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source: XIOS3/trunk/src/io/nc4_data_output.cpp @ 2381

Last change on this file since 2381 was 2381, checked in by jderouillat, 2 years ago
Fix a bug on element names introduced in CGrid::duplicateSentGrid (commit 2351), the bug appeared with many grids in a file.
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: 130.0 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 ( !relElements_.count ( defaultNameKey ) )
127	{
128	// if defaultNameKey not in the map, write the element such as it is defined
129	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, defaultNameKey) ) );
130	}
131	else // look if a hash associated this key is equal
132	{
133	bool elementIsInMap(false);
134	auto defaultNameKeyElements = relElements_.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;
141	// lon/lat names must be updated too, check that its exist, if not "lon"/"lat" (default values) are used
142	StdString lon_name = "lon_"+it->second.second;
143	int ncid = SuperClassWriter::getCurrentGroup();
144	int varId = 0;
145	nc_inq_varid(ncid, lon_name.c_str(), &varId);
146	if (!varId) //lon_name = "lon"
147	{
148	domain->lon_name = "lon";
149	domain->lat_name = "lat";
150	}
151	else
152	{
153	domain->lon_name = "lon_"+it->second.second;
154	domain->lat_name = "lat_"+it->second.second;
155	}
156	elementIsInMap = true;
157	}
158	}
159	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
160	if (!elementIsInMap) // ! in MAP
161	{
162	domain->name = domain->getId();
163	domain->lon_name = "lon_"+domain->getId();
164	domain->lat_name = "lat_"+domain->getId();
165	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain->getDomainOutputName()) ) ) ;// = domain->getId()
166	}
167	}
168	}
169
170
171	std::vector<StdString> dim0, dim1;
172	StdString domid = domain->getDomainOutputName();
173	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
174	if (isWrittenDomain(domid)) return ;
175	else setWrittenDomain(domid);
176
177	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
178
179
180	StdString dimXid, dimYid ;
181
182	nc_type typePrec ;
183	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
184	else if (domain->prec==4) typePrec = NC_FLOAT ;
185	else if (domain->prec==8) typePrec = NC_DOUBLE ;
186
187	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
188	switch (domain->type)
189	{
190	case CDomain::type_attr::curvilinear :
191
192	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
193	else lonName = domain->lon_name;
194
195	if (domain->lat_name.isEmpty()) latName = "nav_lat";
196	else latName = domain->lat_name;
197
198	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
199	else dimXid=domain->dim_i_name.getValue() + appendDomid;
200
201	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
202	else dimYid=domain->dim_j_name.getValue() + appendDomid;
203
204	break ;
205
206	case CDomain::type_attr::rectilinear :
207
208	if (domain->lon_name.isEmpty())
209	{
210	if (domain->dim_i_name.isEmpty())
211	lonName = "lon";
212	else
213	lonName = domain->dim_i_name.getValue();
214	}
215	else lonName = domain->lon_name;
216
217	if (domain->lat_name.isEmpty())
218	{
219	if (domain->dim_j_name.isEmpty())
220	latName = "lat";
221	else
222	latName = domain->dim_j_name.getValue();
223	}
224	else latName = domain->lat_name;
225
226	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
227	else dimXid = domain->dim_i_name.getValue()+appendDomid;
228
229	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
230	else dimYid = domain->dim_j_name.getValue()+appendDomid;
231	break;
232	}
233
234	StdString dimVertId = StdString("nvertex").append(appendDomid);
235
236	string lonid,latid,bounds_lonid,bounds_latid ;
237	string areaId = "area" + appendDomid;
238
239	try
240	{
241	switch (SuperClass::type)
242	{
243	case (MULTI_FILE) :
244	{
245	switch (domain->type)
246	{
247	case CDomain::type_attr::curvilinear :
248	dim0.push_back(dimYid); dim0.push_back(dimXid);
249	lonid = lonName+appendDomid;
250	latid = latName+appendDomid;
251	break ;
252	case CDomain::type_attr::rectilinear :
253	lonid = lonName+appendDomid;
254	latid = latName+appendDomid;
255	dim0.push_back(dimYid);
256	dim1.push_back(dimXid);
257	break;
258	}
259	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
260	else bounds_lonid = "bounds_"+lonName+appendDomid;
261	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
262	else bounds_latid = "bounds_"+latName+appendDomid;
263
264	SuperClassWriter::addDimension(dimXid, domain->ni);
265	SuperClassWriter::addDimension(dimYid, domain->nj);
266
267	if (domain->hasBounds)
268	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
269
270	if (context->intraCommSize_ > 1)
271	{
272	this->writeLocalAttributes(domain->ibegin,
273	domain->ni,
274	domain->jbegin,
275	domain->nj,
276	appendDomid);
277
278	if (singleDomain)
279	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
280	domain->ibegin,
281	domain->ni,
282	domain->jbegin,
283	domain->nj,
284	domain->ni_glo,domain->nj_glo,
285	context->intraCommRank_,context->intraCommSize_);
286	}
287
288	if (domain->hasLonLat)
289	{
290	switch (domain->type)
291	{
292	case CDomain::type_attr::curvilinear :
293	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
294	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
295	break ;
296	case CDomain::type_attr::rectilinear :
297	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
298	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
299	break ;
300	}
301
302	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
303	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
304
305	if (domain->hasBounds)
306	{
307	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
308	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
309
310	dim0.clear();
311	dim0.push_back(dimYid);
312	dim0.push_back(dimXid);
313	dim0.push_back(dimVertId);
314	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
315	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
316	}
317	}
318
319	dim0.clear();
320	dim0.push_back(dimYid);
321	dim0.push_back(dimXid);
322
323	if (domain->hasArea)
324	{
325	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
326	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
327	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
328	}
329
330	SuperClassWriter::definition_end();
331
332	if (domain->hasLonLat)
333	{
334	switch (domain->type)
335	{
336	case CDomain::type_attr::curvilinear :
337	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
338	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
339	break;
340	case CDomain::type_attr::rectilinear :
341	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
342	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
343	CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
344	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
345	break;
346	}
347
348	if (domain->hasBounds)
349	{
350	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
351	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
352	}
353	}
354
355	if (domain->hasArea)
356	{
357	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
358	}
359
360	SuperClassWriter::definition_start();
361
362	break;
363	}
364	case (ONE_FILE) :
365	{
366	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
367	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
368
369	if (domain->hasBounds)
370	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
371
372	if (domain->hasLonLat)
373	{
374	switch (domain->type)
375	{
376	case CDomain::type_attr::curvilinear :
377	dim0.push_back(dimYid); dim0.push_back(dimXid);
378	lonid = lonName+appendDomid;
379	latid = latName+appendDomid;
380	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
381	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
382	break;
383
384	case CDomain::type_attr::rectilinear :
385	dim0.push_back(dimYid);
386	dim1.push_back(dimXid);
387	lonid = lonName+appendDomid;
388	latid = latName+appendDomid;
389	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
390	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
391	break;
392	}
393	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
394	else bounds_lonid = "bounds_"+lonName+appendDomid;
395	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
396	else bounds_latid = "bounds_"+latName+appendDomid;
397
398	this->writeAxisAttributes
399	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
400	this->writeAxisAttributes
401	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
402
403	if (domain->hasBounds)
404	{
405	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
406	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
407
408	dim0.clear();
409	dim0.push_back(dimYid);
410	dim0.push_back(dimXid);
411	dim0.push_back(dimVertId);
412	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
413	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
414	}
415	}
416
417	if (domain->hasArea)
418	{
419	dim0.clear();
420	dim0.push_back(dimYid); dim0.push_back(dimXid);
421	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
422	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
423	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
424	dim0.clear();
425	}
426
427	SuperClassWriter::definition_end();
428
429	switch (domain->type)
430	{
431	case CDomain::type_attr::curvilinear :
432	{
433	std::vector<StdSize> start(2) ;
434	std::vector<StdSize> count(2) ;
435	start[1]=domain->ibegin;
436	start[0]=domain->jbegin;
437	count[1]=domain->ni ; count[0]=domain->nj ;
438
439	if (domain->hasLonLat)
440	{
441	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
442	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
443	}
444	break;
445	}
446	case CDomain::type_attr::rectilinear :
447	{
448	if (domain->hasLonLat)
449	{
450	std::vector<StdSize> start(1) ;
451	std::vector<StdSize> count(1) ;
452
453	start[0]=domain->jbegin;
454	count[0]=domain->nj;
455	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni));
456	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
457
458	start[0]=domain->ibegin;
459	count[0]=domain->ni;
460	CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1));
461	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
462	}
463	break;
464	}
465	}
466
467	if (domain->hasBounds)
468	{
469	std::vector<StdSize> start(3);
470	std::vector<StdSize> count(3);
471	if (domain->isEmpty())
472	{
473	start[2] = start[1] = start[0] = 0;
474	count[2] = count[1] = count[0] = 0;
475	}
476	else
477	{
478	start[2] = 0;
479	start[1] = domain->ibegin;
480	start[0] = domain->jbegin;
481	count[2] = domain->nvertex;
482	count[1] = domain->ni;
483	count[0] = domain->nj;
484	}
485
486	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
487	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
488	}
489
490	if (domain->hasArea)
491	{
492	std::vector<StdSize> start(2);
493	std::vector<StdSize> count(2);
494
495	start[1] = domain->ibegin;
496	start[0] = domain->jbegin;
497	count[1] = domain->ni;
498	count[0] = domain->nj;
499
500	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
501	}
502
503	SuperClassWriter::definition_start();
504	break;
505	}
506	default :
507	ERROR("CNc4DataOutput::writeDomain(domain)",
508	<< "[ type = " << SuperClass::type << "]"
509	<< " not implemented yet !");
510	}
511	}
512	catch (CNetCdfException& e)
513	{
514	StdString msg("On writing the domain : ");
515	msg.append(domid); msg.append("\n");
516	msg.append("In the context : ");
517	msg.append(context->getId()); msg.append("\n");
518	msg.append(e.what());
519	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
520	}
521
522	domain->addRelFile(this->filename);
523	}
524	CATCH
525
526	//--------------------------------------------------------------
527
528	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
529	{
530	CContext* context = CContext::getCurrent() ;
531
532	if (domain->IsWritten(this->filename)) return;
533
534	StdString domid = domain->getDomainOutputName();
535
536	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
537	// Thus the entire mesh connectivity will be generated at once.
538	if (isWrittenDomain(domid)) return ;
539	else setWrittenDomain(domid);
540
541	domain->checkAttributes();
542	if (domain->isEmpty())
543	if (SuperClass::type==MULTI_FILE) return ;
544
545	nc_type typePrec ;
546	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
547	else if (domain->prec==4) typePrec = NC_FLOAT ;
548	else if (domain->prec==8) typePrec = NC_DOUBLE ;
549
550	std::vector<StdString> dim0;
551	StdString domainName = domain->name;
552	domain->assignMesh(domainName, domain->nvertex);
553	domain->mesh->createMeshEpsilon(context->intraComm_, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
554
555	StdString node_x = domainName + "_node_x";
556	StdString node_y = domainName + "_node_y";
557
558	StdString edge_x = domainName + "_edge_x";
559	StdString edge_y = domainName + "_edge_y";
560	StdString edge_nodes = domainName + "_edge_nodes";
561
562	StdString face_x = domainName + "_face_x";
563	StdString face_y = domainName + "_face_y";
564	StdString face_nodes = domainName + "_face_nodes";
565	StdString face_edges = domainName + "_face_edges";
566	StdString edge_faces = domainName + "_edge_face_links";
567	StdString face_faces = domainName + "_face_links";
568
569	StdString dimNode = "n" + domainName + "_node";
570	StdString dimEdge = "n" + domainName + "_edge";
571	StdString dimFace = "n" + domainName + "_face";
572	StdString dimVertex = "n" + domainName + "_vertex";
573	StdString dimTwo = "Two";
574
575	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
576	dim0.clear();
577	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
578	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
579	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
580	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
581	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
582
583	try
584	{
585	switch (SuperClass::type)
586	{
587	case (ONE_FILE) :
588	{
589	// Adding nodes
590	if (domain->nvertex == 1)
591	{
592	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
593	{
594	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
595	dim0.clear();
596	dim0.push_back(dimNode);
597	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
598	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
599	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
600	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
601	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
602	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
603	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
604	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
605	}
606	} // domain->nvertex == 1
607
608	// Adding edges and nodes, if nodes have not been defined previously
609	if (domain->nvertex == 2)
610	{
611	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
612	{
613	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
614	dim0.clear();
615	dim0.push_back(dimNode);
616	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
617	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
618	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
619	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
620	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
621	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
622	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
623	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
624	}
625	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
626	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
627	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
628	dim0.clear();
629	dim0.push_back(dimEdge);
630	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
631	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
632	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
633	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
634	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
635	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
636	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
637	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
638	dim0.clear();
639	dim0.push_back(dimEdge);
640	dim0.push_back(dimTwo);
641	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
642	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
643	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
644	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
645	} // domain->nvertex == 2
646
647	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
648	if (domain->nvertex > 2)
649	{
650	// Nodes
651	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
652	{
653	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
654	dim0.clear();
655	dim0.push_back(dimNode);
656	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
657	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
658	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
659	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
660	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
661	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
662	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
663	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
664	}
665	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
666	{
667	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
668	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
669	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
670	dim0.clear();
671	dim0.push_back(dimEdge);
672	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
673	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
674	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
675	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
676	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
677	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
678	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
679	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
680	dim0.clear();
681	dim0.push_back(dimEdge);
682	dim0.push_back(dimTwo);
683	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
684	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
685	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
686	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
687	}
688	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
689	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
690	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
691	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
692	dim0.clear();
693	dim0.push_back(dimFace);
694	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
695	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
696	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
697	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
698	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
699	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
700	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
701	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
702	dim0.clear();
703	dim0.push_back(dimFace);
704	dim0.push_back(dimVertex);
705	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
706	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
707	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
708	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
709	dim0.clear();
710	dim0.push_back(dimFace);
711	dim0.push_back(dimVertex);
712	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
713	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
714	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
715	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
716	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
717	dim0.clear();
718	dim0.push_back(dimEdge);
719	dim0.push_back(dimTwo);
720	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
721	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
722	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
723	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
724	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
725	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
726	dim0.clear();
727	dim0.push_back(dimFace);
728	dim0.push_back(dimVertex);
729	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
730	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
731	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
732	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
733	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
734	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
735	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
736	} // domain->nvertex > 2
737
738	SuperClassWriter::definition_end();
739
740	std::vector<StdSize> startEdges(1) ;
741	std::vector<StdSize> countEdges(1) ;
742	std::vector<StdSize> startNodes(1) ;
743	std::vector<StdSize> countNodes(1) ;
744	std::vector<StdSize> startFaces(1) ;
745	std::vector<StdSize> countFaces(1) ;
746	std::vector<StdSize> startEdgeNodes(2) ;
747	std::vector<StdSize> countEdgeNodes(2) ;
748	std::vector<StdSize> startEdgeFaces(2) ;
749	std::vector<StdSize> countEdgeFaces(2) ;
750	std::vector<StdSize> startFaceConctv(2) ;
751	std::vector<StdSize> countFaceConctv(2) ;
752
753	if (domain->nvertex == 1)
754	{
755	if (domain->isEmpty())
756	{
757	startNodes[0]=0 ;
758	countNodes[0]=0 ;
759	}
760	else
761	{
762	startNodes[0] = domain->ibegin;
763	countNodes[0] = domain->ni ;
764	}
765
766	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
767	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
768	}
769	else if (domain->nvertex == 2)
770	{
771	if (domain->isEmpty())
772	{
773	startEdges[0]=0 ;
774	countEdges[0]=0 ;
775	startNodes[0]=0 ;
776	countNodes[0]=0 ;
777	startEdgeNodes[0]=0;
778	startEdgeNodes[1]=0;
779	countEdgeNodes[0]=0;
780	countEdgeNodes[1]=0;
781
782	}
783	else
784	{
785	startEdges[0] = domain->ibegin;
786	countEdges[0] = domain->ni;
787	startNodes[0] = domain->mesh->node_start;
788	countNodes[0] = domain->mesh->node_count;
789	startEdgeNodes[0] = domain->ibegin;
790	startEdgeNodes[1] = 0;
791	countEdgeNodes[0] = domain->ni;
792	countEdgeNodes[1] = 2;
793	}
794	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
795	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
796	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
797	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
798	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
799	}
800	else
801	{
802	if (domain->isEmpty())
803	{
804	startFaces[0] = 0 ;
805	countFaces[0] = 0 ;
806	startNodes[0] = 0;
807	countNodes[0] = 0;
808	startEdges[0] = 0;
809	countEdges[0] = 0;
810	startEdgeFaces[0] = 0;
811	startEdgeFaces[1] = 0;
812	countEdgeFaces[0] = 0;
813	countEdgeFaces[1] = 0;
814	startFaceConctv[0] = 0;
815	startFaceConctv[1] = 0;
816	countFaceConctv[0] = 0;
817	countFaceConctv[1] = 0;
818	}
819	else
820	{
821	startFaces[0] = domain->ibegin;
822	countFaces[0] = domain->ni ;
823	startNodes[0] = domain->mesh->node_start;
824	countNodes[0] = domain->mesh->node_count;
825	startEdges[0] = domain->mesh->edge_start;
826	countEdges[0] = domain->mesh->edge_count;
827	startEdgeNodes[0] = domain->mesh->edge_start;
828	startEdgeNodes[1] = 0;
829	countEdgeNodes[0] = domain->mesh->edge_count;
830	countEdgeNodes[1]= 2;
831	startEdgeFaces[0] = domain->mesh->edge_start;
832	startEdgeFaces[1]= 0;
833	countEdgeFaces[0] = domain->mesh->edge_count;
834	countEdgeFaces[1]= 2;
835	startFaceConctv[0] = domain->ibegin;
836	startFaceConctv[1] = 0;
837	countFaceConctv[0] = domain->ni;
838	countFaceConctv[1] = domain->nvertex;
839	}
840	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
841	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
842	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
843	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
844	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
845	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
846	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
847	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
848	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
849	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
850	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
851	}
852	SuperClassWriter::definition_start();
853
854	break;
855	} // ONE_FILE
856
857	case (MULTI_FILE) :
858	{
859	ERROR("CNc4DataOutput::writeDomain(domain)",
860	<< "[ type = multiple_file ]"
861	<< " is not yet implemented for UGRID files !");
862	break;
863	}
864
865	default :
866	ERROR("CNc4DataOutput::writeDomain(domain)",
867	<< "[ type = " << SuperClass::type << "]"
868	<< " not implemented yet !");
869	} // switch
870	} // try
871
872	catch (CNetCdfException& e)
873	{
874	StdString msg("On writing the domain : ");
875	msg.append(domid); msg.append("\n");
876	msg.append("In the context : ");
877	msg.append(context->getId()); msg.append("\n");
878	msg.append(e.what());
879	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
880	}
881
882	domain->addRelFile(this->filename);
883	}
884
885	//--------------------------------------------------------------
886
887	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
888	{
889	CContext* context = CContext::getCurrent() ;
890
891	if (domain->IsWritten(this->filename)) return;
892	domain->checkAttributes();
893
894	if (domain->isEmpty())
895	if (SuperClass::type==MULTI_FILE) return ;
896
897	std::vector<StdString> dim0, dim1;
898	StdString domid = domain->getDomainOutputName();
899	if (isWrittenDomain(domid)) return ;
900	else setWrittenDomain(domid);
901
902	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
903
904	StdString lonName,latName, cellName ;
905	if (domain->lon_name.isEmpty()) lonName = "lon";
906	else lonName = domain->lon_name;
907
908	if (domain->lat_name.isEmpty()) latName = "lat";
909	else latName = domain->lat_name;
910
911	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
912	else cellName="cell";
913	StdString dimXid = cellName+appendDomid;
914	StdString dimVertId = StdString("nvertex").append(appendDomid);
915
916	string lonid,latid,bounds_lonid,bounds_latid ;
917	string areaId = "area" + appendDomid;
918
919	nc_type typePrec ;
920	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
921	else if (domain->prec==4) typePrec = NC_FLOAT ;
922	else if (domain->prec==8) typePrec = NC_DOUBLE ;
923
924	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
925
926	try
927	{
928	switch (SuperClass::type)
929	{
930	case (MULTI_FILE) :
931	{
932	dim0.push_back(dimXid);
933	SuperClassWriter::addDimension(dimXid, domain->ni);
934
935	lonid = lonName+appendDomid;
936	latid = latName+appendDomid;
937	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
938	else bounds_lonid = "bounds_"+lonName+appendDomid;
939	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
940	else bounds_latid = "bounds_"+latName+appendDomid;
941
942	if (domain->hasLonLat)
943	{
944	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
945	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
946	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
947	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
948	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
949	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
950	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
951	}
952	dim0.clear();
953	if (domain->hasBounds)
954	{
955	dim0.push_back(dimXid);
956	dim0.push_back(dimVertId);
957	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
958	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
959	}
960
961	dim0.clear();
962	dim0.push_back(dimXid);
963	if (domain->hasArea)
964	{
965	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
966	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
967	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
968	}
969
970	SuperClassWriter::definition_end();
971
972	if (domain->hasLonLat)
973	{
974	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
975	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
976	if (domain->hasBounds)
977	{
978	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
979	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
980	}
981	}
982
983	if (domain->hasArea)
984	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
985
986	SuperClassWriter::definition_start();
987	break ;
988	}
989
990	case (ONE_FILE) :
991	{
992	lonid = lonName+appendDomid;
993	latid = latName+appendDomid;
994	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
995	else bounds_lonid = "bounds_"+lonName+appendDomid;
996	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
997	else bounds_latid = "bounds_"+latName+appendDomid;
998
999	dim0.push_back(dimXid);
1000	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
1001	if (domain->hasLonLat)
1002	{
1003	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1004	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1005
1006	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1007	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1008	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1009	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1010	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
1011	}
1012	dim0.clear();
1013
1014	if (domain->hasBounds)
1015	{
1016	dim0.push_back(dimXid);
1017	dim0.push_back(dimVertId);
1018	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1019	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1020	}
1021
1022	if (domain->hasArea)
1023	{
1024	dim0.clear();
1025	dim0.push_back(dimXid);
1026	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1027	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1028	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1029	}
1030
1031	SuperClassWriter::definition_end();
1032
1033	std::vector<StdSize> start(1), startBounds(2) ;
1034	std::vector<StdSize> count(1), countBounds(2) ;
1035	if (domain->isEmpty())
1036	{
1037	start[0]=0 ;
1038	count[0]=0 ;
1039	startBounds[1]=0 ;
1040	countBounds[1]=nvertex ;
1041	startBounds[0]=0 ;
1042	countBounds[0]=0 ;
1043	}
1044	else
1045	{
1046	start[0]=domain->ibegin;
1047	count[0]=domain->ni;
1048	startBounds[0]=domain->ibegin;
1049	startBounds[1]=0 ;
1050	countBounds[0]=domain->ni;
1051	countBounds[1]=nvertex ;
1052	}
1053
1054	if (domain->hasLonLat)
1055	{
1056	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
1057	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
1058	if (domain->hasBounds)
1059	{
1060	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1061	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1062	}
1063	}
1064
1065	if (domain->hasArea)
1066	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
1067
1068	SuperClassWriter::definition_start();
1069
1070	break;
1071	}
1072	default :
1073	ERROR("CNc4DataOutput::writeDomain(domain)",
1074	<< "[ type = " << SuperClass::type << "]"
1075	<< " not implemented yet !");
1076	}
1077	}
1078	catch (CNetCdfException& e)
1079	{
1080	StdString msg("On writing the domain : ");
1081	msg.append(domid); msg.append("\n");
1082	msg.append("In the context : ");
1083	msg.append(context->getId()); msg.append("\n");
1084	msg.append(e.what());
1085	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1086	}
1087	domain->addRelFile(this->filename);
1088	}
1089	//--------------------------------------------------------------
1090
1091	void CNc4DataOutput::writeAxis_(CAxis* axis)
1092	{
1093	if (axis->IsWritten(this->filename)) return;
1094
1095	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
1096	if (!axis->value.isEmpty() )
1097	{
1098	int comm_file_rank(0);
1099	MPI_Comm_rank( comm_file, &comm_file_rank );
1100	int comm_file_size(1);
1101	MPI_Comm_size( comm_file, &comm_file_size );
1102
1103	// Get element current FULL view
1104	shared_ptr<CLocalView> srcView = axis->getLocalView(CElementView::FULL) ;
1105	vector<shared_ptr<CLocalView>> srcViews;
1106	srcViews.push_back( srcView );
1107
1108	// Compute a without redundancy element FULL view to enable a consistent hash computation
1109	vector<shared_ptr<CLocalView>> remoteViews;
1110	shared_ptr<CLocalView> remoteView;
1111	// define the remote view without redundancy (naive distribution of the remote view)
1112	int globalSize = axis->n_glo.getValue();
1113	int localSize = globalSize/comm_file_size;
1114	if ( (comm_file_rank==comm_file_size-1) && (localSize*comm_file_size != globalSize ) )
1115	localSize += globalSize-localSize*comm_file_size;
1116	CArray<size_t,1> globalIndex( localSize );
1117	CArray<int,1> index( localSize );
1118	for (int iloc=0; iloc<localSize ; iloc++ )
1119	{
1120	globalIndex(iloc) = comm_file_rank*(globalSize/comm_file_size) + iloc;
1121	index(iloc) = iloc;
1122	}
1123	shared_ptr<CLocalElement> localElement = make_shared<CLocalElement>(comm_file_rank, globalSize, globalIndex) ;
1124	localElement->addView(CElementView::FULL, index) ;
1125	remoteView = localElement->getView(CElementView::FULL) ;
1126	remoteViews.push_back( remoteView );
1127
1128	// Compute the connector between current and without redundancy FULL views
1129	shared_ptr<CGridTransformConnector> gridTransformConnector = make_shared<CGridTransformConnector>(srcViews, remoteViews, comm_file ) ;
1130	gridTransformConnector->computeConnector(true) ; // eliminateRedondant = true
1131	CArray<double,1> distributedValue ;
1132	gridTransformConnector->transfer(axis->value, distributedValue );
1133
1134	// Compute the distributed hash (v0) of the element
1135	// it will be associated to the default element name (= map key), and to the name really written
1136	int localHash = 0;
1137	for (int iloc=0; iloc<localSize ; iloc++ ) localHash+=globalIndex(iloc)*distributedValue(iloc);
1138	int globalHash(0);
1139	globalHash = localHash;
1140	MPI_Allreduce( &localHash, &globalHash, 1, MPI_INT, MPI_SUM, comm_file );
1141
1142	StdString defaultNameKey = axis->getAxisOutputName();
1143	if ( !relElements_.count ( defaultNameKey ) )
1144	{
1145	// if defaultNameKey not in the map, write the element such as it is defined
1146	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, defaultNameKey) ) );
1147	}
1148	else // look if a hash associated this key is equal
1149	{
1150	bool elementIsInMap(false);
1151	auto defaultNameKeyElements = relElements_.equal_range( defaultNameKey );
1152	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
1153	{
1154	if ( it->second.first == globalHash )
1155	{
1156	// if yes, associate the same ids to current element
1157	axis->name = it->second.second;
1158	elementIsInMap = true;
1159	}
1160	}
1161	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
1162	if (!elementIsInMap) // ! in MAP
1163	{
1164	axis->name = axis->getId();
1165	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis->getAxisOutputName()) ) ) ;// = axis->getId()
1166	}
1167	}
1168	}
1169
1170	axis->checkAttributes();
1171
1172	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
1173	: axis->n_glo.getValue();
1174
1175	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
1176
1177	std::vector<StdString> dims;
1178	StdString axisid = axis->getAxisOutputName();
1179	StdString axisDim, axisBoundsId;
1180	if (isWrittenAxis(axisid)) return ;
1181	else setWrittenAxis(axisid);
1182
1183	nc_type typePrec ;
1184	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1185	else if (axis->prec==4) typePrec = NC_FLOAT ;
1186	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1187
1188	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1189	string strId="str_len" ;
1190	try
1191	{
1192	if (axis->dim_name.isEmpty()) axisDim = axisid;
1193	else axisDim=axis->dim_name.getValue();
1194	SuperClassWriter::addDimension(axisDim, size);
1195	dims.push_back(axisDim);
1196
1197	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1198
1199	if (axis->hasValue \|\| !axis->label.isEmpty())
1200	{
1201	if (!axis->label.isEmpty()) dims.push_back(strId);
1202
1203	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1204
1205	if (!axis->name.isEmpty())
1206	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1207
1208	if (!axis->standard_name.isEmpty())
1209	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1210
1211	if (!axis->long_name.isEmpty())
1212	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1213
1214	if (!axis->unit.isEmpty())
1215	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1216
1217	if (!axis->axis_type.isEmpty())
1218	{
1219	switch(axis->axis_type)
1220	{
1221	case CAxis::axis_type_attr::X :
1222	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1223	break;
1224	case CAxis::axis_type_attr::Y :
1225	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1226	break;
1227	case CAxis::axis_type_attr::Z :
1228	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1229	break;
1230	case CAxis::axis_type_attr::T :
1231	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1232	break;
1233	}
1234	}
1235
1236	if (!axis->positive.isEmpty())
1237	{
1238	SuperClassWriter::addAttribute("positive",
1239	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1240	&axisid);
1241	}
1242
1243	if (!axis->formula.isEmpty())
1244	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1245
1246	if (!axis->formula_term.isEmpty())
1247	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
1248
1249	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1250	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1251	{
1252	dims.push_back("axis_nbounds");
1253	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1254	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1255
1256	if (!axis->standard_name.isEmpty())
1257	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1258
1259	if (!axis->unit.isEmpty())
1260	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1261
1262	if (!axis->formula_bounds.isEmpty())
1263	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1264
1265	if (!axis->formula_term_bounds.isEmpty())
1266	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
1267	}
1268	}
1269
1270	SuperClassWriter::definition_end();
1271
1272	switch (SuperClass::type)
1273	{
1274	case MULTI_FILE:
1275	{
1276	if (axis->label.isEmpty())
1277	{
1278	if (!axis->value.isEmpty())
1279	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
1280
1281	if (!axis->bounds.isEmpty())
1282	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
1283	}
1284	else
1285	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
1286
1287	SuperClassWriter::definition_start();
1288	break;
1289	}
1290	case ONE_FILE:
1291	{
1292	std::vector<StdSize> start(1), startBounds(2) ;
1293	std::vector<StdSize> count(1), countBounds(2) ;
1294	start[0] = startBounds[0] = axis->begin;
1295	count[0] = countBounds[0] = axis->n;
1296	startBounds[1] = 0;
1297	countBounds[1] = 2;
1298
1299	if (axis->label.isEmpty())
1300	{
1301	if (!axis->value.isEmpty())
1302	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
1303
1304	if (!axis->bounds.isEmpty())
1305	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1306	}
1307	else
1308	{
1309	std::vector<StdSize> startLabel(2), countLabel(2);
1310	startLabel[0] = start[0]; startLabel[1] = 0;
1311	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1312	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
1313	}
1314
1315	SuperClassWriter::definition_start();
1316
1317	break;
1318	}
1319	default :
1320	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1321	<< "[ type = " << SuperClass::type << "]"
1322	<< " not implemented yet !");
1323	}
1324	}
1325	catch (CNetCdfException& e)
1326	{
1327	StdString msg("On writing the axis : ");
1328	msg.append(axisid); msg.append("\n");
1329	msg.append("In the context : ");
1330	CContext* context = CContext::getCurrent() ;
1331	msg.append(context->getId()); msg.append("\n");
1332	msg.append(e.what());
1333	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1334	}
1335	axis->addRelFile(this->filename);
1336	}
1337
1338	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1339	{
1340	if (scalar->IsWritten(this->filename)) return;
1341	scalar->checkAttributes();
1342	int scalarSize = 1;
1343
1344	StdString scalaId = scalar->getScalarOutputName();
1345	StdString boundsId;
1346	if (isWrittenAxis(scalaId)) return ;
1347	else setWrittenAxis(scalaId);
1348
1349	nc_type typePrec ;
1350	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1351	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1352	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1353
1354	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1355	string strId="str_len" ;
1356
1357	try
1358	{
1359	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1360
1361	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1362	{
1363	std::vector<StdString> dims;
1364	StdString scalarDim = scalaId;
1365
1366	if (!scalar->label.isEmpty()) dims.push_back(strId);
1367
1368	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1369
1370	if (!scalar->name.isEmpty())
1371	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1372
1373	if (!scalar->standard_name.isEmpty())
1374	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1375
1376	if (!scalar->long_name.isEmpty())
1377	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1378
1379	if (!scalar->unit.isEmpty())
1380	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1381
1382	if (!scalar->axis_type.isEmpty())
1383	{
1384	switch(scalar->axis_type)
1385	{
1386	case CScalar::axis_type_attr::X :
1387	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1388	break;
1389	case CScalar::axis_type_attr::Y :
1390	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1391	break;
1392	case CScalar::axis_type_attr::Z :
1393	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1394	break;
1395	case CScalar::axis_type_attr::T :
1396	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1397	break;
1398	}
1399	}
1400
1401	if (!scalar->positive.isEmpty())
1402	{
1403	SuperClassWriter::addAttribute("positive",
1404	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1405	&scalaId);
1406	}
1407
1408	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1409	{
1410	dims.clear();
1411	dims.push_back("axis_nbounds");
1412	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1413	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1414	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1415	}
1416
1417	SuperClassWriter::definition_end();
1418
1419	switch (SuperClass::type)
1420	{
1421	case MULTI_FILE:
1422	{
1423	CArray<double,1> scalarValue(scalarSize);
1424	CArray<string,1> scalarLabel(scalarSize);
1425	CArray<double,1> scalarBounds(scalarSize*2);
1426
1427	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1428	{
1429	scalarValue(0) = scalar->value;
1430	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1431	}
1432
1433	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1434	{
1435	scalarBounds(0) = scalar->bounds(0);
1436	scalarBounds(1) = scalar->bounds(1);
1437	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1438	}
1439
1440	if (!scalar->label.isEmpty())
1441	{
1442	scalarLabel(0) = scalar->label;
1443	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1444	}
1445
1446	SuperClassWriter::definition_start();
1447
1448	break;
1449	}
1450	case ONE_FILE:
1451	{
1452	CArray<double,1> scalarValue(scalarSize);
1453	CArray<string,1> scalarLabel(scalarSize);
1454	CArray<double,1> scalarBounds(scalarSize*2);
1455
1456	std::vector<StdSize> start(1);
1457	std::vector<StdSize> count(1);
1458	start[0] = 0;
1459	count[0] = 1;
1460	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1461	{
1462	scalarValue(0) = scalar->value;
1463	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1464	}
1465	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1466	{
1467	scalarBounds(0) = scalar->bounds(0);
1468	scalarBounds(1) = scalar->bounds(1);
1469	count[0] = 2;
1470	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1471	}
1472	if (!scalar->label.isEmpty())
1473	{
1474	scalarLabel(0) = scalar->label;
1475	count[0] = stringArrayLen;
1476	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1477	}
1478
1479	SuperClassWriter::definition_start();
1480
1481	break;
1482	}
1483	default :
1484	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1485	<< "[ type = " << SuperClass::type << "]"
1486	<< " not implemented yet !");
1487	}
1488	}
1489	}
1490	catch (CNetCdfException& e)
1491	{
1492	StdString msg("On writing the scalar : ");
1493	msg.append(scalaId); msg.append("\n");
1494	msg.append("In the context : ");
1495	CContext* context = CContext::getCurrent() ;
1496	msg.append(context->getId()); msg.append("\n");
1497	msg.append(e.what());
1498	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1499	}
1500	scalar->addRelFile(this->filename);
1501	}
1502
1503	//--------------------------------------------------------------
1504
1505	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1506	{
1507	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1508
1509	// NOTA : The cuurent algorithm to write compress elements of the grid
1510	// will work pretting well when on server side you dont't get
1511	// partial overlap on elements between differents participating process
1512	// So the element must be totally distributed or non distributed
1513	// If an element is partially overlaping betwwen process then the
1514	// total compressed part will apear artificially greater than expected
1515	// For the current implementation of writer which is decomposed only on
1516	// one element, it will work as expected, but for future, it must be
1517	// reconsidered again.
1518	try
1519	{
1520	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1521	std::vector<StdString> domainList = grid->getDomainList();
1522	std::vector<StdString> axisList = grid->getAxisList();
1523	std::vector<StdString> scalarList = grid->getScalarList();
1524	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1525	int commRank ;
1526	MPI_Comm_rank(comm_file,&commRank) ;
1527
1528	std::vector<StdString> dims;
1529
1530	for (int i = 0; i < numElement; ++i)
1531	{
1532	StdString varId, compress;
1533	CArray<size_t, 1> indexes;
1534	bool isDistributed;
1535	size_t nbIndexes, totalNbIndexes, offset;
1536	size_t firstGlobalIndex;
1537
1538	if (2 == axisDomainOrder(i))
1539	{
1540	CDomain* domain = CDomain::get(domainList[idxDomain]);
1541	StdString domId = domain->getDomainOutputName();
1542
1543	if (!domain->isCompressible()
1544	\|\| domain->type == CDomain::type_attr::unstructured
1545	\|\| domain->isWrittenCompressed(this->filename)
1546	\|\| isWrittenCompressedDomain(domId))
1547	continue;
1548
1549	// unstructured grid seems not be taken into account why ?
1550
1551	string lonName,latName ;
1552
1553	if (domain->lon_name.isEmpty())
1554	{
1555	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1556	else lonName = "lon";
1557	}
1558	else lonName = domain->lon_name;
1559
1560	if (domain->lat_name.isEmpty())
1561	{
1562	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1563	else latName = "lat";
1564	}
1565	else latName = domain->lat_name;
1566
1567	StdString appendDomId = singleDomain ? "" : "_" + domId;
1568
1569	varId = domId + "_points";
1570	compress = latName + appendDomId + " " + lonName + appendDomId;
1571
1572	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
1573	workflowView->getGlobalIndexView(indexes) ;
1574	nbIndexes = workflowView->getSize() ;
1575	isDistributed = domain->isDistributed();
1576	if (isDistributed)
1577	{
1578	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1579	if (commRank==0) offset=0 ;
1580	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1581	}
1582	else
1583	{
1584	offset=0 ;
1585	totalNbIndexes = nbIndexes ;
1586	}
1587
1588	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1589
1590	domain->addRelFileCompressed(this->filename);
1591	setWrittenCompressedDomain(domId);
1592	++idxDomain;
1593	}
1594	else if (1 == axisDomainOrder(i))
1595	{
1596	CAxis* axis = CAxis::get(axisList[idxAxis]);
1597	StdString axisId = axis->getAxisOutputName();
1598
1599	if (!axis->isCompressible()
1600	\|\| axis->isWrittenCompressed(this->filename)
1601	\|\| isWrittenCompressedAxis(axisId))
1602	continue;
1603
1604	varId = axisId + "_points";
1605	compress = axisId;
1606
1607	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
1608	workflowView->getGlobalIndexView(indexes) ;
1609	nbIndexes = workflowView->getSize() ;
1610	isDistributed = axis->isDistributed();
1611	if (isDistributed)
1612	{
1613	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1614	if (commRank==0) offset=0 ;
1615	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1616	}
1617	else
1618	{
1619	offset=0 ;
1620	totalNbIndexes = nbIndexes ;
1621	}
1622	firstGlobalIndex = axis->begin;
1623
1624	axis->addRelFileCompressed(this->filename);
1625	setWrittenCompressedAxis(axisId);
1626	++idxAxis;
1627	}
1628	else
1629	{
1630	//for scalar
1631	}
1632
1633	if (!varId.empty())
1634	{
1635	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1636
1637	dims.clear();
1638	dims.push_back(varId);
1639	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
1640
1641	SuperClassWriter::addAttribute("compress", compress, &varId);
1642
1643	switch (SuperClass::type)
1644	{
1645	case (MULTI_FILE):
1646	{
1647	indexes -= firstGlobalIndex;
1648	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1649	break;
1650	}
1651	case (ONE_FILE):
1652	{
1653	std::vector<StdSize> start, count;
1654	start.push_back(offset);
1655	count.push_back(nbIndexes);
1656
1657	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1658	break;
1659	}
1660	}
1661	}
1662	}
1663
1664	grid->addRelFileCompressed(this->filename);
1665	}
1666	catch (CNetCdfException& e)
1667	{
1668	StdString msg("On writing compressed grid : ");
1669	msg.append(grid->getId()); msg.append("\n");
1670	msg.append("In the context : ");
1671	CContext* context = CContext::getCurrent();
1672	msg.append(context->getId()); msg.append("\n");
1673	msg.append(e.what());
1674	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1675	}
1676	}
1677
1678	//--------------------------------------------------------------
1679
1680	void CNc4DataOutput::writeTimeDimension_(void)
1681	{
1682	try
1683	{
1684	SuperClassWriter::addDimension(getTimeCounterName());
1685	}
1686	catch (CNetCdfException& e)
1687	{
1688	StdString msg("On writing time dimension : time_couter\n");
1689	msg.append("In the context : ");
1690	CContext* context = CContext::getCurrent() ;
1691	msg.append(context->getId()); msg.append("\n");
1692	msg.append(e.what());
1693	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1694	}
1695	}
1696
1697	//--------------------------------------------------------------
1698
1699	void CNc4DataOutput::writeField_(CField* field)
1700	{
1701	CContext* context = CContext::getCurrent() ;
1702
1703	std::vector<StdString> dims, coodinates;
1704	CGrid* grid = field->getGrid();
1705	if (!grid->doGridHaveDataToWrite())
1706	if (SuperClass::type==MULTI_FILE) return ;
1707
1708	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1709	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1710	std::vector<StdString> domainList = grid->getDomainList();
1711	std::vector<StdString> axisList = grid->getAxisList();
1712	std::vector<StdString> scalarList = grid->getScalarList();
1713
1714	StdString timeid = getTimeCounterName();
1715	StdString dimXid,dimYid;
1716	std::deque<StdString> dimIdList, dimCoordList;
1717	bool hasArea = false;
1718	StdString cellMeasures = "area:";
1719	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1720
1721	for (int i = 0; i < numElement; ++i)
1722	{
1723	if (2 == axisDomainOrder(i))
1724	{
1725	CDomain* domain = CDomain::get(domainList[idxDomain]);
1726	StdString domId = domain->getDomainOutputName();
1727	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1728	StdString lonName,latName ;
1729	StdString dimIname,dimJname ;
1730
1731	if (domain->lon_name.isEmpty())
1732	{
1733	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1734	else lonName = "lon";
1735	}
1736	else lonName = domain->lon_name;
1737
1738	if (domain->lat_name.isEmpty())
1739	{
1740	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1741	else latName = "lat";
1742	}
1743	else latName = domain->lat_name;
1744
1745	if (domain->dim_i_name.isEmpty())
1746	{
1747	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1748	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1749	else dimIname = lonName;
1750	}
1751	else dimIname = domain->dim_i_name;
1752
1753	if (domain->dim_j_name.isEmpty())
1754	{
1755	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1756	else dimJname = latName;
1757	}
1758	else dimJname = domain->dim_j_name;
1759
1760	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1761	{
1762	dimIdList.push_back(domId + "_points");
1763	field->setUseCompressedOutput();
1764	}
1765
1766	switch (domain->type)
1767	{
1768	case CDomain::type_attr::curvilinear:
1769	if (!compressedOutput \|\| !domain->isCompressible())
1770	{
1771	dimXid=dimIname+appendDomId;
1772	dimYid=dimJname+appendDomId;
1773	dimIdList.push_back(dimXid);
1774	dimIdList.push_back(dimYid);
1775	}
1776	dimCoordList.push_back(lonName+appendDomId);
1777	dimCoordList.push_back(latName+appendDomId);
1778	break ;
1779	case CDomain::type_attr::rectilinear:
1780	if (!compressedOutput \|\| !domain->isCompressible())
1781	{
1782	dimXid = dimIname+appendDomId;
1783	dimYid = dimJname+appendDomId;
1784	dimIdList.push_back(dimXid);
1785	dimIdList.push_back(dimYid);
1786	}
1787	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1788	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1789
1790	break ;
1791	case CDomain::type_attr::unstructured:
1792	{
1793	if (SuperClassWriter::useCFConvention)
1794	{
1795	dimXid = dimIname + appendDomId;
1796	dimIdList.push_back(dimXid);
1797	dimCoordList.push_back(lonName+appendDomId);
1798	dimCoordList.push_back(latName+appendDomId);
1799	}
1800	else
1801	{
1802	StdString domainName = domain->name;
1803	if (domain->nvertex == 1)
1804	{
1805	dimXid = "n" + domainName + "_node";
1806	dimIdList.push_back(dimXid);
1807	dimCoordList.push_back(StdString(domainName + "_node_x"));
1808	dimCoordList.push_back(StdString(domainName + "_node_y"));
1809	}
1810	else if (domain->nvertex == 2)
1811	{
1812	dimXid = "n" + domainName + "_edge";
1813	dimIdList.push_back(dimXid);
1814	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1815	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1816	}
1817	else
1818	{
1819	dimXid = "n" + domainName + "_face";
1820	dimIdList.push_back(dimXid);
1821	dimCoordList.push_back(StdString(domainName + "_face_x"));
1822	dimCoordList.push_back(StdString(domainName + "_face_y"));
1823	}
1824	} // ugrid convention
1825	} // case unstructured domain
1826	}
1827
1828	if (domain->hasArea)
1829	{
1830	hasArea = true;
1831	cellMeasures += " area" + appendDomId;
1832	}
1833	++idxDomain;
1834	}
1835	else if (1 == axisDomainOrder(i))
1836	{
1837	CAxis* axis = CAxis::get(axisList[idxAxis]);
1838	StdString axisId = axis->getAxisOutputName();
1839	StdString axisDim;
1840
1841	if (axis->dim_name.isEmpty()) axisDim = axisId;
1842	else axisDim=axis->dim_name.getValue();
1843
1844	if (compressedOutput && axis->isCompressible())
1845	{
1846	dimIdList.push_back(axisDim + "_points");
1847	field->setUseCompressedOutput();
1848	}
1849	else
1850	dimIdList.push_back(axisDim);
1851
1852	if (axisDim != axisId) dimCoordList.push_back(axisId);
1853	++idxAxis;
1854	}
1855	else
1856	{
1857	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1858	StdString scalarId = scalar->getScalarOutputName();
1859	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1860	dimCoordList.push_back(scalarId);
1861	++idxScalar;
1862	}
1863	}
1864
1865	StdString fieldid = field->getFieldOutputName();
1866
1867	nc_type type ;
1868	if (field->prec.isEmpty()) type = NC_FLOAT ;
1869	else
1870	{
1871	if (field->prec==2) type = NC_SHORT ;
1872	else if (field->prec==4) type = NC_FLOAT ;
1873	else if (field->prec==8) type = NC_DOUBLE ;
1874	}
1875
1876	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1877
1878	if (wtime)
1879	{
1880	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1881	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
1882	dims.push_back(timeid);
1883	}
1884
1885	while (!dimIdList.empty())
1886	{
1887	dims.push_back(dimIdList.back());
1888	dimIdList.pop_back();
1889	}
1890
1891	while (!dimCoordList.empty())
1892	{
1893	coodinates.push_back(dimCoordList.back());
1894	dimCoordList.pop_back();
1895	}
1896
1897	try
1898	{
1899	SuperClassWriter::addVariable(fieldid, type, dims);
1900
1901	if (!field->standard_name.isEmpty())
1902	SuperClassWriter::addAttribute
1903	("standard_name", field->standard_name.getValue(), &fieldid);
1904
1905	if (!field->long_name.isEmpty())
1906	SuperClassWriter::addAttribute
1907	("long_name", field->long_name.getValue(), &fieldid);
1908
1909	if (!field->unit.isEmpty())
1910	SuperClassWriter::addAttribute
1911	("units", field->unit.getValue(), &fieldid);
1912
1913	// Ugrid field attributes "mesh" and "location"
1914	if (!SuperClassWriter::useCFConvention)
1915	{
1916	if (!domainList.empty())
1917	{
1918	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
1919	StdString mesh = domain->name;
1920	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
1921	StdString location;
1922	if (domain->nvertex == 1)
1923	location = "node";
1924	else if (domain->nvertex == 2)
1925	location = "edge";
1926	else if (domain->nvertex > 2)
1927	location = "face";
1928	SuperClassWriter::addAttribute("location", location, &fieldid);
1929	}
1930
1931	}
1932
1933	if (!field->valid_min.isEmpty())
1934	SuperClassWriter::addAttribute
1935	("valid_min", field->valid_min.getValue(), &fieldid);
1936
1937	if (!field->valid_max.isEmpty())
1938	SuperClassWriter::addAttribute
1939	("valid_max", field->valid_max.getValue(), &fieldid);
1940
1941	if (!field->scale_factor.isEmpty())
1942	SuperClassWriter::addAttribute
1943	("scale_factor", field->scale_factor.getValue(), &fieldid);
1944
1945	if (!field->add_offset.isEmpty())
1946	SuperClassWriter::addAttribute
1947	("add_offset", field->add_offset.getValue(), &fieldid);
1948
1949	SuperClassWriter::addAttribute
1950	("online_operation", field->operation.getValue(), &fieldid);
1951
1952	// write child variables as attributes
1953
1954
1955	bool alreadyAddCellMethod = false;
1956	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1957	if (!field->cell_methods.isEmpty())
1958	{
1959	StdString cellMethodString = field->cell_methods;
1960	if (field->cell_methods_mode.isEmpty() \|\|
1961	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1962	{
1963	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1964	alreadyAddCellMethod = true;
1965	}
1966	else
1967	{
1968	switch (field->cell_methods_mode)
1969	{
1970	case (CField::cell_methods_mode_attr::prefix):
1971	cellMethodsPrefix = cellMethodString;
1972	cellMethodsPrefix += " ";
1973	break;
1974	case (CField::cell_methods_mode_attr::suffix):
1975	cellMethodsSuffix = " ";
1976	cellMethodsSuffix += cellMethodString;
1977	break;
1978	case (CField::cell_methods_mode_attr::none):
1979	break;
1980	default:
1981	break;
1982	}
1983	}
1984	}
1985
1986
1987	if (wtime)
1988	{
1989	CDuration freqOp = field->freq_op.getValue();
1990	freqOp.solveTimeStep(*context->calendar);
1991	StdString freqOpStr = freqOp.toStringUDUnits();
1992	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1993
1994	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1995	freqOut.solveTimeStep(*context->calendar);
1996	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1997
1998	StdString cellMethods(cellMethodsPrefix + "time: ");
1999	if (field->operation.getValue() == "instant") cellMethods += "point";
2000	else if (field->operation.getValue() == "average") cellMethods += "mean";
2001	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
2002	else cellMethods += field->operation;
2003	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
2004	cellMethods += " (interval: " + freqOpStr + ")";
2005	cellMethods += cellMethodsSuffix;
2006	if (!alreadyAddCellMethod)
2007	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
2008	}
2009
2010	if (hasArea)
2011	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
2012
2013	if (!field->default_value.isEmpty())
2014	{
2015	double default_value = field->default_value.getValue();
2016	if (type == NC_DOUBLE)
2017	{
2018	SuperClassWriter::setDefaultValue(fieldid, &default_value);
2019	}
2020	else if (type == NC_SHORT)
2021	{
2022	short sdefault_value = (short)default_value;
2023	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
2024	}
2025	else
2026	{
2027	float fdefault_value = (float)default_value;
2028	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
2029	}
2030	}
2031	else
2032	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
2033
2034	if (field->compression_level.isEmpty())
2035	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
2036	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
2037
2038	{ // Ecriture des coordonnes
2039
2040	StdString coordstr; //boost::algorithm::join(coodinates, " ")
2041	std::vector<StdString>::iterator
2042	itc = coodinates.begin(), endc = coodinates.end();
2043
2044	for (; itc!= endc; itc++)
2045	{
2046	StdString & coord = *itc;
2047	if (itc+1 != endc)
2048	coordstr.append(coord).append(" ");
2049	else coordstr.append(coord);
2050	}
2051
2052	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
2053
2054	}
2055
2056	vector<CVariable*> listVars = field->getAllVariables() ;
2057	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
2058
2059	}
2060	catch (CNetCdfException& e)
2061	{
2062	StdString msg("On writing field : ");
2063	msg.append(fieldid); msg.append("\n");
2064	msg.append("In the context : ");
2065	msg.append(context->getId()); msg.append("\n");
2066	msg.append(e.what());
2067	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2068	}
2069	} // writeField_()
2070
2071	//--------------------------------------------------------------
2072
2073	void CNc4DataOutput::writeFile_ (CFile* file)
2074	{
2075	StdString filename = file->getFileOutputName();
2076	StdString description = (!file->description.isEmpty())
2077	? file->description.getValue()
2078	: StdString("Created by xios");
2079
2080	singleDomain = (file->nbDomains == 1);
2081
2082	StdString conv_str ;
2083	if (file->convention_str.isEmpty())
2084	{
2085	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2086	else conv_str="UGRID" ;
2087	}
2088	else conv_str=file->convention_str ;
2089
2090	try
2091	{
2092	if (!appendMode) this->writeFileAttributes(filename, description,
2093	conv_str,
2094	StdString("An IPSL model"),
2095	this->getTimeStamp());
2096
2097	if (!appendMode)
2098	SuperClassWriter::addDimension("axis_nbounds", 2);
2099	}
2100	catch (CNetCdfException& e)
2101	{
2102	StdString msg("On writing file : ");
2103	msg.append(filename); msg.append("\n");
2104	msg.append("In the context : ");
2105	CContext* context = CContext::getCurrent() ;
2106	msg.append(context->getId()); msg.append("\n");
2107	msg.append(e.what());
2108	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2109	}
2110	}
2111
2112	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2113	{
2114	StdString name = var->getVariableOutputName();
2115
2116	try
2117	{
2118	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2119	addAttribute(name, var->getData<int>(), &fieldId);
2120	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2121	addAttribute(name, var->getData<short int>(), &fieldId);
2122	else if (var->type.getValue() == CVariable::type_attr::t_float)
2123	addAttribute(name, var->getData<float>(), &fieldId);
2124	else if (var->type.getValue() == CVariable::type_attr::t_double)
2125	addAttribute(name, var->getData<double>(), &fieldId);
2126	else if (var->type.getValue() == CVariable::type_attr::t_string)
2127	addAttribute(name, var->getData<string>(), &fieldId);
2128	else
2129	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2130	<< "Unsupported variable of type " << var->type.getStringValue());
2131	}
2132	catch (CNetCdfException& e)
2133	{
2134	StdString msg("On writing attributes of variable with name : ");
2135	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2136	msg.append("In the context : ");
2137	CContext* context = CContext::getCurrent() ;
2138	msg.append(context->getId()); msg.append("\n");
2139	msg.append(e.what());
2140	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2141	}
2142	}
2143
2144	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2145	{
2146	StdString name = var->getVariableOutputName();
2147
2148	try
2149	{
2150	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2151	addAttribute(name, var->getData<int>());
2152	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2153	addAttribute(name, var->getData<short int>());
2154	else if (var->type.getValue() == CVariable::type_attr::t_float)
2155	addAttribute(name, var->getData<float>());
2156	else if (var->type.getValue() == CVariable::type_attr::t_double)
2157	addAttribute(name, var->getData<double>());
2158	else if (var->type.getValue() == CVariable::type_attr::t_string)
2159	addAttribute(name, var->getData<string>());
2160	else
2161	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2162	<< "Unsupported variable of type " << var->type.getStringValue());
2163	}
2164	catch (CNetCdfException& e)
2165	{
2166	StdString msg("On writing attributes of variable with name : ");
2167	msg.append(name); msg.append("\n");
2168	msg.append("In the context : ");
2169	CContext* context = CContext::getCurrent() ;
2170	msg.append(context->getId()); msg.append("\n");
2171	msg.append(e.what());
2172	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2173	}
2174	}
2175
2176	void CNc4DataOutput::syncFile_ (void)
2177	{
2178	try
2179	{
2180	SuperClassWriter::sync() ;
2181	}
2182	catch (CNetCdfException& e)
2183	{
2184	StdString msg("On synchronizing the write among processes");
2185	msg.append("In the context : ");
2186	CContext* context = CContext::getCurrent() ;
2187	msg.append(context->getId()); msg.append("\n");
2188	msg.append(e.what());
2189	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2190	}
2191	}
2192
2193	void CNc4DataOutput::closeFile_ (void)
2194	{
2195	try
2196	{
2197	SuperClassWriter::close() ;
2198	}
2199	catch (CNetCdfException& e)
2200	{
2201	StdString msg("On closing file");
2202	msg.append("In the context : ");
2203	CContext* context = CContext::getCurrent() ;
2204	msg.append(context->getId()); msg.append("\n");
2205	msg.append(e.what());
2206	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2207	}
2208
2209	}
2210
2211	//---------------------------------------------------------------
2212
2213	StdString CNc4DataOutput::getTimeStamp(void) const
2214	{
2215	const int buffer_size = 100;
2216	time_t rawtime;
2217	struct tm * timeinfo = NULL;
2218	char buffer [buffer_size];
2219	StdString formatStr;
2220	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2221	else formatStr=file->time_stamp_format;
2222
2223	// time ( &rawtime );
2224	// timeinfo = localtime ( &rawtime );
2225	time ( &rawtime );
2226	timeinfo = gmtime ( &rawtime );
2227	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2228
2229	return (StdString(buffer));
2230	}
2231
2232	//---------------------------------------------------------------
2233
2234	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
2235	const CDate& currentWrite, int nstep)
2236	{
2237	CContext* context = CContext::getCurrent();
2238	CGrid* grid = field->getGrid();
2239
2240	if (nstep<1)
2241	{
2242	return nstep;
2243	}
2244
2245	if (!grid->doGridHaveDataToWrite())
2246	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2247	{
2248	return nstep;
2249	}
2250
2251	StdString fieldid = field->getFieldOutputName();
2252
2253	StdOStringStream oss;
2254	string timeAxisId;
2255	if (field->hasTimeInstant) timeAxisId = "time_instant";
2256	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2257
2258	StdString timeBoundId = getTimeCounterName() + "_bounds";
2259
2260	StdString timeAxisBoundId;
2261	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2262	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2263
2264	if (!field->wasWritten())
2265	{
2266	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
2267	field->getOperationTimeType() != func::CFunctor::once)
2268	{
2269	double factorUnit;
2270	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2271	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2272	else factorUnit=1 ;
2273	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
2274	}
2275
2276	field->setWritten();
2277	}
2278
2279
2280	CArray<double,1> time_data(1);
2281	CArray<double,1> time_data_bound(2);
2282	CArray<double,1> time_counter(1);
2283	CArray<double,1> time_counter_bound(2);
2284
2285	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2286	bool wtimeCounter =false ;
2287	bool wtimeData =false ;
2288
2289
2290	if (wtime)
2291	{
2292
2293	if (field->hasTimeInstant)
2294	{
2295	time_data(0) = time_data_bound(1) = (Time) lastWrite;
2296	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
2297	if (timeCounterType==instant)
2298	{
2299	time_counter(0) = time_data(0);
2300	time_counter_bound(0) = time_data_bound(0);
2301	time_counter_bound(1) = time_data_bound(1);
2302	wtimeCounter=true ;
2303	}
2304	if (hasTimeInstant) wtimeData=true ;
2305	}
2306	else if (field->hasTimeCentered)
2307	{
2308	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
2309	time_data_bound(0) = (Time)lastWrite;
2310	time_data_bound(1) = (Time)currentWrite;
2311	if (timeCounterType==centered)
2312	{
2313	time_counter(0) = time_data(0) ;
2314	time_counter_bound(0) = time_data_bound(0) ;
2315	time_counter_bound(1) = time_data_bound(1) ;
2316	wtimeCounter=true ;
2317	}
2318	if (hasTimeCentered) wtimeData=true ;
2319	}
2320
2321	if (timeCounterType==record)
2322	{
2323	time_counter(0) = nstep - 1;
2324	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
2325	wtimeCounter=true ;
2326	}
2327
2328	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2329	{
2330	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2331	time_data/=secByDay;
2332	time_data_bound/=secByDay;
2333	time_counter/=secByDay;
2334	time_counter_bound/=secByDay;
2335	}
2336	}
2337
2338	bool isRoot = (context->intraCommRank_ == 0);
2339
2340	try
2341	{
2342	switch (SuperClass::type)
2343	{
2344	case (MULTI_FILE) :
2345	{
2346	CTimer::get("Files : writing data").resume();
2347	SuperClassWriter::writeData(data, fieldid, isCollective, nstep - 1);
2348	CTimer::get("Files : writing data").suspend();
2349	if (wtime)
2350	{
2351	CTimer::get("Files : writing time axis").resume();
2352	if ( wtimeData)
2353	{
2354	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2355	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2356	}
2357	if (wtimeCounter)
2358	{
2359	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2360	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2361	}
2362	CTimer::get("Files : writing time axis").suspend();
2363	}
2364	break;
2365	}
2366	case (ONE_FILE) :
2367	{
2368
2369	std::vector<StdSize> start, count;
2370
2371	if (field->getUseCompressedOutput())
2372	{
2373	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2374	std::vector<StdString> domainList = grid->getDomainList();
2375	std::vector<StdString> axisList = grid->getAxisList();
2376	int numElement = axisDomainOrder.numElements();
2377	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2378	int idx = domainList.size() * 2 + axisList.size() - 1;
2379	int commRank ;
2380
2381	MPI_Comm_rank(comm_file,&commRank) ;
2382
2383	start.reserve(idx+1);
2384	count.reserve(idx+1);
2385
2386	for (int i = numElement - 1; i >= 0; --i)
2387	{
2388	if (2 == axisDomainOrder(i))
2389	{
2390	CDomain* domain = CDomain::get(domainList[idxDomain]);
2391
2392	if (domain->isCompressible())
2393	{
2394	size_t offset ;
2395	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
2396	if (domain->isDistributed())
2397	{
2398	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2399	if (commRank==0) offset=0 ;
2400	}
2401	else offset=0 ;
2402
2403	start.push_back(offset);
2404	count.push_back(nbIndexes);
2405	idx -= 2;
2406	}
2407	else
2408	{
2409	if ((domain->type) != CDomain::type_attr::unstructured)
2410	{
2411	start.push_back(domain->jbegin);
2412	count.push_back(domain->nj);
2413	}
2414	--idx;
2415	start.push_back(domain->ibegin);
2416	count.push_back(domain->ni);
2417	--idx;
2418	}
2419	--idxDomain;
2420	}
2421	else if (1 == axisDomainOrder(i))
2422	{
2423	CAxis* axis = CAxis::get(axisList[idxAxis]);
2424
2425	if (axis->isCompressible())
2426	{
2427	size_t offset ;
2428	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
2429	if (axis->isDistributed())
2430	{
2431	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2432	if (commRank==0) offset=0 ;
2433	}
2434	else offset=0 ;
2435
2436	start.push_back(offset);
2437	count.push_back(nbIndexes);
2438	}
2439	else
2440	{
2441	start.push_back(axis->begin);
2442	count.push_back(axis->n);
2443	}
2444	--idxAxis;
2445	--idx;
2446	}
2447	}
2448	}
2449	else
2450	{
2451	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2452	std::vector<StdString> domainList = grid->getDomainList();
2453	std::vector<StdString> axisList = grid->getAxisList();
2454	std::vector<StdString> scalarList = grid->getScalarList() ;
2455	int numElement = axisDomainOrder.numElements();
2456	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2457	int idx = domainList.size() * 2 + axisList.size() - 1;
2458
2459	start.reserve(idx+1);
2460	count.reserve(idx+1);
2461
2462	for (int i = numElement - 1; i >= 0; --i)
2463	{
2464	if (2 == axisDomainOrder(i))
2465	{
2466	CDomain* domain = CDomain::get(domainList[idxDomain]);
2467	if ((domain->type) != CDomain::type_attr::unstructured)
2468	{
2469	start.push_back(domain->jbegin);
2470	count.push_back(domain->nj);
2471	}
2472	--idx ;
2473
2474	start.push_back(domain->ibegin);
2475	count.push_back(domain->ni);
2476	--idx ;
2477	--idxDomain;
2478	}
2479	else if (1 == axisDomainOrder(i))
2480	{
2481	CAxis* axis = CAxis::get(axisList[idxAxis]);
2482	start.push_back(axis->begin);
2483	count.push_back(axis->n);
2484	--idx;
2485	--idxAxis;
2486	}
2487	else
2488	{
2489	if (1 == axisDomainOrder.numElements())
2490	{
2491	CScalar* scalar = CScalar::get(scalarList[scalarList.size()-1]);
2492	start.push_back(0);
2493	count.push_back(scalar->n);
2494	}
2495	--idx;
2496	}
2497	}
2498	}
2499
2500
2501	CTimer::get("Files : writing data").resume();
2502	SuperClassWriter::writeData(data, fieldid, isCollective, nstep - 1, &start, &count);
2503	CTimer::get("Files : writing data").suspend();
2504
2505	if (wtime)
2506	{
2507	CTimer::get("Files : writing time axis").resume();
2508	if ( wtimeData)
2509	{
2510	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2511	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2512	}
2513	if (wtimeCounter)
2514	{
2515	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2516	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2517
2518	}
2519	CTimer::get("Files : writing time axis").suspend();
2520	}
2521
2522	break;
2523	}
2524	}
2525	return nstep ;
2526	}
2527	catch (CNetCdfException& e)
2528	{
2529	StdString msg("On writing field data: ");
2530	msg.append(fieldid); msg.append("\n");
2531	msg.append("In the context : ");
2532	msg.append(context->getId()); msg.append("\n");
2533	msg.append(e.what());
2534	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2535	}
2536	}
2537
2538	//---------------------------------------------------------------
2539
2540	void CNc4DataOutput::writeTimeAxis_
2541	(CField* field,
2542	const std::shared_ptr<CCalendar> cal)
2543	{
2544	StdOStringStream oss;
2545	bool createInstantAxis=false ;
2546	bool createCenteredAxis=false ;
2547	bool createTimeCounterAxis=false ;
2548
2549	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2550
2551
2552	StdString axisId ;
2553	StdString axisBoundId;
2554	StdString timeid(getTimeCounterName());
2555	StdString timeBoundId("axis_nbounds");
2556
2557	StdString strTimeUnits ;
2558	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2559	else strTimeUnits="seconds since " ;
2560
2561	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2562	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2563
2564
2565	if (field->getRelFile()->time_counter.isEmpty())
2566	{
2567	if (timeCounterType==none) createTimeCounterAxis=true ;
2568	if (field->hasTimeCentered)
2569	{
2570	timeCounterType=centered ;
2571	if (!hasTimeCentered) createCenteredAxis=true ;
2572	}
2573	if (field->hasTimeInstant)
2574	{
2575	if (timeCounterType==none) timeCounterType=instant ;
2576	if (!hasTimeInstant) createInstantAxis=true ;
2577	}
2578	}
2579	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
2580	{
2581	if (field->hasTimeCentered)
2582	{
2583	if (!hasTimeCentered) createCenteredAxis=true ;
2584	}
2585	if (field->hasTimeInstant)
2586	{
2587	if (timeCounterType==none) createTimeCounterAxis=true ;
2588	timeCounterType=instant ;
2589	if (!hasTimeInstant) createInstantAxis=true ;
2590	}
2591	}
2592	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
2593	{
2594	if (field->hasTimeCentered)
2595	{
2596	if (timeCounterType==none) createTimeCounterAxis=true ;
2597	timeCounterType=centered ;
2598	if (!hasTimeCentered) createCenteredAxis=true ;
2599	}
2600	if (field->hasTimeInstant)
2601	{
2602	if (!hasTimeInstant) createInstantAxis=true ;
2603	}
2604	}
2605	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
2606	{
2607	if (field->hasTimeCentered)
2608	{
2609	if (!hasTimeCentered) createCenteredAxis=true ;
2610	}
2611	if (field->hasTimeInstant)
2612	{
2613	if (timeCounterType==none) createTimeCounterAxis=true ;
2614	timeCounterType=instant ;
2615	}
2616	}
2617	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
2618	{
2619	if (field->hasTimeCentered)
2620	{
2621	if (timeCounterType==none) createTimeCounterAxis=true ;
2622	timeCounterType=centered ;
2623	}
2624	if (field->hasTimeInstant)
2625	{
2626	if (!hasTimeInstant) createInstantAxis=true ;
2627	}
2628	}
2629	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
2630	{
2631	if (field->hasTimeCentered)
2632	{
2633	if (timeCounterType==none) createTimeCounterAxis=true ;
2634	if (timeCounterType==instant) createInstantAxis=true ;
2635	timeCounterType=centered ;
2636	}
2637	if (field->hasTimeInstant)
2638	{
2639	if (timeCounterType==none)
2640	{
2641	createTimeCounterAxis=true ;
2642	timeCounterType=instant ;
2643	}
2644	if (timeCounterType==centered)
2645	{
2646	if (!hasTimeInstant) createInstantAxis=true ;
2647	}
2648	}
2649	}
2650	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
2651	{
2652	if (field->hasTimeCentered)
2653	{
2654	if (!hasTimeCentered) createCenteredAxis=true ;
2655	}
2656	if (field->hasTimeInstant)
2657	{
2658	if (!hasTimeInstant) createInstantAxis=true ;
2659	}
2660	}
2661	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
2662	{
2663	if (timeCounterType==none) createTimeCounterAxis=true ;
2664	timeCounterType=record ;
2665	if (field->hasTimeCentered)
2666	{
2667	if (!hasTimeCentered) createCenteredAxis=true ;
2668	}
2669	if (field->hasTimeInstant)
2670	{
2671	if (!hasTimeInstant) createInstantAxis=true ;
2672	}
2673	}
2674
2675	if (createInstantAxis)
2676	{
2677	axisId="time_instant" ;
2678	axisBoundId="time_instant_bounds";
2679	hasTimeInstant=true ;
2680	}
2681
2682	if (createCenteredAxis)
2683	{
2684	axisId="time_centered" ;
2685	axisBoundId="time_centered_bounds";
2686	hasTimeCentered=true ;
2687	}
2688
2689
2690	try
2691	{
2692	std::vector<StdString> dims;
2693
2694	if (createInstantAxis \|\| createCenteredAxis)
2695	{
2696	// Adding time_instant or time_centered
2697	dims.push_back(timeid);
2698	if (!SuperClassWriter::varExist(axisId))
2699	{
2700	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2701
2702	CDate timeOrigin=cal->getTimeOrigin() ;
2703	StdOStringStream oss2;
2704	StdString strInitdate=oss2.str() ;
2705	StdString strTimeOrigin=timeOrigin.toString() ;
2706	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2707	strTimeOrigin, axisBoundId);
2708	}
2709
2710	// Adding time_instant_bounds or time_centered_bounds variables
2711	if (!SuperClassWriter::varExist(axisBoundId))
2712	{
2713	dims.clear() ;
2714	dims.push_back(timeid);
2715	dims.push_back(timeBoundId);
2716	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2717	}
2718	}
2719
2720	if (createTimeCounterAxis)
2721	{
2722	// Adding time_counter
2723	axisId = getTimeCounterName();
2724	axisBoundId = getTimeCounterName() + "_bounds";
2725	dims.clear();
2726	dims.push_back(timeid);
2727	if (!SuperClassWriter::varExist(axisId))
2728	{
2729	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2730	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2731
2732	if (field->getRelFile()->time_counter.isEmpty() \|\|
2733	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2734	{
2735	CDate timeOrigin = cal->getTimeOrigin();
2736	StdString strTimeOrigin = timeOrigin.toString();
2737
2738	this->writeTimeAxisAttributes(axisId, cal->getType(),
2739	strTimeUnits+strTimeOrigin,
2740	strTimeOrigin, axisBoundId);
2741	}
2742	}
2743
2744	// Adding time_counter_bound dimension
2745	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2746	{
2747	if (!SuperClassWriter::varExist(axisBoundId))
2748	{
2749	dims.clear();
2750	dims.push_back(timeid);
2751	dims.push_back(timeBoundId);
2752	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2753	}
2754	}
2755	}
2756	}
2757	catch (CNetCdfException& e)
2758	{
2759	StdString msg("On writing time axis data: ");
2760	msg.append("In the context : ");
2761	CContext* context = CContext::getCurrent() ;
2762	msg.append(context->getId()); msg.append("\n");
2763	msg.append(e.what());
2764	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2765	const std::shared_ptr<CCalendar> cal)", << msg);
2766	}
2767	}
2768
2769	//---------------------------------------------------------------
2770
2771	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2772	const StdString & calendar,
2773	const StdString & units,
2774	const StdString & time_origin,
2775	const StdString & time_bounds,
2776	const StdString & standard_name,
2777	const StdString & long_name)
2778	{
2779	try
2780	{
2781	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2782	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2783	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2784	SuperClassWriter::addAttribute("units", units , &axis_name);
2785	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2786	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2787	}
2788	catch (CNetCdfException& e)
2789	{
2790	StdString msg("On writing time axis Attribute: ");
2791	msg.append("In the context : ");
2792	CContext* context = CContext::getCurrent() ;
2793	msg.append(context->getId()); msg.append("\n");
2794	msg.append(e.what());
2795	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2796	const StdString & calendar,\
2797	const StdString & units, \
2798	const StdString & time_origin, \
2799	const StdString & time_bounds, \
2800	const StdString & standard_name, \
2801	const StdString & long_name)", << msg);
2802	}
2803	}
2804
2805	//---------------------------------------------------------------
2806
2807	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2808	const StdString & axis,
2809	const StdString & standard_name,
2810	const StdString & long_name,
2811	const StdString & units,
2812	const StdString & nav_model)
2813	{
2814	try
2815	{
2816	if (!axis.empty())
2817	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2818
2819	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2820	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2821	SuperClassWriter::addAttribute("units" , units , &axis_name);
2822	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2823	}
2824	catch (CNetCdfException& e)
2825	{
2826	StdString msg("On writing Axis Attribute: ");
2827	msg.append("In the context : ");
2828	CContext* context = CContext::getCurrent() ;
2829	msg.append(context->getId()); msg.append("\n");
2830	msg.append(e.what());
2831	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2832	const StdString & axis, \
2833	const StdString & standard_name, \
2834	const StdString & long_name, \
2835	const StdString & units, \
2836	const StdString & nav_model)", << msg);
2837	}
2838	}
2839
2840	//---------------------------------------------------------------
2841
2842	void CNc4DataOutput::writeLocalAttributes
2843	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2844	{
2845	try
2846	{
2847	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2848	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2849	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2850	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2851	}
2852	catch (CNetCdfException& e)
2853	{
2854	StdString msg("On writing Local Attributes: ");
2855	msg.append("In the context : ");
2856	CContext* context = CContext::getCurrent() ;
2857	msg.append(context->getId()); msg.append("\n");
2858	msg.append(e.what());
2859	ERROR("CNc4DataOutput::writeLocalAttributes \
2860	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2861	}
2862
2863	}
2864
2865	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2866	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2867	{
2868	CArray<int,1> array(2) ;
2869
2870	try
2871	{
2872	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2873	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2874	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2875	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2876	array=ni_glo,nj_glo ;
2877	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2878	array=ni,nj ;
2879	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2880	array=ibegin+1,jbegin+1 ;
2881	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2882	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2883	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2884	array=0,0 ;
2885	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2886	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2887	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2888	/*
2889	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2890	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2891	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2892	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2893	*/
2894	}
2895	catch (CNetCdfException& e)
2896	{
2897	StdString msg("On writing Local Attributes IOIPSL \n");
2898	msg.append("In the context : ");
2899	CContext* context = CContext::getCurrent() ;
2900	msg.append(context->getId()); msg.append("\n");
2901	msg.append(e.what());
2902	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2903	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2904	}
2905	}
2906	//---------------------------------------------------------------
2907
2908	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2909	const StdString & description,
2910	const StdString & conventions,
2911	const StdString & production,
2912	const StdString & timeStamp)
2913	{
2914	try
2915	{
2916	SuperClassWriter::addAttribute("name" , name);
2917	SuperClassWriter::addAttribute("description", description);
2918	SuperClassWriter::addAttribute("title" , description);
2919	SuperClassWriter::addAttribute("Conventions", conventions);
2920	// SuperClassWriter::addAttribute("production" , production);
2921
2922	StdString timeStampStr ;
2923	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
2924	else timeStampStr=file->time_stamp_name ;
2925	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
2926
2927	StdString uuidName ;
2928	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
2929	else uuidName=file->uuid_name ;
2930
2931	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
2932	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
2933
2934	}
2935	catch (CNetCdfException& e)
2936	{
2937	StdString msg("On writing File Attributes \n ");
2938	msg.append("In the context : ");
2939	CContext* context = CContext::getCurrent() ;
2940	msg.append(context->getId()); msg.append("\n");
2941	msg.append(e.what());
2942	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2943	const StdString & description, \
2944	const StdString & conventions, \
2945	const StdString & production, \
2946	const StdString & timeStamp)", << msg);
2947	}
2948	}
2949
2950	//---------------------------------------------------------------
2951
2952	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2953	int data_dim,
2954	int data_ni,
2955	int data_nj,
2956	int data_ibegin,
2957	int data_jbegin)
2958	{
2959	try
2960	{
2961	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2962	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2963	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2964	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2965	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2966	}
2967	catch (CNetCdfException& e)
2968	{
2969	StdString msg("On writing Mask Attributes \n ");
2970	msg.append("In the context : ");
2971	CContext* context = CContext::getCurrent() ;
2972	msg.append(context->getId()); msg.append("\n");
2973	msg.append(e.what());
2974	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2975	int data_dim, \
2976	int data_ni, \
2977	int data_nj, \
2978	int data_ibegin, \
2979	int data_jbegin)", << msg);
2980	}
2981	}
2982
2983	///--------------------------------------------------------------
2984
2985	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
2986	{
2987	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2988	if (it == timeToRecordCache.end())
2989	{
2990	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2991	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
2992	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
2993
2994	CArray<double,2> timeAxisBounds;
2995	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
2996
2997	StdSize record = 0;
2998	double dtime(time);
2999	for (int n = dimSize[0] - 1; n >= 0; n--)
3000	{
3001	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3002	timeAxisBounds*=factorUnit ;
3003	if (timeAxisBounds(1, 0) < dtime)
3004	{
3005	record = n + 1;
3006	break;
3007	}
3008	}
3009	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3010	}
3011	return it->second;
3012	}
3013
3014	///--------------------------------------------------------------
3015
3016	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3017	{
3018	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3019	}
3020
3021	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3022	{
3023	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3024	}
3025
3026	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3027	{
3028	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3029	}
3030
3031	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3032	{
3033	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3034	}
3035
3036	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3037	{
3038	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3039	}
3040
3041	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3042	{
3043	this->writtenDomains.insert(domainName);
3044	}
3045
3046	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3047	{
3048	this->writtenCompressedDomains.insert(domainName);
3049	}
3050
3051	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3052	{
3053	this->writtenAxis.insert(axisName);
3054	}
3055
3056	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3057	{
3058	this->writtenCompressedAxis.insert(axisName);
3059	}
3060
3061	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3062	{
3063	this->writtenScalar.insert(scalarName);
3064	}
3065	} // namespace xios

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