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source: XIOS3/trunk/src/io/nc4_data_output.cpp @ 2612

Last change on this file since 2612 was 2600, checked in by jderouillat, 8 months ago
Add a field attribute, conversion_by_NetCDF, to operate type conversion in XIOS, and not in NetCDF
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: 129.3 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	/// ////////////////////// Dfinitions ////////////////////// ///
24	CNc4DataOutput::CNc4DataOutput
25	(CFile* file, const StdString & filename, bool exist)
26	: SuperClass()
27	, SuperClassWriter(filename, exist)
28	, filename(filename)
29	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
30	{
31	SuperClass::type = MULTI_FILE;
32	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
33	}
34
35	CNc4DataOutput::CNc4DataOutput
36	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
37	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
38	: SuperClass()
39	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
40	, comm_file(comm_file)
41	, filename(filename)
42	, isCollective(isCollective)
43	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
44	{
45	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
46	if (file==NULL) compressionLevel = 0 ;
47	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
48	}
49
50	CNc4DataOutput::~CNc4DataOutput(void)
51	{ /* Ne rien faire de plus */ }
52
53	///--------------------------------------------------------------
54
55	const StdString & CNc4DataOutput::getFileName(void) const
56	{
57	return (this->filename);
58	}
59
60	//---------------------------------------------------------------
61
62	void CNc4DataOutput::writeDomain_(CDomain* domain)
63	TRY
64	{
65	StdString lonName,latName ;
66
67	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
68	if (!domain->lonvalue.isEmpty() )
69	{
70	// The hash of the element will be associated to the default element name (= map key), and to the name really written
71	int globalHash = domain->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
72
73	StdString defaultNameKey = domain->getDomainOutputName();
74	if ( !relDomains_.count ( defaultNameKey ) )
75	{
76	// if defaultNameKey not in the map, write the element such as it is defined
77	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) );
78	}
79	else // look if a hash associated this key is equal
80	{
81	bool elementIsInMap(false);
82	auto defaultNameKeyElements = relDomains_.equal_range( defaultNameKey );
83	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
84	{
85	if ( it->second.first == globalHash )
86	{
87	// if yes, associate the same ids to current element
88	domain->renameAttributesBeforeWriting( it->second.second );
89	elementIsInMap = true;
90	}
91	}
92	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
93	if (!elementIsInMap) // ! in MAP
94	{
95	domain->renameAttributesBeforeWriting();
96	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) ) ;
97	}
98	}
99	}
100
101	if (domain->type == CDomain::type_attr::unstructured)
102	{
103	if (SuperClassWriter::useCFConvention)
104	writeUnstructuredDomain(domain) ;
105	else
106	writeUnstructuredDomainUgrid(domain) ;
107	return ;
108	}
109
110	CContext* context = CContext::getCurrent() ;
111	if (domain->IsWritten(this->filename)) return;
112	domain->checkAttributes();
113
114	if (domain->isEmpty())
115	if (SuperClass::type==MULTI_FILE) return;
116
117
118	std::vector<StdString> dim0, dim1;
119	StdString domid = domain->getDomainOutputName();
120	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
121	if (isWrittenDomain(domid)) return ;
122	else setWrittenDomain(domid);
123
124	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
125
126
127	StdString dimXid, dimYid ;
128
129	nc_type typePrec ;
130	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
131	else if (domain->prec==4) typePrec = NC_FLOAT ;
132	else if (domain->prec==8) typePrec = NC_DOUBLE ;
133
134	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
135	switch (domain->type)
136	{
137	case CDomain::type_attr::curvilinear :
138
139	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
140	else lonName = domain->lon_name;
141
142	if (domain->lat_name.isEmpty()) latName = "nav_lat";
143	else latName = domain->lat_name;
144
145	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
146	else dimXid=domain->dim_i_name.getValue() + appendDomid;
147
148	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
149	else dimYid=domain->dim_j_name.getValue() + appendDomid;
150
151	break ;
152
153	case CDomain::type_attr::rectilinear :
154
155	if (domain->lon_name.isEmpty())
156	{
157	if (domain->dim_i_name.isEmpty())
158	lonName = "lon";
159	else
160	lonName = domain->dim_i_name.getValue();
161	}
162	else lonName = domain->lon_name;
163
164	if (domain->lat_name.isEmpty())
165	{
166	if (domain->dim_j_name.isEmpty())
167	latName = "lat";
168	else
169	latName = domain->dim_j_name.getValue();
170	}
171	else latName = domain->lat_name;
172
173	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
174	else dimXid = domain->dim_i_name.getValue()+appendDomid;
175
176	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
177	else dimYid = domain->dim_j_name.getValue()+appendDomid;
178	break;
179	}
180
181	StdString dimVertId = StdString("nvertex").append(appendDomid);
182
183	string lonid,latid,bounds_lonid,bounds_latid ;
184	string areaId = "area" + appendDomid;
185
186	try
187	{
188	switch (SuperClass::type)
189	{
190	case (MULTI_FILE) :
191	{
192	switch (domain->type)
193	{
194	case CDomain::type_attr::curvilinear :
195	dim0.push_back(dimYid); dim0.push_back(dimXid);
196	lonid = lonName+appendDomid;
197	latid = latName+appendDomid;
198	break ;
199	case CDomain::type_attr::rectilinear :
200	lonid = lonName+appendDomid;
201	latid = latName+appendDomid;
202	dim0.push_back(dimYid);
203	dim1.push_back(dimXid);
204	break;
205	}
206	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
207	else bounds_lonid = "bounds_"+lonName+appendDomid;
208	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
209	else bounds_latid = "bounds_"+latName+appendDomid;
210
211	SuperClassWriter::addDimension(dimXid, domain->niValue_);
212	SuperClassWriter::addDimension(dimYid, domain->njValue_);
213
214	if (domain->hasBounds)
215	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
216
217	if (context->intraCommSize_ > 1)
218	{
219	this->writeLocalAttributes(domain->ibeginValue_,
220	domain->niValue_,
221	domain->jbeginValue_,
222	domain->njValue_,
223	appendDomid);
224
225	if (singleDomain)
226	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
227	domain->ibeginValue_,
228	domain->niValue_,
229	domain->jbeginValue_,
230	domain->njValue_,
231	domain->ni_glo,domain->nj_glo,
232	context->intraCommRank_,context->intraCommSize_);
233	}
234
235	if (domain->hasLonLat)
236	{
237	switch (domain->type)
238	{
239	case CDomain::type_attr::curvilinear :
240	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
241	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
242	break ;
243	case CDomain::type_attr::rectilinear :
244	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
245	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
246	break ;
247	}
248
249	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
250	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
251
252	if (domain->hasBounds)
253	{
254	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
255	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
256
257	dim0.clear();
258	dim0.push_back(dimYid);
259	dim0.push_back(dimXid);
260	dim0.push_back(dimVertId);
261	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
262	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
263	}
264	}
265
266	dim0.clear();
267	dim0.push_back(dimYid);
268	dim0.push_back(dimXid);
269
270	if (domain->hasArea)
271	{
272	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
273	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
274	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
275	}
276
277	SuperClassWriter::definition_end();
278
279	if (domain->hasLonLat)
280	{
281	switch (domain->type)
282	{
283	case CDomain::type_attr::curvilinear :
284	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
285	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
286	break;
287	case CDomain::type_attr::rectilinear :
288	//CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
289	CArray<double,1> lat;
290	lat.resize( domain->njValue_);
291	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
292	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
293	//CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
294	CArray<double,1> lon = domain->lonvalue(Range(0,domain->niValue_-1));
295	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
296	break;
297	}
298
299	if (domain->hasBounds)
300	{
301	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
302	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
303	}
304	}
305
306	if (domain->hasArea)
307	{
308	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
309	}
310
311	SuperClassWriter::definition_start();
312
313	break;
314	}
315	case (ONE_FILE) :
316	{
317	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
318	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
319
320	if (domain->hasBounds)
321	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
322
323	if (domain->hasLonLat)
324	{
325	switch (domain->type)
326	{
327	case CDomain::type_attr::curvilinear :
328	dim0.push_back(dimYid); dim0.push_back(dimXid);
329	lonid = lonName+appendDomid;
330	latid = latName+appendDomid;
331	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
332	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
333	break;
334
335	case CDomain::type_attr::rectilinear :
336	dim0.push_back(dimYid);
337	dim1.push_back(dimXid);
338	lonid = lonName+appendDomid;
339	latid = latName+appendDomid;
340	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
341	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
342	break;
343	}
344	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
345	else bounds_lonid = "bounds_"+lonName+appendDomid;
346	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
347	else bounds_latid = "bounds_"+latName+appendDomid;
348
349	this->writeAxisAttributes
350	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
351	this->writeAxisAttributes
352	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
353
354	if (domain->hasBounds)
355	{
356	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
357	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
358
359	dim0.clear();
360	dim0.push_back(dimYid);
361	dim0.push_back(dimXid);
362	dim0.push_back(dimVertId);
363	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
364	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
365	}
366	}
367
368	if (domain->hasArea)
369	{
370	dim0.clear();
371	dim0.push_back(dimYid); dim0.push_back(dimXid);
372	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
373	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
374	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
375	dim0.clear();
376	}
377
378	SuperClassWriter::definition_end();
379
380	switch (domain->type)
381	{
382	case CDomain::type_attr::curvilinear :
383	{
384	std::vector<StdSize> start(2) ;
385	std::vector<StdSize> count(2) ;
386	start[1]=domain->ibeginValue_;
387	start[0]=domain->jbeginValue_;
388	count[1]=domain->niValue_ ; count[0]=domain->njValue_ ;
389
390	if (domain->hasLonLat)
391	{
392	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
393	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
394	}
395	break;
396	}
397	case CDomain::type_attr::rectilinear :
398	{
399	if (domain->hasLonLat)
400	{
401	std::vector<StdSize> start(1) ;
402	std::vector<StdSize> count(1) ;
403
404	start[0]=domain->jbeginValue_;
405	count[0]=domain->njValue_;
406	CArray<double,1> lat;
407	lat.resize( domain->njValue_);
408	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
409	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
410
411	start[0]=domain->ibeginValue_;
412	count[0]=domain->niValue_;
413	CArray<double,1> lon = domain->lonvalue(Range(0,domain->niValue_-1));
414	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
415	}
416	break;
417	}
418	}
419
420	if (domain->hasBounds)
421	{
422	std::vector<StdSize> start(3);
423	std::vector<StdSize> count(3);
424	if (domain->isEmpty())
425	{
426	start[2] = start[1] = start[0] = 0;
427	count[2] = count[1] = count[0] = 0;
428	}
429	else
430	{
431	start[2] = 0;
432	start[1] = domain->ibeginValue_;
433	start[0] = domain->jbeginValue_;
434	count[2] = domain->nvertex;
435	count[1] = domain->niValue_;
436	count[0] = domain->njValue_;
437	}
438
439	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
440	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
441	}
442
443	if (domain->hasArea)
444	{
445	std::vector<StdSize> start(2);
446	std::vector<StdSize> count(2);
447
448	start[1] = domain->ibeginValue_;
449	start[0] = domain->jbeginValue_;
450	count[1] = domain->niValue_;
451	count[0] = domain->njValue_;
452
453	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
454	}
455
456	SuperClassWriter::definition_start();
457	break;
458	}
459	default :
460	ERROR("CNc4DataOutput::writeDomain(domain)",
461	<< "[ type = " << SuperClass::type << "]"
462	<< " not implemented yet !");
463	}
464	}
465	catch (CNetCdfException& e)
466	{
467	StdString msg("On writing the domain : ");
468	msg.append(domid); msg.append("\n");
469	msg.append("In the context : ");
470	msg.append(context->getId()); msg.append("\n");
471	msg.append(e.what());
472	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
473	}
474
475	domain->addRelFile(this->filename);
476	}
477	CATCH
478
479	//--------------------------------------------------------------
480
481	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
482	{
483	CContext* context = CContext::getCurrent() ;
484
485	if (domain->IsWritten(this->filename)) return;
486
487	StdString domid = domain->getDomainOutputName();
488
489	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
490	// Thus the entire mesh connectivity will be generated at once.
491	if (isWrittenDomain(domid)) return ;
492	else setWrittenDomain(domid);
493
494	domain->checkAttributes();
495	if (domain->isEmpty())
496	if (SuperClass::type==MULTI_FILE) return ;
497
498	nc_type typePrec ;
499	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
500	else if (domain->prec==4) typePrec = NC_FLOAT ;
501	else if (domain->prec==8) typePrec = NC_DOUBLE ;
502
503	std::vector<StdString> dim0;
504	StdString domainName = domain->name;
505
506	StdString node_x = domainName + "_node_x";
507	StdString node_y = domainName + "_node_y";
508
509	StdString edge_x = domainName + "_edge_x";
510	StdString edge_y = domainName + "_edge_y";
511	StdString edge_nodes = domainName + "_edge_nodes";
512
513	StdString face_x = domainName + "_face_x";
514	StdString face_y = domainName + "_face_y";
515	StdString face_nodes = domainName + "_face_nodes";
516	StdString face_edges = domainName + "_face_edges";
517	StdString edge_faces = domainName + "_edge_face_links";
518	StdString face_faces = domainName + "_face_links";
519
520	StdString dimNode = "n" + domainName + "_node";
521	StdString dimEdge = "n" + domainName + "_edge";
522	StdString dimFace = "n" + domainName + "_face";
523	StdString dimVertex = "n" + domainName + "_vertex";
524	StdString dimTwo = "Two";
525
526	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
527	dim0.clear();
528	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
529	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
530	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
531	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
532	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
533
534	try
535	{
536	switch (SuperClass::type)
537	{
538	case (ONE_FILE) :
539	{
540	// Adding nodes
541	if (domain->nvertex == 1)
542	{
543	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
544	{
545	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
546	dim0.clear();
547	dim0.push_back(dimNode);
548	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
549	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
550	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
551	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
552	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
553	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
554	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
555	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
556	}
557	} // domain->nvertex == 1
558
559	// Adding edges and nodes, if nodes have not been defined previously
560	if (domain->nvertex == 2)
561	{
562	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
563	{
564	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
565	dim0.clear();
566	dim0.push_back(dimNode);
567	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
568	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
569	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
570	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
571	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
572	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
573	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
574	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
575	}
576	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
577	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
578	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
579	dim0.clear();
580	dim0.push_back(dimEdge);
581	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
582	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
583	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
584	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
585	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
586	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
587	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
588	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
589	dim0.clear();
590	dim0.push_back(dimEdge);
591	dim0.push_back(dimTwo);
592	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
593	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
594	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
595	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
596	} // domain->nvertex == 2
597
598	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
599	if (domain->nvertex > 2)
600	{
601	// Nodes
602	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
603	{
604	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
605	dim0.clear();
606	dim0.push_back(dimNode);
607	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
608	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
609	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
610	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
611	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
612	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
613	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
614	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
615	}
616	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
617	{
618	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
619	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
620	SuperClassWriter::addAttribute("face_edge_connectivity", face_edges, &domainName);
621	SuperClassWriter::addAttribute("edge_face_connectivity", edge_faces, &domainName);
622	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
623	dim0.clear();
624	dim0.push_back(dimEdge);
625	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
626	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
627	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
628	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
629	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
630	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
631	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
632	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
633	dim0.clear();
634	dim0.push_back(dimEdge);
635	dim0.push_back(dimTwo);
636	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
637	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
638	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
639	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
640	}
641	SuperClassWriter::addAttribute("face_face_connectivity", face_faces, &domainName);
642	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
643	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
644	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
645	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
646	dim0.clear();
647	dim0.push_back(dimFace);
648	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
649	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
650	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
651	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
652	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
653	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
654	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
655	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
656	dim0.clear();
657	dim0.push_back(dimFace);
658	dim0.push_back(dimVertex);
659	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
660	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
661	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
662	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
663	dim0.clear();
664	dim0.push_back(dimFace);
665	dim0.push_back(dimVertex);
666	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
667	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
668	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
669	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
670	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
671	dim0.clear();
672	dim0.push_back(dimEdge);
673	dim0.push_back(dimTwo);
674	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
675	SuperClassWriter::addAttribute("cf_role", StdString("edge_face_connectivity"), &edge_faces);
676	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
677	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
678	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
679	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
680	dim0.clear();
681	dim0.push_back(dimFace);
682	dim0.push_back(dimVertex);
683	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
684	SuperClassWriter::addAttribute("cf_role", StdString("face_face_connectivity"), &face_faces);
685	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
686	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
687	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
688	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
689	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
690	} // domain->nvertex > 2
691
692	SuperClassWriter::definition_end();
693
694	std::vector<StdSize> startEdges(1) ;
695	std::vector<StdSize> countEdges(1) ;
696	std::vector<StdSize> startNodes(1) ;
697	std::vector<StdSize> countNodes(1) ;
698	std::vector<StdSize> startFaces(1) ;
699	std::vector<StdSize> countFaces(1) ;
700	std::vector<StdSize> startEdgeNodes(2) ;
701	std::vector<StdSize> countEdgeNodes(2) ;
702	std::vector<StdSize> startEdgeFaces(2) ;
703	std::vector<StdSize> countEdgeFaces(2) ;
704	std::vector<StdSize> startFaceConctv(2) ;
705	std::vector<StdSize> countFaceConctv(2) ;
706
707	if (domain->nvertex == 1)
708	{
709	if (domain->isEmpty())
710	{
711	startNodes[0]=0 ;
712	countNodes[0]=0 ;
713	}
714	else
715	{
716	startNodes[0] = domain->ibeginValue_;
717	countNodes[0] = domain->niValue_ ;
718	}
719
720	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
721	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
722	}
723	else if (domain->nvertex == 2)
724	{
725	if (domain->isEmpty())
726	{
727	startEdges[0]=0 ;
728	countEdges[0]=0 ;
729	startNodes[0]=0 ;
730	countNodes[0]=0 ;
731	startEdgeNodes[0]=0;
732	startEdgeNodes[1]=0;
733	countEdgeNodes[0]=0;
734	countEdgeNodes[1]=0;
735
736	}
737	else
738	{
739	startEdges[0] = domain->ibeginValue_;
740	countEdges[0] = domain->niValue_;
741	startNodes[0] = domain->mesh->node_start;
742	countNodes[0] = domain->mesh->node_count;
743	if (countNodes[0]==0) startNodes[0]=0 ; // for netcdf error
744	startEdgeNodes[0] = domain->ibeginValue_;
745	startEdgeNodes[1] = 0;
746	countEdgeNodes[0] = domain->niValue_;
747	countEdgeNodes[1] = 2;
748	}
749	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
750	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
751	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
752	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
753	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
754	}
755	else
756	{
757	if (domain->isEmpty())
758	{
759	startFaces[0] = 0 ;
760	countFaces[0] = 0 ;
761	startNodes[0] = 0;
762	countNodes[0] = 0;
763	startEdges[0] = 0;
764	countEdges[0] = 0;
765	startEdgeFaces[0] = 0;
766	startEdgeFaces[1] = 0;
767	countEdgeFaces[0] = 0;
768	countEdgeFaces[1] = 0;
769	startFaceConctv[0] = 0;
770	startFaceConctv[1] = 0;
771	countFaceConctv[0] = 0;
772	countFaceConctv[1] = 0;
773	}
774	else
775	{
776	startFaces[0] = domain->ibeginValue_;
777	countFaces[0] = domain->niValue_ ;
778	startNodes[0] = domain->mesh->node_start;
779	countNodes[0] = domain->mesh->node_count;
780	if (countNodes[0]==0) startNodes[0]=0;
781
782	startEdges[0] = domain->mesh->edge_start;
783	countEdges[0] = domain->mesh->edge_count;
784	if (countEdges[0]==0) startEdges[0]=0 ; // for netcdf error
785
786	startEdgeNodes[0] = domain->mesh->edge_start;
787	countEdgeNodes[0] = domain->mesh->edge_count;
788	if (countEdgeNodes[0]==0) startEdgeNodes[0]=0; // for netcdf error
789	startEdgeNodes[1] = 0;
790	countEdgeNodes[1]= 2;
791
792	startEdgeFaces[0] = domain->mesh->edge_start;
793	countEdgeFaces[0] = domain->mesh->edge_count;
794	if (countEdgeFaces[0]==0) startEdgeFaces[0]=0 ; // for netcdf error
795	startEdgeFaces[1]= 0;
796	countEdgeFaces[1]= 2;
797
798	startFaceConctv[0] = domain->ibeginValue_;
799	countFaceConctv[0] = domain->niValue_;
800	startFaceConctv[1] = 0;
801	countFaceConctv[1] = domain->nvertex;
802	}
803	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
804	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
805	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
806	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
807	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
808	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
809	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
810	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
811	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
812	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
813	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
814	}
815	SuperClassWriter::definition_start();
816
817	break;
818	} // ONE_FILE
819
820	case (MULTI_FILE) :
821	{
822	ERROR("CNc4DataOutput::writeDomain(domain)",
823	<< "[ type = multiple_file ]"
824	<< " is not yet implemented for UGRID files !");
825	break;
826	}
827
828	default :
829	ERROR("CNc4DataOutput::writeDomain(domain)",
830	<< "[ type = " << SuperClass::type << "]"
831	<< " not implemented yet !");
832	} // switch
833	} // try
834
835	catch (CNetCdfException& e)
836	{
837	StdString msg("On writing the domain : ");
838	msg.append(domid); msg.append("\n");
839	msg.append("In the context : ");
840	msg.append(context->getId()); msg.append("\n");
841	msg.append(e.what());
842	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
843	}
844
845	domain->addRelFile(this->filename);
846	}
847
848	//--------------------------------------------------------------
849
850	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
851	{
852	CContext* context = CContext::getCurrent() ;
853
854	if (domain->IsWritten(this->filename)) return;
855	domain->checkAttributes();
856
857	if (domain->isEmpty())
858	if (SuperClass::type==MULTI_FILE) return ;
859
860	std::vector<StdString> dim0, dim1;
861	StdString domid = domain->getDomainOutputName();
862	if (isWrittenDomain(domid)) return ;
863	else setWrittenDomain(domid);
864
865	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
866
867	StdString lonName,latName, cellName ;
868	if (domain->lon_name.isEmpty()) lonName = "lon";
869	else lonName = domain->lon_name;
870
871	if (domain->lat_name.isEmpty()) latName = "lat";
872	else latName = domain->lat_name;
873
874	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
875	else cellName="cell";
876	StdString dimXid = cellName+appendDomid;
877	StdString dimVertId;
878	if (domain->nvertex_name.isEmpty()) dimVertId = "nvertex"+appendDomid;
879	else dimVertId = domain->nvertex_name;
880
881	string lonid,latid,bounds_lonid,bounds_latid ;
882	string areaId = "area" + appendDomid;
883
884	nc_type typePrec ;
885	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
886	else if (domain->prec==4) typePrec = NC_FLOAT ;
887	else if (domain->prec==8) typePrec = NC_DOUBLE ;
888
889	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
890
891	try
892	{
893	switch (SuperClass::type)
894	{
895	case (MULTI_FILE) :
896	{
897	dim0.push_back(dimXid);
898	SuperClassWriter::addDimension(dimXid, domain->ni);
899
900	lonid = lonName+appendDomid;
901	latid = latName+appendDomid;
902	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
903	else bounds_lonid = "bounds_"+lonName+appendDomid;
904	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
905	else bounds_latid = "bounds_"+latName+appendDomid;
906
907	if (domain->hasLonLat)
908	{
909	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
910	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
911	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
912	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
913	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
914	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
915	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
916	}
917	dim0.clear();
918	if (domain->hasBounds)
919	{
920	dim0.push_back(dimXid);
921	dim0.push_back(dimVertId);
922	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
923	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
924	}
925
926	dim0.clear();
927	dim0.push_back(dimXid);
928	if (domain->hasArea)
929	{
930	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
931	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
932	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
933	}
934
935	SuperClassWriter::definition_end();
936
937	if (domain->hasLonLat)
938	{
939	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
940	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
941	if (domain->hasBounds)
942	{
943	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
944	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
945	}
946	}
947
948	if (domain->hasArea)
949	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
950
951	SuperClassWriter::definition_start();
952	break ;
953	}
954
955	case (ONE_FILE) :
956	{
957	lonid = lonName+appendDomid;
958	latid = latName+appendDomid;
959	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
960	else bounds_lonid = "bounds_"+lonName+appendDomid;
961	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
962	else bounds_latid = "bounds_"+latName+appendDomid;
963
964	dim0.push_back(dimXid);
965	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
966	if (domain->hasLonLat)
967	{
968	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
969	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
970
971	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
972	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
973	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
974	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
975	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
976	}
977	dim0.clear();
978
979	if (domain->hasBounds)
980	{
981	dim0.push_back(dimXid);
982	dim0.push_back(dimVertId);
983	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
984	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
985	}
986
987	if (domain->hasArea)
988	{
989	dim0.clear();
990	dim0.push_back(dimXid);
991	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
992	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
993	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
994	}
995
996	SuperClassWriter::definition_end();
997
998	std::vector<StdSize> start(1), startBounds(2) ;
999	std::vector<StdSize> count(1), countBounds(2) ;
1000	if (domain->isEmpty())
1001	{
1002	start[0]=0 ;
1003	count[0]=0 ;
1004	startBounds[1]=0 ;
1005	countBounds[1]=nvertex ;
1006	startBounds[0]=0 ;
1007	countBounds[0]=0 ;
1008	}
1009	else
1010	{
1011	start[0]=domain->ibeginValue_;
1012	count[0]=domain->niValue_;
1013	startBounds[0]=domain->ibeginValue_;
1014	startBounds[1]=0 ;
1015	countBounds[0]=domain->niValue_;
1016	countBounds[1]=nvertex ;
1017	}
1018
1019	if (domain->hasLonLat)
1020	{
1021	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
1022	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
1023	if (domain->hasBounds)
1024	{
1025	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1026	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1027	}
1028	}
1029
1030	if (domain->hasArea)
1031	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
1032
1033	SuperClassWriter::definition_start();
1034
1035	break;
1036	}
1037	default :
1038	ERROR("CNc4DataOutput::writeDomain(domain)",
1039	<< "[ type = " << SuperClass::type << "]"
1040	<< " not implemented yet !");
1041	}
1042	}
1043	catch (CNetCdfException& e)
1044	{
1045	StdString msg("On writing the domain : ");
1046	msg.append(domid); msg.append("\n");
1047	msg.append("In the context : ");
1048	msg.append(context->getId()); msg.append("\n");
1049	msg.append(e.what());
1050	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1051	}
1052	domain->addRelFile(this->filename);
1053	}
1054	//--------------------------------------------------------------
1055
1056	void CNc4DataOutput::writeAxis_(CAxis* axis)
1057	{
1058	if (axis->IsWritten(this->filename)) return;
1059
1060	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
1061	if (!axis->value.isEmpty() )
1062	{
1063	// The hash of the element will be associated to the default element name (= map key), and to the name really written
1064	int globalHash = axis->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
1065
1066	StdString defaultNameKey = axis->getAxisOutputName();
1067	if ( !relAxis_.count ( defaultNameKey ) )
1068	{
1069	// if defaultNameKey not in the map, write the element such as it is defined
1070	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) );
1071	}
1072	else // look if a hash associated this key is equal
1073	{
1074	bool elementIsInMap(false);
1075	auto defaultNameKeyElements = relAxis_.equal_range( defaultNameKey );
1076	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
1077	{
1078	if ( it->second.first == globalHash )
1079	{
1080	// if yes, associate the same ids to current element
1081	axis->renameAttributesBeforeWriting( it->second.second );
1082	elementIsInMap = true;
1083	}
1084	}
1085	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
1086	if (!elementIsInMap) // ! in MAP
1087	{
1088	axis->renameAttributesBeforeWriting();
1089	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) ) ;// = axis->getId()
1090	}
1091	}
1092	}
1093
1094	axis->checkAttributes();
1095
1096	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
1097	: axis->n_glo.getValue();
1098
1099	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
1100
1101	std::vector<StdString> dims;
1102	StdString axisid = axis->getAxisOutputName();
1103	StdString axisDim, axisBoundsId;
1104	if (isWrittenAxis(axisid)) return ;
1105	else setWrittenAxis(axisid);
1106
1107	nc_type typePrec ;
1108	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1109	else if (axis->prec==4) typePrec = NC_FLOAT ;
1110	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1111
1112	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1113	string strId="str_len" ;
1114	try
1115	{
1116	if (axis->dim_name.isEmpty()) axisDim = axisid;
1117	else axisDim=axis->dim_name.getValue();
1118	SuperClassWriter::addDimension(axisDim, size);
1119	dims.push_back(axisDim);
1120
1121	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1122
1123	if (axis->hasValue() \|\| !axis->label.isEmpty())
1124	{
1125	if (!axis->label.isEmpty()) dims.push_back(strId);
1126
1127	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1128
1129	if (!axis->name.isEmpty())
1130	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1131
1132	if (!axis->standard_name.isEmpty())
1133	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1134
1135	if (!axis->long_name.isEmpty())
1136	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1137
1138	if (!axis->unit.isEmpty())
1139	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1140
1141	if (!axis->axis_type.isEmpty())
1142	{
1143	switch(axis->axis_type)
1144	{
1145	case CAxis::axis_type_attr::X :
1146	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1147	break;
1148	case CAxis::axis_type_attr::Y :
1149	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1150	break;
1151	case CAxis::axis_type_attr::Z :
1152	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1153	break;
1154	case CAxis::axis_type_attr::T :
1155	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1156	break;
1157	}
1158	}
1159
1160	if (!axis->positive.isEmpty())
1161	{
1162	SuperClassWriter::addAttribute("positive",
1163	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1164	&axisid);
1165	}
1166
1167	if (!axis->formula.isEmpty())
1168	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1169
1170	if (!axis->formula_term.isEmpty())
1171	SuperClassWriter::addAttribute("formula_terms", axis->formula_term.getValue(), &axisid);
1172
1173	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1174	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1175	{
1176	dims.push_back("axis_nbounds");
1177	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1178	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1179
1180	if (!axis->standard_name.isEmpty())
1181	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1182
1183	if (!axis->unit.isEmpty())
1184	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1185
1186	if (!axis->formula_bounds.isEmpty())
1187	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1188
1189	if (!axis->formula_term_bounds.isEmpty())
1190	SuperClassWriter::addAttribute("formula_terms", axis->formula_term_bounds.getValue(), &axisBoundsId);
1191	}
1192	}
1193
1194	SuperClassWriter::definition_end();
1195
1196	switch (SuperClass::type)
1197	{
1198	case MULTI_FILE:
1199	{
1200	if (axis->label.isEmpty())
1201	{
1202	if (!axis->value.isEmpty())
1203	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
1204
1205	if (!axis->bounds.isEmpty())
1206	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
1207	}
1208	else
1209	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
1210
1211	SuperClassWriter::definition_start();
1212	break;
1213	}
1214	case ONE_FILE:
1215	{
1216	std::vector<StdSize> start(1), startBounds(2) ;
1217	std::vector<StdSize> count(1), countBounds(2) ;
1218	start[0] = startBounds[0] = axis->begin;
1219	count[0] = countBounds[0] = axis->n;
1220	startBounds[1] = 0;
1221	countBounds[1] = 2;
1222
1223	if (axis->label.isEmpty())
1224	{
1225	if (!axis->value.isEmpty())
1226	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
1227
1228	if (!axis->bounds.isEmpty())
1229	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1230	}
1231	else
1232	{
1233	std::vector<StdSize> startLabel(2), countLabel(2);
1234	startLabel[0] = start[0]; startLabel[1] = 0;
1235	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1236	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
1237	}
1238
1239	SuperClassWriter::definition_start();
1240
1241	break;
1242	}
1243	default :
1244	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1245	<< "[ type = " << SuperClass::type << "]"
1246	<< " not implemented yet !");
1247	}
1248	}
1249	catch (CNetCdfException& e)
1250	{
1251	StdString msg("On writing the axis : ");
1252	msg.append(axisid); msg.append("\n");
1253	msg.append("In the context : ");
1254	CContext* context = CContext::getCurrent() ;
1255	msg.append(context->getId()); msg.append("\n");
1256	msg.append(e.what());
1257	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1258	}
1259	axis->addRelFile(this->filename);
1260	}
1261
1262	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1263	{
1264	if (scalar->IsWritten(this->filename)) return;
1265	scalar->checkAttributes();
1266	int scalarSize = 1;
1267
1268	StdString scalaId = scalar->getScalarOutputName();
1269	StdString boundsId;
1270	if (isWrittenAxis(scalaId)) return ;
1271	else setWrittenAxis(scalaId);
1272
1273	nc_type typePrec ;
1274	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1275	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1276	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1277
1278	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1279	string strId="str_len" ;
1280
1281	try
1282	{
1283	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1284
1285	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1286	{
1287	std::vector<StdString> dims;
1288	StdString scalarDim = scalaId;
1289
1290	if (!scalar->label.isEmpty()) dims.push_back(strId);
1291
1292	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1293
1294	if (!scalar->name.isEmpty())
1295	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1296
1297	if (!scalar->standard_name.isEmpty())
1298	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1299
1300	if (!scalar->long_name.isEmpty())
1301	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1302
1303	if (!scalar->unit.isEmpty())
1304	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1305
1306	if (!scalar->axis_type.isEmpty())
1307	{
1308	switch(scalar->axis_type)
1309	{
1310	case CScalar::axis_type_attr::X :
1311	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1312	break;
1313	case CScalar::axis_type_attr::Y :
1314	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1315	break;
1316	case CScalar::axis_type_attr::Z :
1317	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1318	break;
1319	case CScalar::axis_type_attr::T :
1320	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1321	break;
1322	}
1323	}
1324
1325	if (!scalar->positive.isEmpty())
1326	{
1327	SuperClassWriter::addAttribute("positive",
1328	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1329	&scalaId);
1330	}
1331
1332	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1333	{
1334	dims.clear();
1335	dims.push_back("axis_nbounds");
1336	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1337	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1338	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1339	}
1340
1341	SuperClassWriter::definition_end();
1342
1343	switch (SuperClass::type)
1344	{
1345	case MULTI_FILE:
1346	{
1347	CArray<double,1> scalarValue(scalarSize);
1348	CArray<string,1> scalarLabel(scalarSize);
1349	CArray<double,1> scalarBounds(scalarSize*2);
1350
1351	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1352	{
1353	scalarValue(0) = scalar->value;
1354	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1355	}
1356
1357	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1358	{
1359	scalarBounds(0) = scalar->bounds(0);
1360	scalarBounds(1) = scalar->bounds(1);
1361	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1362	}
1363
1364	if (!scalar->label.isEmpty())
1365	{
1366	scalarLabel(0) = scalar->label;
1367	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1368	}
1369
1370	SuperClassWriter::definition_start();
1371
1372	break;
1373	}
1374	case ONE_FILE:
1375	{
1376	CArray<double,1> scalarValue(scalarSize);
1377	CArray<string,1> scalarLabel(scalarSize);
1378	CArray<double,1> scalarBounds(scalarSize*2);
1379
1380	std::vector<StdSize> start(1);
1381	std::vector<StdSize> count(1);
1382	start[0] = 0;
1383	count[0] = 1;
1384	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1385	{
1386	scalarValue(0) = scalar->value;
1387	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1388	}
1389	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1390	{
1391	scalarBounds(0) = scalar->bounds(0);
1392	scalarBounds(1) = scalar->bounds(1);
1393	count[0] = 2;
1394	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1395	}
1396	if (!scalar->label.isEmpty())
1397	{
1398	scalarLabel(0) = scalar->label;
1399	count[0] = stringArrayLen;
1400	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1401	}
1402
1403	SuperClassWriter::definition_start();
1404
1405	break;
1406	}
1407	default :
1408	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1409	<< "[ type = " << SuperClass::type << "]"
1410	<< " not implemented yet !");
1411	}
1412	}
1413	}
1414	catch (CNetCdfException& e)
1415	{
1416	StdString msg("On writing the scalar : ");
1417	msg.append(scalaId); msg.append("\n");
1418	msg.append("In the context : ");
1419	CContext* context = CContext::getCurrent() ;
1420	msg.append(context->getId()); msg.append("\n");
1421	msg.append(e.what());
1422	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1423	}
1424	scalar->addRelFile(this->filename);
1425	}
1426
1427	//--------------------------------------------------------------
1428
1429	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1430	{
1431	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1432
1433	// NOTA : The cuurent algorithm to write compress elements of the grid
1434	// will work pretting well when on server side you dont't get
1435	// partial overlap on elements between differents participating process
1436	// So the element must be totally distributed or non distributed
1437	// If an element is partially overlaping betwwen process then the
1438	// total compressed part will apear artificially greater than expected
1439	// For the current implementation of writer which is decomposed only on
1440	// one element, it will work as expected, but for future, it must be
1441	// reconsidered again.
1442	try
1443	{
1444	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1445	std::vector<StdString> domainList = grid->getDomainList();
1446	std::vector<StdString> axisList = grid->getAxisList();
1447	std::vector<StdString> scalarList = grid->getScalarList();
1448	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1449	int commRank ;
1450	MPI_Comm_rank(comm_file,&commRank) ;
1451
1452	std::vector<StdString> dims;
1453
1454	for (int i = 0; i < numElement; ++i)
1455	{
1456	StdString varId, compress;
1457	CArray<size_t, 1> indexes;
1458	bool isDistributed;
1459	size_t nbIndexes, totalNbIndexes, offset;
1460	size_t firstGlobalIndex;
1461
1462	if (2 == axisDomainOrder(i))
1463	{
1464	CDomain* domain = CDomain::get(domainList[idxDomain]);
1465	StdString domId = domain->getDomainOutputName();
1466
1467	if (!domain->isCompressible()
1468	\|\| domain->type == CDomain::type_attr::unstructured
1469	\|\| domain->isWrittenCompressed(this->filename)
1470	\|\| isWrittenCompressedDomain(domId))
1471	continue;
1472
1473	// unstructured grid seems not be taken into account why ?
1474
1475	string lonName,latName ;
1476
1477	if (domain->lon_name.isEmpty())
1478	{
1479	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1480	else lonName = "lon";
1481	}
1482	else lonName = domain->lon_name;
1483
1484	if (domain->lat_name.isEmpty())
1485	{
1486	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1487	else latName = "lat";
1488	}
1489	else latName = domain->lat_name;
1490
1491	StdString appendDomId = singleDomain ? "" : "_" + domId;
1492
1493	varId = domId + "_points";
1494	compress = latName + appendDomId + " " + lonName + appendDomId;
1495
1496	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
1497	workflowView->getGlobalIndexView(indexes) ;
1498	nbIndexes = workflowView->getSize() ;
1499	isDistributed = domain->isDistributed();
1500	if (isDistributed)
1501	{
1502	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1503	if (commRank==0) offset=0 ;
1504	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1505	}
1506	else
1507	{
1508	offset=0 ;
1509	totalNbIndexes = nbIndexes ;
1510	}
1511
1512	firstGlobalIndex = domain->ibeginValue_ + domain->jbeginValue_ * domain->ni_glo;
1513
1514	domain->addRelFileCompressed(this->filename);
1515	setWrittenCompressedDomain(domId);
1516	++idxDomain;
1517	}
1518	else if (1 == axisDomainOrder(i))
1519	{
1520	CAxis* axis = CAxis::get(axisList[idxAxis]);
1521	StdString axisId = axis->getAxisOutputName();
1522
1523	if (!axis->isCompressible()
1524	\|\| axis->isWrittenCompressed(this->filename)
1525	\|\| isWrittenCompressedAxis(axisId))
1526	continue;
1527
1528	varId = axisId + "_points";
1529	compress = axisId;
1530
1531	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
1532	workflowView->getGlobalIndexView(indexes) ;
1533	nbIndexes = workflowView->getSize() ;
1534	isDistributed = axis->isDistributed();
1535	if (isDistributed)
1536	{
1537	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1538	if (commRank==0) offset=0 ;
1539	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1540	}
1541	else
1542	{
1543	offset=0 ;
1544	totalNbIndexes = nbIndexes ;
1545	}
1546	firstGlobalIndex = axis->begin;
1547
1548	axis->addRelFileCompressed(this->filename);
1549	setWrittenCompressedAxis(axisId);
1550	++idxAxis;
1551	}
1552	else
1553	{
1554	//for scalar
1555	}
1556
1557	if (!varId.empty())
1558	{
1559	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1560
1561	dims.clear();
1562	dims.push_back(varId);
1563	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
1564
1565	SuperClassWriter::addAttribute("compress", compress, &varId);
1566
1567	switch (SuperClass::type)
1568	{
1569	case (MULTI_FILE):
1570	{
1571	indexes -= firstGlobalIndex;
1572	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1573	break;
1574	}
1575	case (ONE_FILE):
1576	{
1577	std::vector<StdSize> start, count;
1578	start.push_back(offset);
1579	count.push_back(nbIndexes);
1580
1581	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1582	break;
1583	}
1584	}
1585	}
1586	}
1587
1588	grid->addRelFileCompressed(this->filename);
1589	}
1590	catch (CNetCdfException& e)
1591	{
1592	StdString msg("On writing compressed grid : ");
1593	msg.append(grid->getId()); msg.append("\n");
1594	msg.append("In the context : ");
1595	CContext* context = CContext::getCurrent();
1596	msg.append(context->getId()); msg.append("\n");
1597	msg.append(e.what());
1598	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1599	}
1600	}
1601
1602	//--------------------------------------------------------------
1603
1604	void CNc4DataOutput::writeTimeDimension_(void)
1605	{
1606	try
1607	{
1608	SuperClassWriter::addDimension(getTimeCounterName());
1609	}
1610	catch (CNetCdfException& e)
1611	{
1612	StdString msg("On writing time dimension : time_couter\n");
1613	msg.append("In the context : ");
1614	CContext* context = CContext::getCurrent() ;
1615	msg.append(context->getId()); msg.append("\n");
1616	msg.append(e.what());
1617	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1618	}
1619	}
1620
1621	//--------------------------------------------------------------
1622
1623	void CNc4DataOutput::writeField_(CField* field)
1624	{
1625	CContext* context = CContext::getCurrent() ;
1626
1627	std::vector<StdString> dims, coodinates;
1628	CGrid* grid = field->getGrid();
1629	if (!grid->doGridHaveDataToWrite())
1630	if (SuperClass::type==MULTI_FILE) return ;
1631
1632	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1633	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1634	std::vector<StdString> domainList = grid->getDomainList();
1635	std::vector<StdString> axisList = grid->getAxisList();
1636	std::vector<StdString> scalarList = grid->getScalarList();
1637
1638	StdString timeid = getTimeCounterName();
1639	StdString dimXid,dimYid;
1640	std::deque<StdString> dimIdList, dimCoordList;
1641	bool hasArea = false;
1642	StdString cellMeasures = "area:";
1643	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1644
1645	for (int i = 0; i < numElement; ++i)
1646	{
1647	if (2 == axisDomainOrder(i))
1648	{
1649	CDomain* domain = CDomain::get(domainList[idxDomain]);
1650	StdString domId = domain->getDomainOutputName();
1651	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1652	StdString lonName,latName ;
1653	StdString dimIname,dimJname ;
1654
1655	if (domain->lon_name.isEmpty())
1656	{
1657	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1658	else lonName = "lon";
1659	}
1660	else lonName = domain->lon_name;
1661
1662	if (domain->lat_name.isEmpty())
1663	{
1664	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1665	else latName = "lat";
1666	}
1667	else latName = domain->lat_name;
1668
1669	if (domain->dim_i_name.isEmpty())
1670	{
1671	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1672	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1673	else dimIname = lonName;
1674	}
1675	else dimIname = domain->dim_i_name;
1676
1677	if (domain->dim_j_name.isEmpty())
1678	{
1679	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1680	else dimJname = latName;
1681	}
1682	else dimJname = domain->dim_j_name;
1683
1684	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1685	{
1686	dimIdList.push_back(domId + "_points");
1687	field->setUseCompressedOutput();
1688	}
1689
1690	switch (domain->type)
1691	{
1692	case CDomain::type_attr::curvilinear:
1693	if (!compressedOutput \|\| !domain->isCompressible())
1694	{
1695	dimXid=dimIname+appendDomId;
1696	dimYid=dimJname+appendDomId;
1697	dimIdList.push_back(dimXid);
1698	dimIdList.push_back(dimYid);
1699	}
1700	dimCoordList.push_back(lonName+appendDomId);
1701	dimCoordList.push_back(latName+appendDomId);
1702	break ;
1703	case CDomain::type_attr::rectilinear:
1704	if (!compressedOutput \|\| !domain->isCompressible())
1705	{
1706	dimXid = dimIname+appendDomId;
1707	dimYid = dimJname+appendDomId;
1708	dimIdList.push_back(dimXid);
1709	dimIdList.push_back(dimYid);
1710	}
1711	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1712	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1713
1714	break ;
1715	case CDomain::type_attr::unstructured:
1716	{
1717	if (SuperClassWriter::useCFConvention)
1718	{
1719	dimXid = dimIname + appendDomId;
1720	dimIdList.push_back(dimXid);
1721	dimCoordList.push_back(lonName+appendDomId);
1722	dimCoordList.push_back(latName+appendDomId);
1723	}
1724	else
1725	{
1726	StdString domainName = domain->name;
1727	if (domain->nvertex == 1)
1728	{
1729	dimXid = "n" + domainName + "_node";
1730	dimIdList.push_back(dimXid);
1731	dimCoordList.push_back(StdString(domainName + "_node_x"));
1732	dimCoordList.push_back(StdString(domainName + "_node_y"));
1733	}
1734	else if (domain->nvertex == 2)
1735	{
1736	dimXid = "n" + domainName + "_edge";
1737	dimIdList.push_back(dimXid);
1738	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1739	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1740	}
1741	else
1742	{
1743	dimXid = "n" + domainName + "_face";
1744	dimIdList.push_back(dimXid);
1745	dimCoordList.push_back(StdString(domainName + "_face_x"));
1746	dimCoordList.push_back(StdString(domainName + "_face_y"));
1747	}
1748	} // ugrid convention
1749	} // case unstructured domain
1750	}
1751
1752	if (domain->hasArea)
1753	{
1754	hasArea = true;
1755	cellMeasures += " area" + appendDomId;
1756	}
1757	++idxDomain;
1758	}
1759	else if (1 == axisDomainOrder(i))
1760	{
1761	CAxis* axis = CAxis::get(axisList[idxAxis]);
1762	StdString axisId = axis->getAxisOutputName();
1763	StdString axisDim;
1764
1765	if (axis->dim_name.isEmpty()) axisDim = axisId;
1766	else axisDim=axis->dim_name.getValue();
1767
1768	if (compressedOutput && axis->isCompressible())
1769	{
1770	dimIdList.push_back(axisDim + "_points");
1771	field->setUseCompressedOutput();
1772	}
1773	else
1774	dimIdList.push_back(axisDim);
1775
1776	if (axisDim != axisId) dimCoordList.push_back(axisId);
1777	++idxAxis;
1778	}
1779	else
1780	{
1781	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1782	StdString scalarId = scalar->getScalarOutputName();
1783	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1784	dimCoordList.push_back(scalarId);
1785	++idxScalar;
1786	}
1787	}
1788
1789	StdString fieldid = field->getFieldOutputName();
1790
1791	nc_type type ;
1792	if (field->prec.isEmpty()) type = NC_FLOAT ;
1793	else
1794	{
1795	if (field->prec==2) type = NC_SHORT ;
1796	else if (field->prec==4) type = NC_FLOAT ;
1797	else if (field->prec==8) type = NC_DOUBLE ;
1798	}
1799
1800	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1801
1802	if (wtime)
1803	{
1804	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1805	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
1806	dims.push_back(timeid);
1807	}
1808
1809	while (!dimIdList.empty())
1810	{
1811	dims.push_back(dimIdList.back());
1812	dimIdList.pop_back();
1813	}
1814
1815	while (!dimCoordList.empty())
1816	{
1817	coodinates.push_back(dimCoordList.back());
1818	dimCoordList.pop_back();
1819	}
1820
1821	try
1822	{
1823	SuperClassWriter::addVariable(fieldid, type, dims, false);
1824	SuperClassWriter::addChunk(field, type, dims);
1825
1826	if (!field->standard_name.isEmpty())
1827	SuperClassWriter::addAttribute
1828	("standard_name", field->standard_name.getValue(), &fieldid);
1829
1830	if (!field->long_name.isEmpty())
1831	SuperClassWriter::addAttribute
1832	("long_name", field->long_name.getValue(), &fieldid);
1833
1834	if (!field->unit.isEmpty())
1835	SuperClassWriter::addAttribute
1836	("units", field->unit.getValue(), &fieldid);
1837
1838	// Ugrid field attributes "mesh" and "location"
1839	if (!SuperClassWriter::useCFConvention)
1840	{
1841	if (!domainList.empty())
1842	{
1843	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
1844	StdString mesh = domain->name;
1845	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
1846	StdString location;
1847	if (domain->nvertex == 1)
1848	location = "node";
1849	else if (domain->nvertex == 2)
1850	location = "edge";
1851	else if (domain->nvertex > 2)
1852	location = "face";
1853	SuperClassWriter::addAttribute("location", location, &fieldid);
1854	}
1855
1856	}
1857
1858	if (!field->valid_min.isEmpty())
1859	SuperClassWriter::addAttribute
1860	("valid_min", field->valid_min.getValue(), &fieldid);
1861
1862	if (!field->valid_max.isEmpty())
1863	SuperClassWriter::addAttribute
1864	("valid_max", field->valid_max.getValue(), &fieldid);
1865
1866	if (!field->scale_factor.isEmpty())
1867	SuperClassWriter::addAttribute
1868	("scale_factor", field->scale_factor.getValue(), &fieldid);
1869
1870	if (!field->add_offset.isEmpty())
1871	SuperClassWriter::addAttribute
1872	("add_offset", field->add_offset.getValue(), &fieldid);
1873
1874	SuperClassWriter::addAttribute
1875	("online_operation", field->operation.getValue(), &fieldid);
1876
1877	// write child variables as attributes
1878
1879
1880	bool alreadyAddCellMethod = false;
1881	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1882	if (!field->cell_methods.isEmpty())
1883	{
1884	StdString cellMethodString = field->cell_methods;
1885	if (field->cell_methods_mode.isEmpty() \|\|
1886	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1887	{
1888	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1889	alreadyAddCellMethod = true;
1890	}
1891	else
1892	{
1893	switch (field->cell_methods_mode)
1894	{
1895	case (CField::cell_methods_mode_attr::prefix):
1896	cellMethodsPrefix = cellMethodString;
1897	cellMethodsPrefix += " ";
1898	break;
1899	case (CField::cell_methods_mode_attr::suffix):
1900	cellMethodsSuffix = " ";
1901	cellMethodsSuffix += cellMethodString;
1902	break;
1903	case (CField::cell_methods_mode_attr::none):
1904	break;
1905	default:
1906	break;
1907	}
1908	}
1909	}
1910
1911
1912	if (wtime)
1913	{
1914	CDuration freqOp = field->freq_op.getValue();
1915	freqOp.solveTimeStep(*context->calendar);
1916	StdString freqOpStr = freqOp.toStringUDUnits();
1917	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1918
1919	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1920	freqOut.solveTimeStep(*context->calendar);
1921	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1922
1923	StdString cellMethods(cellMethodsPrefix + "time: ");
1924	if (field->operation.getValue() == "instant") cellMethods += "point";
1925	else if (field->operation.getValue() == "average") cellMethods += "mean";
1926	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1927	else cellMethods += field->operation;
1928	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1929	cellMethods += " (interval: " + freqOpStr + ")";
1930	cellMethods += cellMethodsSuffix;
1931	if (!alreadyAddCellMethod)
1932	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1933	}
1934
1935	if (hasArea)
1936	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1937
1938	if (!field->default_value.isEmpty())
1939	{
1940	double default_value = field->default_value.getValue();
1941	if (type == NC_DOUBLE)
1942	{
1943	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1944	}
1945	else if (type == NC_SHORT)
1946	{
1947	short sdefault_value = (short)default_value;
1948	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
1949	}
1950	else
1951	{
1952	float fdefault_value = (float)default_value;
1953	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1954	}
1955	}
1956	else
1957	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1958
1959	if (field->compression_level.isEmpty())
1960	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
1961	if ( (field->compression_level.getValue()>0)&&(field->compression_type.isEmpty()) )
1962	field->compression_type.setValue( "gzip" );
1963	if (field->compression_type.isEmpty())
1964	field->compression_type = "None";
1965	if (field->compression_params.isEmpty())
1966	field->compression_params.resize( 0 );
1967	SuperClassWriter::setCompressionLevel(fieldid, field->compression_type, field->compression_level, field->compression_params);
1968
1969	{ // Ecriture des coordonnes
1970
1971	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1972	std::vector<StdString>::iterator
1973	itc = coodinates.begin(), endc = coodinates.end();
1974
1975	for (; itc!= endc; itc++)
1976	{
1977	StdString & coord = *itc;
1978	if (itc+1 != endc)
1979	coordstr.append(coord).append(" ");
1980	else coordstr.append(coord);
1981	}
1982
1983	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1984
1985	}
1986
1987	vector<CVariable*> listVars = field->getAllVariables() ;
1988	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1989
1990	}
1991	catch (CNetCdfException& e)
1992	{
1993	StdString msg("On writing field : ");
1994	msg.append(fieldid); msg.append("\n");
1995	msg.append("In the context : ");
1996	msg.append(context->getId()); msg.append("\n");
1997	msg.append(e.what());
1998	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1999	}
2000	} // writeField_()
2001
2002	//--------------------------------------------------------------
2003
2004	void CNc4DataOutput::writeFile_ (CFile* file)
2005	{
2006	StdString filename = file->getFileOutputName();
2007	StdString description = (!file->description.isEmpty())
2008	? file->description.getValue()
2009	: StdString("Created by xios");
2010
2011	singleDomain = (file->nbDomains == 1);
2012
2013	StdString conv_str ;
2014	if (file->convention_str.isEmpty())
2015	{
2016	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2017	else conv_str="UGRID" ;
2018	}
2019	else conv_str=file->convention_str ;
2020
2021	try
2022	{
2023	if (!appendMode) this->writeFileAttributes(filename, description,
2024	conv_str,
2025	StdString("An IPSL model"),
2026	this->getTimeStamp());
2027
2028	if (!appendMode)
2029	SuperClassWriter::addDimension("axis_nbounds", 2);
2030	}
2031	catch (CNetCdfException& e)
2032	{
2033	StdString msg("On writing file : ");
2034	msg.append(filename); msg.append("\n");
2035	msg.append("In the context : ");
2036	CContext* context = CContext::getCurrent() ;
2037	msg.append(context->getId()); msg.append("\n");
2038	msg.append(e.what());
2039	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2040	}
2041	}
2042
2043	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2044	{
2045	StdString name = var->getVariableOutputName();
2046
2047	try
2048	{
2049	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2050	addAttribute(name, var->getData<int>(), &fieldId);
2051	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2052	addAttribute(name, var->getData<short int>(), &fieldId);
2053	else if (var->type.getValue() == CVariable::type_attr::t_float)
2054	addAttribute(name, var->getData<float>(), &fieldId);
2055	else if (var->type.getValue() == CVariable::type_attr::t_double)
2056	addAttribute(name, var->getData<double>(), &fieldId);
2057	else if (var->type.getValue() == CVariable::type_attr::t_string)
2058	addAttribute(name, var->getData<string>(), &fieldId);
2059	else
2060	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2061	<< "Unsupported variable of type " << var->type.getStringValue());
2062	}
2063	catch (CNetCdfException& e)
2064	{
2065	StdString msg("On writing attributes of variable with name : ");
2066	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2067	msg.append("In the context : ");
2068	CContext* context = CContext::getCurrent() ;
2069	msg.append(context->getId()); msg.append("\n");
2070	msg.append(e.what());
2071	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2072	}
2073	}
2074
2075	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2076	{
2077	StdString name = var->getVariableOutputName();
2078
2079	try
2080	{
2081	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2082	addAttribute(name, var->getData<int>());
2083	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2084	addAttribute(name, var->getData<short int>());
2085	else if (var->type.getValue() == CVariable::type_attr::t_float)
2086	addAttribute(name, var->getData<float>());
2087	else if (var->type.getValue() == CVariable::type_attr::t_double)
2088	addAttribute(name, var->getData<double>());
2089	else if (var->type.getValue() == CVariable::type_attr::t_string)
2090	addAttribute(name, var->getData<string>());
2091	else
2092	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2093	<< "Unsupported variable of type " << var->type.getStringValue());
2094	}
2095	catch (CNetCdfException& e)
2096	{
2097	StdString msg("On writing attributes of variable with name : ");
2098	msg.append(name); msg.append("\n");
2099	msg.append("In the context : ");
2100	CContext* context = CContext::getCurrent() ;
2101	msg.append(context->getId()); msg.append("\n");
2102	msg.append(e.what());
2103	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2104	}
2105	}
2106
2107	void CNc4DataOutput::syncFile_ (void)
2108	{
2109	try
2110	{
2111	SuperClassWriter::sync() ;
2112	}
2113	catch (CNetCdfException& e)
2114	{
2115	StdString msg("On synchronizing the write among processes");
2116	msg.append("In the context : ");
2117	CContext* context = CContext::getCurrent() ;
2118	msg.append(context->getId()); msg.append("\n");
2119	msg.append(e.what());
2120	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2121	}
2122	}
2123
2124	void CNc4DataOutput::closeFile_ (void)
2125	{
2126	try
2127	{
2128	SuperClassWriter::close() ;
2129	}
2130	catch (CNetCdfException& e)
2131	{
2132	StdString msg("On closing file");
2133	msg.append("In the context : ");
2134	CContext* context = CContext::getCurrent() ;
2135	msg.append(context->getId()); msg.append("\n");
2136	msg.append(e.what());
2137	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2138	}
2139
2140	}
2141
2142	//---------------------------------------------------------------
2143
2144	StdString CNc4DataOutput::getTimeStamp(void) const
2145	{
2146	const int buffer_size = 100;
2147	time_t rawtime;
2148	struct tm * timeinfo = NULL;
2149	char buffer [buffer_size];
2150	StdString formatStr;
2151	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2152	else formatStr=file->time_stamp_format;
2153
2154	// time ( &rawtime );
2155	// timeinfo = localtime ( &rawtime );
2156	time ( &rawtime );
2157	timeinfo = gmtime ( &rawtime );
2158	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2159
2160	return (StdString(buffer));
2161	}
2162
2163	//---------------------------------------------------------------
2164
2165	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
2166	const CDate& currentWrite, int nstep)
2167	{
2168	CContext* context = CContext::getCurrent();
2169	CGrid* grid = field->getGrid();
2170
2171	if (nstep<1)
2172	{
2173	return nstep;
2174	}
2175
2176	if (!grid->doGridHaveDataToWrite())
2177	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2178	{
2179	return nstep;
2180	}
2181
2182	StdString fieldid = field->getFieldOutputName();
2183
2184	StdOStringStream oss;
2185	string timeAxisId;
2186	if (field->hasTimeInstant) timeAxisId = "time_instant";
2187	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2188
2189	StdString timeBoundId = getTimeCounterName() + "_bounds";
2190
2191	StdString timeAxisBoundId;
2192	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2193	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2194
2195	if (!field->wasWritten())
2196	{
2197	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
2198	field->getOperationTimeType() != func::CFunctor::once)
2199	{
2200	double factorUnit;
2201	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2202	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2203	else factorUnit=1 ;
2204	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
2205	}
2206
2207	field->setWritten();
2208	}
2209
2210
2211	CArray<double,1> time_data(1);
2212	CArray<double,1> time_data_bound(2);
2213	CArray<double,1> time_counter(1);
2214	CArray<double,1> time_counter_bound(2);
2215
2216	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2217	bool wtimeCounter =false ;
2218	bool wtimeData =false ;
2219
2220
2221	if (wtime)
2222	{
2223
2224	if (field->hasTimeInstant)
2225	{
2226	time_data(0) = time_data_bound(1) = (Time) currentWrite;
2227	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
2228	if (timeCounterType==instant)
2229	{
2230	time_counter(0) = time_data(0);
2231	time_counter_bound(0) = time_data_bound(0);
2232	time_counter_bound(1) = time_data_bound(1);
2233	wtimeCounter=true ;
2234	}
2235	if (hasTimeInstant) wtimeData=true ;
2236	}
2237	else if (field->hasTimeCentered)
2238	{
2239	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
2240	time_data_bound(0) = (Time)lastWrite;
2241	time_data_bound(1) = (Time)currentWrite;
2242	if (timeCounterType==centered)
2243	{
2244	time_counter(0) = time_data(0) ;
2245	time_counter_bound(0) = time_data_bound(0) ;
2246	time_counter_bound(1) = time_data_bound(1) ;
2247	wtimeCounter=true ;
2248	}
2249	if (hasTimeCentered) wtimeData=true ;
2250	}
2251
2252	if (timeCounterType==record)
2253	{
2254	time_counter(0) = nstep - 1;
2255	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
2256	wtimeCounter=true ;
2257	}
2258
2259	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2260	{
2261	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2262	time_data/=secByDay;
2263	time_data_bound/=secByDay;
2264	time_counter/=secByDay;
2265	time_counter_bound/=secByDay;
2266	}
2267	}
2268
2269	bool isRoot = (context->intraCommRank_ == 0);
2270
2271	try
2272	{
2273	switch (SuperClass::type)
2274	{
2275	case (MULTI_FILE) :
2276	{
2277	CTimer::get("Files : writing data").resume();
2278	writeAndConvertData(field, data, nstep - 1);
2279	CTimer::get("Files : writing data").suspend();
2280	if (wtime)
2281	{
2282	CTimer::get("Files : writing time axis").resume();
2283	if ( wtimeData)
2284	{
2285	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2286	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2287	}
2288	if (wtimeCounter)
2289	{
2290	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2291	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2292	}
2293	CTimer::get("Files : writing time axis").suspend();
2294	}
2295	break;
2296	}
2297	case (ONE_FILE) :
2298	{
2299
2300	std::vector<StdSize> start, count;
2301
2302	if (field->getUseCompressedOutput())
2303	{
2304	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2305	std::vector<StdString> domainList = grid->getDomainList();
2306	std::vector<StdString> axisList = grid->getAxisList();
2307	int numElement = axisDomainOrder.numElements();
2308	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2309	int idx = domainList.size() * 2 + axisList.size() - 1;
2310	int commRank ;
2311
2312	MPI_Comm_rank(comm_file,&commRank) ;
2313
2314	start.reserve(idx+1);
2315	count.reserve(idx+1);
2316
2317	for (int i = numElement - 1; i >= 0; --i)
2318	{
2319	if (2 == axisDomainOrder(i))
2320	{
2321	CDomain* domain = CDomain::get(domainList[idxDomain]);
2322
2323	if (domain->isCompressible())
2324	{
2325	size_t offset ;
2326	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
2327	if (domain->isDistributed())
2328	{
2329	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2330	if (commRank==0) offset=0 ;
2331	}
2332	else offset=0 ;
2333
2334	start.push_back(offset);
2335	count.push_back(nbIndexes);
2336	idx -= 2;
2337	}
2338	else
2339	{
2340	if ((domain->type) != CDomain::type_attr::unstructured)
2341	{
2342	start.push_back(domain->jbeginValue_);
2343	count.push_back(domain->njValue_);
2344	}
2345	--idx;
2346	start.push_back(domain->ibeginValue_);
2347	count.push_back(domain->niValue_);
2348	--idx;
2349	}
2350	--idxDomain;
2351	}
2352	else if (1 == axisDomainOrder(i))
2353	{
2354	CAxis* axis = CAxis::get(axisList[idxAxis]);
2355
2356	if (axis->isCompressible())
2357	{
2358	size_t offset ;
2359	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
2360	if (axis->isDistributed())
2361	{
2362	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2363	if (commRank==0) offset=0 ;
2364	}
2365	else offset=0 ;
2366
2367	start.push_back(offset);
2368	count.push_back(nbIndexes);
2369	}
2370	else
2371	{
2372	start.push_back(axis->begin);
2373	count.push_back(axis->n);
2374	}
2375	--idxAxis;
2376	--idx;
2377	}
2378	}
2379	}
2380	else
2381	{
2382	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2383	std::vector<StdString> domainList = grid->getDomainList();
2384	std::vector<StdString> axisList = grid->getAxisList();
2385	std::vector<StdString> scalarList = grid->getScalarList() ;
2386	int numElement = axisDomainOrder.numElements();
2387	int idxDomain = domainList.size() - 1 ;
2388	int idxAxis = axisList.size() - 1 ;
2389	int idxScalar = scalarList.size() - 1 ;
2390	int idx = domainList.size() * 2 + axisList.size() - 1;
2391
2392	start.reserve(idx+1);
2393	count.reserve(idx+1);
2394
2395	for (int i = numElement - 1; i >= 0; --i)
2396	{
2397	if (2 == axisDomainOrder(i))
2398	{
2399	CDomain* domain = CDomain::get(domainList[idxDomain]);
2400	if ((domain->type) != CDomain::type_attr::unstructured)
2401	{
2402	start.push_back(domain->jbeginValue_);
2403	count.push_back(domain->njValue_);
2404	}
2405	--idx ;
2406
2407	start.push_back(domain->ibeginValue_);
2408	count.push_back(domain->niValue_);
2409	--idx ;
2410	--idxDomain;
2411	}
2412	else if (1 == axisDomainOrder(i))
2413	{
2414	CAxis* axis = CAxis::get(axisList[idxAxis]);
2415	start.push_back(axis->begin);
2416	count.push_back(axis->n);
2417	--idx;
2418	--idxAxis;
2419	}
2420	else
2421	{
2422	if (idx ==-1)
2423	{
2424	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
2425	start.push_back(0);
2426	count.push_back(scalar->n);
2427	idx-- ;
2428	}
2429	else if (idx<-1)
2430	{
2431	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
2432	count.back()*=scalar->n;
2433	idx-- ;
2434	}
2435	--idxScalar;
2436	}
2437	}
2438	}
2439
2440
2441	CTimer::get("Files : writing data").resume();
2442	writeAndConvertData(field, data, nstep - 1, &start, &count);
2443	CTimer::get("Files : writing data").suspend();
2444
2445	if (wtime)
2446	{
2447	CTimer::get("Files : writing time axis").resume();
2448	if ( wtimeData)
2449	{
2450	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2451	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2452	}
2453	if (wtimeCounter)
2454	{
2455	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2456	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2457
2458	}
2459	CTimer::get("Files : writing time axis").suspend();
2460	}
2461
2462	break;
2463	}
2464	}
2465	return nstep ;
2466	}
2467	catch (CNetCdfException& e)
2468	{
2469	StdString msg("On writing field data: ");
2470	msg.append(fieldid); msg.append("\n");
2471	msg.append("In the context : ");
2472	msg.append(context->getId()); msg.append("\n");
2473	msg.append(e.what());
2474	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2475	}
2476	}
2477
2478	void CNc4DataOutput::writeAndConvertData(CField* field, const CArray<double,1>& data, StdSize record, const std::vector<StdSize> start, const std::vector<StdSize> count)
2479	{
2480	StdString fieldid = field->getFieldOutputName();
2481	nc_type type ;
2482	if (field->prec.isEmpty()) type = NC_FLOAT ;
2483	else
2484	{
2485	if (field->prec==2) type = NC_SHORT ;
2486	else if (field->prec==4) type = NC_FLOAT ;
2487	else if (field->prec==8) type = NC_DOUBLE ;
2488	}
2489
2490	bool conversionByNetCDF = true; // default : conversion operated by NetCDF for now (legacy behaviour)
2491	if (!field->conversion_by_NetCDF.isEmpty())
2492	{
2493	// use conversion_by_NetCDF = ".false." to bypass NetCDF conversion
2494	// poor performances from NC_DOUBLE to NC_FLOAT with isgreater/isless in recent NetCDF available at TGCC
2495	conversionByNetCDF = field->conversion_by_NetCDF;
2496	}
2497	if ( ( type == NC_DOUBLE ) \|\| ( conversionByNetCDF ) )
2498	{
2499	SuperClassWriter::writeData(data, fieldid, isCollective, record, start, count);
2500	}
2501	else if ( type == NC_FLOAT )
2502	{
2503	CArray<float,1> f_data;
2504	f_data.resize( data.numElements() );
2505	for (int i = 0; i < data.numElements(); i++)
2506	{
2507	if (data(i) <= X_FLOAT_MAX \|\| data(i) >= X_FLOAT_MIN)
2508	f_data(i) = data(i);
2509	else if (data(i) > X_FLOAT_MAX)
2510	f_data(i) = X_FLOAT_MAX;
2511	else if (data(i) < X_FLOAT_MIN)
2512	f_data(i) = X_FLOAT_MIN;
2513	}
2514	SuperClassWriter::writeData(f_data, fieldid, isCollective, record, start, count);
2515	}
2516	else if ( type == NC_SHORT )
2517	{
2518	CArray<short,1> s_data;
2519	s_data.resize( data.numElements() );
2520	for (int i = 0; i < data.numElements(); i++)
2521	{
2522	if (data(i) <= X_SHORT_MAX \|\| data(i) >= X_SHORT_MIN)
2523	s_data(i) = data(i);
2524	else if (data(i) > X_SHORT_MAX)
2525	s_data(i) = X_SHORT_MAX;
2526	else if (data(i) < X_SHORT_MIN)
2527	s_data(i) = X_SHORT_MIN;
2528	}
2529	SuperClassWriter::writeData(s_data, fieldid, isCollective, record, start, count);
2530	}
2531	else
2532	{
2533	ERROR("CNc4DataOutput::writeAndConvertData(...)", << "Type conversion not managed for " << fieldid );
2534	}
2535
2536	}
2537
2538	//---------------------------------------------------------------
2539
2540	void CNc4DataOutput::writeTimeAxis_
2541	(CField* field,
2542	const std::shared_ptr<CCalendar> cal)
2543	{
2544	StdOStringStream oss;
2545	bool createInstantAxis=false ;
2546	bool createCenteredAxis=false ;
2547	bool createTimeCounterAxis=false ;
2548
2549	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2550
2551
2552	StdString axisId ;
2553	StdString axisBoundId;
2554	StdString timeid(getTimeCounterName());
2555	StdString timeBoundId("axis_nbounds");
2556
2557	StdString strTimeUnits ;
2558	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2559	else strTimeUnits="seconds since " ;
2560
2561	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2562	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2563
2564
2565	if (field->getRelFile()->time_counter.isEmpty())
2566	{
2567	if (timeCounterType==none) createTimeCounterAxis=true ;
2568	if (field->hasTimeCentered)
2569	{
2570	timeCounterType=centered ;
2571	if (!hasTimeCentered) createCenteredAxis=true ;
2572	}
2573	if (field->hasTimeInstant)
2574	{
2575	if (timeCounterType==none) timeCounterType=instant ;
2576	if (!hasTimeInstant) createInstantAxis=true ;
2577	}
2578	}
2579	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
2580	{
2581	if (field->hasTimeCentered)
2582	{
2583	if (!hasTimeCentered) createCenteredAxis=true ;
2584	}
2585	if (field->hasTimeInstant)
2586	{
2587	if (timeCounterType==none) createTimeCounterAxis=true ;
2588	timeCounterType=instant ;
2589	if (!hasTimeInstant) createInstantAxis=true ;
2590	}
2591	}
2592	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
2593	{
2594	if (field->hasTimeCentered)
2595	{
2596	if (timeCounterType==none) createTimeCounterAxis=true ;
2597	timeCounterType=centered ;
2598	if (!hasTimeCentered) createCenteredAxis=true ;
2599	}
2600	if (field->hasTimeInstant)
2601	{
2602	if (!hasTimeInstant) createInstantAxis=true ;
2603	}
2604	}
2605	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
2606	{
2607	if (field->hasTimeCentered)
2608	{
2609	if (!hasTimeCentered) createCenteredAxis=true ;
2610	}
2611	if (field->hasTimeInstant)
2612	{
2613	if (timeCounterType==none) createTimeCounterAxis=true ;
2614	timeCounterType=instant ;
2615	}
2616	}
2617	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
2618	{
2619	if (field->hasTimeCentered)
2620	{
2621	if (timeCounterType==none) createTimeCounterAxis=true ;
2622	timeCounterType=centered ;
2623	}
2624	if (field->hasTimeInstant)
2625	{
2626	if (!hasTimeInstant) createInstantAxis=true ;
2627	}
2628	}
2629	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
2630	{
2631	if (field->hasTimeCentered)
2632	{
2633	if (timeCounterType==none) createTimeCounterAxis=true ;
2634	if (timeCounterType==instant) createInstantAxis=true ;
2635	timeCounterType=centered ;
2636	}
2637	if (field->hasTimeInstant)
2638	{
2639	if (timeCounterType==none)
2640	{
2641	createTimeCounterAxis=true ;
2642	timeCounterType=instant ;
2643	}
2644	if (timeCounterType==centered)
2645	{
2646	if (!hasTimeInstant) createInstantAxis=true ;
2647	}
2648	}
2649	}
2650	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
2651	{
2652	if (field->hasTimeCentered)
2653	{
2654	if (!hasTimeCentered) createCenteredAxis=true ;
2655	}
2656	if (field->hasTimeInstant)
2657	{
2658	if (!hasTimeInstant) createInstantAxis=true ;
2659	}
2660	}
2661	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
2662	{
2663	if (timeCounterType==none) createTimeCounterAxis=true ;
2664	timeCounterType=record ;
2665	if (field->hasTimeCentered)
2666	{
2667	if (!hasTimeCentered) createCenteredAxis=true ;
2668	}
2669	if (field->hasTimeInstant)
2670	{
2671	if (!hasTimeInstant) createInstantAxis=true ;
2672	}
2673	}
2674
2675	if (createInstantAxis)
2676	{
2677	axisId="time_instant" ;
2678	axisBoundId="time_instant_bounds";
2679	hasTimeInstant=true ;
2680	}
2681
2682	if (createCenteredAxis)
2683	{
2684	axisId="time_centered" ;
2685	axisBoundId="time_centered_bounds";
2686	hasTimeCentered=true ;
2687	}
2688
2689
2690	try
2691	{
2692	std::vector<StdString> dims;
2693
2694	if (createInstantAxis \|\| createCenteredAxis)
2695	{
2696	// Adding time_instant or time_centered
2697	dims.push_back(timeid);
2698	if (!SuperClassWriter::varExist(axisId))
2699	{
2700	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2701
2702	CDate timeOrigin=cal->getTimeOrigin() ;
2703	StdOStringStream oss2;
2704	StdString strInitdate=oss2.str() ;
2705	StdString strTimeOrigin=timeOrigin.toString() ;
2706	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2707	strTimeOrigin, axisBoundId);
2708	}
2709
2710	// Adding time_instant_bounds or time_centered_bounds variables
2711	if (!SuperClassWriter::varExist(axisBoundId))
2712	{
2713	dims.clear() ;
2714	dims.push_back(timeid);
2715	dims.push_back(timeBoundId);
2716	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2717	}
2718	}
2719
2720	if (createTimeCounterAxis)
2721	{
2722	// Adding time_counter
2723	axisId = getTimeCounterName();
2724	axisBoundId = getTimeCounterName() + "_bounds";
2725	dims.clear();
2726	dims.push_back(timeid);
2727	if (!SuperClassWriter::varExist(axisId))
2728	{
2729	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2730	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2731
2732	if (field->getRelFile()->time_counter.isEmpty() \|\|
2733	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2734	{
2735	CDate timeOrigin = cal->getTimeOrigin();
2736	StdString strTimeOrigin = timeOrigin.toString();
2737
2738	this->writeTimeAxisAttributes(axisId, cal->getType(),
2739	strTimeUnits+strTimeOrigin,
2740	strTimeOrigin, axisBoundId);
2741	}
2742	}
2743
2744	// Adding time_counter_bound dimension
2745	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2746	{
2747	if (!SuperClassWriter::varExist(axisBoundId))
2748	{
2749	dims.clear();
2750	dims.push_back(timeid);
2751	dims.push_back(timeBoundId);
2752	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2753	}
2754	}
2755	}
2756	}
2757	catch (CNetCdfException& e)
2758	{
2759	StdString msg("On writing time axis data: ");
2760	msg.append("In the context : ");
2761	CContext* context = CContext::getCurrent() ;
2762	msg.append(context->getId()); msg.append("\n");
2763	msg.append(e.what());
2764	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2765	const std::shared_ptr<CCalendar> cal)", << msg);
2766	}
2767	}
2768
2769	//---------------------------------------------------------------
2770
2771	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2772	const StdString & calendar,
2773	const StdString & units,
2774	const StdString & time_origin,
2775	const StdString & time_bounds,
2776	const StdString & standard_name,
2777	const StdString & long_name)
2778	{
2779	try
2780	{
2781	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2782	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2783	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2784	SuperClassWriter::addAttribute("units", units , &axis_name);
2785	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2786	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2787	}
2788	catch (CNetCdfException& e)
2789	{
2790	StdString msg("On writing time axis Attribute: ");
2791	msg.append("In the context : ");
2792	CContext* context = CContext::getCurrent() ;
2793	msg.append(context->getId()); msg.append("\n");
2794	msg.append(e.what());
2795	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2796	const StdString & calendar,\
2797	const StdString & units, \
2798	const StdString & time_origin, \
2799	const StdString & time_bounds, \
2800	const StdString & standard_name, \
2801	const StdString & long_name)", << msg);
2802	}
2803	}
2804
2805	//---------------------------------------------------------------
2806
2807	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2808	const StdString & axis,
2809	const StdString & standard_name,
2810	const StdString & long_name,
2811	const StdString & units,
2812	const StdString & nav_model)
2813	{
2814	try
2815	{
2816	if (!axis.empty())
2817	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2818
2819	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2820	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2821	SuperClassWriter::addAttribute("units" , units , &axis_name);
2822	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2823	}
2824	catch (CNetCdfException& e)
2825	{
2826	StdString msg("On writing Axis Attribute: ");
2827	msg.append("In the context : ");
2828	CContext* context = CContext::getCurrent() ;
2829	msg.append(context->getId()); msg.append("\n");
2830	msg.append(e.what());
2831	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2832	const StdString & axis, \
2833	const StdString & standard_name, \
2834	const StdString & long_name, \
2835	const StdString & units, \
2836	const StdString & nav_model)", << msg);
2837	}
2838	}
2839
2840	//---------------------------------------------------------------
2841
2842	void CNc4DataOutput::writeLocalAttributes
2843	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2844	{
2845	try
2846	{
2847	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2848	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2849	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2850	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2851	}
2852	catch (CNetCdfException& e)
2853	{
2854	StdString msg("On writing Local Attributes: ");
2855	msg.append("In the context : ");
2856	CContext* context = CContext::getCurrent() ;
2857	msg.append(context->getId()); msg.append("\n");
2858	msg.append(e.what());
2859	ERROR("CNc4DataOutput::writeLocalAttributes \
2860	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2861	}
2862
2863	}
2864
2865	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2866	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2867	{
2868	CArray<int,1> array(2) ;
2869
2870	try
2871	{
2872	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2873	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2874	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2875	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2876	array=ni_glo,nj_glo ;
2877	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2878	array=ni,nj ;
2879	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2880	array=ibegin+1,jbegin+1 ;
2881	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2882	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2883	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2884	array=0,0 ;
2885	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2886	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2887	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2888	/*
2889	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2890	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2891	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2892	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2893	*/
2894	}
2895	catch (CNetCdfException& e)
2896	{
2897	StdString msg("On writing Local Attributes IOIPSL \n");
2898	msg.append("In the context : ");
2899	CContext* context = CContext::getCurrent() ;
2900	msg.append(context->getId()); msg.append("\n");
2901	msg.append(e.what());
2902	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2903	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2904	}
2905	}
2906	//---------------------------------------------------------------
2907
2908	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2909	const StdString & description,
2910	const StdString & conventions,
2911	const StdString & production,
2912	const StdString & timeStamp)
2913	{
2914	try
2915	{
2916	SuperClassWriter::addAttribute("name" , name);
2917	SuperClassWriter::addAttribute("description", description);
2918	SuperClassWriter::addAttribute("title" , description);
2919	SuperClassWriter::addAttribute("Conventions", conventions);
2920	// SuperClassWriter::addAttribute("production" , production);
2921
2922	StdString timeStampStr ;
2923	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
2924	else timeStampStr=file->time_stamp_name ;
2925	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
2926
2927	StdString uuidName ;
2928	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
2929	else uuidName=file->uuid_name ;
2930
2931	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
2932	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
2933
2934	}
2935	catch (CNetCdfException& e)
2936	{
2937	StdString msg("On writing File Attributes \n ");
2938	msg.append("In the context : ");
2939	CContext* context = CContext::getCurrent() ;
2940	msg.append(context->getId()); msg.append("\n");
2941	msg.append(e.what());
2942	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2943	const StdString & description, \
2944	const StdString & conventions, \
2945	const StdString & production, \
2946	const StdString & timeStamp)", << msg);
2947	}
2948	}
2949
2950	//---------------------------------------------------------------
2951
2952	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2953	int data_dim,
2954	int data_ni,
2955	int data_nj,
2956	int data_ibegin,
2957	int data_jbegin)
2958	{
2959	try
2960	{
2961	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2962	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2963	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2964	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2965	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2966	}
2967	catch (CNetCdfException& e)
2968	{
2969	StdString msg("On writing Mask Attributes \n ");
2970	msg.append("In the context : ");
2971	CContext* context = CContext::getCurrent() ;
2972	msg.append(context->getId()); msg.append("\n");
2973	msg.append(e.what());
2974	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2975	int data_dim, \
2976	int data_ni, \
2977	int data_nj, \
2978	int data_ibegin, \
2979	int data_jbegin)", << msg);
2980	}
2981	}
2982
2983	///--------------------------------------------------------------
2984
2985	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
2986	{
2987	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2988	if (it == timeToRecordCache.end())
2989	{
2990	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2991	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
2992	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
2993
2994	CArray<double,2> timeAxisBounds;
2995	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
2996
2997	StdSize record = 0;
2998	double dtime(time);
2999	for (int n = dimSize[0] - 1; n >= 0; n--)
3000	{
3001	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3002	timeAxisBounds*=factorUnit ;
3003	if (timeAxisBounds(1, 0) < dtime)
3004	{
3005	record = n + 1;
3006	break;
3007	}
3008	}
3009	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3010	}
3011	return it->second;
3012	}
3013
3014	///--------------------------------------------------------------
3015
3016	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3017	{
3018	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3019	}
3020
3021	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3022	{
3023	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3024	}
3025
3026	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3027	{
3028	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3029	}
3030
3031	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3032	{
3033	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3034	}
3035
3036	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3037	{
3038	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3039	}
3040
3041	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3042	{
3043	this->writtenDomains.insert(domainName);
3044	}
3045
3046	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3047	{
3048	this->writtenCompressedDomains.insert(domainName);
3049	}
3050
3051	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3052	{
3053	this->writtenAxis.insert(axisName);
3054	}
3055
3056	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3057	{
3058	this->writtenCompressedAxis.insert(axisName);
3059	}
3060
3061	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3062	{
3063	this->writtenScalar.insert(scalarName);
3064	}
3065	} // namespace xios

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