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source: XIOS3/trunk/src/io/nc4_data_output.cpp @ 2628

Last change on this file since 2628 was 2628, checked in by jderouillat, 7 weeks ago
New timers integration/reporting
Property copyright set to Software name : XIOS (Xml I/O Server) http://forge.ipsl.jussieu.fr/ioserver Creation date : January 2009 Licence : CeCCIL version2 see license file in root directory : Licence_CeCILL_V2-en.txt or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement) CNRS/IPSL (Institut Pierre Simon Laplace) Project Manager : Yann Meurdesoif yann.meurdesoif@cea.fr Property svn:executable set to ``*
File size: 129.6 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
15	#include <limits.h>
16	#define X_FLOAT_MAX FLT_MAX
17	#define X_FLOAT_MIN FLT_MIN
18	#define X_SHORT_MAX SHRT_MAX
19	#define X_SHORT_MIN SHRT_MIN
20
21	namespace xios
22	{
23	extern CLogType logProfile ;
24	/// ////////////////////// Dfinitions ////////////////////// ///
25	CNc4DataOutput::CNc4DataOutput
26	(CFile* file, const StdString & filename, bool exist)
27	: SuperClass()
28	, SuperClassWriter(filename, exist)
29	, filename(filename)
30	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
31	{
32	SuperClass::type = MULTI_FILE;
33	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
34	}
35
36	CNc4DataOutput::CNc4DataOutput
37	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
38	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
39	: SuperClass()
40	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
41	, comm_file(comm_file)
42	, filename(filename)
43	, isCollective(isCollective)
44	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
45	{
46	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
47	if (file==NULL) compressionLevel = 0 ;
48	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
49	}
50
51	CNc4DataOutput::~CNc4DataOutput(void)
52	{ /* Ne rien faire de plus */ }
53
54	///--------------------------------------------------------------
55
56	const StdString & CNc4DataOutput::getFileName(void) const
57	{
58	return (this->filename);
59	}
60
61	//---------------------------------------------------------------
62
63	void CNc4DataOutput::writeDomain_(CDomain* domain)
64	TRY
65	{
66	StdString lonName,latName ;
67
68	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
69	if (!domain->lonvalue.isEmpty() )
70	{
71	// The hash of the element will be associated to the default element name (= map key), and to the name really written
72	int globalHash = domain->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
73
74	StdString defaultNameKey = domain->getDomainOutputName();
75	if ( !relDomains_.count ( defaultNameKey ) )
76	{
77	// if defaultNameKey not in the map, write the element such as it is defined
78	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) );
79	}
80	else // look if a hash associated this key is equal
81	{
82	bool elementIsInMap(false);
83	auto defaultNameKeyElements = relDomains_.equal_range( defaultNameKey );
84	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
85	{
86	if ( it->second.first == globalHash )
87	{
88	// if yes, associate the same ids to current element
89	domain->renameAttributesBeforeWriting( it->second.second );
90	elementIsInMap = true;
91	}
92	}
93	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
94	if (!elementIsInMap) // ! in MAP
95	{
96	domain->renameAttributesBeforeWriting();
97	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) ) ;
98	}
99	}
100	}
101
102	if (domain->type == CDomain::type_attr::unstructured)
103	{
104	if (SuperClassWriter::useCFConvention)
105	writeUnstructuredDomain(domain) ;
106	else
107	writeUnstructuredDomainUgrid(domain) ;
108	return ;
109	}
110
111	CContext* context = CContext::getCurrent() ;
112	if (domain->IsWritten(this->filename)) return;
113	domain->checkAttributes();
114
115	if (domain->isEmpty())
116	if (SuperClass::type==MULTI_FILE) return;
117
118
119	std::vector<StdString> dim0, dim1;
120	StdString domid = domain->getDomainOutputName();
121	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
122	if (isWrittenDomain(domid)) return ;
123	else setWrittenDomain(domid);
124
125	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
126
127
128	StdString dimXid, dimYid ;
129
130	nc_type typePrec ;
131	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
132	else if (domain->prec==4) typePrec = NC_FLOAT ;
133	else if (domain->prec==8) typePrec = NC_DOUBLE ;
134
135	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
136	switch (domain->type)
137	{
138	case CDomain::type_attr::curvilinear :
139
140	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
141	else lonName = domain->lon_name;
142
143	if (domain->lat_name.isEmpty()) latName = "nav_lat";
144	else latName = domain->lat_name;
145
146	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
147	else dimXid=domain->dim_i_name.getValue() + appendDomid;
148
149	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
150	else dimYid=domain->dim_j_name.getValue() + appendDomid;
151
152	break ;
153
154	case CDomain::type_attr::rectilinear :
155
156	if (domain->lon_name.isEmpty())
157	{
158	if (domain->dim_i_name.isEmpty())
159	lonName = "lon";
160	else
161	lonName = domain->dim_i_name.getValue();
162	}
163	else lonName = domain->lon_name;
164
165	if (domain->lat_name.isEmpty())
166	{
167	if (domain->dim_j_name.isEmpty())
168	latName = "lat";
169	else
170	latName = domain->dim_j_name.getValue();
171	}
172	else latName = domain->lat_name;
173
174	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
175	else dimXid = domain->dim_i_name.getValue()+appendDomid;
176
177	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
178	else dimYid = domain->dim_j_name.getValue()+appendDomid;
179	break;
180	}
181
182	StdString dimVertId = StdString("nvertex").append(appendDomid);
183
184	string lonid,latid,bounds_lonid,bounds_latid ;
185	string areaId = "area" + appendDomid;
186
187	try
188	{
189	switch (SuperClass::type)
190	{
191	case (MULTI_FILE) :
192	{
193	switch (domain->type)
194	{
195	case CDomain::type_attr::curvilinear :
196	dim0.push_back(dimYid); dim0.push_back(dimXid);
197	lonid = lonName+appendDomid;
198	latid = latName+appendDomid;
199	break ;
200	case CDomain::type_attr::rectilinear :
201	lonid = lonName+appendDomid;
202	latid = latName+appendDomid;
203	dim0.push_back(dimYid);
204	dim1.push_back(dimXid);
205	break;
206	}
207	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
208	else bounds_lonid = "bounds_"+lonName+appendDomid;
209	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
210	else bounds_latid = "bounds_"+latName+appendDomid;
211
212	SuperClassWriter::addDimension(dimXid, domain->niValue_);
213	SuperClassWriter::addDimension(dimYid, domain->njValue_);
214
215	if (domain->hasBounds)
216	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
217
218	if (context->intraCommSize_ > 1)
219	{
220	this->writeLocalAttributes(domain->ibeginValue_,
221	domain->niValue_,
222	domain->jbeginValue_,
223	domain->njValue_,
224	appendDomid);
225
226	if (singleDomain)
227	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
228	domain->ibeginValue_,
229	domain->niValue_,
230	domain->jbeginValue_,
231	domain->njValue_,
232	domain->ni_glo,domain->nj_glo,
233	context->intraCommRank_,context->intraCommSize_);
234	}
235
236	if (domain->hasLonLat)
237	{
238	switch (domain->type)
239	{
240	case CDomain::type_attr::curvilinear :
241	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
242	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
243	break ;
244	case CDomain::type_attr::rectilinear :
245	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
246	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
247	break ;
248	}
249
250	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
251	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
252
253	if (domain->hasBounds)
254	{
255	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
256	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
257
258	dim0.clear();
259	dim0.push_back(dimYid);
260	dim0.push_back(dimXid);
261	dim0.push_back(dimVertId);
262	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
263	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
264	}
265	}
266
267	dim0.clear();
268	dim0.push_back(dimYid);
269	dim0.push_back(dimXid);
270
271	if (domain->hasArea)
272	{
273	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
274	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
275	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
276	}
277
278	SuperClassWriter::definition_end();
279
280	if (domain->hasLonLat)
281	{
282	switch (domain->type)
283	{
284	case CDomain::type_attr::curvilinear :
285	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
286	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
287	break;
288	case CDomain::type_attr::rectilinear :
289	//CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
290	CArray<double,1> lat;
291	lat.resize( domain->njValue_);
292	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
293	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
294	//CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
295	CArray<double,1> lon = domain->lonvalue(Range(0,domain->niValue_-1));
296	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
297	break;
298	}
299
300	if (domain->hasBounds)
301	{
302	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
303	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
304	}
305	}
306
307	if (domain->hasArea)
308	{
309	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
310	}
311
312	SuperClassWriter::definition_start();
313
314	break;
315	}
316	case (ONE_FILE) :
317	{
318	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
319	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
320
321	if (domain->hasBounds)
322	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
323
324	if (domain->hasLonLat)
325	{
326	switch (domain->type)
327	{
328	case CDomain::type_attr::curvilinear :
329	dim0.push_back(dimYid); dim0.push_back(dimXid);
330	lonid = lonName+appendDomid;
331	latid = latName+appendDomid;
332	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
333	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
334	break;
335
336	case CDomain::type_attr::rectilinear :
337	dim0.push_back(dimYid);
338	dim1.push_back(dimXid);
339	lonid = lonName+appendDomid;
340	latid = latName+appendDomid;
341	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
342	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
343	break;
344	}
345	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
346	else bounds_lonid = "bounds_"+lonName+appendDomid;
347	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
348	else bounds_latid = "bounds_"+latName+appendDomid;
349
350	this->writeAxisAttributes
351	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
352	this->writeAxisAttributes
353	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
354
355	if (domain->hasBounds)
356	{
357	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
358	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
359
360	dim0.clear();
361	dim0.push_back(dimYid);
362	dim0.push_back(dimXid);
363	dim0.push_back(dimVertId);
364	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
365	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
366	}
367	}
368
369	if (domain->hasArea)
370	{
371	dim0.clear();
372	dim0.push_back(dimYid); dim0.push_back(dimXid);
373	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
374	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
375	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
376	dim0.clear();
377	}
378
379	SuperClassWriter::definition_end();
380
381	switch (domain->type)
382	{
383	case CDomain::type_attr::curvilinear :
384	{
385	std::vector<StdSize> start(2) ;
386	std::vector<StdSize> count(2) ;
387	start[1]=domain->ibeginValue_;
388	start[0]=domain->jbeginValue_;
389	count[1]=domain->niValue_ ; count[0]=domain->njValue_ ;
390
391	if (domain->hasLonLat)
392	{
393	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
394	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
395	}
396	break;
397	}
398	case CDomain::type_attr::rectilinear :
399	{
400	if (domain->hasLonLat)
401	{
402	std::vector<StdSize> start(1) ;
403	std::vector<StdSize> count(1) ;
404
405	start[0]=domain->jbeginValue_;
406	count[0]=domain->njValue_;
407	CArray<double,1> lat;
408	lat.resize( domain->njValue_);
409	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
410	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
411
412	start[0]=domain->ibeginValue_;
413	count[0]=domain->niValue_;
414	CArray<double,1> lon;
415	lon.resize( domain->niValue_);
416	for (int i=0;i<domain->niValue_;i++) lon(i) = domain->lonvalue(i);
417	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
418	}
419	break;
420	}
421	}
422
423	if (domain->hasBounds)
424	{
425	std::vector<StdSize> start(3);
426	std::vector<StdSize> count(3);
427	if (domain->isEmpty())
428	{
429	start[2] = start[1] = start[0] = 0;
430	count[2] = count[1] = count[0] = 0;
431	}
432	else
433	{
434	start[2] = 0;
435	start[1] = domain->ibeginValue_;
436	start[0] = domain->jbeginValue_;
437	count[2] = domain->nvertex;
438	count[1] = domain->niValue_;
439	count[0] = domain->njValue_;
440	}
441
442	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
443	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
444	}
445
446	if (domain->hasArea)
447	{
448	std::vector<StdSize> start(2);
449	std::vector<StdSize> count(2);
450
451	start[1] = domain->ibeginValue_;
452	start[0] = domain->jbeginValue_;
453	count[1] = domain->niValue_;
454	count[0] = domain->njValue_;
455
456	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
457	}
458
459	SuperClassWriter::definition_start();
460	break;
461	}
462	default :
463	ERROR("CNc4DataOutput::writeDomain(domain)",
464	<< "[ type = " << SuperClass::type << "]"
465	<< " not implemented yet !");
466	}
467	}
468	catch (CNetCdfException& e)
469	{
470	StdString msg("On writing the domain : ");
471	msg.append(domid); msg.append("\n");
472	msg.append("In the context : ");
473	msg.append(context->getId()); msg.append("\n");
474	msg.append(e.what());
475	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
476	}
477
478	domain->addRelFile(this->filename);
479	}
480	CATCH
481
482	//--------------------------------------------------------------
483
484	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
485	{
486	CContext* context = CContext::getCurrent() ;
487
488	if (domain->IsWritten(this->filename)) return;
489
490	StdString domid = domain->getDomainOutputName();
491
492	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
493	// Thus the entire mesh connectivity will be generated at once.
494	if (isWrittenDomain(domid)) return ;
495	else setWrittenDomain(domid);
496
497	domain->checkAttributes();
498	if (domain->isEmpty())
499	if (SuperClass::type==MULTI_FILE) return ;
500
501	nc_type typePrec ;
502	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
503	else if (domain->prec==4) typePrec = NC_FLOAT ;
504	else if (domain->prec==8) typePrec = NC_DOUBLE ;
505
506	std::vector<StdString> dim0;
507	StdString domainName = domain->name;
508
509	StdString node_x = domainName + "_node_x";
510	StdString node_y = domainName + "_node_y";
511
512	StdString edge_x = domainName + "_edge_x";
513	StdString edge_y = domainName + "_edge_y";
514	StdString edge_nodes = domainName + "_edge_nodes";
515
516	StdString face_x = domainName + "_face_x";
517	StdString face_y = domainName + "_face_y";
518	StdString face_nodes = domainName + "_face_nodes";
519	StdString face_edges = domainName + "_face_edges";
520	StdString edge_faces = domainName + "_edge_face_links";
521	StdString face_faces = domainName + "_face_links";
522
523	StdString dimNode = "n" + domainName + "_node";
524	StdString dimEdge = "n" + domainName + "_edge";
525	StdString dimFace = "n" + domainName + "_face";
526	StdString dimVertex = "n" + domainName + "_vertex";
527	StdString dimTwo = "Two";
528
529	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
530	dim0.clear();
531	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
532	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
533	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
534	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
535	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
536
537	try
538	{
539	switch (SuperClass::type)
540	{
541	case (ONE_FILE) :
542	{
543	// Adding nodes
544	if (domain->nvertex == 1)
545	{
546	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
547	{
548	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
549	dim0.clear();
550	dim0.push_back(dimNode);
551	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
552	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
553	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
554	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
555	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
556	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
557	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
558	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
559	}
560	} // domain->nvertex == 1
561
562	// Adding edges and nodes, if nodes have not been defined previously
563	if (domain->nvertex == 2)
564	{
565	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
566	{
567	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
568	dim0.clear();
569	dim0.push_back(dimNode);
570	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
571	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
572	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
573	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
574	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
575	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
576	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
577	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
578	}
579	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
580	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
581	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
582	dim0.clear();
583	dim0.push_back(dimEdge);
584	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
585	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
586	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
587	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
588	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
589	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
590	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
591	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
592	dim0.clear();
593	dim0.push_back(dimEdge);
594	dim0.push_back(dimTwo);
595	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
596	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
597	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
598	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
599	} // domain->nvertex == 2
600
601	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
602	if (domain->nvertex > 2)
603	{
604	// Nodes
605	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
606	{
607	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
608	dim0.clear();
609	dim0.push_back(dimNode);
610	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
611	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
612	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
613	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
614	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
615	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
616	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
617	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
618	}
619	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
620	{
621	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
622	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
623	SuperClassWriter::addAttribute("face_edge_connectivity", face_edges, &domainName);
624	SuperClassWriter::addAttribute("edge_face_connectivity", edge_faces, &domainName);
625	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
626	dim0.clear();
627	dim0.push_back(dimEdge);
628	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
629	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
630	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
631	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
632	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
633	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
634	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
635	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
636	dim0.clear();
637	dim0.push_back(dimEdge);
638	dim0.push_back(dimTwo);
639	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
640	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
641	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
642	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
643	}
644	SuperClassWriter::addAttribute("face_face_connectivity", face_faces, &domainName);
645	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
646	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
647	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
648	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
649	dim0.clear();
650	dim0.push_back(dimFace);
651	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
652	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
653	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
654	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
655	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
656	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
657	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
658	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
659	dim0.clear();
660	dim0.push_back(dimFace);
661	dim0.push_back(dimVertex);
662	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
663	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
664	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
665	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
666	dim0.clear();
667	dim0.push_back(dimFace);
668	dim0.push_back(dimVertex);
669	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
670	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
671	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
672	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
673	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
674	dim0.clear();
675	dim0.push_back(dimEdge);
676	dim0.push_back(dimTwo);
677	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
678	SuperClassWriter::addAttribute("cf_role", StdString("edge_face_connectivity"), &edge_faces);
679	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
680	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
681	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
682	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
683	dim0.clear();
684	dim0.push_back(dimFace);
685	dim0.push_back(dimVertex);
686	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
687	SuperClassWriter::addAttribute("cf_role", StdString("face_face_connectivity"), &face_faces);
688	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
689	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
690	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
691	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
692	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
693	} // domain->nvertex > 2
694
695	SuperClassWriter::definition_end();
696
697	std::vector<StdSize> startEdges(1) ;
698	std::vector<StdSize> countEdges(1) ;
699	std::vector<StdSize> startNodes(1) ;
700	std::vector<StdSize> countNodes(1) ;
701	std::vector<StdSize> startFaces(1) ;
702	std::vector<StdSize> countFaces(1) ;
703	std::vector<StdSize> startEdgeNodes(2) ;
704	std::vector<StdSize> countEdgeNodes(2) ;
705	std::vector<StdSize> startEdgeFaces(2) ;
706	std::vector<StdSize> countEdgeFaces(2) ;
707	std::vector<StdSize> startFaceConctv(2) ;
708	std::vector<StdSize> countFaceConctv(2) ;
709
710	if (domain->nvertex == 1)
711	{
712	if (domain->isEmpty())
713	{
714	startNodes[0]=0 ;
715	countNodes[0]=0 ;
716	}
717	else
718	{
719	startNodes[0] = domain->ibeginValue_;
720	countNodes[0] = domain->niValue_ ;
721	}
722
723	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
724	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
725	}
726	else if (domain->nvertex == 2)
727	{
728	if (domain->isEmpty())
729	{
730	startEdges[0]=0 ;
731	countEdges[0]=0 ;
732	startNodes[0]=0 ;
733	countNodes[0]=0 ;
734	startEdgeNodes[0]=0;
735	startEdgeNodes[1]=0;
736	countEdgeNodes[0]=0;
737	countEdgeNodes[1]=0;
738
739	}
740	else
741	{
742	startEdges[0] = domain->ibeginValue_;
743	countEdges[0] = domain->niValue_;
744	startNodes[0] = domain->mesh->node_start;
745	countNodes[0] = domain->mesh->node_count;
746	if (countNodes[0]==0) startNodes[0]=0 ; // for netcdf error
747	startEdgeNodes[0] = domain->ibeginValue_;
748	startEdgeNodes[1] = 0;
749	countEdgeNodes[0] = domain->niValue_;
750	countEdgeNodes[1] = 2;
751	}
752	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
753	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
754	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
755	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
756	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
757	}
758	else
759	{
760	if (domain->isEmpty())
761	{
762	startFaces[0] = 0 ;
763	countFaces[0] = 0 ;
764	startNodes[0] = 0;
765	countNodes[0] = 0;
766	startEdges[0] = 0;
767	countEdges[0] = 0;
768	startEdgeFaces[0] = 0;
769	startEdgeFaces[1] = 0;
770	countEdgeFaces[0] = 0;
771	countEdgeFaces[1] = 0;
772	startFaceConctv[0] = 0;
773	startFaceConctv[1] = 0;
774	countFaceConctv[0] = 0;
775	countFaceConctv[1] = 0;
776	}
777	else
778	{
779	startFaces[0] = domain->ibeginValue_;
780	countFaces[0] = domain->niValue_ ;
781	startNodes[0] = domain->mesh->node_start;
782	countNodes[0] = domain->mesh->node_count;
783	if (countNodes[0]==0) startNodes[0]=0;
784
785	startEdges[0] = domain->mesh->edge_start;
786	countEdges[0] = domain->mesh->edge_count;
787	if (countEdges[0]==0) startEdges[0]=0 ; // for netcdf error
788
789	startEdgeNodes[0] = domain->mesh->edge_start;
790	countEdgeNodes[0] = domain->mesh->edge_count;
791	if (countEdgeNodes[0]==0) startEdgeNodes[0]=0; // for netcdf error
792	startEdgeNodes[1] = 0;
793	countEdgeNodes[1]= 2;
794
795	startEdgeFaces[0] = domain->mesh->edge_start;
796	countEdgeFaces[0] = domain->mesh->edge_count;
797	if (countEdgeFaces[0]==0) startEdgeFaces[0]=0 ; // for netcdf error
798	startEdgeFaces[1]= 0;
799	countEdgeFaces[1]= 2;
800
801	startFaceConctv[0] = domain->ibeginValue_;
802	countFaceConctv[0] = domain->niValue_;
803	startFaceConctv[1] = 0;
804	countFaceConctv[1] = domain->nvertex;
805	}
806	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
807	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
808	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
809	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
810	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
811	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
812	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
813	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
814	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
815	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
816	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
817	}
818	SuperClassWriter::definition_start();
819
820	break;
821	} // ONE_FILE
822
823	case (MULTI_FILE) :
824	{
825	ERROR("CNc4DataOutput::writeDomain(domain)",
826	<< "[ type = multiple_file ]"
827	<< " is not yet implemented for UGRID files !");
828	break;
829	}
830
831	default :
832	ERROR("CNc4DataOutput::writeDomain(domain)",
833	<< "[ type = " << SuperClass::type << "]"
834	<< " not implemented yet !");
835	} // switch
836	} // try
837
838	catch (CNetCdfException& e)
839	{
840	StdString msg("On writing the domain : ");
841	msg.append(domid); msg.append("\n");
842	msg.append("In the context : ");
843	msg.append(context->getId()); msg.append("\n");
844	msg.append(e.what());
845	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
846	}
847
848	domain->addRelFile(this->filename);
849	}
850
851	//--------------------------------------------------------------
852
853	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
854	{
855	CContext* context = CContext::getCurrent() ;
856
857	if (domain->IsWritten(this->filename)) return;
858	domain->checkAttributes();
859
860	if (domain->isEmpty())
861	if (SuperClass::type==MULTI_FILE) return ;
862
863	std::vector<StdString> dim0, dim1;
864	StdString domid = domain->getDomainOutputName();
865	if (isWrittenDomain(domid)) return ;
866	else setWrittenDomain(domid);
867
868	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
869
870	StdString lonName,latName, cellName ;
871	if (domain->lon_name.isEmpty()) lonName = "lon";
872	else lonName = domain->lon_name;
873
874	if (domain->lat_name.isEmpty()) latName = "lat";
875	else latName = domain->lat_name;
876
877	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
878	else cellName="cell";
879	StdString dimXid = cellName+appendDomid;
880	StdString dimVertId;
881	if (domain->nvertex_name.isEmpty()) dimVertId = "nvertex"+appendDomid;
882	else dimVertId = domain->nvertex_name;
883
884	string lonid,latid,bounds_lonid,bounds_latid ;
885	string areaId = "area" + appendDomid;
886
887	nc_type typePrec ;
888	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
889	else if (domain->prec==4) typePrec = NC_FLOAT ;
890	else if (domain->prec==8) typePrec = NC_DOUBLE ;
891
892	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
893
894	try
895	{
896	switch (SuperClass::type)
897	{
898	case (MULTI_FILE) :
899	{
900	dim0.push_back(dimXid);
901	SuperClassWriter::addDimension(dimXid, domain->ni);
902
903	lonid = lonName+appendDomid;
904	latid = latName+appendDomid;
905	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
906	else bounds_lonid = "bounds_"+lonName+appendDomid;
907	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
908	else bounds_latid = "bounds_"+latName+appendDomid;
909
910	if (domain->hasLonLat)
911	{
912	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
913	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
914	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
915	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
916	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
917	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
918	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
919	}
920	dim0.clear();
921	if (domain->hasBounds)
922	{
923	dim0.push_back(dimXid);
924	dim0.push_back(dimVertId);
925	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
926	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
927	}
928
929	dim0.clear();
930	dim0.push_back(dimXid);
931	if (domain->hasArea)
932	{
933	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
934	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
935	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
936	}
937
938	SuperClassWriter::definition_end();
939
940	if (domain->hasLonLat)
941	{
942	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
943	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
944	if (domain->hasBounds)
945	{
946	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
947	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
948	}
949	}
950
951	if (domain->hasArea)
952	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
953
954	SuperClassWriter::definition_start();
955	break ;
956	}
957
958	case (ONE_FILE) :
959	{
960	lonid = lonName+appendDomid;
961	latid = latName+appendDomid;
962	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
963	else bounds_lonid = "bounds_"+lonName+appendDomid;
964	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
965	else bounds_latid = "bounds_"+latName+appendDomid;
966
967	dim0.push_back(dimXid);
968	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
969	if (domain->hasLonLat)
970	{
971	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
972	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
973
974	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
975	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
976	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
977	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
978	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
979	}
980	dim0.clear();
981
982	if (domain->hasBounds)
983	{
984	dim0.push_back(dimXid);
985	dim0.push_back(dimVertId);
986	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
987	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
988	}
989
990	if (domain->hasArea)
991	{
992	dim0.clear();
993	dim0.push_back(dimXid);
994	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
995	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
996	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
997	}
998
999	SuperClassWriter::definition_end();
1000
1001	std::vector<StdSize> start(1), startBounds(2) ;
1002	std::vector<StdSize> count(1), countBounds(2) ;
1003	if (domain->isEmpty())
1004	{
1005	start[0]=0 ;
1006	count[0]=0 ;
1007	startBounds[1]=0 ;
1008	countBounds[1]=nvertex ;
1009	startBounds[0]=0 ;
1010	countBounds[0]=0 ;
1011	}
1012	else
1013	{
1014	start[0]=domain->ibeginValue_;
1015	count[0]=domain->niValue_;
1016	startBounds[0]=domain->ibeginValue_;
1017	startBounds[1]=0 ;
1018	countBounds[0]=domain->niValue_;
1019	countBounds[1]=nvertex ;
1020	}
1021
1022	if (domain->hasLonLat)
1023	{
1024	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
1025	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
1026	if (domain->hasBounds)
1027	{
1028	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1029	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1030	}
1031	}
1032
1033	if (domain->hasArea)
1034	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
1035
1036	SuperClassWriter::definition_start();
1037
1038	break;
1039	}
1040	default :
1041	ERROR("CNc4DataOutput::writeDomain(domain)",
1042	<< "[ type = " << SuperClass::type << "]"
1043	<< " not implemented yet !");
1044	}
1045	}
1046	catch (CNetCdfException& e)
1047	{
1048	StdString msg("On writing the domain : ");
1049	msg.append(domid); msg.append("\n");
1050	msg.append("In the context : ");
1051	msg.append(context->getId()); msg.append("\n");
1052	msg.append(e.what());
1053	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1054	}
1055	domain->addRelFile(this->filename);
1056	}
1057	//--------------------------------------------------------------
1058
1059	void CNc4DataOutput::writeAxis_(CAxis* axis)
1060	{
1061	if (axis->IsWritten(this->filename)) return;
1062
1063	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
1064	if (!axis->value.isEmpty() )
1065	{
1066	// The hash of the element will be associated to the default element name (= map key), and to the name really written
1067	int globalHash = axis->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
1068
1069	StdString defaultNameKey = axis->getAxisOutputName();
1070	if ( !relAxis_.count ( defaultNameKey ) )
1071	{
1072	// if defaultNameKey not in the map, write the element such as it is defined
1073	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) );
1074	}
1075	else // look if a hash associated this key is equal
1076	{
1077	bool elementIsInMap(false);
1078	auto defaultNameKeyElements = relAxis_.equal_range( defaultNameKey );
1079	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
1080	{
1081	if ( it->second.first == globalHash )
1082	{
1083	// if yes, associate the same ids to current element
1084	axis->renameAttributesBeforeWriting( it->second.second );
1085	elementIsInMap = true;
1086	}
1087	}
1088	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
1089	if (!elementIsInMap) // ! in MAP
1090	{
1091	axis->renameAttributesBeforeWriting();
1092	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) ) ;// = axis->getId()
1093	}
1094	}
1095	}
1096
1097	axis->checkAttributes();
1098
1099	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
1100	: axis->n_glo.getValue();
1101
1102	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
1103
1104	std::vector<StdString> dims;
1105	StdString axisid = axis->getAxisOutputName();
1106	StdString axisDim, axisBoundsId;
1107	if (isWrittenAxis(axisid)) return ;
1108	else setWrittenAxis(axisid);
1109
1110	nc_type typePrec ;
1111	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1112	else if (axis->prec==4) typePrec = NC_FLOAT ;
1113	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1114
1115	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1116	string strId="str_len" ;
1117	try
1118	{
1119	if (axis->dim_name.isEmpty()) axisDim = axisid;
1120	else axisDim=axis->dim_name.getValue();
1121	SuperClassWriter::addDimension(axisDim, size);
1122	dims.push_back(axisDim);
1123
1124	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1125
1126	if (axis->hasValue() \|\| !axis->label.isEmpty())
1127	{
1128	if (!axis->label.isEmpty()) dims.push_back(strId);
1129
1130	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1131
1132	if (!axis->name.isEmpty())
1133	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1134
1135	if (!axis->standard_name.isEmpty())
1136	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1137
1138	if (!axis->long_name.isEmpty())
1139	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1140
1141	if (!axis->unit.isEmpty())
1142	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1143
1144	if (!axis->axis_type.isEmpty())
1145	{
1146	switch(axis->axis_type)
1147	{
1148	case CAxis::axis_type_attr::X :
1149	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1150	break;
1151	case CAxis::axis_type_attr::Y :
1152	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1153	break;
1154	case CAxis::axis_type_attr::Z :
1155	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1156	break;
1157	case CAxis::axis_type_attr::T :
1158	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1159	break;
1160	}
1161	}
1162
1163	if (!axis->positive.isEmpty())
1164	{
1165	SuperClassWriter::addAttribute("positive",
1166	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1167	&axisid);
1168	}
1169
1170	if (!axis->formula.isEmpty())
1171	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1172
1173	if (!axis->formula_term.isEmpty())
1174	SuperClassWriter::addAttribute("formula_terms", axis->formula_term.getValue(), &axisid);
1175
1176	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1177	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1178	{
1179	dims.push_back("axis_nbounds");
1180	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1181	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1182
1183	if (!axis->standard_name.isEmpty())
1184	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1185
1186	if (!axis->unit.isEmpty())
1187	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1188
1189	if (!axis->formula_bounds.isEmpty())
1190	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1191
1192	if (!axis->formula_term_bounds.isEmpty())
1193	SuperClassWriter::addAttribute("formula_terms", axis->formula_term_bounds.getValue(), &axisBoundsId);
1194	}
1195	}
1196
1197	SuperClassWriter::definition_end();
1198
1199	switch (SuperClass::type)
1200	{
1201	case MULTI_FILE:
1202	{
1203	if (axis->label.isEmpty())
1204	{
1205	if (!axis->value.isEmpty())
1206	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
1207
1208	if (!axis->bounds.isEmpty())
1209	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
1210	}
1211	else
1212	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
1213
1214	SuperClassWriter::definition_start();
1215	break;
1216	}
1217	case ONE_FILE:
1218	{
1219	std::vector<StdSize> start(1), startBounds(2) ;
1220	std::vector<StdSize> count(1), countBounds(2) ;
1221	start[0] = startBounds[0] = axis->begin;
1222	count[0] = countBounds[0] = axis->n;
1223	startBounds[1] = 0;
1224	countBounds[1] = 2;
1225
1226	if (axis->label.isEmpty())
1227	{
1228	if (!axis->value.isEmpty())
1229	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
1230
1231	if (!axis->bounds.isEmpty())
1232	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1233	}
1234	else
1235	{
1236	std::vector<StdSize> startLabel(2), countLabel(2);
1237	startLabel[0] = start[0]; startLabel[1] = 0;
1238	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1239	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
1240	}
1241
1242	SuperClassWriter::definition_start();
1243
1244	break;
1245	}
1246	default :
1247	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1248	<< "[ type = " << SuperClass::type << "]"
1249	<< " not implemented yet !");
1250	}
1251	}
1252	catch (CNetCdfException& e)
1253	{
1254	StdString msg("On writing the axis : ");
1255	msg.append(axisid); msg.append("\n");
1256	msg.append("In the context : ");
1257	CContext* context = CContext::getCurrent() ;
1258	msg.append(context->getId()); msg.append("\n");
1259	msg.append(e.what());
1260	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1261	}
1262	axis->addRelFile(this->filename);
1263	}
1264
1265	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1266	{
1267	if (scalar->IsWritten(this->filename)) return;
1268	scalar->checkAttributes();
1269	int scalarSize = 1;
1270
1271	StdString scalaId = scalar->getScalarOutputName();
1272	StdString boundsId;
1273	if (isWrittenAxis(scalaId)) return ;
1274	else setWrittenAxis(scalaId);
1275
1276	nc_type typePrec ;
1277	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1278	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1279	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1280
1281	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1282	string strId="str_len" ;
1283
1284	try
1285	{
1286	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1287
1288	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1289	{
1290	std::vector<StdString> dims;
1291	StdString scalarDim = scalaId;
1292
1293	if (!scalar->label.isEmpty()) dims.push_back(strId);
1294
1295	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1296
1297	if (!scalar->name.isEmpty())
1298	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1299
1300	if (!scalar->standard_name.isEmpty())
1301	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1302
1303	if (!scalar->long_name.isEmpty())
1304	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1305
1306	if (!scalar->unit.isEmpty())
1307	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1308
1309	if (!scalar->axis_type.isEmpty())
1310	{
1311	switch(scalar->axis_type)
1312	{
1313	case CScalar::axis_type_attr::X :
1314	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1315	break;
1316	case CScalar::axis_type_attr::Y :
1317	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1318	break;
1319	case CScalar::axis_type_attr::Z :
1320	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1321	break;
1322	case CScalar::axis_type_attr::T :
1323	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1324	break;
1325	}
1326	}
1327
1328	if (!scalar->positive.isEmpty())
1329	{
1330	SuperClassWriter::addAttribute("positive",
1331	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1332	&scalaId);
1333	}
1334
1335	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1336	{
1337	dims.clear();
1338	dims.push_back("axis_nbounds");
1339	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1340	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1341	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1342	}
1343
1344	SuperClassWriter::definition_end();
1345
1346	switch (SuperClass::type)
1347	{
1348	case MULTI_FILE:
1349	{
1350	CArray<double,1> scalarValue(scalarSize);
1351	CArray<string,1> scalarLabel(scalarSize);
1352	CArray<double,1> scalarBounds(scalarSize*2);
1353
1354	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1355	{
1356	scalarValue(0) = scalar->value;
1357	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1358	}
1359
1360	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1361	{
1362	scalarBounds(0) = scalar->bounds(0);
1363	scalarBounds(1) = scalar->bounds(1);
1364	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1365	}
1366
1367	if (!scalar->label.isEmpty())
1368	{
1369	scalarLabel(0) = scalar->label;
1370	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1371	}
1372
1373	SuperClassWriter::definition_start();
1374
1375	break;
1376	}
1377	case ONE_FILE:
1378	{
1379	CArray<double,1> scalarValue(scalarSize);
1380	CArray<string,1> scalarLabel(scalarSize);
1381	CArray<double,1> scalarBounds(scalarSize*2);
1382
1383	std::vector<StdSize> start(1);
1384	std::vector<StdSize> count(1);
1385	start[0] = 0;
1386	count[0] = 1;
1387	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1388	{
1389	scalarValue(0) = scalar->value;
1390	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1391	}
1392	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1393	{
1394	scalarBounds(0) = scalar->bounds(0);
1395	scalarBounds(1) = scalar->bounds(1);
1396	count[0] = 2;
1397	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1398	}
1399	if (!scalar->label.isEmpty())
1400	{
1401	scalarLabel(0) = scalar->label;
1402	count[0] = stringArrayLen;
1403	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1404	}
1405
1406	SuperClassWriter::definition_start();
1407
1408	break;
1409	}
1410	default :
1411	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1412	<< "[ type = " << SuperClass::type << "]"
1413	<< " not implemented yet !");
1414	}
1415	}
1416	}
1417	catch (CNetCdfException& e)
1418	{
1419	StdString msg("On writing the scalar : ");
1420	msg.append(scalaId); msg.append("\n");
1421	msg.append("In the context : ");
1422	CContext* context = CContext::getCurrent() ;
1423	msg.append(context->getId()); msg.append("\n");
1424	msg.append(e.what());
1425	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1426	}
1427	scalar->addRelFile(this->filename);
1428	}
1429
1430	//--------------------------------------------------------------
1431
1432	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1433	{
1434	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1435
1436	// NOTA : The cuurent algorithm to write compress elements of the grid
1437	// will work pretting well when on server side you dont't get
1438	// partial overlap on elements between differents participating process
1439	// So the element must be totally distributed or non distributed
1440	// If an element is partially overlaping betwwen process then the
1441	// total compressed part will apear artificially greater than expected
1442	// For the current implementation of writer which is decomposed only on
1443	// one element, it will work as expected, but for future, it must be
1444	// reconsidered again.
1445	try
1446	{
1447	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1448	std::vector<StdString> domainList = grid->getDomainList();
1449	std::vector<StdString> axisList = grid->getAxisList();
1450	std::vector<StdString> scalarList = grid->getScalarList();
1451	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1452	int commRank ;
1453	MPI_Comm_rank(comm_file,&commRank) ;
1454
1455	std::vector<StdString> dims;
1456
1457	for (int i = 0; i < numElement; ++i)
1458	{
1459	StdString varId, compress;
1460	CArray<size_t, 1> indexes;
1461	bool isDistributed;
1462	size_t nbIndexes, totalNbIndexes, offset;
1463	size_t firstGlobalIndex;
1464
1465	if (2 == axisDomainOrder(i))
1466	{
1467	CDomain* domain = CDomain::get(domainList[idxDomain]);
1468	StdString domId = domain->getDomainOutputName();
1469
1470	if (!domain->isCompressible()
1471	\|\| domain->type == CDomain::type_attr::unstructured
1472	\|\| domain->isWrittenCompressed(this->filename)
1473	\|\| isWrittenCompressedDomain(domId))
1474	continue;
1475
1476	// unstructured grid seems not be taken into account why ?
1477
1478	string lonName,latName ;
1479
1480	if (domain->lon_name.isEmpty())
1481	{
1482	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1483	else lonName = "lon";
1484	}
1485	else lonName = domain->lon_name;
1486
1487	if (domain->lat_name.isEmpty())
1488	{
1489	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1490	else latName = "lat";
1491	}
1492	else latName = domain->lat_name;
1493
1494	StdString appendDomId = singleDomain ? "" : "_" + domId;
1495
1496	varId = domId + "_points";
1497	compress = latName + appendDomId + " " + lonName + appendDomId;
1498
1499	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
1500	workflowView->getGlobalIndexView(indexes) ;
1501	nbIndexes = workflowView->getSize() ;
1502	isDistributed = domain->isDistributed();
1503	if (isDistributed)
1504	{
1505	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1506	if (commRank==0) offset=0 ;
1507	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1508	}
1509	else
1510	{
1511	offset=0 ;
1512	totalNbIndexes = nbIndexes ;
1513	}
1514
1515	firstGlobalIndex = domain->ibeginValue_ + domain->jbeginValue_ * domain->ni_glo;
1516
1517	domain->addRelFileCompressed(this->filename);
1518	setWrittenCompressedDomain(domId);
1519	++idxDomain;
1520	}
1521	else if (1 == axisDomainOrder(i))
1522	{
1523	CAxis* axis = CAxis::get(axisList[idxAxis]);
1524	StdString axisId = axis->getAxisOutputName();
1525
1526	if (!axis->isCompressible()
1527	\|\| axis->isWrittenCompressed(this->filename)
1528	\|\| isWrittenCompressedAxis(axisId))
1529	continue;
1530
1531	varId = axisId + "_points";
1532	compress = axisId;
1533
1534	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
1535	workflowView->getGlobalIndexView(indexes) ;
1536	nbIndexes = workflowView->getSize() ;
1537	isDistributed = axis->isDistributed();
1538	if (isDistributed)
1539	{
1540	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1541	if (commRank==0) offset=0 ;
1542	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1543	}
1544	else
1545	{
1546	offset=0 ;
1547	totalNbIndexes = nbIndexes ;
1548	}
1549	firstGlobalIndex = axis->begin;
1550
1551	axis->addRelFileCompressed(this->filename);
1552	setWrittenCompressedAxis(axisId);
1553	++idxAxis;
1554	}
1555	else
1556	{
1557	//for scalar
1558	}
1559
1560	if (!varId.empty())
1561	{
1562	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1563
1564	dims.clear();
1565	dims.push_back(varId);
1566	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
1567
1568	SuperClassWriter::addAttribute("compress", compress, &varId);
1569
1570	switch (SuperClass::type)
1571	{
1572	case (MULTI_FILE):
1573	{
1574	indexes -= firstGlobalIndex;
1575	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1576	break;
1577	}
1578	case (ONE_FILE):
1579	{
1580	std::vector<StdSize> start, count;
1581	start.push_back(offset);
1582	count.push_back(nbIndexes);
1583
1584	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1585	break;
1586	}
1587	}
1588	}
1589	}
1590
1591	grid->addRelFileCompressed(this->filename);
1592	}
1593	catch (CNetCdfException& e)
1594	{
1595	StdString msg("On writing compressed grid : ");
1596	msg.append(grid->getId()); msg.append("\n");
1597	msg.append("In the context : ");
1598	CContext* context = CContext::getCurrent();
1599	msg.append(context->getId()); msg.append("\n");
1600	msg.append(e.what());
1601	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1602	}
1603	}
1604
1605	//--------------------------------------------------------------
1606
1607	void CNc4DataOutput::writeTimeDimension_(void)
1608	{
1609	try
1610	{
1611	SuperClassWriter::addDimension(getTimeCounterName());
1612	}
1613	catch (CNetCdfException& e)
1614	{
1615	StdString msg("On writing time dimension : time_couter\n");
1616	msg.append("In the context : ");
1617	CContext* context = CContext::getCurrent() ;
1618	msg.append(context->getId()); msg.append("\n");
1619	msg.append(e.what());
1620	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1621	}
1622	}
1623
1624	//--------------------------------------------------------------
1625
1626	void CNc4DataOutput::writeField_(CField* field)
1627	{
1628	CContext* context = CContext::getCurrent() ;
1629
1630	std::vector<StdString> dims, coodinates;
1631	CGrid* grid = field->getGrid();
1632	if (!grid->doGridHaveDataToWrite())
1633	if (SuperClass::type==MULTI_FILE) return ;
1634
1635	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1636	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1637	std::vector<StdString> domainList = grid->getDomainList();
1638	std::vector<StdString> axisList = grid->getAxisList();
1639	std::vector<StdString> scalarList = grid->getScalarList();
1640
1641	StdString timeid = getTimeCounterName();
1642	StdString dimXid,dimYid;
1643	std::deque<StdString> dimIdList, dimCoordList;
1644	bool hasArea = false;
1645	StdString cellMeasures = "area:";
1646	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1647
1648	for (int i = 0; i < numElement; ++i)
1649	{
1650	if (2 == axisDomainOrder(i))
1651	{
1652	CDomain* domain = CDomain::get(domainList[idxDomain]);
1653	StdString domId = domain->getDomainOutputName();
1654	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1655	StdString lonName,latName ;
1656	StdString dimIname,dimJname ;
1657
1658	if (domain->lon_name.isEmpty())
1659	{
1660	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1661	else lonName = "lon";
1662	}
1663	else lonName = domain->lon_name;
1664
1665	if (domain->lat_name.isEmpty())
1666	{
1667	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1668	else latName = "lat";
1669	}
1670	else latName = domain->lat_name;
1671
1672	if (domain->dim_i_name.isEmpty())
1673	{
1674	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1675	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1676	else dimIname = lonName;
1677	}
1678	else dimIname = domain->dim_i_name;
1679
1680	if (domain->dim_j_name.isEmpty())
1681	{
1682	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1683	else dimJname = latName;
1684	}
1685	else dimJname = domain->dim_j_name;
1686
1687	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1688	{
1689	dimIdList.push_back(domId + "_points");
1690	field->setUseCompressedOutput();
1691	}
1692
1693	switch (domain->type)
1694	{
1695	case CDomain::type_attr::curvilinear:
1696	if (!compressedOutput \|\| !domain->isCompressible())
1697	{
1698	dimXid=dimIname+appendDomId;
1699	dimYid=dimJname+appendDomId;
1700	dimIdList.push_back(dimXid);
1701	dimIdList.push_back(dimYid);
1702	}
1703	dimCoordList.push_back(lonName+appendDomId);
1704	dimCoordList.push_back(latName+appendDomId);
1705	break ;
1706	case CDomain::type_attr::rectilinear:
1707	if (!compressedOutput \|\| !domain->isCompressible())
1708	{
1709	dimXid = dimIname+appendDomId;
1710	dimYid = dimJname+appendDomId;
1711	dimIdList.push_back(dimXid);
1712	dimIdList.push_back(dimYid);
1713	}
1714	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1715	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1716
1717	break ;
1718	case CDomain::type_attr::unstructured:
1719	{
1720	if (SuperClassWriter::useCFConvention)
1721	{
1722	dimXid = dimIname + appendDomId;
1723	dimIdList.push_back(dimXid);
1724	dimCoordList.push_back(lonName+appendDomId);
1725	dimCoordList.push_back(latName+appendDomId);
1726	}
1727	else
1728	{
1729	StdString domainName = domain->name;
1730	if (domain->nvertex == 1)
1731	{
1732	dimXid = "n" + domainName + "_node";
1733	dimIdList.push_back(dimXid);
1734	dimCoordList.push_back(StdString(domainName + "_node_x"));
1735	dimCoordList.push_back(StdString(domainName + "_node_y"));
1736	}
1737	else if (domain->nvertex == 2)
1738	{
1739	dimXid = "n" + domainName + "_edge";
1740	dimIdList.push_back(dimXid);
1741	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1742	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1743	}
1744	else
1745	{
1746	dimXid = "n" + domainName + "_face";
1747	dimIdList.push_back(dimXid);
1748	dimCoordList.push_back(StdString(domainName + "_face_x"));
1749	dimCoordList.push_back(StdString(domainName + "_face_y"));
1750	}
1751	} // ugrid convention
1752	} // case unstructured domain
1753	}
1754
1755	if (domain->hasArea)
1756	{
1757	hasArea = true;
1758	cellMeasures += " area" + appendDomId;
1759	}
1760	++idxDomain;
1761	}
1762	else if (1 == axisDomainOrder(i))
1763	{
1764	CAxis* axis = CAxis::get(axisList[idxAxis]);
1765	StdString axisId = axis->getAxisOutputName();
1766	StdString axisDim;
1767
1768	if (axis->dim_name.isEmpty()) axisDim = axisId;
1769	else axisDim=axis->dim_name.getValue();
1770
1771	if (compressedOutput && axis->isCompressible())
1772	{
1773	dimIdList.push_back(axisDim + "_points");
1774	field->setUseCompressedOutput();
1775	}
1776	else
1777	dimIdList.push_back(axisDim);
1778
1779	if (axisDim != axisId) dimCoordList.push_back(axisId);
1780	++idxAxis;
1781	}
1782	else
1783	{
1784	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1785	StdString scalarId = scalar->getScalarOutputName();
1786	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1787	dimCoordList.push_back(scalarId);
1788	++idxScalar;
1789	}
1790	}
1791
1792	StdString fieldid = field->getFieldOutputName();
1793
1794	nc_type type ;
1795	if (field->prec.isEmpty()) type = NC_FLOAT ;
1796	else
1797	{
1798	if (field->prec==2) type = NC_SHORT ;
1799	else if (field->prec==4) type = NC_FLOAT ;
1800	else if (field->prec==8) type = NC_DOUBLE ;
1801	}
1802
1803	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1804
1805	if (wtime)
1806	{
1807	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1808	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
1809	dims.push_back(timeid);
1810	}
1811
1812	while (!dimIdList.empty())
1813	{
1814	dims.push_back(dimIdList.back());
1815	dimIdList.pop_back();
1816	}
1817
1818	while (!dimCoordList.empty())
1819	{
1820	coodinates.push_back(dimCoordList.back());
1821	dimCoordList.pop_back();
1822	}
1823
1824	try
1825	{
1826	SuperClassWriter::addVariable(fieldid, type, dims, false);
1827	SuperClassWriter::addChunk(field, type, dims);
1828
1829	if (!field->standard_name.isEmpty())
1830	SuperClassWriter::addAttribute
1831	("standard_name", field->standard_name.getValue(), &fieldid);
1832
1833	if (!field->long_name.isEmpty())
1834	SuperClassWriter::addAttribute
1835	("long_name", field->long_name.getValue(), &fieldid);
1836
1837	if (!field->unit.isEmpty())
1838	SuperClassWriter::addAttribute
1839	("units", field->unit.getValue(), &fieldid);
1840
1841	// Ugrid field attributes "mesh" and "location"
1842	if (!SuperClassWriter::useCFConvention)
1843	{
1844	if (!domainList.empty())
1845	{
1846	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
1847	StdString mesh = domain->name;
1848	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
1849	StdString location;
1850	if (domain->nvertex == 1)
1851	location = "node";
1852	else if (domain->nvertex == 2)
1853	location = "edge";
1854	else if (domain->nvertex > 2)
1855	location = "face";
1856	SuperClassWriter::addAttribute("location", location, &fieldid);
1857	}
1858
1859	}
1860
1861	if (!field->valid_min.isEmpty())
1862	SuperClassWriter::addAttribute
1863	("valid_min", field->valid_min.getValue(), &fieldid);
1864
1865	if (!field->valid_max.isEmpty())
1866	SuperClassWriter::addAttribute
1867	("valid_max", field->valid_max.getValue(), &fieldid);
1868
1869	if (!field->scale_factor.isEmpty())
1870	SuperClassWriter::addAttribute
1871	("scale_factor", field->scale_factor.getValue(), &fieldid);
1872
1873	if (!field->add_offset.isEmpty())
1874	SuperClassWriter::addAttribute
1875	("add_offset", field->add_offset.getValue(), &fieldid);
1876
1877	SuperClassWriter::addAttribute
1878	("online_operation", field->operation.getValue(), &fieldid);
1879
1880	// write child variables as attributes
1881
1882
1883	bool alreadyAddCellMethod = false;
1884	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1885	if (!field->cell_methods.isEmpty())
1886	{
1887	StdString cellMethodString = field->cell_methods;
1888	if (field->cell_methods_mode.isEmpty() \|\|
1889	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1890	{
1891	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1892	alreadyAddCellMethod = true;
1893	}
1894	else
1895	{
1896	switch (field->cell_methods_mode)
1897	{
1898	case (CField::cell_methods_mode_attr::prefix):
1899	cellMethodsPrefix = cellMethodString;
1900	cellMethodsPrefix += " ";
1901	break;
1902	case (CField::cell_methods_mode_attr::suffix):
1903	cellMethodsSuffix = " ";
1904	cellMethodsSuffix += cellMethodString;
1905	break;
1906	case (CField::cell_methods_mode_attr::none):
1907	break;
1908	default:
1909	break;
1910	}
1911	}
1912	}
1913
1914
1915	if (wtime)
1916	{
1917	CDuration freqOp = field->freq_op.getValue();
1918	freqOp.solveTimeStep(*context->calendar);
1919	StdString freqOpStr = freqOp.toStringUDUnits();
1920	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1921
1922	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1923	freqOut.solveTimeStep(*context->calendar);
1924	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1925
1926	StdString cellMethods(cellMethodsPrefix + "time: ");
1927	if (field->operation.getValue() == "instant") cellMethods += "point";
1928	else if (field->operation.getValue() == "average") cellMethods += "mean";
1929	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1930	else cellMethods += field->operation;
1931	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1932	cellMethods += " (interval: " + freqOpStr + ")";
1933	cellMethods += cellMethodsSuffix;
1934	if (!alreadyAddCellMethod)
1935	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1936	}
1937
1938	if (hasArea)
1939	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1940
1941	if (!field->default_value.isEmpty())
1942	{
1943	double default_value = field->default_value.getValue();
1944	if (type == NC_DOUBLE)
1945	{
1946	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1947	}
1948	else if (type == NC_SHORT)
1949	{
1950	short sdefault_value = (short)default_value;
1951	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
1952	}
1953	else
1954	{
1955	float fdefault_value = (float)default_value;
1956	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1957	}
1958	}
1959	else
1960	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1961
1962	if (field->compression_level.isEmpty())
1963	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
1964	if ( (field->compression_level.getValue()>0)&&(field->compression_type.isEmpty()) )
1965	field->compression_type.setValue( "gzip" );
1966	if (field->compression_type.isEmpty())
1967	field->compression_type = "None";
1968	if (field->compression_params.isEmpty())
1969	field->compression_params.resize( 0 );
1970	SuperClassWriter::setCompressionLevel(fieldid, field->compression_type, field->compression_level, field->compression_params);
1971
1972	{ // Ecriture des coordonnes
1973
1974	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1975	std::vector<StdString>::iterator
1976	itc = coodinates.begin(), endc = coodinates.end();
1977
1978	for (; itc!= endc; itc++)
1979	{
1980	StdString & coord = *itc;
1981	if (itc+1 != endc)
1982	coordstr.append(coord).append(" ");
1983	else coordstr.append(coord);
1984	}
1985
1986	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1987
1988	}
1989
1990	vector<CVariable*> listVars = field->getAllVariables() ;
1991	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1992
1993	}
1994	catch (CNetCdfException& e)
1995	{
1996	StdString msg("On writing field : ");
1997	msg.append(fieldid); msg.append("\n");
1998	msg.append("In the context : ");
1999	msg.append(context->getId()); msg.append("\n");
2000	msg.append(e.what());
2001	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2002	}
2003	} // writeField_()
2004
2005	//--------------------------------------------------------------
2006
2007	void CNc4DataOutput::writeFile_ (CFile* file)
2008	{
2009	StdString filename = file->getFileOutputName();
2010	StdString description = (!file->description.isEmpty())
2011	? file->description.getValue()
2012	: StdString("Created by xios");
2013
2014	singleDomain = (file->nbDomains == 1);
2015
2016	StdString conv_str ;
2017	if (file->convention_str.isEmpty())
2018	{
2019	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2020	else conv_str="UGRID" ;
2021	}
2022	else conv_str=file->convention_str ;
2023
2024	try
2025	{
2026	if (!appendMode) this->writeFileAttributes(filename, description,
2027	conv_str,
2028	StdString("An IPSL model"),
2029	this->getTimeStamp());
2030
2031	if (!appendMode)
2032	SuperClassWriter::addDimension("axis_nbounds", 2);
2033	}
2034	catch (CNetCdfException& e)
2035	{
2036	StdString msg("On writing file : ");
2037	msg.append(filename); msg.append("\n");
2038	msg.append("In the context : ");
2039	CContext* context = CContext::getCurrent() ;
2040	msg.append(context->getId()); msg.append("\n");
2041	msg.append(e.what());
2042	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2043	}
2044	}
2045
2046	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2047	{
2048	StdString name = var->getVariableOutputName();
2049
2050	try
2051	{
2052	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2053	addAttribute(name, var->getData<int>(), &fieldId);
2054	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2055	addAttribute(name, var->getData<short int>(), &fieldId);
2056	else if (var->type.getValue() == CVariable::type_attr::t_float)
2057	addAttribute(name, var->getData<float>(), &fieldId);
2058	else if (var->type.getValue() == CVariable::type_attr::t_double)
2059	addAttribute(name, var->getData<double>(), &fieldId);
2060	else if (var->type.getValue() == CVariable::type_attr::t_string)
2061	addAttribute(name, var->getData<string>(), &fieldId);
2062	else
2063	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2064	<< "Unsupported variable of type " << var->type.getStringValue());
2065	}
2066	catch (CNetCdfException& e)
2067	{
2068	StdString msg("On writing attributes of variable with name : ");
2069	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2070	msg.append("In the context : ");
2071	CContext* context = CContext::getCurrent() ;
2072	msg.append(context->getId()); msg.append("\n");
2073	msg.append(e.what());
2074	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2075	}
2076	}
2077
2078	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2079	{
2080	StdString name = var->getVariableOutputName();
2081
2082	try
2083	{
2084	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2085	addAttribute(name, var->getData<int>());
2086	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2087	addAttribute(name, var->getData<short int>());
2088	else if (var->type.getValue() == CVariable::type_attr::t_float)
2089	addAttribute(name, var->getData<float>());
2090	else if (var->type.getValue() == CVariable::type_attr::t_double)
2091	addAttribute(name, var->getData<double>());
2092	else if (var->type.getValue() == CVariable::type_attr::t_string)
2093	addAttribute(name, var->getData<string>());
2094	else
2095	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2096	<< "Unsupported variable of type " << var->type.getStringValue());
2097	}
2098	catch (CNetCdfException& e)
2099	{
2100	StdString msg("On writing attributes of variable with name : ");
2101	msg.append(name); msg.append("\n");
2102	msg.append("In the context : ");
2103	CContext* context = CContext::getCurrent() ;
2104	msg.append(context->getId()); msg.append("\n");
2105	msg.append(e.what());
2106	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2107	}
2108	}
2109
2110	void CNc4DataOutput::syncFile_ (void)
2111	{
2112	try
2113	{
2114	SuperClassWriter::sync() ;
2115	}
2116	catch (CNetCdfException& e)
2117	{
2118	StdString msg("On synchronizing the write among processes");
2119	msg.append("In the context : ");
2120	CContext* context = CContext::getCurrent() ;
2121	msg.append(context->getId()); msg.append("\n");
2122	msg.append(e.what());
2123	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2124	}
2125	}
2126
2127	void CNc4DataOutput::closeFile_ (void)
2128	{
2129	try
2130	{
2131	SuperClassWriter::close() ;
2132	}
2133	catch (CNetCdfException& e)
2134	{
2135	StdString msg("On closing file");
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::syncFile_ (void)", << msg);
2141	}
2142
2143	}
2144
2145	//---------------------------------------------------------------
2146
2147	StdString CNc4DataOutput::getTimeStamp(void) const
2148	{
2149	const int buffer_size = 100;
2150	time_t rawtime;
2151	struct tm * timeinfo = NULL;
2152	char buffer [buffer_size];
2153	StdString formatStr;
2154	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2155	else formatStr=file->time_stamp_format;
2156
2157	// time ( &rawtime );
2158	// timeinfo = localtime ( &rawtime );
2159	time ( &rawtime );
2160	timeinfo = gmtime ( &rawtime );
2161	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2162
2163	return (StdString(buffer));
2164	}
2165
2166	//---------------------------------------------------------------
2167
2168	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
2169	const CDate& currentWrite, int nstep)
2170	{
2171	CContext* context = CContext::getCurrent();
2172	CGrid* grid = field->getGrid();
2173
2174	if (nstep<1)
2175	{
2176	return nstep;
2177	}
2178
2179	if (!grid->doGridHaveDataToWrite())
2180	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2181	{
2182	return nstep;
2183	}
2184
2185	StdString fieldid = field->getFieldOutputName();
2186
2187	StdOStringStream oss;
2188	string timeAxisId;
2189	if (field->hasTimeInstant) timeAxisId = "time_instant";
2190	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2191
2192	StdString timeBoundId = getTimeCounterName() + "_bounds";
2193
2194	StdString timeAxisBoundId;
2195	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2196	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2197
2198	if (!field->wasWritten())
2199	{
2200	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
2201	field->getOperationTimeType() != func::CFunctor::once)
2202	{
2203	double factorUnit;
2204	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2205	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2206	else factorUnit=1 ;
2207	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
2208	}
2209
2210	field->setWritten();
2211	}
2212
2213
2214	CArray<double,1> time_data(1);
2215	CArray<double,1> time_data_bound(2);
2216	CArray<double,1> time_counter(1);
2217	CArray<double,1> time_counter_bound(2);
2218
2219	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2220	bool wtimeCounter =false ;
2221	bool wtimeData =false ;
2222
2223
2224	if (wtime)
2225	{
2226
2227	if (field->hasTimeInstant)
2228	{
2229	time_data(0) = time_data_bound(1) = (Time) currentWrite;
2230	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
2231	if (timeCounterType==instant)
2232	{
2233	time_counter(0) = time_data(0);
2234	time_counter_bound(0) = time_data_bound(0);
2235	time_counter_bound(1) = time_data_bound(1);
2236	wtimeCounter=true ;
2237	}
2238	if (hasTimeInstant) wtimeData=true ;
2239	}
2240	else if (field->hasTimeCentered)
2241	{
2242	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
2243	time_data_bound(0) = (Time)lastWrite;
2244	time_data_bound(1) = (Time)currentWrite;
2245	if (timeCounterType==centered)
2246	{
2247	time_counter(0) = time_data(0) ;
2248	time_counter_bound(0) = time_data_bound(0) ;
2249	time_counter_bound(1) = time_data_bound(1) ;
2250	wtimeCounter=true ;
2251	}
2252	if (hasTimeCentered) wtimeData=true ;
2253	}
2254
2255	if (timeCounterType==record)
2256	{
2257	time_counter(0) = nstep - 1;
2258	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
2259	wtimeCounter=true ;
2260	}
2261
2262	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2263	{
2264	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2265	time_data/=secByDay;
2266	time_data_bound/=secByDay;
2267	time_counter/=secByDay;
2268	time_counter_bound/=secByDay;
2269	}
2270	}
2271
2272	bool isRoot = (context->intraCommRank_ == 0);
2273
2274	try
2275	{
2276	switch (SuperClass::type)
2277	{
2278	case (MULTI_FILE) :
2279	{
2280	if (info.isActive(logProfile)) CTimer::get("Files : writing data").resume();
2281	writeAndConvertData(field, data, nstep - 1);
2282	if (info.isActive(logProfile)) CTimer::get("Files : writing data").suspend();
2283	if (wtime)
2284	{
2285	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").resume();
2286	if ( wtimeData)
2287	{
2288	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2289	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2290	}
2291	if (wtimeCounter)
2292	{
2293	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2294	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2295	}
2296	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").suspend();
2297	}
2298	break;
2299	}
2300	case (ONE_FILE) :
2301	{
2302
2303	std::vector<StdSize> start, count;
2304
2305	if (field->getUseCompressedOutput())
2306	{
2307	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2308	std::vector<StdString> domainList = grid->getDomainList();
2309	std::vector<StdString> axisList = grid->getAxisList();
2310	int numElement = axisDomainOrder.numElements();
2311	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2312	int idx = domainList.size() * 2 + axisList.size() - 1;
2313	int commRank ;
2314
2315	MPI_Comm_rank(comm_file,&commRank) ;
2316
2317	start.reserve(idx+1);
2318	count.reserve(idx+1);
2319
2320	for (int i = numElement - 1; i >= 0; --i)
2321	{
2322	if (2 == axisDomainOrder(i))
2323	{
2324	CDomain* domain = CDomain::get(domainList[idxDomain]);
2325
2326	if (domain->isCompressible())
2327	{
2328	size_t offset ;
2329	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
2330	if (domain->isDistributed())
2331	{
2332	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2333	if (commRank==0) offset=0 ;
2334	}
2335	else offset=0 ;
2336
2337	start.push_back(offset);
2338	count.push_back(nbIndexes);
2339	idx -= 2;
2340	}
2341	else
2342	{
2343	if ((domain->type) != CDomain::type_attr::unstructured)
2344	{
2345	start.push_back(domain->jbeginValue_);
2346	count.push_back(domain->njValue_);
2347	}
2348	--idx;
2349	start.push_back(domain->ibeginValue_);
2350	count.push_back(domain->niValue_);
2351	--idx;
2352	}
2353	--idxDomain;
2354	}
2355	else if (1 == axisDomainOrder(i))
2356	{
2357	CAxis* axis = CAxis::get(axisList[idxAxis]);
2358
2359	if (axis->isCompressible())
2360	{
2361	size_t offset ;
2362	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
2363	if (axis->isDistributed())
2364	{
2365	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2366	if (commRank==0) offset=0 ;
2367	}
2368	else offset=0 ;
2369
2370	start.push_back(offset);
2371	count.push_back(nbIndexes);
2372	}
2373	else
2374	{
2375	start.push_back(axis->begin);
2376	count.push_back(axis->n);
2377	}
2378	--idxAxis;
2379	--idx;
2380	}
2381	}
2382	}
2383	else
2384	{
2385	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2386	std::vector<StdString> domainList = grid->getDomainList();
2387	std::vector<StdString> axisList = grid->getAxisList();
2388	std::vector<StdString> scalarList = grid->getScalarList() ;
2389	int numElement = axisDomainOrder.numElements();
2390	int idxDomain = domainList.size() - 1 ;
2391	int idxAxis = axisList.size() - 1 ;
2392	int idxScalar = scalarList.size() - 1 ;
2393	int idx = domainList.size() * 2 + axisList.size() - 1;
2394
2395	start.reserve(idx+1);
2396	count.reserve(idx+1);
2397
2398	for (int i = numElement - 1; i >= 0; --i)
2399	{
2400	if (2 == axisDomainOrder(i))
2401	{
2402	CDomain* domain = CDomain::get(domainList[idxDomain]);
2403	if ((domain->type) != CDomain::type_attr::unstructured)
2404	{
2405	start.push_back(domain->jbeginValue_);
2406	count.push_back(domain->njValue_);
2407	}
2408	--idx ;
2409
2410	start.push_back(domain->ibeginValue_);
2411	count.push_back(domain->niValue_);
2412	--idx ;
2413	--idxDomain;
2414	}
2415	else if (1 == axisDomainOrder(i))
2416	{
2417	CAxis* axis = CAxis::get(axisList[idxAxis]);
2418	start.push_back(axis->begin);
2419	count.push_back(axis->n);
2420	--idx;
2421	--idxAxis;
2422	}
2423	else
2424	{
2425	if (idx ==-1)
2426	{
2427	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
2428	start.push_back(0);
2429	count.push_back(scalar->n);
2430	idx-- ;
2431	}
2432	else if (idx<-1)
2433	{
2434	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
2435	count.back()*=scalar->n;
2436	idx-- ;
2437	}
2438	--idxScalar;
2439	}
2440	}
2441	}
2442
2443
2444	if (info.isActive(logProfile)) CTimer::get("Files : writing data").resume();
2445	writeAndConvertData(field, data, nstep - 1, &start, &count);
2446	if (info.isActive(logProfile)) CTimer::get("Files : writing data").suspend();
2447
2448	if (wtime)
2449	{
2450	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").resume();
2451	if ( wtimeData)
2452	{
2453	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2454	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2455	}
2456	if (wtimeCounter)
2457	{
2458	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2459	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2460
2461	}
2462	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").suspend();
2463	}
2464
2465	break;
2466	}
2467	}
2468	return nstep ;
2469	}
2470	catch (CNetCdfException& e)
2471	{
2472	StdString msg("On writing field data: ");
2473	msg.append(fieldid); msg.append("\n");
2474	msg.append("In the context : ");
2475	msg.append(context->getId()); msg.append("\n");
2476	msg.append(e.what());
2477	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2478	}
2479	}
2480
2481	void CNc4DataOutput::writeAndConvertData(CField* field, const CArray<double,1>& data, StdSize record, const std::vector<StdSize> start, const std::vector<StdSize> count)
2482	{
2483	StdString fieldid = field->getFieldOutputName();
2484	nc_type type ;
2485	if (field->prec.isEmpty()) type = NC_FLOAT ;
2486	else
2487	{
2488	if (field->prec==2) type = NC_SHORT ;
2489	else if (field->prec==4) type = NC_FLOAT ;
2490	else if (field->prec==8) type = NC_DOUBLE ;
2491	}
2492
2493	bool conversionByNetCDF = true; // default : conversion operated by NetCDF for now (legacy behaviour)
2494	if (!field->conversion_by_netcdf.isEmpty())
2495	{
2496	// use conversion_by_netcdf = ".false." to bypass NetCDF conversion
2497	// poor performances from NC_DOUBLE to NC_FLOAT with isgreater/isless in recent NetCDF available at TGCC
2498	conversionByNetCDF = field->conversion_by_netcdf;
2499	}
2500	if ( ( type == NC_DOUBLE ) \|\| ( conversionByNetCDF ) )
2501	{
2502	SuperClassWriter::writeData(data, fieldid, isCollective, record, start, count);
2503	}
2504	else if ( type == NC_FLOAT )
2505	{
2506	CArray<float,1> f_data;
2507	f_data.resize( data.numElements() );
2508	for (int i = 0; i < data.numElements(); i++)
2509	{
2510	if (data(i) <= X_FLOAT_MAX \|\| data(i) >= X_FLOAT_MIN)
2511	f_data(i) = data(i);
2512	else if (data(i) > X_FLOAT_MAX)
2513	f_data(i) = X_FLOAT_MAX;
2514	else if (data(i) < X_FLOAT_MIN)
2515	f_data(i) = X_FLOAT_MIN;
2516	}
2517	SuperClassWriter::writeData(f_data, fieldid, isCollective, record, start, count);
2518	}
2519	else if ( type == NC_SHORT )
2520	{
2521	CArray<short,1> s_data;
2522	s_data.resize( data.numElements() );
2523	for (int i = 0; i < data.numElements(); i++)
2524	{
2525	if (data(i) <= X_SHORT_MAX \|\| data(i) >= X_SHORT_MIN)
2526	s_data(i) = data(i);
2527	else if (data(i) > X_SHORT_MAX)
2528	s_data(i) = X_SHORT_MAX;
2529	else if (data(i) < X_SHORT_MIN)
2530	s_data(i) = X_SHORT_MIN;
2531	}
2532	SuperClassWriter::writeData(s_data, fieldid, isCollective, record, start, count);
2533	}
2534	else
2535	{
2536	ERROR("CNc4DataOutput::writeAndConvertData(...)", << "Type conversion not managed for " << fieldid );
2537	}
2538
2539	}
2540
2541	//---------------------------------------------------------------
2542
2543	void CNc4DataOutput::writeTimeAxis_
2544	(CField* field,
2545	const std::shared_ptr<CCalendar> cal)
2546	{
2547	StdOStringStream oss;
2548	bool createInstantAxis=false ;
2549	bool createCenteredAxis=false ;
2550	bool createTimeCounterAxis=false ;
2551
2552	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2553
2554
2555	StdString axisId ;
2556	StdString axisBoundId;
2557	StdString timeid(getTimeCounterName());
2558	StdString timeBoundId("axis_nbounds");
2559
2560	StdString strTimeUnits ;
2561	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2562	else strTimeUnits="seconds since " ;
2563
2564	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2565	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2566
2567
2568	if (field->getRelFile()->time_counter.isEmpty())
2569	{
2570	if (timeCounterType==none) createTimeCounterAxis=true ;
2571	if (field->hasTimeCentered)
2572	{
2573	timeCounterType=centered ;
2574	if (!hasTimeCentered) createCenteredAxis=true ;
2575	}
2576	if (field->hasTimeInstant)
2577	{
2578	if (timeCounterType==none) timeCounterType=instant ;
2579	if (!hasTimeInstant) createInstantAxis=true ;
2580	}
2581	}
2582	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
2583	{
2584	if (field->hasTimeCentered)
2585	{
2586	if (!hasTimeCentered) createCenteredAxis=true ;
2587	}
2588	if (field->hasTimeInstant)
2589	{
2590	if (timeCounterType==none) createTimeCounterAxis=true ;
2591	timeCounterType=instant ;
2592	if (!hasTimeInstant) createInstantAxis=true ;
2593	}
2594	}
2595	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
2596	{
2597	if (field->hasTimeCentered)
2598	{
2599	if (timeCounterType==none) createTimeCounterAxis=true ;
2600	timeCounterType=centered ;
2601	if (!hasTimeCentered) createCenteredAxis=true ;
2602	}
2603	if (field->hasTimeInstant)
2604	{
2605	if (!hasTimeInstant) createInstantAxis=true ;
2606	}
2607	}
2608	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
2609	{
2610	if (field->hasTimeCentered)
2611	{
2612	if (!hasTimeCentered) createCenteredAxis=true ;
2613	}
2614	if (field->hasTimeInstant)
2615	{
2616	if (timeCounterType==none) createTimeCounterAxis=true ;
2617	timeCounterType=instant ;
2618	}
2619	}
2620	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
2621	{
2622	if (field->hasTimeCentered)
2623	{
2624	if (timeCounterType==none) createTimeCounterAxis=true ;
2625	timeCounterType=centered ;
2626	}
2627	if (field->hasTimeInstant)
2628	{
2629	if (!hasTimeInstant) createInstantAxis=true ;
2630	}
2631	}
2632	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
2633	{
2634	if (field->hasTimeCentered)
2635	{
2636	if (timeCounterType==none) createTimeCounterAxis=true ;
2637	if (timeCounterType==instant) createInstantAxis=true ;
2638	timeCounterType=centered ;
2639	}
2640	if (field->hasTimeInstant)
2641	{
2642	if (timeCounterType==none)
2643	{
2644	createTimeCounterAxis=true ;
2645	timeCounterType=instant ;
2646	}
2647	if (timeCounterType==centered)
2648	{
2649	if (!hasTimeInstant) createInstantAxis=true ;
2650	}
2651	}
2652	}
2653	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
2654	{
2655	if (field->hasTimeCentered)
2656	{
2657	if (!hasTimeCentered) createCenteredAxis=true ;
2658	}
2659	if (field->hasTimeInstant)
2660	{
2661	if (!hasTimeInstant) createInstantAxis=true ;
2662	}
2663	}
2664	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
2665	{
2666	if (timeCounterType==none) createTimeCounterAxis=true ;
2667	timeCounterType=record ;
2668	if (field->hasTimeCentered)
2669	{
2670	if (!hasTimeCentered) createCenteredAxis=true ;
2671	}
2672	if (field->hasTimeInstant)
2673	{
2674	if (!hasTimeInstant) createInstantAxis=true ;
2675	}
2676	}
2677
2678	if (createInstantAxis)
2679	{
2680	axisId="time_instant" ;
2681	axisBoundId="time_instant_bounds";
2682	hasTimeInstant=true ;
2683	}
2684
2685	if (createCenteredAxis)
2686	{
2687	axisId="time_centered" ;
2688	axisBoundId="time_centered_bounds";
2689	hasTimeCentered=true ;
2690	}
2691
2692
2693	try
2694	{
2695	std::vector<StdString> dims;
2696
2697	if (createInstantAxis \|\| createCenteredAxis)
2698	{
2699	// Adding time_instant or time_centered
2700	dims.push_back(timeid);
2701	if (!SuperClassWriter::varExist(axisId))
2702	{
2703	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2704
2705	CDate timeOrigin=cal->getTimeOrigin() ;
2706	StdOStringStream oss2;
2707	StdString strInitdate=oss2.str() ;
2708	StdString strTimeOrigin=timeOrigin.toString() ;
2709	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2710	strTimeOrigin, axisBoundId);
2711	}
2712
2713	// Adding time_instant_bounds or time_centered_bounds variables
2714	if (!SuperClassWriter::varExist(axisBoundId))
2715	{
2716	dims.clear() ;
2717	dims.push_back(timeid);
2718	dims.push_back(timeBoundId);
2719	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2720	}
2721	}
2722
2723	if (createTimeCounterAxis)
2724	{
2725	// Adding time_counter
2726	axisId = getTimeCounterName();
2727	axisBoundId = getTimeCounterName() + "_bounds";
2728	dims.clear();
2729	dims.push_back(timeid);
2730	if (!SuperClassWriter::varExist(axisId))
2731	{
2732	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2733	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2734
2735	if (field->getRelFile()->time_counter.isEmpty() \|\|
2736	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2737	{
2738	CDate timeOrigin = cal->getTimeOrigin();
2739	StdString strTimeOrigin = timeOrigin.toString();
2740
2741	this->writeTimeAxisAttributes(axisId, cal->getType(),
2742	strTimeUnits+strTimeOrigin,
2743	strTimeOrigin, axisBoundId);
2744	}
2745	}
2746
2747	// Adding time_counter_bound dimension
2748	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2749	{
2750	if (!SuperClassWriter::varExist(axisBoundId))
2751	{
2752	dims.clear();
2753	dims.push_back(timeid);
2754	dims.push_back(timeBoundId);
2755	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2756	}
2757	}
2758	}
2759	}
2760	catch (CNetCdfException& e)
2761	{
2762	StdString msg("On writing time axis data: ");
2763	msg.append("In the context : ");
2764	CContext* context = CContext::getCurrent() ;
2765	msg.append(context->getId()); msg.append("\n");
2766	msg.append(e.what());
2767	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2768	const std::shared_ptr<CCalendar> cal)", << msg);
2769	}
2770	}
2771
2772	//---------------------------------------------------------------
2773
2774	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2775	const StdString & calendar,
2776	const StdString & units,
2777	const StdString & time_origin,
2778	const StdString & time_bounds,
2779	const StdString & standard_name,
2780	const StdString & long_name)
2781	{
2782	try
2783	{
2784	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2785	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2786	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2787	SuperClassWriter::addAttribute("units", units , &axis_name);
2788	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2789	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2790	}
2791	catch (CNetCdfException& e)
2792	{
2793	StdString msg("On writing time axis Attribute: ");
2794	msg.append("In the context : ");
2795	CContext* context = CContext::getCurrent() ;
2796	msg.append(context->getId()); msg.append("\n");
2797	msg.append(e.what());
2798	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2799	const StdString & calendar,\
2800	const StdString & units, \
2801	const StdString & time_origin, \
2802	const StdString & time_bounds, \
2803	const StdString & standard_name, \
2804	const StdString & long_name)", << msg);
2805	}
2806	}
2807
2808	//---------------------------------------------------------------
2809
2810	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2811	const StdString & axis,
2812	const StdString & standard_name,
2813	const StdString & long_name,
2814	const StdString & units,
2815	const StdString & nav_model)
2816	{
2817	try
2818	{
2819	if (!axis.empty())
2820	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2821
2822	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2823	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2824	SuperClassWriter::addAttribute("units" , units , &axis_name);
2825	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2826	}
2827	catch (CNetCdfException& e)
2828	{
2829	StdString msg("On writing Axis Attribute: ");
2830	msg.append("In the context : ");
2831	CContext* context = CContext::getCurrent() ;
2832	msg.append(context->getId()); msg.append("\n");
2833	msg.append(e.what());
2834	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2835	const StdString & axis, \
2836	const StdString & standard_name, \
2837	const StdString & long_name, \
2838	const StdString & units, \
2839	const StdString & nav_model)", << msg);
2840	}
2841	}
2842
2843	//---------------------------------------------------------------
2844
2845	void CNc4DataOutput::writeLocalAttributes
2846	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2847	{
2848	try
2849	{
2850	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2851	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2852	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2853	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2854	}
2855	catch (CNetCdfException& e)
2856	{
2857	StdString msg("On writing Local Attributes: ");
2858	msg.append("In the context : ");
2859	CContext* context = CContext::getCurrent() ;
2860	msg.append(context->getId()); msg.append("\n");
2861	msg.append(e.what());
2862	ERROR("CNc4DataOutput::writeLocalAttributes \
2863	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2864	}
2865
2866	}
2867
2868	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2869	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2870	{
2871	CArray<int,1> array(2) ;
2872
2873	try
2874	{
2875	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2876	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2877	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2878	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2879	array=ni_glo,nj_glo ;
2880	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2881	array=ni,nj ;
2882	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2883	array=ibegin+1,jbegin+1 ;
2884	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2885	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2886	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2887	array=0,0 ;
2888	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2889	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2890	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2891	/*
2892	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2893	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2894	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2895	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2896	*/
2897	}
2898	catch (CNetCdfException& e)
2899	{
2900	StdString msg("On writing Local Attributes IOIPSL \n");
2901	msg.append("In the context : ");
2902	CContext* context = CContext::getCurrent() ;
2903	msg.append(context->getId()); msg.append("\n");
2904	msg.append(e.what());
2905	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2906	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2907	}
2908	}
2909	//---------------------------------------------------------------
2910
2911	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2912	const StdString & description,
2913	const StdString & conventions,
2914	const StdString & production,
2915	const StdString & timeStamp)
2916	{
2917	try
2918	{
2919	SuperClassWriter::addAttribute("name" , name);
2920	SuperClassWriter::addAttribute("description", description);
2921	SuperClassWriter::addAttribute("title" , description);
2922	SuperClassWriter::addAttribute("Conventions", conventions);
2923	// SuperClassWriter::addAttribute("production" , production);
2924
2925	StdString timeStampStr ;
2926	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
2927	else timeStampStr=file->time_stamp_name ;
2928	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
2929
2930	StdString uuidName ;
2931	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
2932	else uuidName=file->uuid_name ;
2933
2934	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
2935	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
2936
2937	}
2938	catch (CNetCdfException& e)
2939	{
2940	StdString msg("On writing File Attributes \n ");
2941	msg.append("In the context : ");
2942	CContext* context = CContext::getCurrent() ;
2943	msg.append(context->getId()); msg.append("\n");
2944	msg.append(e.what());
2945	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2946	const StdString & description, \
2947	const StdString & conventions, \
2948	const StdString & production, \
2949	const StdString & timeStamp)", << msg);
2950	}
2951	}
2952
2953	//---------------------------------------------------------------
2954
2955	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2956	int data_dim,
2957	int data_ni,
2958	int data_nj,
2959	int data_ibegin,
2960	int data_jbegin)
2961	{
2962	try
2963	{
2964	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2965	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2966	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2967	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2968	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2969	}
2970	catch (CNetCdfException& e)
2971	{
2972	StdString msg("On writing Mask Attributes \n ");
2973	msg.append("In the context : ");
2974	CContext* context = CContext::getCurrent() ;
2975	msg.append(context->getId()); msg.append("\n");
2976	msg.append(e.what());
2977	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2978	int data_dim, \
2979	int data_ni, \
2980	int data_nj, \
2981	int data_ibegin, \
2982	int data_jbegin)", << msg);
2983	}
2984	}
2985
2986	///--------------------------------------------------------------
2987
2988	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
2989	{
2990	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2991	if (it == timeToRecordCache.end())
2992	{
2993	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2994	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
2995	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
2996
2997	CArray<double,2> timeAxisBounds;
2998	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
2999
3000	StdSize record = 0;
3001	double dtime(time);
3002	for (int n = dimSize[0] - 1; n >= 0; n--)
3003	{
3004	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3005	timeAxisBounds*=factorUnit ;
3006	if (timeAxisBounds(1, 0) < dtime)
3007	{
3008	record = n + 1;
3009	break;
3010	}
3011	}
3012	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3013	}
3014	return it->second;
3015	}
3016
3017	///--------------------------------------------------------------
3018
3019	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3020	{
3021	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3022	}
3023
3024	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3025	{
3026	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3027	}
3028
3029	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3030	{
3031	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3032	}
3033
3034	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3035	{
3036	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3037	}
3038
3039	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3040	{
3041	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3042	}
3043
3044	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3045	{
3046	this->writtenDomains.insert(domainName);
3047	}
3048
3049	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3050	{
3051	this->writtenCompressedDomains.insert(domainName);
3052	}
3053
3054	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3055	{
3056	this->writtenAxis.insert(axisName);
3057	}
3058
3059	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3060	{
3061	this->writtenCompressedAxis.insert(axisName);
3062	}
3063
3064	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3065	{
3066	this->writtenScalar.insert(scalarName);
3067	}
3068	} // namespace xios

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