim0.clear();
583	dim0.push_back(dimNode);
584	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
585	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
586	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
587	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
588	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
589	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
590	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
591	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
592	}
593	} // domain->nvertex == 1
594
595	// Adding edges and nodes, if nodes have not been defined previously
596	if (domain->nvertex == 2)
597	{
598	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
599	{
600	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
601	dim0.clear();
602	dim0.push_back(dimNode);
603	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
604	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
605	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
606	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
607	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
608	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
609	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
610	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
611	}
612	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
613	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
614	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
615	dim0.clear();
616	dim0.push_back(dimEdge);
617	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
618	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
619	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
620	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
621	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
622	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
623	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
624	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
625	dim0.clear();
626	dim0.push_back(dimEdge);
627	dim0.push_back(dimTwo);
628	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
629	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
630	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
631	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
632	} // domain->nvertex == 2
633
634	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
635	if (domain->nvertex > 2)
636	{
637	// Nodes
638	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
639	{
640	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
641	dim0.clear();
642	dim0.push_back(dimNode);
643	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
644	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
645	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
646	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
647	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
648	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
649	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
650	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
651	}
652	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
653	{
654	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
655	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
656	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
657	dim0.clear();
658	dim0.push_back(dimEdge);
659	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
660	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
661	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
662	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
663	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
664	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
665	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
666	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
667	dim0.clear();
668	dim0.push_back(dimEdge);
669	dim0.push_back(dimTwo);
670	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
671	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
672	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
673	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
674	}
675	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
676	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
677	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
678	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
679	dim0.clear();
680	dim0.push_back(dimFace);
681	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
682	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
683	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
684	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
685	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
686	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
687	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
688	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
689	dim0.clear();
690	dim0.push_back(dimFace);
691	dim0.push_back(dimVertex);
692	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
693	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
694	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
695	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
696	dim0.clear();
697	dim0.push_back(dimFace);
698	dim0.push_back(dimVertex);
699	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
700	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
701	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
702	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
703	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
704	dim0.clear();
705	dim0.push_back(dimEdge);
706	dim0.push_back(dimTwo);
707	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
708	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
709	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
710	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
711	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
712	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
713	dim0.clear();
714	dim0.push_back(dimFace);
715	dim0.push_back(dimVertex);
716	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
717	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
718	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
719	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
720	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
721	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
722	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
723	} // domain->nvertex > 2
724
725	SuperClassWriter::definition_end();
726
727	std::vector<StdSize> startEdges(1) ;
728	std::vector<StdSize> countEdges(1) ;
729	std::vector<StdSize> startNodes(1) ;
730	std::vector<StdSize> countNodes(1) ;
731	std::vector<StdSize> startFaces(1) ;
732	std::vector<StdSize> countFaces(1) ;
733	std::vector<StdSize> startEdgeNodes(2) ;
734	std::vector<StdSize> countEdgeNodes(2) ;
735	std::vector<StdSize> startEdgeFaces(2) ;
736	std::vector<StdSize> countEdgeFaces(2) ;
737	std::vector<StdSize> startFaceConctv(2) ;
738	std::vector<StdSize> countFaceConctv(2) ;
739
740	if (domain->nvertex == 1)
741	{
742	if (domain->isEmpty())
743	{
744	startNodes[0]=0 ;
745	countNodes[0]=0 ;
746	}
747	else
748	{
749	startNodes[0] = domain->ibegin;
750	countNodes[0] = domain->ni ;
751	}
752
753	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
754	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
755	}
756	else if (domain->nvertex == 2)
757	{
758	if (domain->isEmpty())
759	{
760	startEdges[0]=0 ;
761	countEdges[0]=0 ;
762	startNodes[0]=0 ;
763	countNodes[0]=0 ;
764	startEdgeNodes[0]=0;
765	startEdgeNodes[1]=0;
766	countEdgeNodes[0]=0;
767	countEdgeNodes[1]=0;
768
769	}
770	else
771	{
772	startEdges[0] = domain->ibegin;
773	countEdges[0] = domain->ni;
774	startNodes[0] = domain->mesh->node_start;
775	countNodes[0] = domain->mesh->node_count;
776	startEdgeNodes[0] = domain->ibegin;
777	startEdgeNodes[1] = 0;
778	countEdgeNodes[0] = domain->ni;
779	countEdgeNodes[1] = 2;
780	}
781	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
782	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
783	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
784	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
785	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
786	}
787	else
788	{
789	if (domain->isEmpty())
790	{
791	startFaces[0] = 0 ;
792	countFaces[0] = 0 ;
793	startNodes[0] = 0;
794	countNodes[0] = 0;
795	startEdges[0] = 0;
796	countEdges[0] = 0;
797	startEdgeFaces[0] = 0;
798	startEdgeFaces[1] = 0;
799	countEdgeFaces[0] = 0;
800	countEdgeFaces[1] = 0;
801	startFaceConctv[0] = 0;
802	startFaceConctv[1] = 0;
803	countFaceConctv[0] = 0;
804	countFaceConctv[1] = 0;
805	}
806	else
807	{
808	startFaces[0] = domain->ibegin;
809	countFaces[0] = domain->ni ;
810	startNodes[0] = domain->mesh->node_start;
811	countNodes[0] = domain->mesh->node_count;
812	startEdges[0] = domain->mesh->edge_start;
813	countEdges[0] = domain->mesh->edge_count;
814	startEdgeNodes[0] = domain->mesh->edge_start;
815	startEdgeNodes[1] = 0;
816	countEdgeNodes[0] = domain->mesh->edge_count;
817	countEdgeNodes[1]= 2;
818	startEdgeFaces[0] = domain->mesh->edge_start;
819	startEdgeFaces[1]= 0;
820	countEdgeFaces[0] = domain->mesh->edge_count;
821	countEdgeFaces[1]= 2;
822	startFaceConctv[0] = domain->ibegin;
823	startFaceConctv[1] = 0;
824	countFaceConctv[0] = domain->ni;
825	countFaceConctv[1] = domain->nvertex;
826	}
827	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
828	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
829	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
830	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
831	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
832	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
833	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
834	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
835	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
836	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
837	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
838	}
839	SuperClassWriter::definition_start();
840
841	break;
842	} // ONE_FILE
843
844	case (MULTI_FILE) :
845	{
846	ERROR("CNc4DataOutput::writeDomain(domain)",
847	<< "[ type = multiple_file ]"
848	<< " is not yet implemented for UGRID files !");
849	break;
850	}
851
852	default :
853	ERROR("CNc4DataOutput::writeDomain(domain)",
854	<< "[ type = " << SuperClass::type << "]"
855	<< " not implemented yet !");
856	} // switch
857	} // try
858
859	catch (CNetCdfException& e)
860	{
861	StdString msg("On writing the domain : ");
862	msg.append(domid); msg.append("\n");
863	msg.append("In the context : ");
864	msg.append(context->getId()); msg.append("\n");
865	msg.append(e.what());
866	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
867	}
868
869	domain->addRelFile(this->filename);
870	}
871
872	//--------------------------------------------------------------
873
874	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
875	{
876	CContext* context = CContext::getCurrent() ;
877
878	if (domain->IsWritten(this->filename)) return;
879	domain->checkAttributes();
880
881	if (domain->isEmpty())
882	if (SuperClass::type==MULTI_FILE) return ;
883
884	std::vector<StdString> dim0, dim1;
885	StdString domid = domain->getDomainOutputName();
886	if (isWrittenDomain(domid)) return ;
887	else setWrittenDomain(domid);
888
889	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
890
891	StdString lonName,latName, cellName ;
892	if (domain->lon_name.isEmpty()) lonName = "lon";
893	else lonName = domain->lon_name;
894
895	if (domain->lat_name.isEmpty()) latName = "lat";
896	else latName = domain->lat_name;
897
898	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
899	else cellName="cell";
900	StdString dimXid = cellName+appendDomid;
901	StdString dimVertId = StdString("nvertex").append(appendDomid);
902
903	string lonid,latid,bounds_lonid,bounds_latid ;
904	string areaId = "area" + appendDomid;
905
906	nc_type typePrec ;
907	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
908	else if (domain->prec==4) typePrec = NC_FLOAT ;
909	else if (domain->prec==8) typePrec = NC_DOUBLE ;
910
911	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
912
913	try
914	{
915	switch (SuperClass::type)
916	{
917	case (MULTI_FILE) :
918	{
919	dim0.push_back(dimXid);
920	SuperClassWriter::addDimension(dimXid, domain->ni);
921
922	lonid = lonName+appendDomid;
923	latid = latName+appendDomid;
924	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
925	else bounds_lonid = "bounds_"+lonName+appendDomid;
926	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
927	else bounds_latid = "bounds_"+latName+appendDomid;
928
929	if (domain->hasLonLat)
930	{
931	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
932	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
933	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
934	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
935	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
936	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
937	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
938	}
939	dim0.clear();
940	if (domain->hasBounds)
941	{
942	dim0.push_back(dimXid);
943	dim0.push_back(dimVertId);
944	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
945	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
946	}
947
948	dim0.clear();
949	dim0.push_back(dimXid);
950	if (domain->hasArea)
951	{
952	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
953	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
954	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
955	}
956
957	SuperClassWriter::definition_end();
958
959	if (domain->hasLonLat)
960	{
961	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
962	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
963	if (domain->hasBounds)
964	{
965	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
966	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
967	}
968	}
969
970	if (domain->hasArea)
971	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
972
973	SuperClassWriter::definition_start();
974	break ;
975	}
976
977	case (ONE_FILE) :
978	{
979	lonid = lonName+appendDomid;
980	latid = latName+appendDomid;
981	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
982	else bounds_lonid = "bounds_"+lonName+appendDomid;
983	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
984	else bounds_latid = "bounds_"+latName+appendDomid;
985
986	dim0.push_back(dimXid);
987	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
988	if (domain->hasLonLat)
989	{
990	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
991	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
992
993	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
994	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
995	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
996	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
997	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
998	}
999	dim0.clear();
1000
1001	if (domain->hasBounds)
1002	{
1003	dim0.push_back(dimXid);
1004	dim0.push_back(dimVertId);
1005	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1006	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1007	}
1008
1009	if (domain->hasArea)
1010	{
1011	dim0.clear();
1012	dim0.push_back(dimXid);
1013	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1014	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1015	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1016	}
1017
1018	SuperClassWriter::definition_end();
1019
1020	std::vector<StdSize> start(1), startBounds(2) ;
1021	std::vector<StdSize> count(1), countBounds(2) ;
1022	if (domain->isEmpty())
1023	{
1024	start[0]=0 ;
1025	count[0]=0 ;
1026	startBounds[1]=0 ;
1027	countBounds[1]=nvertex ;
1028	startBounds[0]=0 ;
1029	countBounds[0]=0 ;
1030	}
1031	else
1032	{
1033	start[0]=domain->ibegin;
1034	count[0]=domain->ni;
1035	startBounds[0]=domain->ibegin;
1036	startBounds[1]=0 ;
1037	countBounds[0]=domain->ni;
1038	countBounds[1]=nvertex ;
1039	}
1040
1041	if (domain->hasLonLat)
1042	{
1043	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
1044	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
1045	if (domain->hasBounds)
1046	{
1047	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1048	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1049	}
1050	}
1051
1052	if (domain->hasArea)
1053	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
1054
1055	SuperClassWriter::definition_start();
1056
1057	break;
1058	}
1059	default :
1060	ERROR("CNc4DataOutput::writeDomain(domain)",
1061	<< "[ type = " << SuperClass::type << "]"
1062	<< " not implemented yet !");
1063	}
1064	}
1065	catch (CNetCdfException& e)
1066	{
1067	StdString msg("On writing the domain : ");
1068	msg.append(domid); msg.append("\n");
1069	msg.append("In the context : ");
1070	msg.append(context->getId()); msg.append("\n");
1071	msg.append(e.what());
1072	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1073	}
1074	domain->addRelFile(this->filename);
1075	}
1076	//--------------------------------------------------------------
1077
1078	void CNc4DataOutput::writeAxis_(CAxis* axis)
1079	{
1080	if (axis->IsWritten(this->filename)) return;
1081
1082	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
1083	if (!axis->value.isEmpty() )
1084	{
1085	int comm_file_rank(0);
1086	MPI_Comm_rank( comm_file, &comm_file_rank );
1087	int comm_file_size(1);
1088	MPI_Comm_size( comm_file, &comm_file_size );
1089
1090	// Get element current FULL view
1091	shared_ptr<CLocalView> srcView = axis->getLocalView(CElementView::FULL) ;
1092	vector<shared_ptr<CLocalView>> srcViews;
1093	srcViews.push_back( srcView );
1094
1095	// Compute a without redundancy element FULL view to enable a consistent hash computation
1096	vector<shared_ptr<CLocalView>> remoteViews;
1097	shared_ptr<CLocalView> remoteView;
1098	// define the remote view without redundancy (naive distribution of the remote view)
1099	int globalSize = axis->n_glo.getValue();
1100	int localSize = globalSize/comm_file_size;
1101	if ( (comm_file_rank==comm_file_size-1) && (localSize*comm_file_size != globalSize ) )
1102	localSize += globalSize-localSize*comm_file_size;
1103	CArray<size_t,1> globalIndex( localSize );
1104	CArray<int,1> index( localSize );
1105	for (int iloc=0; iloc<localSize ; iloc++ )
1106	{
1107	globalIndex(iloc) = comm_file_rank*(globalSize/comm_file_size) + iloc;
1108	index(iloc) = iloc;
1109	}
1110	shared_ptr<CLocalElement> localElement = make_shared<CLocalElement>(comm_file_rank, globalSize, globalIndex) ;
1111	localElement->addView(CElementView::FULL, index) ;
1112	remoteView = localElement->getView(CElementView::FULL) ;
1113	remoteViews.push_back( remoteView );
1114
1115	// Compute the connector between current and without redundancy FULL views
1116	shared_ptr<CGridTransformConnector> gridTransformConnector = make_shared<CGridTransformConnector>(srcViews, remoteViews, comm_file ) ;
1117	gridTransformConnector->computeConnector(true) ; // eliminateRedondant = true
1118	CArray<double,1> distributedValue ;
1119	gridTransformConnector->transfer(axis->value, distributedValue );
1120
1121	// Compute the distributed hash (v0) of the element
1122	// it will be associated to the default element name (= map key), and to the name really written
1123	int localHash = 0;
1124	for (int iloc=0; iloc<localSize ; iloc++ ) localHash+=globalIndex(iloc)*distributedValue(iloc);
1125	int globalHash(0);
1126	globalHash = localHash;
1127	MPI_Allreduce( &localHash, &globalHash, 1, MPI_INT, MPI_SUM, comm_file );
1128
1129	StdString defaultNameKey = axis->getAxisOutputName();
1130	if ( !relElements_.count ( defaultNameKey ) )
1131	{
1132	// if defaultNameKey not in the map, write the element such as it is defined
1133	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, defaultNameKey) ) );
1134	}
1135	else // look if a hash associated this key is equal
1136	{
1137	bool elementIsInMap(false);
1138	auto defaultNameKeyElements = relElements_.equal_range( defaultNameKey );
1139	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
1140	{
1141	if ( it->second.first == globalHash )
1142	{
1143	// if yes, associate the same ids to current element
1144	axis->name = it->second.second;
1145	elementIsInMap = true;
1146	}
1147	}
1148	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
1149	if (!elementIsInMap) // ! in MAP
1150	{
1151	axis->name = axis->getId();
1152	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis->getAxisOutputName()) ) ) ;// = axis->getId()
1153	}
1154	}
1155	}
1156
1157	axis->checkAttributes();
1158
1159	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
1160	: axis->n_glo.getValue();
1161
1162	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
1163
1164	std::vector<StdString> dims;
1165	StdString axisid = axis->getAxisOutputName();
1166	StdString axisDim, axisBoundsId;
1167	if (isWrittenAxis(axisid)) return ;
1168	else setWrittenAxis(axisid);
1169
1170	nc_type typePrec ;
1171	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1172	else if (axis->prec==4) typePrec = NC_FLOAT ;
1173	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1174
1175	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1176	string strId="str_len" ;
1177	try
1178	{
1179	if (axis->dim_name.isEmpty()) axisDim = axisid;
1180	else axisDim=axis->dim_name.getValue();
1181	SuperClassWriter::addDimension(axisDim, size);
1182	dims.push_back(axisDim);
1183
1184	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1185
1186	if (axis->hasValue \|\| !axis->label.isEmpty())
1187	{
1188	if (!axis->label.isEmpty()) dims.push_back(strId);
1189
1190	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1191
1192	if (!axis->name.isEmpty())
1193	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1194
1195	if (!axis->standard_name.isEmpty())
1196	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1197
1198	if (!axis->long_name.isEmpty())
1199	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1200
1201	if (!axis->unit.isEmpty())
1202	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1203
1204	if (!axis->axis_type.isEmpty())
1205	{
1206	switch(axis->axis_type)
1207	{
1208	case CAxis::axis_type_attr::X :
1209	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1210	break;
1211	case CAxis::axis_type_attr::Y :
1212	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1213	break;
1214	case CAxis::axis_type_attr::Z :
1215	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1216	break;
1217	case CAxis::axis_type_attr::T :
1218	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1219	break;
1220	}
1221	}
1222
1223	if (!axis->positive.isEmpty())
1224	{
1225	SuperClassWriter::addAttribute("positive",
1226	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1227	&axisid);
1228	}
1229
1230	if (!axis->formula.isEmpty())
1231	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1232
1233	if (!axis->formula_term.isEmpty())
1234	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
1235
1236	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1237	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1238	{
1239	dims.push_back("axis_nbounds");
1240	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1241	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1242
1243	if (!axis->standard_name.isEmpty())
1244	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1245
1246	if (!axis->unit.isEmpty())
1247	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1248
1249	if (!axis->formula_bounds.isEmpty())
1250	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1251
1252	if (!axis->formula_term_bounds.isEmpty())
1253	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
1254	}
1255	}
1256
1257	SuperClassWriter::definition_end();
1258
1259	switch (SuperClass::type)
1260	{
1261	case MULTI_FILE:
1262	{
1263	if (axis->label.isEmpty())
1264	{
1265	if (!axis->value.isEmpty())
1266	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
1267
1268	if (!axis->bounds.isEmpty())
1269	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
1270	}
1271	else
1272	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
1273
1274	SuperClassWriter::definition_start();
1275	break;
1276	}
1277	case ONE_FILE:
1278	{
1279	std::vector<StdSize> start(1), startBounds(2) ;
1280	std::vector<StdSize> count(1), countBounds(2) ;
1281	start[0] = startBounds[0] = axis->begin;
1282	count[0] = countBounds[0] = axis->n;
1283	startBounds[1] = 0;
1284	countBounds[1] = 2;
1285
1286	if (axis->label.isEmpty())
1287	{
1288	if (!axis->value.isEmpty())
1289	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
1290
1291	if (!axis->bounds.isEmpty())
1292	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1293	}
1294	else
1295	{
1296	std::vector<StdSize> startLabel(2), countLabel(2);
1297	startLabel[0] = start[0]; startLabel[1] = 0;
1298	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1299	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
1300	}
1301
1302	SuperClassWriter::definition_start();
1303
1304	break;
1305	}
1306	default :
1307	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1308	<< "[ type = " << SuperClass::type << "]"
1309	<< " not implemented yet !");
1310	}
1311	}
1312	catch (CNetCdfException& e)
1313	{
1314	StdString msg("On writing the axis : ");
1315	msg.append(axisid); msg.append("\n");
1316	msg.append("In the context : ");
1317	CContext* context = CContext::getCurrent() ;
1318	msg.append(context->getId()); msg.append("\n");
1319	msg.append(e.what());
1320	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1321	}
1322	axis->addRelFile(this->filename);
1323	}
1324
1325	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1326	{
1327	if (scalar->IsWritten(this->filename)) return;
1328	scalar->checkAttributes();
1329	int scalarSize = 1;
1330
1331	StdString scalaId = scalar->getScalarOutputName();
1332	StdString boundsId;
1333	if (isWrittenAxis(scalaId)) return ;
1334	else setWrittenAxis(scalaId);
1335
1336	nc_type typePrec ;
1337	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1338	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1339	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1340
1341	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1342	string strId="str_len" ;
1343
1344	try
1345	{
1346	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1347
1348	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1349	{
1350	std::vector<StdString> dims;
1351	StdString scalarDim = scalaId;
1352
1353	if (!scalar->label.isEmpty()) dims.push_back(strId);
1354
1355	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1356
1357	if (!scalar->name.isEmpty())
1358	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1359
1360	if (!scalar->standard_name.isEmpty())
1361	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1362
1363	if (!scalar->long_name.isEmpty())
1364	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1365
1366	if (!scalar->unit.isEmpty())
1367	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1368
1369	if (!scalar->axis_type.isEmpty())
1370	{
1371	switch(scalar->axis_type)
1372	{
1373	case CScalar::axis_type_attr::X :
1374	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1375	break;
1376	case CScalar::axis_type_attr::Y :
1377	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1378	break;
1379	case CScalar::axis_type_attr::Z :
1380	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1381	break;
1382	case CScalar::axis_type_attr::T :
1383	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1384	break;
1385	}
1386	}
1387
1388	if (!scalar->positive.isEmpty())
1389	{
1390	SuperClassWriter::addAttribute("positive",
1391	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1392	&scalaId);
1393	}
1394
1395	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1396	{
1397	dims.clear();
1398	dims.push_back("axis_nbounds");
1399	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1400	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1401	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1402	}
1403
1404	SuperClassWriter::definition_end();
1405
1406	switch (SuperClass::type)
1407	{
1408	case MULTI_FILE:
1409	{
1410	CArray<double,1> scalarValue(scalarSize);
1411	CArray<string,1> scalarLabel(scalarSize);
1412	CArray<double,1> scalarBounds(scalarSize*2);
1413
1414	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1415	{
1416	scalarValue(0) = scalar->value;
1417	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1418	}
1419
1420	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1421	{
1422	scalarBounds(0) = scalar->bounds(0);
1423	scalarBounds(1) = scalar->bounds(1);
1424	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1425	}
1426
1427	if (!scalar->label.isEmpty())
1428	{
1429	scalarLabel(0) = scalar->label;
1430	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1431	}
1432
1433	SuperClassWriter::definition_start();
1434
1435	break;
1436	}
1437	case ONE_FILE:
1438	{
1439	CArray<double,1> scalarValue(scalarSize);
1440	CArray<string,1> scalarLabel(scalarSize);
1441	CArray<double,1> scalarBounds(scalarSize*2);
1442
1443	std::vector<StdSize> start(1);
1444	std::vector<StdSize> count(1);
1445	start[0] = 0;
1446	count[0] = 1;
1447	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1448	{
1449	scalarValue(0) = scalar->value;
1450	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1451	}
1452	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1453	{
1454	scalarBounds(0) = scalar->bounds(0);
1455	scalarBounds(1) = scalar->bounds(1);
1456	count[0] = 2;
1457	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1458	}
1459	if (!scalar->label.isEmpty())
1460	{
1461	scalarLabel(0) = scalar->label;
1462	count[0] = stringArrayLen;
1463	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1464	}
1465
1466	SuperClassWriter::definition_start();
1467
1468	break;
1469	}
1470	default :
1471	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1472	<< "[ type = " << SuperClass::type << "]"
1473	<< " not implemented yet !");
1474	}
1475	}
1476	}
1477	catch (CNetCdfException& e)
1478	{
1479	StdString msg("On writing the scalar : ");
1480	msg.append(scalaId); msg.append("\n");
1481	msg.append("In the context : ");
1482	CContext* context = CContext::getCurrent() ;
1483	msg.append(context->getId()); msg.append("\n");
1484	msg.append(e.what());
1485	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1486	}
1487	scalar->addRelFile(this->filename);
1488	}
1489
1490	//--------------------------------------------------------------
1491
1492	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1493	{
1494	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1495
1496	// NOTA : The cuurent algorithm to write compress elements of the grid
1497	// will work pretting well when on server side you dont't get
1498	// partial overlap on elements between differents participating process
1499	// So the element must be totally distributed or non distributed
1500	// If an element is partially overlaping betwwen process then the
1501	// total compressed part will apear artificially greater than expected
1502	// For the current implementation of writer which is decomposed only on
1503	// one element, it will work as expected, but for future, it must be
1504	// reconsidered again.
1505	try
1506	{
1507	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1508	std::vector<StdString> domainList = grid->getDomainList();
1509	std::vector<StdString> axisList = grid->getAxisList();
1510	std::vector<StdString> scalarList = grid->getScalarList();
1511	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1512	int commRank ;
1513	MPI_Comm_rank(comm_file,&commRank) ;
1514
1515	std::vector<StdString> dims;
1516
1517	for (int i = 0; i < numElement; ++i)
1518	{
1519	StdString varId, compress;
1520	CArray<size_t, 1> indexes;
1521	bool isDistributed;
1522	size_t nbIndexes, totalNbIndexes, offset;
1523	size_t firstGlobalIndex;
1524
1525	if (2 == axisDomainOrder(i))
1526	{
1527	CDomain* domain = CDomain::get(domainList[idxDomain]);
1528	StdString domId = domain->getDomainOutputName();
1529
1530	if (!domain->isCompressible()
1531	\|\| domain->type == CDomain::type_attr::unstructured
1532	\|\| domain->isWrittenCompressed(this->filename)
1533	\|\| isWrittenCompressedDomain(domId))
1534	continue;
1535
1536	// unstructured grid seems not be taken into account why ?
1537
1538	string lonName,latName ;
1539
1540	if (domain->lon_name.isEmpty())
1541	{
1542	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1543	else lonName = "lon";
1544	}
1545	else lonName = domain->lon_name;
1546
1547	if (domain->lat_name.isEmpty())
1548	{
1549	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1550	else latName = "lat";
1551	}
1552	else latName = domain->lat_name;
1553
1554	StdString appendDomId = singleDomain ? "" : "_" + domId;
1555
1556	varId = domId + "_points";
1557	compress = latName + appendDomId + " " + lonName + appendDomId;
1558
1559	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
1560	workflowView->getGlobalIndexView(indexes) ;
1561	nbIndexes = workflowView->getSize() ;
1562	isDistributed = domain->isDistributed();
1563	if (isDistributed)
1564	{
1565	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1566	if (commRank==0) offset=0 ;
1567	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1568	}
1569	else
1570	{
1571	offset=0 ;
1572	totalNbIndexes = nbIndexes ;
1573	}
1574
1575	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1576
1577	domain->addRelFileCompressed(this->filename);
1578	setWrittenCompressedDomain(domId);
1579	++idxDomain;
1580	}
1581	else if (1 == axisDomainOrder(i))
1582	{
1583	CAxis* axis = CAxis::get(axisList[idxAxis]);
1584	StdString axisId = axis->getAxisOutputName();
1585
1586	if (!axis->isCompressible()
1587	\|\| axis->isWrittenCompressed(this->filename)
1588	\|\| isWrittenCompressedAxis(axisId))
1589	continue;
1590
1591	varId = axisId + "_points";
1592	compress = axisId;
1593
1594	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
1595	workflowView->getGlobalIndexView(indexes) ;
1596	nbIndexes = workflowView->getSize() ;
1597	isDistributed = axis->isDistributed();
1598	if (isDistributed)
1599	{
1600	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1601	if (commRank==0) offset=0 ;
1602	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1603	}
1604	else
1605	{
1606	offset=0 ;
1607	totalNbIndexes = nbIndexes ;
1608	}
1609	firstGlobalIndex = axis->begin;
1610
1611	axis->addRelFileCompressed(this->filename);
1612	setWrittenCompressedAxis(axisId);
1613	++idxAxis;
1614	}
1615	else
1616	{
1617	//for scalar
1618	}
1619
1620	if (!varId.empty())
1621	{
1622	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1623
1624	dims.clear();
1625	dims.push_back(varId);
1626	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
1627
1628	SuperClassWriter::addAttribute("compress", compress, &varId);
1629
1630	switch (SuperClass::type)
1631	{
1632	case (MULTI_FILE):
1633	{
1634	indexes -= firstGlobalIndex;
1635	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1636	break;
1637	}
1638	case (ONE_FILE):
1639	{
1640	std::vector<StdSize> start, count;
1641	start.push_back(offset);
1642	count.push_back(nbIndexes);
1643
1644	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1645	break;
1646	}
1647	}
1648	}
1649	}
1650
1651	grid->addRelFileCompressed(this->filename);
1652	}
1653	catch (CNetCdfException& e)
1654	{
1655	StdString msg("On writing compressed grid : ");
1656	msg.append(grid->getId()); msg.append("\n");
1657	msg.append("In the context : ");
1658	CContext* context = CContext::getCurrent();
1659	msg.append(context->getId()); msg.append("\n");
1660	msg.append(e.what());
1661	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1662	}
1663	}
1664
1665	//--------------------------------------------------------------
1666
1667	void CNc4DataOutput::writeTimeDimension_(void)
1668	{
1669	try
1670	{
1671	SuperClassWriter::addDimension(getTimeCounterName());
1672	}
1673	catch (CNetCdfException& e)
1674	{
1675	StdString msg("On writing time dimension : time_couter\n");
1676	msg.append("In the context : ");
1677	CContext* context = CContext::getCurrent() ;
1678	msg.append(context->getId()); msg.append("\n");
1679	msg.append(e.what());
1680	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1681	}
1682	}
1683
1684	//--------------------------------------------------------------
1685
1686	void CNc4DataOutput::writeField_(CField* field)
1687	{
1688	CContext* context = CContext::getCurrent() ;
1689
1690	std::vector<StdString> dims, coodinates;
1691	CGrid* grid = field->getGrid();
1692	if (!grid->doGridHaveDataToWrite())
1693	if (SuperClass::type==MULTI_FILE) return ;
1694
1695	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1696	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1697	std::vector<StdString> domainList = grid->getDomainList();
1698	std::vector<StdString> axisList = grid->getAxisList();
1699	std::vector<StdString> scalarList = grid->getScalarList();
1700
1701	StdString timeid = getTimeCounterName();
1702	StdString dimXid,dimYid;
1703	std::deque<StdString> dimIdList, dimCoordList;
1704	bool hasArea = false;
1705	StdString cellMeasures = "area:";
1706	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1707
1708	for (int i = 0; i < numElement; ++i)
1709	{
1710	if (2 == axisDomainOrder(i))
1711	{
1712	CDomain* domain = CDomain::get(domainList[idxDomain]);
1713	StdString domId = domain->getDomainOutputName();
1714	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1715	StdString lonName,latName ;
1716	StdString dimIname,dimJname ;
1717
1718	if (domain->lon_name.isEmpty())
1719	{
1720	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1721	else lonName = "lon";
1722	}
1723	else lonName = domain->lon_name;
1724
1725	if (domain->lat_name.isEmpty())
1726	{
1727	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1728	else latName = "lat";
1729	}
1730	else latName = domain->lat_name;
1731
1732	if (domain->dim_i_name.isEmpty())
1733	{
1734	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1735	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1736	else dimIname = lonName;
1737	}
1738	else dimIname = domain->dim_i_name;
1739
1740	if (domain->dim_j_name.isEmpty())
1741	{
1742	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1743	else dimJname = latName;
1744	}
1745	else dimJname = domain->dim_j_name;
1746
1747	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1748	{
1749	dimIdList.push_back(domId + "_points");
1750	field->setUseCompressedOutput();
1751	}
1752
1753	switch (domain->type)
1754	{
1755	case CDomain::type_attr::curvilinear:
1756	if (!compressedOutput \|\| !domain->isCompressible())
1757	{
1758	dimXid=dimIname+appendDomId;
1759	dimYid=dimJname+appendDomId;
1760	dimIdList.push_back(dimXid);
1761	dimIdList.push_back(dimYid);
1762	}
1763	dimCoordList.push_back(lonName+appendDomId);
1764	dimCoordList.push_back(latName+appendDomId);
1765	break ;
1766	case CDomain::type_attr::rectilinear:
1767	if (!compressedOutput \|\| !domain->isCompressible())
1768	{
1769	dimXid = dimIname+appendDomId;
1770	dimYid = dimJname+appendDomId;
1771	dimIdList.push_back(dimXid);
1772	dimIdList.push_back(dimYid);
1773	}
1774	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1775	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1776
1777	break ;
1778	case CDomain::type_attr::unstructured:
1779	{
1780	if (SuperClassWriter::useCFConvention)
1781	{
1782	dimXid = dimIname + appendDomId;
1783	dimIdList.push_back(dimXid);
1784	dimCoordList.push_back(lonName+appendDomId);
1785	dimCoordList.push_back(latName+appendDomId);
1786	}
1787	else
1788	{
1789	StdString domainName = domain->name;
1790	if (domain->nvertex == 1)
1791	{
1792	dimXid = "n" + domainName + "_node";
1793	dimIdList.push_back(dimXid);
1794	dimCoordList.push_back(StdString(domainName + "_node_x"));
1795	dimCoordList.push_back(StdString(domainName + "_node_y"));
1796	}
1797	else if (domain->nvertex == 2)
1798	{
1799	dimXid = "n" + domainName + "_edge";
1800	dimIdList.push_back(dimXid);
1801	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1802	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1803	}
1804	else
1805	{
1806	dimXid = "n" + domainName + "_face";
1807	dimIdList.push_back(dimXid);
1808	dimCoordList.push_back(StdString(domainName + "_face_x"));
1809	dimCoordList.push_back(StdString(domainName + "_face_y"));
1810	}
1811	} // ugrid convention
1812	} // case unstructured domain
1813	}
1814
1815	if (domain->hasArea)
1816	{
1817	hasArea = true;
1818	cellMeasures += " area" + appendDomId;
1819	}
1820	++idxDomain;
1821	}
1822	else if (1 == axisDomainOrder(i))
1823	{
1824	CAxis* axis = CAxis::get(axisList[idxAxis]);
1825	StdString axisId = axis->getAxisOutputName();
1826	StdString axisDim;
1827
1828	if (axis->dim_name.isEmpty()) axisDim = axisId;
1829	else axisDim=axis->dim_name.getValue();
1830
1831	if (compressedOutput && axis->isCompressible())
1832	{
1833	dimIdList.push_back(axisDim + "_points");
1834	field->setUseCompressedOutput();
1835	}
1836	else
1837	dimIdList.push_back(axisDim);
1838
1839	if (axisDim != axisId) dimCoordList.push_back(axisId);
1840	++idxAxis;
1841	}
1842	else
1843	{
1844	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1845	StdString scalarId = scalar->getScalarOutputName();
1846	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1847	dimCoordList.push_back(scalarId);
1848	++idxScalar;
1849	}
1850	}
1851
1852	StdString fieldid = field->getFieldOutputName();
1853
1854	nc_type type ;
1855	if (field->prec.isEmpty()) type = NC_FLOAT ;
1856	else
1857	{
1858	if (field->prec==2) type = NC_SHORT ;
1859	else if (field->prec==4) type = NC_FLOAT ;
1860	else if (field->prec==8) type = NC_DOUBLE ;
1861	}
1862
1863	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1864
1865	if (wtime)
1866	{
1867	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1868	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
1869	dims.push_back(timeid);
1870	}
1871
1872	while (!dimIdList.empty())
1873	{
1874	dims.push_back(dimIdList.back());
1875	dimIdList.pop_back();
1876	}
1877
1878	while (!dimCoordList.empty())
1879	{
1880	coodinates.push_back(dimCoordList.back());
1881	dimCoordList.pop_back();
1882	}
1883
1884	try
1885	{
1886	SuperClassWriter::addVariable(fieldid, type, dims);
1887
1888	if (!field->standard_name.isEmpty())
1889	SuperClassWriter::addAttribute
1890	("standard_name", field->standard_name.getValue(), &fieldid);
1891
1892	if (!field->long_name.isEmpty())
1893	SuperClassWriter::addAttribute
1894	("long_name", field->long_name.getValue(), &fieldid);
1895
1896	if (!field->unit.isEmpty())
1897	SuperClassWriter::addAttribute
1898	("units", field->unit.getValue(), &fieldid);
1899
1900	// Ugrid field attributes "mesh" and "location"
1901	if (!SuperClassWriter::useCFConvention)
1902	{
1903	if (!domainList.empty())
1904	{
1905	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
1906	StdString mesh = domain->name;
1907	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
1908	StdString location;
1909	if (domain->nvertex == 1)
1910	location = "node";
1911	else if (domain->nvertex == 2)
1912	location = "edge";
1913	else if (domain->nvertex > 2)
1914	location = "face";
1915	SuperClassWriter::addAttribute("location", location, &fieldid);
1916	}
1917
1918	}
1919
1920	if (!field->valid_min.isEmpty())
1921	SuperClassWriter::addAttribute
1922	("valid_min", field->valid_min.getValue(), &fieldid);
1923
1924	if (!field->valid_max.isEmpty())
1925	SuperClassWriter::addAttribute
1926	("valid_max", field->valid_max.getValue(), &fieldid);
1927
1928	if (!field->scale_factor.isEmpty())
1929	SuperClassWriter::addAttribute
1930	("scale_factor", field->scale_factor.getValue(), &fieldid);
1931
1932	if (!field->add_offset.isEmpty())
1933	SuperClassWriter::addAttribute
1934	("add_offset", field->add_offset.getValue(), &fieldid);
1935
1936	SuperClassWriter::addAttribute
1937	("online_operation", field->operation.getValue(), &fieldid);
1938
1939	// write child variables as attributes
1940
1941
1942	bool alreadyAddCellMethod = false;
1943	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1944	if (!field->cell_methods.isEmpty())
1945	{
1946	StdString cellMethodString = field->cell_methods;
1947	if (field->cell_methods_mode.isEmpty() \|\|
1948	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1949	{
1950	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1951	alreadyAddCellMethod = true;
1952	}
1953	else
1954	{
1955	switch (field->cell_methods_mode)
1956	{
1957	case (CField::cell_methods_mode_attr::prefix):
1958	cellMethodsPrefix = cellMethodString;
1959	cellMethodsPrefix += " ";
1960	break;
1961	case (CField::cell_methods_mode_attr::suffix):
1962	cellMethodsSuffix = " ";
1963	cellMethodsSuffix += cellMethodString;
1964	break;
1965	case (CField::cell_methods_mode_attr::none):
1966	break;
1967	default:
1968	break;
1969	}
1970	}
1971	}
1972
1973
1974	if (wtime)
1975	{
1976	CDuration freqOp = field->freq_op.getValue();
1977	freqOp.solveTimeStep(*context->calendar);
1978	StdString freqOpStr = freqOp.toStringUDUnits();
1979	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1980
1981	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1982	freqOut.solveTimeStep(*context->calendar);
1983	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1984
1985	StdString cellMethods(cellMethodsPrefix + "time: ");
1986	if (field->operation.getValue() == "instant") cellMethods += "point";
1987	else if (field->operation.getValue() == "average") cellMethods += "mean";
1988	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1989	else cellMethods += field->operation;
1990	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1991	cellMethods += " (interval: " + freqOpStr + ")";
1992	cellMethods += cellMethodsSuffix;
1993	if (!alreadyAddCellMethod)
1994	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1995	}
1996
1997	if (hasArea)
1998	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1999
2000	if (!field->default_value.isEmpty())
2001	{
2002	double default_value = field->default_value.getValue();
2003	if (type == NC_DOUBLE)
2004	{
2005	SuperClassWriter::setDefaultValue(fieldid, &default_value);
2006	}
2007	else if (type == NC_SHORT)
2008	{
2009	short sdefault_value = (short)default_value;
2010	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
2011	}
2012	else
2013	{
2014	float fdefault_value = (float)default_value;
2015	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
2016	}
2017	}
2018	else
2019	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
2020
2021	if (field->compression_level.isEmpty())
2022	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
2023	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
2024
2025	{ // Ecriture des coordonnes
2026
2027	StdString coordstr; //boost::algorithm::join(coodinates, " ")
2028	std::vector<StdString>::iterator
2029	itc = coodinates.begin(), endc = coodinates.end();
2030
2031	for (; itc!= endc; itc++)
2032	{
2033	StdString & coord = *itc;
2034	if (itc+1 != endc)
2035	coordstr.append(coord).append(" ");
2036	else coordstr.append(coord);
2037	}
2038
2039	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
2040
2041	}
2042
2043	vector<CVariable*> listVars = field->getAllVariables() ;
2044	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
2045
2046	}
2047	catch (CNetCdfException& e)
2048	{
2049	StdString msg("On writing field : ");
2050	msg.append(fieldid); msg.append("\n");
2051	msg.append("In the context : ");
2052	msg.append(context->getId()); msg.append("\n");
2053	msg.append(e.what());
2054	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2055	}
2056	} // writeField_()
2057
2058	//--------------------------------------------------------------
2059
2060	void CNc4DataOutput::writeFile_ (CFile* file)
2061	{
2062	StdString filename = file->getFileOutputName();
2063	StdString description = (!file->description.isEmpty())
2064	? file->description.getValue()
2065	: StdString("Created by xios");
2066
2067	singleDomain = (file->nbDomains == 1);
2068
2069	StdString conv_str ;
2070	if (file->convention_str.isEmpty())
2071	{
2072	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2073	else conv_str="UGRID" ;
2074	}
2075	else conv_str=file->convention_str ;
2076
2077	try
2078	{
2079	if (!appendMode) this->writeFileAttributes(filename, description,
2080	conv_str,
2081	StdString("An IPSL model"),
2082	this->getTimeStamp());
2083
2084	if (!appendMode)
2085	SuperClassWriter::addDimension("axis_nbounds", 2);
2086	}
2087	catch (CNetCdfException& e)
2088	{
2089	StdString msg("On writing file : ");
2090	msg.append(filename); msg.append("\n");
2091	msg.append("In the context : ");
2092	CContext* context = CContext::getCurrent() ;
2093	msg.append(context->getId()); msg.append("\n");
2094	msg.append(e.what());
2095	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2096	}
2097	}
2098
2099	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2100	{
2101	StdString name = var->getVariableOutputName();
2102
2103	try
2104	{
2105	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2106	addAttribute(name, var->getData<int>(), &fieldId);
2107	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2108	addAttribute(name, var->getData<short int>(), &fieldId);
2109	else if (var->type.getValue() == CVariable::type_attr::t_float)
2110	addAttribute(name, var->getData<float>(), &fieldId);
2111	else if (var->type.getValue() == CVariable::type_attr::t_double)
2112	addAttribute(name, var->getData<double>(), &fieldId);
2113	else if (var->type.getValue() == CVariable::type_attr::t_string)
2114	addAttribute(name, var->getData<string>(), &fieldId);
2115	else
2116	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2117	<< "Unsupported variable of type " << var->type.getStringValue());
2118	}
2119	catch (CNetCdfException& e)
2120	{
2121	StdString msg("On writing attributes of variable with name : ");
2122	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2123	msg.append("In the context : ");
2124	CContext* context = CContext::getCurrent() ;
2125	msg.append(context->getId()); msg.append("\n");
2126	msg.append(e.what());
2127	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2128	}
2129	}
2130
2131	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2132	{
2133	StdString name = var->getVariableOutputName();
2134
2135	try
2136	{
2137	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2138	addAttribute(name, var->getData<int>());
2139	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2140	addAttribute(name, var->getData<short int>());
2141	else if (var->type.getValue() == CVariable::type_attr::t_float)
2142	addAttribute(name, var->getData<float>());
2143	else if (var->type.getValue() == CVariable::type_attr::t_double)
2144	addAttribute(name, var->getData<double>());
2145	else if (var->type.getValue() == CVariable::type_attr::t_string)
2146	addAttribute(name, var->getData<string>());
2147	else
2148	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2149	<< "Unsupported variable of type " << var->type.getStringValue());
2150	}
2151	catch (CNetCdfException& e)
2152	{
2153	StdString msg("On writing attributes of variable with name : ");
2154	msg.append(name); msg.append("\n");
2155	msg.append("In the context : ");
2156	CContext* context = CContext::getCurrent() ;
2157	msg.append(context->getId()); msg.append("\n");
2158	msg.append(e.what());
2159	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2160	}
2161	}
2162
2163	void CNc4DataOutput::syncFile_ (void)
2164	{
2165	try
2166	{
2167	SuperClassWriter::sync() ;
2168	}
2169	catch (CNetCdfException& e)
2170	{
2171	StdString msg("On synchronizing the write among processes");
2172	msg.append("In the context : ");
2173	CContext* context = CContext::getCurrent() ;
2174	msg.append(context->getId()); msg.append("\n");
2175	msg.append(e.what());
2176	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2177	}
2178	}
2179
2180	void CNc4DataOutput::closeFile_ (void)
2181	{
2182	try
2183	{
2184	SuperClassWriter::close() ;
2185	}
2186	catch (CNetCdfException& e)
2187	{
2188	StdString msg("On closing file");
2189	msg.append("In the context : ");
2190	CContext* context = CContext::getCurrent() ;
2191	msg.append(context->getId()); msg.append("\n");
2192	msg.append(e.what());
2193	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2194	}
2195
2196	}
2197
2198	//---------------------------------------------------------------
2199
2200	StdString CNc4DataOutput::getTimeStamp(void) const
2201	{
2202	const int buffer_size = 100;
2203	time_t rawtime;
2204	struct tm * timeinfo = NULL;
2205	char buffer [buffer_size];
2206	StdString formatStr;
2207	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2208	else formatStr=file->time_stamp_format;
2209
2210	// time ( &rawtime );
2211	// timeinfo = localtime ( &rawtime );
2212	time ( &rawtime );
2213	timeinfo = gmtime ( &rawtime );
2214	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2215
2216	return (StdString(buffer));
2217	}
2218
2219	//---------------------------------------------------------------
2220
2221	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
2222	const CDate& currentWrite, int nstep)
2223	{
2224	CContext* context = CContext::getCurrent();
2225	CGrid* grid = field->getGrid();
2226
2227	if (nstep<1)
2228	{
2229	return nstep;
2230	}
2231
2232	if (!grid->doGridHaveDataToWrite())
2233	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2234	{
2235	return nstep;
2236	}
2237
2238	StdString fieldid = field->getFieldOutputName();
2239
2240	StdOStringStream oss;
2241	string timeAxisId;
2242	if (field->hasTimeInstant) timeAxisId = "time_instant";
2243	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2244
2245	StdString timeBoundId = getTimeCounterName() + "_bounds";
2246
2247	StdString timeAxisBoundId;
2248	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2249	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2250
2251	if (!field->wasWritten())
2252	{
2253	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
2254	field->getOperationTimeType() != func::CFunctor::once)
2255	{
2256	double factorUnit;
2257	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2258	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2259	else factorUnit=1 ;
2260	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
2261	}
2262
2263	field->setWritten();
2264	}
2265
2266
2267	CArray<double,1> time_data(1);
2268	CArray<double,1> time_data_bound(2);
2269	CArray<double,1> time_counter(1);
2270	CArray<double,1> time_counter_bound(2);
2271
2272	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2273	bool wtimeCounter =false ;
2274	bool wtimeData =false ;
2275
2276
2277	if (wtime)
2278	{
2279
2280	if (field->hasTimeInstant)
2281	{
2282	time_data(0) = time_data_bound(1) = (Time) lastWrite;
2283	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
2284	if (timeCounterType==instant)
2285	{
2286	time_counter(0) = time_data(0);
2287	time_counter_bound(0) = time_data_bound(0);
2288	time_counter_bound(1) = time_data_bound(1);
2289	wtimeCounter=true ;
2290	}
2291	if (hasTimeInstant) wtimeData=true ;
2292	}
2293	else if (field->hasTimeCentered)
2294	{
2295	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
2296	time_data_bound(0) = (Time)lastWrite;
2297	time_data_bound(1) = (Time)currentWrite;
2298	if (timeCounterType==centered)
2299	{
2300	time_counter(0) = time_data(0) ;
2301	time_counter_bound(0) = time_data_bound(0) ;
2302	time_counter_bound(1) = time_data_bound(1) ;
2303	wtimeCounter=true ;
2304	}
2305	if (hasTimeCentered) wtimeData=true ;
2306	}
2307
2308	if (timeCounterType==record)
2309	{
2310	time_counter(0) = nstep - 1;
2311	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
2312	wtimeCounter=true ;
2313	}
2314
2315	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2316	{
2317	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2318	time_data/=secByDay;
2319	time_data_bound/=secByDay;
2320	time_counter/=secByDay;
2321	time_counter_bound/=secByDay;
2322	}
2323	}
2324
2325	bool isRoot = (context->intraCommRank_ == 0);
2326
2327	try
2328	{
2329	switch (SuperClass::type)
2330	{
2331	case (MULTI_FILE) :
2332	{
2333	CTimer::get("Files : writing data").resume();
2334	SuperClassWriter::writeData(data, fieldid, isCollective, nstep - 1);
2335	CTimer::get("Files : writing data").suspend();
2336	if (wtime)
2337	{
2338	CTimer::get("Files : writing time axis").resume();
2339	if ( wtimeData)
2340	{
2341	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2342	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2343	}
2344	if (wtimeCounter)
2345	{
2346	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2347	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2348	}
2349	CTimer::get("Files : writing time axis").suspend();
2350	}
2351	break;
2352	}
2353	case (ONE_FILE) :
2354	{
2355
2356	std::vector<StdSize> start, count;
2357
2358	if (field->getUseCompressedOutput())
2359	{
2360	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2361	std::vector<StdString> domainList = grid->getDomainList();
2362	std::vector<StdString> axisList = grid->getAxisList();
2363	int numElement = axisDomainOrder.numElements();
2364	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2365	int idx = domainList.size() * 2 + axisList.size() - 1;
2366	int commRank ;
2367
2368	MPI_Comm_rank(comm_file,&commRank) ;
2369
2370	start.reserve(idx+1);
2371	count.reserve(idx+1);
2372
2373	for (int i = numElement - 1; i >= 0; --i)
2374	{
2375	if (2 == axisDomainOrder(i))
2376	{
2377	CDomain* domain = CDomain::get(domainList[idxDomain]);
2378
2379	if (domain->isCompressible())
2380	{
2381	size_t offset ;
2382	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
2383	if (domain->isDistributed())
2384	{
2385	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2386	if (commRank==0) offset=0 ;
2387	}
2388	else offset=0 ;
2389
2390	start.push_back(offset);
2391	count.push_back(nbIndexes);
2392	idx -= 2;
2393	}
2394	else
2395	{
2396	if ((domain->type) != CDomain::type_attr::unstructured)
2397	{
2398	start.push_back(domain->jbegin);
2399	count.push_back(domain->nj);
2400	}
2401	--idx;
2402	start.push_back(domain->ibegin);
2403	count.push_back(domain->ni);
2404	--idx;
2405	}
2406	--idxDomain;
2407	}
2408	else if (1 == axisDomainOrder(i))
2409	{
2410	CAxis* axis = CAxis::get(axisList[idxAxis]);
2411
2412	if (axis->isCompressible())
2413	{
2414	size_t offset ;
2415	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
2416	if (axis->isDistributed())
2417	{
2418	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2419	if (commRank==0) offset=0 ;
2420	}
2421	else offset=0 ;
2422
2423	start.push_back(offset);
2424	count.push_back(nbIndexes);
2425	}
2426	else
2427	{
2428	start.push_back(axis->begin);
2429	count.push_back(axis->n);
2430	}
2431	--idxAxis;
2432	--idx;
2433	}
2434	}
2435	}
2436	else
2437	{
2438	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2439	std::vector<StdString> domainList = grid->getDomainList();
2440	std::vector<StdString> axisList = grid->getAxisList();
2441	std::vector<StdString> scalarList = grid->getScalarList() ;
2442	int numElement = axisDomainOrder.numElements();
2443	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2444	int idx = domainList.size() * 2 + axisList.size() - 1;
2445
2446	start.reserve(idx+1);
2447	count.reserve(idx+1);
2448
2449	for (int i = numElement - 1; i >= 0; --i)
2450	{
2451	if (2 == axisDomainOrder(i))
2452	{
2453	CDomain* domain = CDomain::get(domainList[idxDomain]);
2454	if ((domain->type) != CDomain::type_attr::unstructured)
2455	{
2456	start.push_back(domain->jbegin);
2457	count.push_back(domain->nj);
2458	}
2459	--idx ;
2460
2461	start.push_back(domain->ibegin);
2462	count.push_back(domain->ni);
2463	--idx ;
2464	--idxDomain;
2465	}
2466	else if (1 == axisDomainOrder(i))
2467	{
2468	CAxis* axis = CAxis::get(axisList[idxAxis]);
2469	start.push_back(axis->begin);
2470	count.push_back(axis->n);
2471	--idx;
2472	--idxAxis;
2473	}
2474	else
2475	{
2476	if (1 == axisDomainOrder.numElements())
2477	{
2478	CScalar* scalar = CScalar::get(scalarList[scalarList.size()-1]);
2479	start.push_back(0);
2480	count.push_back(scalar->n);
2481	}
2482	--idx;
2483	}
2484	}
2485	}
2486
2487
2488	CTimer::get("Files : writing data").resume();
2489	SuperClassWriter::writeData(data, fieldid, isCollective, nstep - 1, &start, &count);
2490	CTimer::get("Files : writing data").suspend();
2491
2492	if (wtime)
2493	{
2494	CTimer::get("Files : writing time axis").resume();
2495	if ( wtimeData)
2496	{
2497	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2498	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2499	}
2500	if (wtimeCounter)
2501	{
2502	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2503	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2504
2505	}
2506	CTimer::get("Files : writing time axis").suspend();
2507	}
2508
2509	break;
2510	}
2511	}
2512	return nstep ;
2513	}
2514	catch (CNetCdfException& e)
2515	{
2516	StdString msg("On writing field data: ");
2517	msg.append(fieldid); msg.append("\n");
2518	msg.append("In the context : ");
2519	msg.append(context->getId()); msg.append("\n");
2520	msg.append(e.what());
2521	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2522	}
2523	}
2524
2525	//---------------------------------------------------------------
2526
2527	void CNc4DataOutput::writeTimeAxis_
2528	(CField* field,
2529	const std::shared_ptr<CCalendar> cal)
2530	{
2531	StdOStringStream oss;
2532	bool createInstantAxis=false ;
2533	bool createCenteredAxis=false ;
2534	bool createTimeCounterAxis=false ;
2535
2536	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2537
2538
2539	StdString axisId ;
2540	StdString axisBoundId;
2541	StdString timeid(getTimeCounterName());
2542	StdString timeBoundId("axis_nbounds");
2543
2544	StdString strTimeUnits ;
2545	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2546	else strTimeUnits="seconds since " ;
2547
2548	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2549	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2550
2551
2552	if (field->getRelFile()->time_counter.isEmpty())
2553	{
2554	if (timeCounterType==none) createTimeCounterAxis=true ;
2555	if (field->hasTimeCentered)
2556	{
2557	timeCounterType=centered ;
2558	if (!hasTimeCentered) createCenteredAxis=true ;
2559	}
2560	if (field->hasTimeInstant)
2561	{
2562	if (timeCounterType==none) timeCounterType=instant ;
2563	if (!hasTimeInstant) createInstantAxis=true ;
2564	}
2565	}
2566	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
2567	{
2568	if (field->hasTimeCentered)
2569	{
2570	if (!hasTimeCentered) createCenteredAxis=true ;
2571	}
2572	if (field->hasTimeInstant)
2573	{
2574	if (timeCounterType==none) createTimeCounterAxis=true ;
2575	timeCounterType=instant ;
2576	if (!hasTimeInstant) createInstantAxis=true ;
2577	}
2578	}
2579	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
2580	{
2581	if (field->hasTimeCentered)
2582	{
2583	if (timeCounterType==none) createTimeCounterAxis=true ;
2584	timeCounterType=centered ;
2585	if (!hasTimeCentered) createCenteredAxis=true ;
2586	}
2587	if (field->hasTimeInstant)
2588	{
2589	if (!hasTimeInstant) createInstantAxis=true ;
2590	}
2591	}
2592	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
2593	{
2594	if (field->hasTimeCentered)
2595	{
2596	if (!hasTimeCentered) createCenteredAxis=true ;
2597	}
2598	if (field->hasTimeInstant)
2599	{
2600	if (timeCounterType==none) createTimeCounterAxis=true ;
2601	timeCounterType=instant ;
2602	}
2603	}
2604	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
2605	{
2606	if (field->hasTimeCentered)
2607	{
2608	if (timeCounterType==none) createTimeCounterAxis=true ;
2609	timeCounterType=centered ;
2610	}
2611	if (field->hasTimeInstant)
2612	{
2613	if (!hasTimeInstant) createInstantAxis=true ;
2614	}
2615	}
2616	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
2617	{
2618	if (field->hasTimeCentered)
2619	{
2620	if (timeCounterType==none) createTimeCounterAxis=true ;
2621	if (timeCounterType==instant) createInstantAxis=true ;
2622	timeCounterType=centered ;
2623	}
2624	if (field->hasTimeInstant)
2625	{
2626	if (timeCounterType==none)
2627	{
2628	createTimeCounterAxis=true ;
2629	timeCounterType=instant ;
2630	}
2631	if (timeCounterType==centered)
2632	{
2633	if (!hasTimeInstant) createInstantAxis=true ;
2634	}
2635	}
2636	}
2637	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
2638	{
2639	if (field->hasTimeCentered)
2640	{
2641	if (!hasTimeCentered) createCenteredAxis=true ;
2642	}
2643	if (field->hasTimeInstant)
2644	{
2645	if (!hasTimeInstant) createInstantAxis=true ;
2646	}
2647	}
2648	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
2649	{
2650	if (timeCounterType==none) createTimeCounterAxis=true ;
2651	timeCounterType=record ;
2652	if (field->hasTimeCentered)
2653	{
2654	if (!hasTimeCentered) createCenteredAxis=true ;
2655	}
2656	if (field->hasTimeInstant)
2657	{
2658	if (!hasTimeInstant) createInstantAxis=true ;
2659	}
2660	}
2661
2662	if (createInstantAxis)
2663	{
2664	axisId="time_instant" ;
2665	axisBoundId="time_instant_bounds";
2666	hasTimeInstant=true ;
2667	}
2668
2669	if (createCenteredAxis)
2670	{
2671	axisId="time_centered" ;
2672	axisBoundId="time_centered_bounds";
2673	hasTimeCentered=true ;
2674	}
2675
2676
2677	try
2678	{
2679	std::vector<StdString> dims;
2680
2681	if (createInstantAxis \|\| createCenteredAxis)
2682	{
2683	// Adding time_instant or time_centered
2684	dims.push_back(timeid);
2685	if (!SuperClassWriter::varExist(axisId))
2686	{
2687	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2688
2689	CDate timeOrigin=cal->getTimeOrigin() ;
2690	StdOStringStream oss2;
2691	StdString strInitdate=oss2.str() ;
2692	StdString strTimeOrigin=timeOrigin.toString() ;
2693	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2694	strTimeOrigin, axisBoundId);
2695	}
2696
2697	// Adding time_instant_bounds or time_centered_bounds variables
2698	if (!SuperClassWriter::varExist(axisBoundId))
2699	{
2700	dims.clear() ;
2701	dims.push_back(timeid);
2702	dims.push_back(timeBoundId);
2703	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2704	}
2705	}
2706
2707	if (createTimeCounterAxis)
2708	{
2709	// Adding time_counter
2710	axisId = getTimeCounterName();
2711	axisBoundId = getTimeCounterName() + "_bounds";
2712	dims.clear();
2713	dims.push_back(timeid);
2714	if (!SuperClassWriter::varExist(axisId))
2715	{
2716	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2717	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2718
2719	if (field->getRelFile()->time_counter.isEmpty() \|\|
2720	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2721	{
2722	CDate timeOrigin = cal->getTimeOrigin();
2723	StdString strTimeOrigin = timeOrigin.toString();
2724
2725	this->writeTimeAxisAttributes(axisId, cal->getType(),
2726	strTimeUnits+strTimeOrigin,
2727	strTimeOrigin, axisBoundId);
2728	}
2729	}
2730
2731	// Adding time_counter_bound dimension
2732	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2733	{
2734	if (!SuperClassWriter::varExist(axisBoundId))
2735	{
2736	dims.clear();
2737	dims.push_back(timeid);
2738	dims.push_back(timeBoundId);
2739	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2740	}
2741	}
2742	}
2743	}
2744	catch (CNetCdfException& e)
2745	{
2746	StdString msg("On writing time axis data: ");
2747	msg.append("In the context : ");
2748	CContext* context = CContext::getCurrent() ;
2749	msg.append(context->getId()); msg.append("\n");
2750	msg.append(e.what());
2751	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2752	const std::shared_ptr<CCalendar> cal)", << msg);
2753	}
2754	}
2755
2756	//---------------------------------------------------------------
2757
2758	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2759	const StdString & calendar,
2760	const StdString & units,
2761	const StdString & time_origin,
2762	const StdString & time_bounds,
2763	const StdString & standard_name,
2764	const StdString & long_name)
2765	{
2766	try
2767	{
2768	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2769	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2770	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2771	SuperClassWriter::addAttribute("units", units , &axis_name);
2772	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2773	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2774	}
2775	catch (CNetCdfException& e)
2776	{
2777	StdString msg("On writing time axis Attribute: ");
2778	msg.append("In the context : ");
2779	CContext* context = CContext::getCurrent() ;
2780	msg.append(context->getId()); msg.append("\n");
2781	msg.append(e.what());
2782	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2783	const StdString & calendar,\
2784	const StdString & units, \
2785	const StdString & time_origin, \
2786	const StdString & time_bounds, \
2787	const StdString & standard_name, \
2788	const StdString & long_name)", << msg);
2789	}
2790	}
2791
2792	//---------------------------------------------------------------
2793
2794	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2795	const StdString & axis,
2796	const StdString & standard_name,
2797	const StdString & long_name,
2798	const StdString & units,
2799	const StdString & nav_model)
2800	{
2801	try
2802	{
2803	if (!axis.empty())
2804	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2805
2806	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2807	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2808	SuperClassWriter::addAttribute("units" , units , &axis_name);
2809	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2810	}
2811	catch (CNetCdfException& e)
2812	{
2813	StdString msg("On writing Axis Attribute: ");
2814	msg.append("In the context : ");
2815	CContext* context = CContext::getCurrent() ;
2816	msg.append(context->getId()); msg.append("\n");
2817	msg.append(e.what());
2818	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2819	const StdString & axis, \
2820	const StdString & standard_name, \
2821	const StdString & long_name, \
2822	const StdString & units, \
2823	const StdString & nav_model)", << msg);
2824	}
2825	}
2826
2827	//---------------------------------------------------------------
2828
2829	void CNc4DataOutput::writeLocalAttributes
2830	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2831	{
2832	try
2833	{
2834	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2835	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2836	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2837	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2838	}
2839	catch (CNetCdfException& e)
2840	{
2841	StdString msg("On writing Local Attributes: ");
2842	msg.append("In the context : ");
2843	CContext* context = CContext::getCurrent() ;
2844	msg.append(context->getId()); msg.append("\n");
2845	msg.append(e.what());
2846	ERROR("CNc4DataOutput::writeLocalAttributes \
2847	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2848	}
2849
2850	}
2851
2852	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2853	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2854	{
2855	CArray<int,1> array(2) ;
2856
2857	try
2858	{
2859	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2860	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2861	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2862	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2863	array=ni_glo,nj_glo ;
2864	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2865	array=ni,nj ;
2866	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2867	array=ibegin+1,jbegin+1 ;
2868	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2869	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2870	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2871	array=0,0 ;
2872	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2873	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2874	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2875	/*
2876	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2877	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2878	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2879	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2880	*/
2881	}
2882	catch (CNetCdfException& e)
2883	{
2884	StdString msg("On writing Local Attributes IOIPSL \n");
2885	msg.append("In the context : ");
2886	CContext* context = CContext::getCurrent() ;
2887	msg.append(context->getId()); msg.append("\n");
2888	msg.append(e.what());
2889	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2890	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2891	}
2892	}
2893	//---------------------------------------------------------------
2894
2895	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2896	const StdString & description,
2897	const StdString & conventions,
2898	const StdString & production,
2899	const StdString & timeStamp)
2900	{
2901	try
2902	{
2903	SuperClassWriter::addAttribute("name" , name);
2904	SuperClassWriter::addAttribute("description", description);
2905	SuperClassWriter::addAttribute("title" , description);
2906	SuperClassWriter::addAttribute("Conventions", conventions);
2907	// SuperClassWriter::addAttribute("production" , production);
2908
2909	StdString timeStampStr ;
2910	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
2911	else timeStampStr=file->time_stamp_name ;
2912	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
2913
2914	StdString uuidName ;
2915	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
2916	else uuidName=file->uuid_name ;
2917
2918	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
2919	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
2920
2921	}
2922	catch (CNetCdfException& e)
2923	{
2924	StdString msg("On writing File Attributes \n ");
2925	msg.append("In the context : ");
2926	CContext* context = CContext::getCurrent() ;
2927	msg.append(context->getId()); msg.append("\n");
2928	msg.append(e.what());
2929	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2930	const StdString & description, \
2931	const StdString & conventions, \
2932	const StdString & production, \
2933	const StdString & timeStamp)", << msg);
2934	}
2935	}
2936
2937	//---------------------------------------------------------------
2938
2939	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2940	int data_dim,
2941	int data_ni,
2942	int data_nj,
2943	int data_ibegin,
2944	int data_jbegin)
2945	{
2946	try
2947	{
2948	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2949	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2950	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2951	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2952	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2953	}
2954	catch (CNetCdfException& e)
2955	{
2956	StdString msg("On writing Mask Attributes \n ");
2957	msg.append("In the context : ");
2958	CContext* context = CContext::getCurrent() ;
2959	msg.append(context->getId()); msg.append("\n");
2960	msg.append(e.what());
2961	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2962	int data_dim, \
2963	int data_ni, \
2964	int data_nj, \
2965	int data_ibegin, \
2966	int data_jbegin)", << msg);
2967	}
2968	}
2969
2970	///--------------------------------------------------------------
2971
2972	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
2973	{
2974	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2975	if (it == timeToRecordCache.end())
2976	{
2977	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2978	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
2979	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
2980
2981	CArray<double,2> timeAxisBounds;
2982	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
2983
2984	StdSize record = 0;
2985	double dtime(time);
2986	for (int n = dimSize[0] - 1; n >= 0; n--)
2987	{
2988	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
2989	timeAxisBounds*=factorUnit ;
2990	if (timeAxisBounds(1, 0) < dtime)
2991	{
2992	record = n + 1;
2993	break;
2994	}
2995	}
2996	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2997	}
2998	return it->second;
2999	}
3000
3001	///--------------------------------------------------------------
3002
3003	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3004	{
3005	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3006	}
3007
3008	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3009	{
3010	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3011	}
3012
3013	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3014	{
3015	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3016	}
3017
3018	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3019	{
3020	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3021	}
3022
3023	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3024	{
3025	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3026	}
3027
3028	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3029	{
3030	this->writtenDomains.insert(domainName);
3031	}
3032
3033	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3034	{
3035	this->writtenCompressedDomains.insert(domainName);
3036	}
3037
3038	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3039	{
3040	this->writtenAxis.insert(axisName);
3041	}
3042
3043	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3044	{
3045	this->writtenCompressedAxis.insert(axisName);
3046	}
3047
3048	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3049	{
3050	this->writtenScalar.insert(scalarName);
3051	}
3052	} // namespace xios

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