Context Navigation

← Previous Revision
Next Revision →
Blame
Revision Log

nc4_data_output.cpp

Last change on this file was 2629, checked in by jderouillat, 2 months ago
Delete boost dependencies, the few features used are replaced by functions stored in extern/boost_extraction
Property copyright set to Software name : XIOS (Xml I/O Server) http://forge.ipsl.jussieu.fr/ioserver Creation date : January 2009 Licence : CeCCIL version2 see license file in root directory : Licence_CeCILL_V2-en.txt or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement) CNRS/IPSL (Institut Pierre Simon Laplace) Project Manager : Yann Meurdesoif yann.meurdesoif@cea.fr Property svn:executable set to ``*
File size: 129.6 KB

Line
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	#include <cfloat>
17	#define X_FLOAT_MAX FLT_MAX
18	#define X_FLOAT_MIN FLT_MIN
19	#define X_SHORT_MAX SHRT_MAX
20	#define X_SHORT_MIN SHRT_MIN
21
22	namespace xios
23	{
24	extern CLogType logProfile ;
25	/// ////////////////////// Dfinitions ////////////////////// ///
26	CNc4DataOutput::CNc4DataOutput
27	(CFile* file, const StdString & filename, bool exist)
28	: SuperClass()
29	, SuperClassWriter(filename, exist)
30	, filename(filename)
31	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
32	{
33	SuperClass::type = MULTI_FILE;
34	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
35	}
36
37	CNc4DataOutput::CNc4DataOutput
38	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
39	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
40	: SuperClass()
41	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
42	, comm_file(comm_file)
43	, filename(filename)
44	, isCollective(isCollective)
45	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
46	{
47	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
48	if (file==NULL) compressionLevel = 0 ;
49	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
50	}
51
52	CNc4DataOutput::~CNc4DataOutput(void)
53	{ /* Ne rien faire de plus */ }
54
55	///--------------------------------------------------------------
56
57	const StdString & CNc4DataOutput::getFileName(void) const
58	{
59	return (this->filename);
60	}
61
62	//---------------------------------------------------------------
63
64	void CNc4DataOutput::writeDomain_(CDomain* domain)
65	TRY
66	{
67	StdString lonName,latName ;
68
69	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
70	if (!domain->lonvalue.isEmpty() )
71	{
72	// The hash of the element will be associated to the default element name (= map key), and to the name really written
73	int globalHash = domain->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
74
75	StdString defaultNameKey = domain->getDomainOutputName();
76	if ( !relDomains_.count ( defaultNameKey ) )
77	{
78	// if defaultNameKey not in the map, write the element such as it is defined
79	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) );
80	}
81	else // look if a hash associated this key is equal
82	{
83	bool elementIsInMap(false);
84	auto defaultNameKeyElements = relDomains_.equal_range( defaultNameKey );
85	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
86	{
87	if ( it->second.first == globalHash )
88	{
89	// if yes, associate the same ids to current element
90	domain->renameAttributesBeforeWriting( it->second.second );
91	elementIsInMap = true;
92	}
93	}
94	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
95	if (!elementIsInMap) // ! in MAP
96	{
97	domain->renameAttributesBeforeWriting();
98	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) ) ;
99	}
100	}
101	}
102
103	if (domain->type == CDomain::type_attr::unstructured)
104	{
105	if (SuperClassWriter::useCFConvention)
106	writeUnstructuredDomain(domain) ;
107	else
108	writeUnstructuredDomainUgrid(domain) ;
109	return ;
110	}
111
112	CContext* context = CContext::getCurrent() ;
113	if (domain->IsWritten(this->filename)) return;
114	domain->checkAttributes();
115
116	if (domain->isEmpty())
117	if (SuperClass::type==MULTI_FILE) return;
118
119
120	std::vector<StdString> dim0, dim1;
121	StdString domid = domain->getDomainOutputName();
122	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
123	if (isWrittenDomain(domid)) return ;
124	else setWrittenDomain(domid);
125
126	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
127
128
129	StdString dimXid, dimYid ;
130
131	nc_type typePrec ;
132	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
133	else if (domain->prec==4) typePrec = NC_FLOAT ;
134	else if (domain->prec==8) typePrec = NC_DOUBLE ;
135
136	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
137	switch (domain->type)
138	{
139	case CDomain::type_attr::curvilinear :
140
141	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
142	else lonName = domain->lon_name;
143
144	if (domain->lat_name.isEmpty()) latName = "nav_lat";
145	else latName = domain->lat_name;
146
147	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
148	else dimXid=domain->dim_i_name.getValue() + appendDomid;
149
150	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
151	else dimYid=domain->dim_j_name.getValue() + appendDomid;
152
153	break ;
154
155	case CDomain::type_attr::rectilinear :
156
157	if (domain->lon_name.isEmpty())
158	{
159	if (domain->dim_i_name.isEmpty())
160	lonName = "lon";
161	else
162	lonName = domain->dim_i_name.getValue();
163	}
164	else lonName = domain->lon_name;
165
166	if (domain->lat_name.isEmpty())
167	{
168	if (domain->dim_j_name.isEmpty())
169	latName = "lat";
170	else
171	latName = domain->dim_j_name.getValue();
172	}
173	else latName = domain->lat_name;
174
175	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
176	else dimXid = domain->dim_i_name.getValue()+appendDomid;
177
178	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
179	else dimYid = domain->dim_j_name.getValue()+appendDomid;
180	break;
181	}
182
183	StdString dimVertId = StdString("nvertex").append(appendDomid);
184
185	string lonid,latid,bounds_lonid,bounds_latid ;
186	string areaId = "area" + appendDomid;
187
188	try
189	{
190	switch (SuperClass::type)
191	{
192	case (MULTI_FILE) :
193	{
194	switch (domain->type)
195	{
196	case CDomain::type_attr::curvilinear :
197	dim0.push_back(dimYid); dim0.push_back(dimXid);
198	lonid = lonName+appendDomid;
199	latid = latName+appendDomid;
200	break ;
201	case CDomain::type_attr::rectilinear :
202	lonid = lonName+appendDomid;
203	latid = latName+appendDomid;
204	dim0.push_back(dimYid);
205	dim1.push_back(dimXid);
206	break;
207	}
208	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
209	else bounds_lonid = "bounds_"+lonName+appendDomid;
210	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
211	else bounds_latid = "bounds_"+latName+appendDomid;
212
213	SuperClassWriter::addDimension(dimXid, domain->niValue_);
214	SuperClassWriter::addDimension(dimYid, domain->njValue_);
215
216	if (domain->hasBounds)
217	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
218
219	if (context->intraCommSize_ > 1)
220	{
221	this->writeLocalAttributes(domain->ibeginValue_,
222	domain->niValue_,
223	domain->jbeginValue_,
224	domain->njValue_,
225	appendDomid);
226
227	if (singleDomain)
228	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
229	domain->ibeginValue_,
230	domain->niValue_,
231	domain->jbeginValue_,
232	domain->njValue_,
233	domain->ni_glo,domain->nj_glo,
234	context->intraCommRank_,context->intraCommSize_);
235	}
236
237	if (domain->hasLonLat)
238	{
239	switch (domain->type)
240	{
241	case CDomain::type_attr::curvilinear :
242	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
243	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
244	break ;
245	case CDomain::type_attr::rectilinear :
246	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
247	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
248	break ;
249	}
250
251	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
252	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
253
254	if (domain->hasBounds)
255	{
256	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
257	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
258
259	dim0.clear();
260	dim0.push_back(dimYid);
261	dim0.push_back(dimXid);
262	dim0.push_back(dimVertId);
263	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
264	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
265	}
266	}
267
268	dim0.clear();
269	dim0.push_back(dimYid);
270	dim0.push_back(dimXid);
271
272	if (domain->hasArea)
273	{
274	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
275	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
276	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
277	}
278
279	SuperClassWriter::definition_end();
280
281	if (domain->hasLonLat)
282	{
283	switch (domain->type)
284	{
285	case CDomain::type_attr::curvilinear :
286	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
287	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
288	break;
289	case CDomain::type_attr::rectilinear :
290	//CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
291	CArray<double,1> lat;
292	lat.resize( domain->njValue_);
293	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
294	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
295	//CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
296	CArray<double,1> lon = domain->lonvalue(Range(0,domain->niValue_-1));
297	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
298	break;
299	}
300
301	if (domain->hasBounds)
302	{
303	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
304	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
305	}
306	}
307
308	if (domain->hasArea)
309	{
310	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
311	}
312
313	SuperClassWriter::definition_start();
314
315	break;
316	}
317	case (ONE_FILE) :
318	{
319	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
320	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
321
322	if (domain->hasBounds)
323	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
324
325	if (domain->hasLonLat)
326	{
327	switch (domain->type)
328	{
329	case CDomain::type_attr::curvilinear :
330	dim0.push_back(dimYid); dim0.push_back(dimXid);
331	lonid = lonName+appendDomid;
332	latid = latName+appendDomid;
333	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
334	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
335	break;
336
337	case CDomain::type_attr::rectilinear :
338	dim0.push_back(dimYid);
339	dim1.push_back(dimXid);
340	lonid = lonName+appendDomid;
341	latid = latName+appendDomid;
342	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
343	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
344	break;
345	}
346	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
347	else bounds_lonid = "bounds_"+lonName+appendDomid;
348	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
349	else bounds_latid = "bounds_"+latName+appendDomid;
350
351	this->writeAxisAttributes
352	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
353	this->writeAxisAttributes
354	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
355
356	if (domain->hasBounds)
357	{
358	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
359	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
360
361	dim0.clear();
362	dim0.push_back(dimYid);
363	dim0.push_back(dimXid);
364	dim0.push_back(dimVertId);
365	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
366	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
367	}
368	}
369
370	if (domain->hasArea)
371	{
372	dim0.clear();
373	dim0.push_back(dimYid); dim0.push_back(dimXid);
374	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
375	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
376	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
377	dim0.clear();
378	}
379
380	SuperClassWriter::definition_end();
381
382	switch (domain->type)
383	{
384	case CDomain::type_attr::curvilinear :
385	{
386	std::vector<StdSize> start(2) ;
387	std::vector<StdSize> count(2) ;
388	start[1]=domain->ibeginValue_;
389	start[0]=domain->jbeginValue_;
390	count[1]=domain->niValue_ ; count[0]=domain->njValue_ ;
391
392	if (domain->hasLonLat)
393	{
394	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
395	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
396	}
397	break;
398	}
399	case CDomain::type_attr::rectilinear :
400	{
401	if (domain->hasLonLat)
402	{
403	std::vector<StdSize> start(1) ;
404	std::vector<StdSize> count(1) ;
405
406	start[0]=domain->jbeginValue_;
407	count[0]=domain->njValue_;
408	CArray<double,1> lat;
409	lat.resize( domain->njValue_);
410	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
411	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
412
413	start[0]=domain->ibeginValue_;
414	count[0]=domain->niValue_;
415	CArray<double,1> lon;
416	lon.resize( domain->niValue_);
417	for (int i=0;i<domain->niValue_;i++) lon(i) = domain->lonvalue(i);
418	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
419	}
420	break;
421	}
422	}
423
424	if (domain->hasBounds)
425	{
426	std::vector<StdSize> start(3);
427	std::vector<StdSize> count(3);
428	if (domain->isEmpty())
429	{
430	start[2] = start[1] = start[0] = 0;
431	count[2] = count[1] = count[0] = 0;
432	}
433	else
434	{
435	start[2] = 0;
436	start[1] = domain->ibeginValue_;
437	start[0] = domain->jbeginValue_;
438	count[2] = domain->nvertex;
439	count[1] = domain->niValue_;
440	count[0] = domain->njValue_;
441	}
442
443	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
444	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
445	}
446
447	if (domain->hasArea)
448	{
449	std::vector<StdSize> start(2);
450	std::vector<StdSize> count(2);
451
452	start[1] = domain->ibeginValue_;
453	start[0] = domain->jbeginValue_;
454	count[1] = domain->niValue_;
455	count[0] = domain->njValue_;
456
457	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
458	}
459
460	SuperClassWriter::definition_start();
461	break;
462	}
463	default :
464	ERROR("CNc4DataOutput::writeDomain(domain)",
465	<< "[ type = " << SuperClass::type << "]"
466	<< " not implemented yet !");
467	}
468	}
469	catch (CNetCdfException& e)
470	{
471	StdString msg("On writing the domain : ");
472	msg.append(domid); msg.append("\n");
473	msg.append("In the context : ");
474	msg.append(context->getId()); msg.append("\n");
475	msg.append(e.what());
476	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
477	}
478
479	domain->addRelFile(this->filename);
480	}
481	CATCH
482
483	//--------------------------------------------------------------
484
485	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
486	{
487	CContext* context = CContext::getCurrent() ;
488
489	if (domain->IsWritten(this->filename)) return;
490
491	StdString domid = domain->getDomainOutputName();
492
493	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
494	// Thus the entire mesh connectivity will be generated at once.
495	if (isWrittenDomain(domid)) return ;
496	else setWrittenDomain(domid);
497
498	domain->checkAttributes();
499	if (domain->isEmpty())
500	if (SuperClass::type==MULTI_FILE) return ;
501
502	nc_type typePrec ;
503	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
504	else if (domain->prec==4) typePrec = NC_FLOAT ;
505	else if (domain->prec==8) typePrec = NC_DOUBLE ;
506
507	std::vector<StdString> dim0;
508	StdString domainName = domain->name;
509
510	StdString node_x = domainName + "_node_x";
511	StdString node_y = domainName + "_node_y";
512
513	StdString edge_x = domainName + "_edge_x";
514	StdString edge_y = domainName + "_edge_y";
515	StdString edge_nodes = domainName + "_edge_nodes";
516
517	StdString face_x = domainName + "_face_x";
518	StdString face_y = domainName + "_face_y";
519	StdString face_nodes = domainName + "_face_nodes";
520	StdString face_edges = domainName + "_face_edges";
521	StdString edge_faces = domainName + "_edge_face_links";
522	StdString face_faces = domainName + "_face_links";
523
524	StdString dimNode = "n" + domainName + "_node";
525	StdString dimEdge = "n" + domainName + "_edge";
526	StdString dimFace = "n" + domainName + "_face";
527	StdString dimVertex = "n" + domainName + "_vertex";
528	StdString dimTwo = "Two";
529
530	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
531	dim0.clear();
532	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
533	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
534	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
535	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
536	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
537
538	try
539	{
540	switch (SuperClass::type)
541	{
542	case (ONE_FILE) :
543	{
544	// Adding nodes
545	if (domain->nvertex == 1)
546	{
547	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
548	{
549	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
550	dim0.clear();
551	dim0.push_back(dimNode);
552	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
553	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
554	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
555	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
556	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
557	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
558	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
559	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
560	}
561	} // domain->nvertex == 1
562
563	// Adding edges and nodes, if nodes have not been defined previously
564	if (domain->nvertex == 2)
565	{
566	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
567	{
568	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
569	dim0.clear();
570	dim0.push_back(dimNode);
571	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
572	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
573	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
574	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
575	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
576	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
577	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
578	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
579	}
580	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
581	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
582	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
583	dim0.clear();
584	dim0.push_back(dimEdge);
585	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
586	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
587	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
588	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
589	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
590	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
591	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
592	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
593	dim0.clear();
594	dim0.push_back(dimEdge);
595	dim0.push_back(dimTwo);
596	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
597	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
598	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
599	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
600	} // domain->nvertex == 2
601
602	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
603	if (domain->nvertex > 2)
604	{
605	// Nodes
606	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
607	{
608	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
609	dim0.clear();
610	dim0.push_back(dimNode);
611	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
612	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
613	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
614	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
615	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
616	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
617	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
618	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
619	}
620	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
621	{
622	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
623	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
624	SuperClassWriter::addAttribute("face_edge_connectivity", face_edges, &domainName);
625	SuperClassWriter::addAttribute("edge_face_connectivity", edge_faces, &domainName);
626	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
627	dim0.clear();
628	dim0.push_back(dimEdge);
629	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
630	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
631	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
632	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
633	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
634	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
635	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
636	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
637	dim0.clear();
638	dim0.push_back(dimEdge);
639	dim0.push_back(dimTwo);
640	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
641	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
642	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
643	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
644	}
645	SuperClassWriter::addAttribute("face_face_connectivity", face_faces, &domainName);
646	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
647	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
648	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
649	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
650	dim0.clear();
651	dim0.push_back(dimFace);
652	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
653	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
654	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
655	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
656	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
657	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
658	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
659	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
660	dim0.clear();
661	dim0.push_back(dimFace);
662	dim0.push_back(dimVertex);
663	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
664	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
665	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
666	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
667	dim0.clear();
668	dim0.push_back(dimFace);
669	dim0.push_back(dimVertex);
670	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
671	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
672	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
673	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
674	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
675	dim0.clear();
676	dim0.push_back(dimEdge);
677	dim0.push_back(dimTwo);
678	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
679	SuperClassWriter::addAttribute("cf_role", StdString("edge_face_connectivity"), &edge_faces);
680	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
681	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
682	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
683	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
684	dim0.clear();
685	dim0.push_back(dimFace);
686	dim0.push_back(dimVertex);
687	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
688	SuperClassWriter::addAttribute("cf_role", StdString("face_face_connectivity"), &face_faces);
689	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
690	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
691	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
692	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
693	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
694	} // domain->nvertex > 2
695
696	SuperClassWriter::definition_end();
697
698	std::vector<StdSize> startEdges(1) ;
699	std::vector<StdSize> countEdges(1) ;
700	std::vector<StdSize> startNodes(1) ;
701	std::vector<StdSize> countNodes(1) ;
702	std::vector<StdSize> startFaces(1) ;
703	std::vector<StdSize> countFaces(1) ;
704	std::vector<StdSize> startEdgeNodes(2) ;
705	std::vector<StdSize> countEdgeNodes(2) ;
706	std::vector<StdSize> startEdgeFaces(2) ;
707	std::vector<StdSize> countEdgeFaces(2) ;
708	std::vector<StdSize> startFaceConctv(2) ;
709	std::vector<StdSize> countFaceConctv(2) ;
710
711	if (domain->nvertex == 1)
712	{
713	if (domain->isEmpty())
714	{
715	startNodes[0]=0 ;
716	countNodes[0]=0 ;
717	}
718	else
719	{
720	startNodes[0] = domain->ibeginValue_;
721	countNodes[0] = domain->niValue_ ;
722	}
723
724	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
725	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
726	}
727	else if (domain->nvertex == 2)
728	{
729	if (domain->isEmpty())
730	{
731	startEdges[0]=0 ;
732	countEdges[0]=0 ;
733	startNodes[0]=0 ;
734	countNodes[0]=0 ;
735	startEdgeNodes[0]=0;
736	startEdgeNodes[1]=0;
737	countEdgeNodes[0]=0;
738	countEdgeNodes[1]=0;
739
740	}
741	else
742	{
743	startEdges[0] = domain->ibeginValue_;
744	countEdges[0] = domain->niValue_;
745	startNodes[0] = domain->mesh->node_start;
746	countNodes[0] = domain->mesh->node_count;
747	if (countNodes[0]==0) startNodes[0]=0 ; // for netcdf error
748	startEdgeNodes[0] = domain->ibeginValue_;
749	startEdgeNodes[1] = 0;
750	countEdgeNodes[0] = domain->niValue_;
751	countEdgeNodes[1] = 2;
752	}
753	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
754	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
755	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
756	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
757	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
758	}
759	else
760	{
761	if (domain->isEmpty())
762	{
763	startFaces[0] = 0 ;
764	countFaces[0] = 0 ;
765	startNodes[0] = 0;
766	countNodes[0] = 0;
767	startEdges[0] = 0;
768	countEdges[0] = 0;
769	startEdgeFaces[0] = 0;
770	startEdgeFaces[1] = 0;
771	countEdgeFaces[0] = 0;
772	countEdgeFaces[1] = 0;
773	startFaceConctv[0] = 0;
774	startFaceConctv[1] = 0;
775	countFaceConctv[0] = 0;
776	countFaceConctv[1] = 0;
777	}
778	else
779	{
780	startFaces[0] = domain->ibeginValue_;
781	countFaces[0] = domain->niValue_ ;
782	startNodes[0] = domain->mesh->node_start;
783	countNodes[0] = domain->mesh->node_count;
784	if (countNodes[0]==0) startNodes[0]=0;
785
786	startEdges[0] = domain->mesh->edge_start;
787	countEdges[0] = domain->mesh->edge_count;
788	if (countEdges[0]==0) startEdges[0]=0 ; // for netcdf error
789
790	startEdgeNodes[0] = domain->mesh->edge_start;
791	countEdgeNodes[0] = domain->mesh->edge_count;
792	if (countEdgeNodes[0]==0) startEdgeNodes[0]=0; // for netcdf error
793	startEdgeNodes[1] = 0;
794	countEdgeNodes[1]= 2;
795
796	startEdgeFaces[0] = domain->mesh->edge_start;
797	countEdgeFaces[0] = domain->mesh->edge_count;
798	if (countEdgeFaces[0]==0) startEdgeFaces[0]=0 ; // for netcdf error
799	startEdgeFaces[1]= 0;
800	countEdgeFaces[1]= 2;
801
802	startFaceConctv[0] = domain->ibeginValue_;
803	countFaceConctv[0] = domain->niValue_;
804	startFaceConctv[1] = 0;
805	countFaceConctv[1] = domain->nvertex;
806	}
807	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
808	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
809	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
810	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
811	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
812	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
813	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
814	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
815	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
816	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
817	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
818	}
819	SuperClassWriter::definition_start();
820
821	break;
822	} // ONE_FILE
823
824	case (MULTI_FILE) :
825	{
826	ERROR("CNc4DataOutput::writeDomain(domain)",
827	<< "[ type = multiple_file ]"
828	<< " is not yet implemented for UGRID files !");
829	break;
830	}
831
832	default :
833	ERROR("CNc4DataOutput::writeDomain(domain)",
834	<< "[ type = " << SuperClass::type << "]"
835	<< " not implemented yet !");
836	} // switch
837	} // try
838
839	catch (CNetCdfException& e)
840	{
841	StdString msg("On writing the domain : ");
842	msg.append(domid); msg.append("\n");
843	msg.append("In the context : ");
844	msg.append(context->getId()); msg.append("\n");
845	msg.append(e.what());
846	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
847	}
848
849	domain->addRelFile(this->filename);
850	}
851
852	//--------------------------------------------------------------
853
854	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
855	{
856	CContext* context = CContext::getCurrent() ;
857
858	if (domain->IsWritten(this->filename)) return;
859	domain->checkAttributes();
860
861	if (domain->isEmpty())
862	if (SuperClass::type==MULTI_FILE) return ;
863
864	std::vector<StdString> dim0, dim1;
865	StdString domid = domain->getDomainOutputName();
866	if (isWrittenDomain(domid)) return ;
867	else setWrittenDomain(domid);
868
869	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
870
871	StdString lonName,latName, cellName ;
872	if (domain->lon_name.isEmpty()) lonName = "lon";
873	else lonName = domain->lon_name;
874
875	if (domain->lat_name.isEmpty()) latName = "lat";
876	else latName = domain->lat_name;
877
878	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
879	else cellName="cell";
880	StdString dimXid = cellName+appendDomid;
881	StdString dimVertId;
882	if (domain->nvertex_name.isEmpty()) dimVertId = "nvertex"+appendDomid;
883	else dimVertId = domain->nvertex_name;
884
885	string lonid,latid,bounds_lonid,bounds_latid ;
886	string areaId = "area" + appendDomid;
887
888	nc_type typePrec ;
889	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
890	else if (domain->prec==4) typePrec = NC_FLOAT ;
891	else if (domain->prec==8) typePrec = NC_DOUBLE ;
892
893	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
894
895	try
896	{
897	switch (SuperClass::type)
898	{
899	case (MULTI_FILE) :
900	{
901	dim0.push_back(dimXid);
902	SuperClassWriter::addDimension(dimXid, domain->ni);
903
904	lonid = lonName+appendDomid;
905	latid = latName+appendDomid;
906	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
907	else bounds_lonid = "bounds_"+lonName+appendDomid;
908	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
909	else bounds_latid = "bounds_"+latName+appendDomid;
910
911	if (domain->hasLonLat)
912	{
913	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
914	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
915	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
916	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
917	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
918	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
919	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
920	}
921	dim0.clear();
922	if (domain->hasBounds)
923	{
924	dim0.push_back(dimXid);
925	dim0.push_back(dimVertId);
926	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
927	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
928	}
929
930	dim0.clear();
931	dim0.push_back(dimXid);
932	if (domain->hasArea)
933	{
934	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
935	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
936	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
937	}
938
939	SuperClassWriter::definition_end();
940
941	if (domain->hasLonLat)
942	{
943	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
944	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
945	if (domain->hasBounds)
946	{
947	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
948	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
949	}
950	}
951
952	if (domain->hasArea)
953	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
954
955	SuperClassWriter::definition_start();
956	break ;
957	}
958
959	case (ONE_FILE) :
960	{
961	lonid = lonName+appendDomid;
962	latid = latName+appendDomid;
963	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
964	else bounds_lonid = "bounds_"+lonName+appendDomid;
965	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
966	else bounds_latid = "bounds_"+latName+appendDomid;
967
968	dim0.push_back(dimXid);
969	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
970	if (domain->hasLonLat)
971	{
972	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
973	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
974
975	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
976	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
977	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
978	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
979	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
980	}
981	dim0.clear();
982
983	if (domain->hasBounds)
984	{
985	dim0.push_back(dimXid);
986	dim0.push_back(dimVertId);
987	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
988	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
989	}
990
991	if (domain->hasArea)
992	{
993	dim0.clear();
994	dim0.push_back(dimXid);
995	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
996	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
997	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
998	}
999
1000	SuperClassWriter::definition_end();
1001
1002	std::vector<StdSize> start(1), startBounds(2) ;
1003	std::vector<StdSize> count(1), countBounds(2) ;
1004	if (domain->isEmpty())
1005	{
1006	start[0]=0 ;
1007	count[0]=0 ;
1008	startBounds[1]=0 ;
1009	countBounds[1]=nvertex ;
1010	startBounds[0]=0 ;
1011	countBounds[0]=0 ;
1012	}
1013	else
1014	{
1015	start[0]=domain->ibeginValue_;
1016	count[0]=domain->niValue_;
1017	startBounds[0]=domain->ibeginValue_;
1018	startBounds[1]=0 ;
1019	countBounds[0]=domain->niValue_;
1020	countBounds[1]=nvertex ;
1021	}
1022
1023	if (domain->hasLonLat)
1024	{
1025	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
1026	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
1027	if (domain->hasBounds)
1028	{
1029	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1030	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1031	}
1032	}
1033
1034	if (domain->hasArea)
1035	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
1036
1037	SuperClassWriter::definition_start();
1038
1039	break;
1040	}
1041	default :
1042	ERROR("CNc4DataOutput::writeDomain(domain)",
1043	<< "[ type = " << SuperClass::type << "]"
1044	<< " not implemented yet !");
1045	}
1046	}
1047	catch (CNetCdfException& e)
1048	{
1049	StdString msg("On writing the domain : ");
1050	msg.append(domid); msg.append("\n");
1051	msg.append("In the context : ");
1052	msg.append(context->getId()); msg.append("\n");
1053	msg.append(e.what());
1054	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1055	}
1056	domain->addRelFile(this->filename);
1057	}
1058	//--------------------------------------------------------------
1059
1060	void CNc4DataOutput::writeAxis_(CAxis* axis)
1061	{
1062	if (axis->IsWritten(this->filename)) return;
1063
1064	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
1065	if (!axis->value.isEmpty() )
1066	{
1067	// The hash of the element will be associated to the default element name (= map key), and to the name really written
1068	int globalHash = axis->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
1069
1070	StdString defaultNameKey = axis->getAxisOutputName();
1071	if ( !relAxis_.count ( defaultNameKey ) )
1072	{
1073	// if defaultNameKey not in the map, write the element such as it is defined
1074	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) );
1075	}
1076	else // look if a hash associated this key is equal
1077	{
1078	bool elementIsInMap(false);
1079	auto defaultNameKeyElements = relAxis_.equal_range( defaultNameKey );
1080	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
1081	{
1082	if ( it->second.first == globalHash )
1083	{
1084	// if yes, associate the same ids to current element
1085	axis->renameAttributesBeforeWriting( it->second.second );
1086	elementIsInMap = true;
1087	}
1088	}
1089	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
1090	if (!elementIsInMap) // ! in MAP
1091	{
1092	axis->renameAttributesBeforeWriting();
1093	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) ) ;// = axis->getId()
1094	}
1095	}
1096	}
1097
1098	axis->checkAttributes();
1099
1100	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
1101	: axis->n_glo.getValue();
1102
1103	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
1104
1105	std::vector<StdString> dims;
1106	StdString axisid = axis->getAxisOutputName();
1107	StdString axisDim, axisBoundsId;
1108	if (isWrittenAxis(axisid)) return ;
1109	else setWrittenAxis(axisid);
1110
1111	nc_type typePrec ;
1112	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1113	else if (axis->prec==4) typePrec = NC_FLOAT ;
1114	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1115
1116	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1117	string strId="str_len" ;
1118	try
1119	{
1120	if (axis->dim_name.isEmpty()) axisDim = axisid;
1121	else axisDim=axis->dim_name.getValue();
1122	SuperClassWriter::addDimension(axisDim, size);
1123	dims.push_back(axisDim);
1124
1125	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1126
1127	if (axis->hasValue() \|\| !axis->label.isEmpty())
1128	{
1129	if (!axis->label.isEmpty()) dims.push_back(strId);
1130
1131	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1132
1133	if (!axis->name.isEmpty())
1134	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1135
1136	if (!axis->standard_name.isEmpty())
1137	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1138
1139	if (!axis->long_name.isEmpty())
1140	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1141
1142	if (!axis->unit.isEmpty())
1143	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1144
1145	if (!axis->axis_type.isEmpty())
1146	{
1147	switch(axis->axis_type)
1148	{
1149	case CAxis::axis_type_attr::X :
1150	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1151	break;
1152	case CAxis::axis_type_attr::Y :
1153	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1154	break;
1155	case CAxis::axis_type_attr::Z :
1156	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1157	break;
1158	case CAxis::axis_type_attr::T :
1159	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1160	break;
1161	}
1162	}
1163
1164	if (!axis->positive.isEmpty())
1165	{
1166	SuperClassWriter::addAttribute("positive",
1167	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1168	&axisid);
1169	}
1170
1171	if (!axis->formula.isEmpty())
1172	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1173
1174	if (!axis->formula_term.isEmpty())
1175	SuperClassWriter::addAttribute("formula_terms", axis->formula_term.getValue(), &axisid);
1176
1177	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1178	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1179	{
1180	dims.push_back("axis_nbounds");
1181	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1182	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1183
1184	if (!axis->standard_name.isEmpty())
1185	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1186
1187	if (!axis->unit.isEmpty())
1188	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1189
1190	if (!axis->formula_bounds.isEmpty())
1191	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1192
1193	if (!axis->formula_term_bounds.isEmpty())
1194	SuperClassWriter::addAttribute("formula_terms", axis->formula_term_bounds.getValue(), &axisBoundsId);
1195	}
1196	}
1197
1198	SuperClassWriter::definition_end();
1199
1200	switch (SuperClass::type)
1201	{
1202	case MULTI_FILE:
1203	{
1204	if (axis->label.isEmpty())
1205	{
1206	if (!axis->value.isEmpty())
1207	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
1208
1209	if (!axis->bounds.isEmpty())
1210	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
1211	}
1212	else
1213	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
1214
1215	SuperClassWriter::definition_start();
1216	break;
1217	}
1218	case ONE_FILE:
1219	{
1220	std::vector<StdSize> start(1), startBounds(2) ;
1221	std::vector<StdSize> count(1), countBounds(2) ;
1222	start[0] = startBounds[0] = axis->begin;
1223	count[0] = countBounds[0] = axis->n;
1224	startBounds[1] = 0;
1225	countBounds[1] = 2;
1226
1227	if (axis->label.isEmpty())
1228	{
1229	if (!axis->value.isEmpty())
1230	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
1231
1232	if (!axis->bounds.isEmpty())
1233	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1234	}
1235	else
1236	{
1237	std::vector<StdSize> startLabel(2), countLabel(2);
1238	startLabel[0] = start[0]; startLabel[1] = 0;
1239	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1240	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
1241	}
1242
1243	SuperClassWriter::definition_start();
1244
1245	break;
1246	}
1247	default :
1248	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1249	<< "[ type = " << SuperClass::type << "]"
1250	<< " not implemented yet !");
1251	}
1252	}
1253	catch (CNetCdfException& e)
1254	{
1255	StdString msg("On writing the axis : ");
1256	msg.append(axisid); msg.append("\n");
1257	msg.append("In the context : ");
1258	CContext* context = CContext::getCurrent() ;
1259	msg.append(context->getId()); msg.append("\n");
1260	msg.append(e.what());
1261	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1262	}
1263	axis->addRelFile(this->filename);
1264	}
1265
1266	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1267	{
1268	if (scalar->IsWritten(this->filename)) return;
1269	scalar->checkAttributes();
1270	int scalarSize = 1;
1271
1272	StdString scalaId = scalar->getScalarOutputName();
1273	StdString boundsId;
1274	if (isWrittenAxis(scalaId)) return ;
1275	else setWrittenAxis(scalaId);
1276
1277	nc_type typePrec ;
1278	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1279	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1280	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1281
1282	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1283	string strId="str_len" ;
1284
1285	try
1286	{
1287	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1288
1289	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1290	{
1291	std::vector<StdString> dims;
1292	StdString scalarDim = scalaId;
1293
1294	if (!scalar->label.isEmpty()) dims.push_back(strId);
1295
1296	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1297
1298	if (!scalar->name.isEmpty())
1299	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1300
1301	if (!scalar->standard_name.isEmpty())
1302	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1303
1304	if (!scalar->long_name.isEmpty())
1305	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1306
1307	if (!scalar->unit.isEmpty())
1308	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1309
1310	if (!scalar->axis_type.isEmpty())
1311	{
1312	switch(scalar->axis_type)
1313	{
1314	case CScalar::axis_type_attr::X :
1315	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1316	break;
1317	case CScalar::axis_type_attr::Y :
1318	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1319	break;
1320	case CScalar::axis_type_attr::Z :
1321	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1322	break;
1323	case CScalar::axis_type_attr::T :
1324	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1325	break;
1326	}
1327	}
1328
1329	if (!scalar->positive.isEmpty())
1330	{
1331	SuperClassWriter::addAttribute("positive",
1332	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1333	&scalaId);
1334	}
1335
1336	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1337	{
1338	dims.clear();
1339	dims.push_back("axis_nbounds");
1340	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1341	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1342	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1343	}
1344
1345	SuperClassWriter::definition_end();
1346
1347	switch (SuperClass::type)
1348	{
1349	case MULTI_FILE:
1350	{
1351	CArray<double,1> scalarValue(scalarSize);
1352	CArray<string,1> scalarLabel(scalarSize);
1353	CArray<double,1> scalarBounds(scalarSize*2);
1354
1355	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1356	{
1357	scalarValue(0) = scalar->value;
1358	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1359	}
1360
1361	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1362	{
1363	scalarBounds(0) = scalar->bounds(0);
1364	scalarBounds(1) = scalar->bounds(1);
1365	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1366	}
1367
1368	if (!scalar->label.isEmpty())
1369	{
1370	scalarLabel(0) = scalar->label;
1371	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1372	}
1373
1374	SuperClassWriter::definition_start();
1375
1376	break;
1377	}
1378	case ONE_FILE:
1379	{
1380	CArray<double,1> scalarValue(scalarSize);
1381	CArray<string,1> scalarLabel(scalarSize);
1382	CArray<double,1> scalarBounds(scalarSize*2);
1383
1384	std::vector<StdSize> start(1);
1385	std::vector<StdSize> count(1);
1386	start[0] = 0;
1387	count[0] = 1;
1388	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1389	{
1390	scalarValue(0) = scalar->value;
1391	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1392	}
1393	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1394	{
1395	scalarBounds(0) = scalar->bounds(0);
1396	scalarBounds(1) = scalar->bounds(1);
1397	count[0] = 2;
1398	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1399	}
1400	if (!scalar->label.isEmpty())
1401	{
1402	scalarLabel(0) = scalar->label;
1403	count[0] = stringArrayLen;
1404	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1405	}
1406
1407	SuperClassWriter::definition_start();
1408
1409	break;
1410	}
1411	default :
1412	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1413	<< "[ type = " << SuperClass::type << "]"
1414	<< " not implemented yet !");
1415	}
1416	}
1417	}
1418	catch (CNetCdfException& e)
1419	{
1420	StdString msg("On writing the scalar : ");
1421	msg.append(scalaId); msg.append("\n");
1422	msg.append("In the context : ");
1423	CContext* context = CContext::getCurrent() ;
1424	msg.append(context->getId()); msg.append("\n");
1425	msg.append(e.what());
1426	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1427	}
1428	scalar->addRelFile(this->filename);
1429	}
1430
1431	//--------------------------------------------------------------
1432
1433	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1434	{
1435	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1436
1437	// NOTA : The cuurent algorithm to write compress elements of the grid
1438	// will work pretting well when on server side you dont't get
1439	// partial overlap on elements between differents participating process
1440	// So the element must be totally distributed or non distributed
1441	// If an element is partially overlaping betwwen process then the
1442	// total compressed part will apear artificially greater than expected
1443	// For the current implementation of writer which is decomposed only on
1444	// one element, it will work as expected, but for future, it must be
1445	// reconsidered again.
1446	try
1447	{
1448	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1449	std::vector<StdString> domainList = grid->getDomainList();
1450	std::vector<StdString> axisList = grid->getAxisList();
1451	std::vector<StdString> scalarList = grid->getScalarList();
1452	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1453	int commRank ;
1454	MPI_Comm_rank(comm_file,&commRank) ;
1455
1456	std::vector<StdString> dims;
1457
1458	for (int i = 0; i < numElement; ++i)
1459	{
1460	StdString varId, compress;
1461	CArray<size_t, 1> indexes;
1462	bool isDistributed;
1463	size_t nbIndexes, totalNbIndexes, offset;
1464	size_t firstGlobalIndex;
1465
1466	if (2 == axisDomainOrder(i))
1467	{
1468	CDomain* domain = CDomain::get(domainList[idxDomain]);
1469	StdString domId = domain->getDomainOutputName();
1470
1471	if (!domain->isCompressible()
1472	\|\| domain->type == CDomain::type_attr::unstructured
1473	\|\| domain->isWrittenCompressed(this->filename)
1474	\|\| isWrittenCompressedDomain(domId))
1475	continue;
1476
1477	// unstructured grid seems not be taken into account why ?
1478
1479	string lonName,latName ;
1480
1481	if (domain->lon_name.isEmpty())
1482	{
1483	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1484	else lonName = "lon";
1485	}
1486	else lonName = domain->lon_name;
1487
1488	if (domain->lat_name.isEmpty())
1489	{
1490	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1491	else latName = "lat";
1492	}
1493	else latName = domain->lat_name;
1494
1495	StdString appendDomId = singleDomain ? "" : "_" + domId;
1496
1497	varId = domId + "_points";
1498	compress = latName + appendDomId + " " + lonName + appendDomId;
1499
1500	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
1501	workflowView->getGlobalIndexView(indexes) ;
1502	nbIndexes = workflowView->getSize() ;
1503	isDistributed = domain->isDistributed();
1504	if (isDistributed)
1505	{
1506	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1507	if (commRank==0) offset=0 ;
1508	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1509	}
1510	else
1511	{
1512	offset=0 ;
1513	totalNbIndexes = nbIndexes ;
1514	}
1515
1516	firstGlobalIndex = domain->ibeginValue_ + domain->jbeginValue_ * domain->ni_glo;
1517
1518	domain->addRelFileCompressed(this->filename);
1519	setWrittenCompressedDomain(domId);
1520	++idxDomain;
1521	}
1522	else if (1 == axisDomainOrder(i))
1523	{
1524	CAxis* axis = CAxis::get(axisList[idxAxis]);
1525	StdString axisId = axis->getAxisOutputName();
1526
1527	if (!axis->isCompressible()
1528	\|\| axis->isWrittenCompressed(this->filename)
1529	\|\| isWrittenCompressedAxis(axisId))
1530	continue;
1531
1532	varId = axisId + "_points";
1533	compress = axisId;
1534
1535	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
1536	workflowView->getGlobalIndexView(indexes) ;
1537	nbIndexes = workflowView->getSize() ;
1538	isDistributed = axis->isDistributed();
1539	if (isDistributed)
1540	{
1541	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
1542	if (commRank==0) offset=0 ;
1543	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
1544	}
1545	else
1546	{
1547	offset=0 ;
1548	totalNbIndexes = nbIndexes ;
1549	}
1550	firstGlobalIndex = axis->begin;
1551
1552	axis->addRelFileCompressed(this->filename);
1553	setWrittenCompressedAxis(axisId);
1554	++idxAxis;
1555	}
1556	else
1557	{
1558	//for scalar
1559	}
1560
1561	if (!varId.empty())
1562	{
1563	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1564
1565	dims.clear();
1566	dims.push_back(varId);
1567	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
1568
1569	SuperClassWriter::addAttribute("compress", compress, &varId);
1570
1571	switch (SuperClass::type)
1572	{
1573	case (MULTI_FILE):
1574	{
1575	indexes -= firstGlobalIndex;
1576	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1577	break;
1578	}
1579	case (ONE_FILE):
1580	{
1581	std::vector<StdSize> start, count;
1582	start.push_back(offset);
1583	count.push_back(nbIndexes);
1584
1585	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1586	break;
1587	}
1588	}
1589	}
1590	}
1591
1592	grid->addRelFileCompressed(this->filename);
1593	}
1594	catch (CNetCdfException& e)
1595	{
1596	StdString msg("On writing compressed grid : ");
1597	msg.append(grid->getId()); msg.append("\n");
1598	msg.append("In the context : ");
1599	CContext* context = CContext::getCurrent();
1600	msg.append(context->getId()); msg.append("\n");
1601	msg.append(e.what());
1602	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1603	}
1604	}
1605
1606	//--------------------------------------------------------------
1607
1608	void CNc4DataOutput::writeTimeDimension_(void)
1609	{
1610	try
1611	{
1612	SuperClassWriter::addDimension(getTimeCounterName());
1613	}
1614	catch (CNetCdfException& e)
1615	{
1616	StdString msg("On writing time dimension : time_couter\n");
1617	msg.append("In the context : ");
1618	CContext* context = CContext::getCurrent() ;
1619	msg.append(context->getId()); msg.append("\n");
1620	msg.append(e.what());
1621	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1622	}
1623	}
1624
1625	//--------------------------------------------------------------
1626
1627	void CNc4DataOutput::writeField_(CField* field)
1628	{
1629	CContext* context = CContext::getCurrent() ;
1630
1631	std::vector<StdString> dims, coodinates;
1632	CGrid* grid = field->getGrid();
1633	if (!grid->doGridHaveDataToWrite())
1634	if (SuperClass::type==MULTI_FILE) return ;
1635
1636	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1637	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1638	std::vector<StdString> domainList = grid->getDomainList();
1639	std::vector<StdString> axisList = grid->getAxisList();
1640	std::vector<StdString> scalarList = grid->getScalarList();
1641
1642	StdString timeid = getTimeCounterName();
1643	StdString dimXid,dimYid;
1644	std::deque<StdString> dimIdList, dimCoordList;
1645	bool hasArea = false;
1646	StdString cellMeasures = "area:";
1647	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1648
1649	for (int i = 0; i < numElement; ++i)
1650	{
1651	if (2 == axisDomainOrder(i))
1652	{
1653	CDomain* domain = CDomain::get(domainList[idxDomain]);
1654	StdString domId = domain->getDomainOutputName();
1655	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1656	StdString lonName,latName ;
1657	StdString dimIname,dimJname ;
1658
1659	if (domain->lon_name.isEmpty())
1660	{
1661	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1662	else lonName = "lon";
1663	}
1664	else lonName = domain->lon_name;
1665
1666	if (domain->lat_name.isEmpty())
1667	{
1668	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1669	else latName = "lat";
1670	}
1671	else latName = domain->lat_name;
1672
1673	if (domain->dim_i_name.isEmpty())
1674	{
1675	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1676	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1677	else dimIname = lonName;
1678	}
1679	else dimIname = domain->dim_i_name;
1680
1681	if (domain->dim_j_name.isEmpty())
1682	{
1683	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1684	else dimJname = latName;
1685	}
1686	else dimJname = domain->dim_j_name;
1687
1688	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1689	{
1690	dimIdList.push_back(domId + "_points");
1691	field->setUseCompressedOutput();
1692	}
1693
1694	switch (domain->type)
1695	{
1696	case CDomain::type_attr::curvilinear:
1697	if (!compressedOutput \|\| !domain->isCompressible())
1698	{
1699	dimXid=dimIname+appendDomId;
1700	dimYid=dimJname+appendDomId;
1701	dimIdList.push_back(dimXid);
1702	dimIdList.push_back(dimYid);
1703	}
1704	dimCoordList.push_back(lonName+appendDomId);
1705	dimCoordList.push_back(latName+appendDomId);
1706	break ;
1707	case CDomain::type_attr::rectilinear:
1708	if (!compressedOutput \|\| !domain->isCompressible())
1709	{
1710	dimXid = dimIname+appendDomId;
1711	dimYid = dimJname+appendDomId;
1712	dimIdList.push_back(dimXid);
1713	dimIdList.push_back(dimYid);
1714	}
1715	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1716	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1717
1718	break ;
1719	case CDomain::type_attr::unstructured:
1720	{
1721	if (SuperClassWriter::useCFConvention)
1722	{
1723	dimXid = dimIname + appendDomId;
1724	dimIdList.push_back(dimXid);
1725	dimCoordList.push_back(lonName+appendDomId);
1726	dimCoordList.push_back(latName+appendDomId);
1727	}
1728	else
1729	{
1730	StdString domainName = domain->name;
1731	if (domain->nvertex == 1)
1732	{
1733	dimXid = "n" + domainName + "_node";
1734	dimIdList.push_back(dimXid);
1735	dimCoordList.push_back(StdString(domainName + "_node_x"));
1736	dimCoordList.push_back(StdString(domainName + "_node_y"));
1737	}
1738	else if (domain->nvertex == 2)
1739	{
1740	dimXid = "n" + domainName + "_edge";
1741	dimIdList.push_back(dimXid);
1742	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1743	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1744	}
1745	else
1746	{
1747	dimXid = "n" + domainName + "_face";
1748	dimIdList.push_back(dimXid);
1749	dimCoordList.push_back(StdString(domainName + "_face_x"));
1750	dimCoordList.push_back(StdString(domainName + "_face_y"));
1751	}
1752	} // ugrid convention
1753	} // case unstructured domain
1754	}
1755
1756	if (domain->hasArea)
1757	{
1758	hasArea = true;
1759	cellMeasures += " area" + appendDomId;
1760	}
1761	++idxDomain;
1762	}
1763	else if (1 == axisDomainOrder(i))
1764	{
1765	CAxis* axis = CAxis::get(axisList[idxAxis]);
1766	StdString axisId = axis->getAxisOutputName();
1767	StdString axisDim;
1768
1769	if (axis->dim_name.isEmpty()) axisDim = axisId;
1770	else axisDim=axis->dim_name.getValue();
1771
1772	if (compressedOutput && axis->isCompressible())
1773	{
1774	dimIdList.push_back(axisDim + "_points");
1775	field->setUseCompressedOutput();
1776	}
1777	else
1778	dimIdList.push_back(axisDim);
1779
1780	if (axisDim != axisId) dimCoordList.push_back(axisId);
1781	++idxAxis;
1782	}
1783	else
1784	{
1785	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1786	StdString scalarId = scalar->getScalarOutputName();
1787	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1788	dimCoordList.push_back(scalarId);
1789	++idxScalar;
1790	}
1791	}
1792
1793	StdString fieldid = field->getFieldOutputName();
1794
1795	nc_type type ;
1796	if (field->prec.isEmpty()) type = NC_FLOAT ;
1797	else
1798	{
1799	if (field->prec==2) type = NC_SHORT ;
1800	else if (field->prec==4) type = NC_FLOAT ;
1801	else if (field->prec==8) type = NC_DOUBLE ;
1802	}
1803
1804	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1805
1806	if (wtime)
1807	{
1808	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1809	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
1810	dims.push_back(timeid);
1811	}
1812
1813	while (!dimIdList.empty())
1814	{
1815	dims.push_back(dimIdList.back());
1816	dimIdList.pop_back();
1817	}
1818
1819	while (!dimCoordList.empty())
1820	{
1821	coodinates.push_back(dimCoordList.back());
1822	dimCoordList.pop_back();
1823	}
1824
1825	try
1826	{
1827	SuperClassWriter::addVariable(fieldid, type, dims, false);
1828	SuperClassWriter::addChunk(field, type, dims);
1829
1830	if (!field->standard_name.isEmpty())
1831	SuperClassWriter::addAttribute
1832	("standard_name", field->standard_name.getValue(), &fieldid);
1833
1834	if (!field->long_name.isEmpty())
1835	SuperClassWriter::addAttribute
1836	("long_name", field->long_name.getValue(), &fieldid);
1837
1838	if (!field->unit.isEmpty())
1839	SuperClassWriter::addAttribute
1840	("units", field->unit.getValue(), &fieldid);
1841
1842	// Ugrid field attributes "mesh" and "location"
1843	if (!SuperClassWriter::useCFConvention)
1844	{
1845	if (!domainList.empty())
1846	{
1847	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
1848	StdString mesh = domain->name;
1849	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
1850	StdString location;
1851	if (domain->nvertex == 1)
1852	location = "node";
1853	else if (domain->nvertex == 2)
1854	location = "edge";
1855	else if (domain->nvertex > 2)
1856	location = "face";
1857	SuperClassWriter::addAttribute("location", location, &fieldid);
1858	}
1859
1860	}
1861
1862	if (!field->valid_min.isEmpty())
1863	SuperClassWriter::addAttribute
1864	("valid_min", field->valid_min.getValue(), &fieldid);
1865
1866	if (!field->valid_max.isEmpty())
1867	SuperClassWriter::addAttribute
1868	("valid_max", field->valid_max.getValue(), &fieldid);
1869
1870	if (!field->scale_factor.isEmpty())
1871	SuperClassWriter::addAttribute
1872	("scale_factor", field->scale_factor.getValue(), &fieldid);
1873
1874	if (!field->add_offset.isEmpty())
1875	SuperClassWriter::addAttribute
1876	("add_offset", field->add_offset.getValue(), &fieldid);
1877
1878	SuperClassWriter::addAttribute
1879	("online_operation", field->operation.getValue(), &fieldid);
1880
1881	// write child variables as attributes
1882
1883
1884	bool alreadyAddCellMethod = false;
1885	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1886	if (!field->cell_methods.isEmpty())
1887	{
1888	StdString cellMethodString = field->cell_methods;
1889	if (field->cell_methods_mode.isEmpty() \|\|
1890	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1891	{
1892	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1893	alreadyAddCellMethod = true;
1894	}
1895	else
1896	{
1897	switch (field->cell_methods_mode)
1898	{
1899	case (CField::cell_methods_mode_attr::prefix):
1900	cellMethodsPrefix = cellMethodString;
1901	cellMethodsPrefix += " ";
1902	break;
1903	case (CField::cell_methods_mode_attr::suffix):
1904	cellMethodsSuffix = " ";
1905	cellMethodsSuffix += cellMethodString;
1906	break;
1907	case (CField::cell_methods_mode_attr::none):
1908	break;
1909	default:
1910	break;
1911	}
1912	}
1913	}
1914
1915
1916	if (wtime)
1917	{
1918	CDuration freqOp = field->freq_op.getValue();
1919	freqOp.solveTimeStep(*context->calendar);
1920	StdString freqOpStr = freqOp.toStringUDUnits();
1921	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1922
1923	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1924	freqOut.solveTimeStep(*context->calendar);
1925	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1926
1927	StdString cellMethods(cellMethodsPrefix + "time: ");
1928	if (field->operation.getValue() == "instant") cellMethods += "point";
1929	else if (field->operation.getValue() == "average") cellMethods += "mean";
1930	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1931	else cellMethods += field->operation;
1932	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1933	cellMethods += " (interval: " + freqOpStr + ")";
1934	cellMethods += cellMethodsSuffix;
1935	if (!alreadyAddCellMethod)
1936	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1937	}
1938
1939	if (hasArea)
1940	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1941
1942	if (!field->default_value.isEmpty())
1943	{
1944	double default_value = field->default_value.getValue();
1945	if (type == NC_DOUBLE)
1946	{
1947	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1948	}
1949	else if (type == NC_SHORT)
1950	{
1951	short sdefault_value = (short)default_value;
1952	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
1953	}
1954	else
1955	{
1956	float fdefault_value = (float)default_value;
1957	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1958	}
1959	}
1960	else
1961	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1962
1963	if (field->compression_level.isEmpty())
1964	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
1965	if ( (field->compression_level.getValue()>0)&&(field->compression_type.isEmpty()) )
1966	field->compression_type.setValue( "gzip" );
1967	if (field->compression_type.isEmpty())
1968	field->compression_type = "None";
1969	if (field->compression_params.isEmpty())
1970	field->compression_params.resize( 0 );
1971	SuperClassWriter::setCompressionLevel(fieldid, field->compression_type, field->compression_level, field->compression_params);
1972
1973	{ // Ecriture des coordonnes
1974
1975	StdString coordstr;
1976	std::vector<StdString>::iterator
1977	itc = coodinates.begin(), endc = coodinates.end();
1978
1979	for (; itc!= endc; itc++)
1980	{
1981	StdString & coord = *itc;
1982	if (itc+1 != endc)
1983	coordstr.append(coord).append(" ");
1984	else coordstr.append(coord);
1985	}
1986
1987	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1988
1989	}
1990
1991	vector<CVariable*> listVars = field->getAllVariables() ;
1992	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1993
1994	}
1995	catch (CNetCdfException& e)
1996	{
1997	StdString msg("On writing field : ");
1998	msg.append(fieldid); msg.append("\n");
1999	msg.append("In the context : ");
2000	msg.append(context->getId()); msg.append("\n");
2001	msg.append(e.what());
2002	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2003	}
2004	} // writeField_()
2005
2006	//--------------------------------------------------------------
2007
2008	void CNc4DataOutput::writeFile_ (CFile* file)
2009	{
2010	StdString filename = file->getFileOutputName();
2011	StdString description = (!file->description.isEmpty())
2012	? file->description.getValue()
2013	: StdString("Created by xios");
2014
2015	singleDomain = (file->nbDomains == 1);
2016
2017	StdString conv_str ;
2018	if (file->convention_str.isEmpty())
2019	{
2020	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2021	else conv_str="UGRID" ;
2022	}
2023	else conv_str=file->convention_str ;
2024
2025	try
2026	{
2027	if (!appendMode) this->writeFileAttributes(filename, description,
2028	conv_str,
2029	StdString("An IPSL model"),
2030	this->getTimeStamp());
2031
2032	if (!appendMode)
2033	SuperClassWriter::addDimension("axis_nbounds", 2);
2034	}
2035	catch (CNetCdfException& e)
2036	{
2037	StdString msg("On writing file : ");
2038	msg.append(filename); msg.append("\n");
2039	msg.append("In the context : ");
2040	CContext* context = CContext::getCurrent() ;
2041	msg.append(context->getId()); msg.append("\n");
2042	msg.append(e.what());
2043	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2044	}
2045	}
2046
2047	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2048	{
2049	StdString name = var->getVariableOutputName();
2050
2051	try
2052	{
2053	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2054	addAttribute(name, var->getData<int>(), &fieldId);
2055	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2056	addAttribute(name, var->getData<short int>(), &fieldId);
2057	else if (var->type.getValue() == CVariable::type_attr::t_float)
2058	addAttribute(name, var->getData<float>(), &fieldId);
2059	else if (var->type.getValue() == CVariable::type_attr::t_double)
2060	addAttribute(name, var->getData<double>(), &fieldId);
2061	else if (var->type.getValue() == CVariable::type_attr::t_string)
2062	addAttribute(name, var->getData<string>(), &fieldId);
2063	else
2064	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2065	<< "Unsupported variable of type " << var->type.getStringValue());
2066	}
2067	catch (CNetCdfException& e)
2068	{
2069	StdString msg("On writing attributes of variable with name : ");
2070	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2071	msg.append("In the context : ");
2072	CContext* context = CContext::getCurrent() ;
2073	msg.append(context->getId()); msg.append("\n");
2074	msg.append(e.what());
2075	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2076	}
2077	}
2078
2079	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2080	{
2081	StdString name = var->getVariableOutputName();
2082
2083	try
2084	{
2085	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2086	addAttribute(name, var->getData<int>());
2087	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2088	addAttribute(name, var->getData<short int>());
2089	else if (var->type.getValue() == CVariable::type_attr::t_float)
2090	addAttribute(name, var->getData<float>());
2091	else if (var->type.getValue() == CVariable::type_attr::t_double)
2092	addAttribute(name, var->getData<double>());
2093	else if (var->type.getValue() == CVariable::type_attr::t_string)
2094	addAttribute(name, var->getData<string>());
2095	else
2096	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2097	<< "Unsupported variable of type " << var->type.getStringValue());
2098	}
2099	catch (CNetCdfException& e)
2100	{
2101	StdString msg("On writing attributes of variable with name : ");
2102	msg.append(name); msg.append("\n");
2103	msg.append("In the context : ");
2104	CContext* context = CContext::getCurrent() ;
2105	msg.append(context->getId()); msg.append("\n");
2106	msg.append(e.what());
2107	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2108	}
2109	}
2110
2111	void CNc4DataOutput::syncFile_ (void)
2112	{
2113	try
2114	{
2115	SuperClassWriter::sync() ;
2116	}
2117	catch (CNetCdfException& e)
2118	{
2119	StdString msg("On synchronizing the write among processes");
2120	msg.append("In the context : ");
2121	CContext* context = CContext::getCurrent() ;
2122	msg.append(context->getId()); msg.append("\n");
2123	msg.append(e.what());
2124	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2125	}
2126	}
2127
2128	void CNc4DataOutput::closeFile_ (void)
2129	{
2130	try
2131	{
2132	SuperClassWriter::close() ;
2133	}
2134	catch (CNetCdfException& e)
2135	{
2136	StdString msg("On closing file");
2137	msg.append("In the context : ");
2138	CContext* context = CContext::getCurrent() ;
2139	msg.append(context->getId()); msg.append("\n");
2140	msg.append(e.what());
2141	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2142	}
2143
2144	}
2145
2146	//---------------------------------------------------------------
2147
2148	StdString CNc4DataOutput::getTimeStamp(void) const
2149	{
2150	const int buffer_size = 100;
2151	time_t rawtime;
2152	struct tm * timeinfo = NULL;
2153	char buffer [buffer_size];
2154	StdString formatStr;
2155	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2156	else formatStr=file->time_stamp_format;
2157
2158	// time ( &rawtime );
2159	// timeinfo = localtime ( &rawtime );
2160	time ( &rawtime );
2161	timeinfo = gmtime ( &rawtime );
2162	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2163
2164	return (StdString(buffer));
2165	}
2166
2167	//---------------------------------------------------------------
2168
2169	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
2170	const CDate& currentWrite, int nstep)
2171	{
2172	CContext* context = CContext::getCurrent();
2173	CGrid* grid = field->getGrid();
2174
2175	if (nstep<1)
2176	{
2177	return nstep;
2178	}
2179
2180	if (!grid->doGridHaveDataToWrite())
2181	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2182	{
2183	return nstep;
2184	}
2185
2186	StdString fieldid = field->getFieldOutputName();
2187
2188	StdOStringStream oss;
2189	string timeAxisId;
2190	if (field->hasTimeInstant) timeAxisId = "time_instant";
2191	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2192
2193	StdString timeBoundId = getTimeCounterName() + "_bounds";
2194
2195	StdString timeAxisBoundId;
2196	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2197	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2198
2199	if (!field->wasWritten())
2200	{
2201	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
2202	field->getOperationTimeType() != func::CFunctor::once)
2203	{
2204	double factorUnit;
2205	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2206	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2207	else factorUnit=1 ;
2208	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
2209	}
2210
2211	field->setWritten();
2212	}
2213
2214
2215	CArray<double,1> time_data(1);
2216	CArray<double,1> time_data_bound(2);
2217	CArray<double,1> time_counter(1);
2218	CArray<double,1> time_counter_bound(2);
2219
2220	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2221	bool wtimeCounter =false ;
2222	bool wtimeData =false ;
2223
2224
2225	if (wtime)
2226	{
2227
2228	if (field->hasTimeInstant)
2229	{
2230	time_data(0) = time_data_bound(1) = (Time) currentWrite;
2231	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
2232	if (timeCounterType==instant)
2233	{
2234	time_counter(0) = time_data(0);
2235	time_counter_bound(0) = time_data_bound(0);
2236	time_counter_bound(1) = time_data_bound(1);
2237	wtimeCounter=true ;
2238	}
2239	if (hasTimeInstant) wtimeData=true ;
2240	}
2241	else if (field->hasTimeCentered)
2242	{
2243	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
2244	time_data_bound(0) = (Time)lastWrite;
2245	time_data_bound(1) = (Time)currentWrite;
2246	if (timeCounterType==centered)
2247	{
2248	time_counter(0) = time_data(0) ;
2249	time_counter_bound(0) = time_data_bound(0) ;
2250	time_counter_bound(1) = time_data_bound(1) ;
2251	wtimeCounter=true ;
2252	}
2253	if (hasTimeCentered) wtimeData=true ;
2254	}
2255
2256	if (timeCounterType==record)
2257	{
2258	time_counter(0) = nstep - 1;
2259	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
2260	wtimeCounter=true ;
2261	}
2262
2263	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
2264	{
2265	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2266	time_data/=secByDay;
2267	time_data_bound/=secByDay;
2268	time_counter/=secByDay;
2269	time_counter_bound/=secByDay;
2270	}
2271	}
2272
2273	bool isRoot = (context->intraCommRank_ == 0);
2274
2275	try
2276	{
2277	switch (SuperClass::type)
2278	{
2279	case (MULTI_FILE) :
2280	{
2281	if (info.isActive(logProfile)) CTimer::get("Files : writing data").resume();
2282	writeAndConvertData(field, data, nstep - 1);
2283	if (info.isActive(logProfile)) CTimer::get("Files : writing data").suspend();
2284	if (wtime)
2285	{
2286	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").resume();
2287	if ( wtimeData)
2288	{
2289	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2290	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2291	}
2292	if (wtimeCounter)
2293	{
2294	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2295	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2296	}
2297	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").suspend();
2298	}
2299	break;
2300	}
2301	case (ONE_FILE) :
2302	{
2303
2304	std::vector<StdSize> start, count;
2305
2306	if (field->getUseCompressedOutput())
2307	{
2308	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2309	std::vector<StdString> domainList = grid->getDomainList();
2310	std::vector<StdString> axisList = grid->getAxisList();
2311	int numElement = axisDomainOrder.numElements();
2312	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2313	int idx = domainList.size() * 2 + axisList.size() - 1;
2314	int commRank ;
2315
2316	MPI_Comm_rank(comm_file,&commRank) ;
2317
2318	start.reserve(idx+1);
2319	count.reserve(idx+1);
2320
2321	for (int i = numElement - 1; i >= 0; --i)
2322	{
2323	if (2 == axisDomainOrder(i))
2324	{
2325	CDomain* domain = CDomain::get(domainList[idxDomain]);
2326
2327	if (domain->isCompressible())
2328	{
2329	size_t offset ;
2330	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
2331	if (domain->isDistributed())
2332	{
2333	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2334	if (commRank==0) offset=0 ;
2335	}
2336	else offset=0 ;
2337
2338	start.push_back(offset);
2339	count.push_back(nbIndexes);
2340	idx -= 2;
2341	}
2342	else
2343	{
2344	if ((domain->type) != CDomain::type_attr::unstructured)
2345	{
2346	start.push_back(domain->jbeginValue_);
2347	count.push_back(domain->njValue_);
2348	}
2349	--idx;
2350	start.push_back(domain->ibeginValue_);
2351	count.push_back(domain->niValue_);
2352	--idx;
2353	}
2354	--idxDomain;
2355	}
2356	else if (1 == axisDomainOrder(i))
2357	{
2358	CAxis* axis = CAxis::get(axisList[idxAxis]);
2359
2360	if (axis->isCompressible())
2361	{
2362	size_t offset ;
2363	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
2364	if (axis->isDistributed())
2365	{
2366	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
2367	if (commRank==0) offset=0 ;
2368	}
2369	else offset=0 ;
2370
2371	start.push_back(offset);
2372	count.push_back(nbIndexes);
2373	}
2374	else
2375	{
2376	start.push_back(axis->begin);
2377	count.push_back(axis->n);
2378	}
2379	--idxAxis;
2380	--idx;
2381	}
2382	}
2383	}
2384	else
2385	{
2386	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2387	std::vector<StdString> domainList = grid->getDomainList();
2388	std::vector<StdString> axisList = grid->getAxisList();
2389	std::vector<StdString> scalarList = grid->getScalarList() ;
2390	int numElement = axisDomainOrder.numElements();
2391	int idxDomain = domainList.size() - 1 ;
2392	int idxAxis = axisList.size() - 1 ;
2393	int idxScalar = scalarList.size() - 1 ;
2394	int idx = domainList.size() * 2 + axisList.size() - 1;
2395
2396	start.reserve(idx+1);
2397	count.reserve(idx+1);
2398
2399	for (int i = numElement - 1; i >= 0; --i)
2400	{
2401	if (2 == axisDomainOrder(i))
2402	{
2403	CDomain* domain = CDomain::get(domainList[idxDomain]);
2404	if ((domain->type) != CDomain::type_attr::unstructured)
2405	{
2406	start.push_back(domain->jbeginValue_);
2407	count.push_back(domain->njValue_);
2408	}
2409	--idx ;
2410
2411	start.push_back(domain->ibeginValue_);
2412	count.push_back(domain->niValue_);
2413	--idx ;
2414	--idxDomain;
2415	}
2416	else if (1 == axisDomainOrder(i))
2417	{
2418	CAxis* axis = CAxis::get(axisList[idxAxis]);
2419	start.push_back(axis->begin);
2420	count.push_back(axis->n);
2421	--idx;
2422	--idxAxis;
2423	}
2424	else
2425	{
2426	if (idx ==-1)
2427	{
2428	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
2429	start.push_back(0);
2430	count.push_back(scalar->n);
2431	idx-- ;
2432	}
2433	else if (idx<-1)
2434	{
2435	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
2436	count.back()*=scalar->n;
2437	idx-- ;
2438	}
2439	--idxScalar;
2440	}
2441	}
2442	}
2443
2444
2445	if (info.isActive(logProfile)) CTimer::get("Files : writing data").resume();
2446	writeAndConvertData(field, data, nstep - 1, &start, &count);
2447	if (info.isActive(logProfile)) CTimer::get("Files : writing data").suspend();
2448
2449	if (wtime)
2450	{
2451	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").resume();
2452	if ( wtimeData)
2453	{
2454	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
2455	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
2456	}
2457	if (wtimeCounter)
2458	{
2459	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
2460	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
2461
2462	}
2463	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").suspend();
2464	}
2465
2466	break;
2467	}
2468	}
2469	return nstep ;
2470	}
2471	catch (CNetCdfException& e)
2472	{
2473	StdString msg("On writing field data: ");
2474	msg.append(fieldid); msg.append("\n");
2475	msg.append("In the context : ");
2476	msg.append(context->getId()); msg.append("\n");
2477	msg.append(e.what());
2478	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2479	}
2480	}
2481
2482	void CNc4DataOutput::writeAndConvertData(CField* field, const CArray<double,1>& data, StdSize record, const std::vector<StdSize> start, const std::vector<StdSize> count)
2483	{
2484	StdString fieldid = field->getFieldOutputName();
2485	nc_type type ;
2486	if (field->prec.isEmpty()) type = NC_FLOAT ;
2487	else
2488	{
2489	if (field->prec==2) type = NC_SHORT ;
2490	else if (field->prec==4) type = NC_FLOAT ;
2491	else if (field->prec==8) type = NC_DOUBLE ;
2492	}
2493
2494	bool conversionByNetCDF = true; // default : conversion operated by NetCDF for now (legacy behaviour)
2495	if (!field->conversion_by_netcdf.isEmpty())
2496	{
2497	// use conversion_by_netcdf = ".false." to bypass NetCDF conversion
2498	// poor performances from NC_DOUBLE to NC_FLOAT with isgreater/isless in recent NetCDF available at TGCC
2499	conversionByNetCDF = field->conversion_by_netcdf;
2500	}
2501	if ( ( type == NC_DOUBLE ) \|\| ( conversionByNetCDF ) )
2502	{
2503	SuperClassWriter::writeData(data, fieldid, isCollective, record, start, count);
2504	}
2505	else if ( type == NC_FLOAT )
2506	{
2507	CArray<float,1> f_data;
2508	f_data.resize( data.numElements() );
2509	for (int i = 0; i < data.numElements(); i++)
2510	{
2511	if (data(i) <= X_FLOAT_MAX \|\| data(i) >= X_FLOAT_MIN)
2512	f_data(i) = data(i);
2513	else if (data(i) > X_FLOAT_MAX)
2514	f_data(i) = X_FLOAT_MAX;
2515	else if (data(i) < X_FLOAT_MIN)
2516	f_data(i) = X_FLOAT_MIN;
2517	}
2518	SuperClassWriter::writeData(f_data, fieldid, isCollective, record, start, count);
2519	}
2520	else if ( type == NC_SHORT )
2521	{
2522	CArray<short,1> s_data;
2523	s_data.resize( data.numElements() );
2524	for (int i = 0; i < data.numElements(); i++)
2525	{
2526	if (data(i) <= X_SHORT_MAX \|\| data(i) >= X_SHORT_MIN)
2527	s_data(i) = data(i);
2528	else if (data(i) > X_SHORT_MAX)
2529	s_data(i) = X_SHORT_MAX;
2530	else if (data(i) < X_SHORT_MIN)
2531	s_data(i) = X_SHORT_MIN;
2532	}
2533	SuperClassWriter::writeData(s_data, fieldid, isCollective, record, start, count);
2534	}
2535	else
2536	{
2537	ERROR("CNc4DataOutput::writeAndConvertData(...)", << "Type conversion not managed for " << fieldid );
2538	}
2539
2540	}
2541
2542	//---------------------------------------------------------------
2543
2544	void CNc4DataOutput::writeTimeAxis_
2545	(CField* field,
2546	const std::shared_ptr<CCalendar> cal)
2547	{
2548	StdOStringStream oss;
2549	bool createInstantAxis=false ;
2550	bool createCenteredAxis=false ;
2551	bool createTimeCounterAxis=false ;
2552
2553	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2554
2555
2556	StdString axisId ;
2557	StdString axisBoundId;
2558	StdString timeid(getTimeCounterName());
2559	StdString timeBoundId("axis_nbounds");
2560
2561	StdString strTimeUnits ;
2562	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2563	else strTimeUnits="seconds since " ;
2564
2565	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2566	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2567
2568
2569	if (field->getRelFile()->time_counter.isEmpty())
2570	{
2571	if (timeCounterType==none) createTimeCounterAxis=true ;
2572	if (field->hasTimeCentered)
2573	{
2574	timeCounterType=centered ;
2575	if (!hasTimeCentered) createCenteredAxis=true ;
2576	}
2577	if (field->hasTimeInstant)
2578	{
2579	if (timeCounterType==none) timeCounterType=instant ;
2580	if (!hasTimeInstant) createInstantAxis=true ;
2581	}
2582	}
2583	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
2584	{
2585	if (field->hasTimeCentered)
2586	{
2587	if (!hasTimeCentered) createCenteredAxis=true ;
2588	}
2589	if (field->hasTimeInstant)
2590	{
2591	if (timeCounterType==none) createTimeCounterAxis=true ;
2592	timeCounterType=instant ;
2593	if (!hasTimeInstant) createInstantAxis=true ;
2594	}
2595	}
2596	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
2597	{
2598	if (field->hasTimeCentered)
2599	{
2600	if (timeCounterType==none) createTimeCounterAxis=true ;
2601	timeCounterType=centered ;
2602	if (!hasTimeCentered) createCenteredAxis=true ;
2603	}
2604	if (field->hasTimeInstant)
2605	{
2606	if (!hasTimeInstant) createInstantAxis=true ;
2607	}
2608	}
2609	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
2610	{
2611	if (field->hasTimeCentered)
2612	{
2613	if (!hasTimeCentered) createCenteredAxis=true ;
2614	}
2615	if (field->hasTimeInstant)
2616	{
2617	if (timeCounterType==none) createTimeCounterAxis=true ;
2618	timeCounterType=instant ;
2619	}
2620	}
2621	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
2622	{
2623	if (field->hasTimeCentered)
2624	{
2625	if (timeCounterType==none) createTimeCounterAxis=true ;
2626	timeCounterType=centered ;
2627	}
2628	if (field->hasTimeInstant)
2629	{
2630	if (!hasTimeInstant) createInstantAxis=true ;
2631	}
2632	}
2633	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
2634	{
2635	if (field->hasTimeCentered)
2636	{
2637	if (timeCounterType==none) createTimeCounterAxis=true ;
2638	if (timeCounterType==instant) createInstantAxis=true ;
2639	timeCounterType=centered ;
2640	}
2641	if (field->hasTimeInstant)
2642	{
2643	if (timeCounterType==none)
2644	{
2645	createTimeCounterAxis=true ;
2646	timeCounterType=instant ;
2647	}
2648	if (timeCounterType==centered)
2649	{
2650	if (!hasTimeInstant) createInstantAxis=true ;
2651	}
2652	}
2653	}
2654	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
2655	{
2656	if (field->hasTimeCentered)
2657	{
2658	if (!hasTimeCentered) createCenteredAxis=true ;
2659	}
2660	if (field->hasTimeInstant)
2661	{
2662	if (!hasTimeInstant) createInstantAxis=true ;
2663	}
2664	}
2665	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
2666	{
2667	if (timeCounterType==none) createTimeCounterAxis=true ;
2668	timeCounterType=record ;
2669	if (field->hasTimeCentered)
2670	{
2671	if (!hasTimeCentered) createCenteredAxis=true ;
2672	}
2673	if (field->hasTimeInstant)
2674	{
2675	if (!hasTimeInstant) createInstantAxis=true ;
2676	}
2677	}
2678
2679	if (createInstantAxis)
2680	{
2681	axisId="time_instant" ;
2682	axisBoundId="time_instant_bounds";
2683	hasTimeInstant=true ;
2684	}
2685
2686	if (createCenteredAxis)
2687	{
2688	axisId="time_centered" ;
2689	axisBoundId="time_centered_bounds";
2690	hasTimeCentered=true ;
2691	}
2692
2693
2694	try
2695	{
2696	std::vector<StdString> dims;
2697
2698	if (createInstantAxis \|\| createCenteredAxis)
2699	{
2700	// Adding time_instant or time_centered
2701	dims.push_back(timeid);
2702	if (!SuperClassWriter::varExist(axisId))
2703	{
2704	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2705
2706	CDate timeOrigin=cal->getTimeOrigin() ;
2707	StdOStringStream oss2;
2708	StdString strInitdate=oss2.str() ;
2709	StdString strTimeOrigin=timeOrigin.toString() ;
2710	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2711	strTimeOrigin, axisBoundId);
2712	}
2713
2714	// Adding time_instant_bounds or time_centered_bounds variables
2715	if (!SuperClassWriter::varExist(axisBoundId))
2716	{
2717	dims.clear() ;
2718	dims.push_back(timeid);
2719	dims.push_back(timeBoundId);
2720	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2721	}
2722	}
2723
2724	if (createTimeCounterAxis)
2725	{
2726	// Adding time_counter
2727	axisId = getTimeCounterName();
2728	axisBoundId = getTimeCounterName() + "_bounds";
2729	dims.clear();
2730	dims.push_back(timeid);
2731	if (!SuperClassWriter::varExist(axisId))
2732	{
2733	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2734	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2735
2736	if (field->getRelFile()->time_counter.isEmpty() \|\|
2737	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2738	{
2739	CDate timeOrigin = cal->getTimeOrigin();
2740	StdString strTimeOrigin = timeOrigin.toString();
2741
2742	this->writeTimeAxisAttributes(axisId, cal->getType(),
2743	strTimeUnits+strTimeOrigin,
2744	strTimeOrigin, axisBoundId);
2745	}
2746	}
2747
2748	// Adding time_counter_bound dimension
2749	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
2750	{
2751	if (!SuperClassWriter::varExist(axisBoundId))
2752	{
2753	dims.clear();
2754	dims.push_back(timeid);
2755	dims.push_back(timeBoundId);
2756	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2757	}
2758	}
2759	}
2760	}
2761	catch (CNetCdfException& e)
2762	{
2763	StdString msg("On writing time axis data: ");
2764	msg.append("In the context : ");
2765	CContext* context = CContext::getCurrent() ;
2766	msg.append(context->getId()); msg.append("\n");
2767	msg.append(e.what());
2768	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2769	const std::shared_ptr<CCalendar> cal)", << msg);
2770	}
2771	}
2772
2773	//---------------------------------------------------------------
2774
2775	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2776	const StdString & calendar,
2777	const StdString & units,
2778	const StdString & time_origin,
2779	const StdString & time_bounds,
2780	const StdString & standard_name,
2781	const StdString & long_name)
2782	{
2783	try
2784	{
2785	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2786	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2787	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2788	SuperClassWriter::addAttribute("units", units , &axis_name);
2789	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2790	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2791	}
2792	catch (CNetCdfException& e)
2793	{
2794	StdString msg("On writing time axis Attribute: ");
2795	msg.append("In the context : ");
2796	CContext* context = CContext::getCurrent() ;
2797	msg.append(context->getId()); msg.append("\n");
2798	msg.append(e.what());
2799	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2800	const StdString & calendar,\
2801	const StdString & units, \
2802	const StdString & time_origin, \
2803	const StdString & time_bounds, \
2804	const StdString & standard_name, \
2805	const StdString & long_name)", << msg);
2806	}
2807	}
2808
2809	//---------------------------------------------------------------
2810
2811	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2812	const StdString & axis,
2813	const StdString & standard_name,
2814	const StdString & long_name,
2815	const StdString & units,
2816	const StdString & nav_model)
2817	{
2818	try
2819	{
2820	if (!axis.empty())
2821	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2822
2823	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2824	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2825	SuperClassWriter::addAttribute("units" , units , &axis_name);
2826	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2827	}
2828	catch (CNetCdfException& e)
2829	{
2830	StdString msg("On writing Axis Attribute: ");
2831	msg.append("In the context : ");
2832	CContext* context = CContext::getCurrent() ;
2833	msg.append(context->getId()); msg.append("\n");
2834	msg.append(e.what());
2835	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2836	const StdString & axis, \
2837	const StdString & standard_name, \
2838	const StdString & long_name, \
2839	const StdString & units, \
2840	const StdString & nav_model)", << msg);
2841	}
2842	}
2843
2844	//---------------------------------------------------------------
2845
2846	void CNc4DataOutput::writeLocalAttributes
2847	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2848	{
2849	try
2850	{
2851	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2852	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2853	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2854	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2855	}
2856	catch (CNetCdfException& e)
2857	{
2858	StdString msg("On writing Local Attributes: ");
2859	msg.append("In the context : ");
2860	CContext* context = CContext::getCurrent() ;
2861	msg.append(context->getId()); msg.append("\n");
2862	msg.append(e.what());
2863	ERROR("CNc4DataOutput::writeLocalAttributes \
2864	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2865	}
2866
2867	}
2868
2869	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2870	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2871	{
2872	CArray<int,1> array(2) ;
2873
2874	try
2875	{
2876	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2877	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2878	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2879	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2880	array=ni_glo,nj_glo ;
2881	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2882	array=ni,nj ;
2883	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2884	array=ibegin+1,jbegin+1 ;
2885	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2886	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2887	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2888	array=0,0 ;
2889	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2890	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2891	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2892	/*
2893	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2894	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2895	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2896	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2897	*/
2898	}
2899	catch (CNetCdfException& e)
2900	{
2901	StdString msg("On writing Local Attributes IOIPSL \n");
2902	msg.append("In the context : ");
2903	CContext* context = CContext::getCurrent() ;
2904	msg.append(context->getId()); msg.append("\n");
2905	msg.append(e.what());
2906	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2907	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2908	}
2909	}
2910	//---------------------------------------------------------------
2911
2912	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2913	const StdString & description,
2914	const StdString & conventions,
2915	const StdString & production,
2916	const StdString & timeStamp)
2917	{
2918	try
2919	{
2920	SuperClassWriter::addAttribute("name" , name);
2921	SuperClassWriter::addAttribute("description", description);
2922	SuperClassWriter::addAttribute("title" , description);
2923	SuperClassWriter::addAttribute("Conventions", conventions);
2924	// SuperClassWriter::addAttribute("production" , production);
2925
2926	StdString timeStampStr ;
2927	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
2928	else timeStampStr=file->time_stamp_name ;
2929	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
2930
2931	StdString uuidName ;
2932	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
2933	else uuidName=file->uuid_name ;
2934
2935	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
2936	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
2937
2938	}
2939	catch (CNetCdfException& e)
2940	{
2941	StdString msg("On writing File Attributes \n ");
2942	msg.append("In the context : ");
2943	CContext* context = CContext::getCurrent() ;
2944	msg.append(context->getId()); msg.append("\n");
2945	msg.append(e.what());
2946	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2947	const StdString & description, \
2948	const StdString & conventions, \
2949	const StdString & production, \
2950	const StdString & timeStamp)", << msg);
2951	}
2952	}
2953
2954	//---------------------------------------------------------------
2955
2956	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2957	int data_dim,
2958	int data_ni,
2959	int data_nj,
2960	int data_ibegin,
2961	int data_jbegin)
2962	{
2963	try
2964	{
2965	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2966	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2967	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2968	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2969	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2970	}
2971	catch (CNetCdfException& e)
2972	{
2973	StdString msg("On writing Mask Attributes \n ");
2974	msg.append("In the context : ");
2975	CContext* context = CContext::getCurrent() ;
2976	msg.append(context->getId()); msg.append("\n");
2977	msg.append(e.what());
2978	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2979	int data_dim, \
2980	int data_ni, \
2981	int data_nj, \
2982	int data_ibegin, \
2983	int data_jbegin)", << msg);
2984	}
2985	}
2986
2987	///--------------------------------------------------------------
2988
2989	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
2990	{
2991	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2992	if (it == timeToRecordCache.end())
2993	{
2994	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2995	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
2996	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
2997
2998	CArray<double,2> timeAxisBounds;
2999	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
3000
3001	StdSize record = 0;
3002	double dtime(time);
3003	for (int n = dimSize[0] - 1; n >= 0; n--)
3004	{
3005	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3006	timeAxisBounds*=factorUnit ;
3007	if (timeAxisBounds(1, 0) < dtime)
3008	{
3009	record = n + 1;
3010	break;
3011	}
3012	}
3013	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3014	}
3015	return it->second;
3016	}
3017
3018	///--------------------------------------------------------------
3019
3020	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3021	{
3022	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3023	}
3024
3025	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3026	{
3027	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3028	}
3029
3030	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3031	{
3032	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3033	}
3034
3035	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3036	{
3037	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3038	}
3039
3040	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3041	{
3042	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3043	}
3044
3045	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3046	{
3047	this->writtenDomains.insert(domainName);
3048	}
3049
3050	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3051	{
3052	this->writtenCompressedDomains.insert(domainName);
3053	}
3054
3055	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3056	{
3057	this->writtenAxis.insert(axisName);
3058	}
3059
3060	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3061	{
3062	this->writtenCompressedAxis.insert(axisName);
3063	}
3064
3065	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3066	{
3067	this->writtenScalar.insert(scalarName);
3068	}
3069	} // namespace xios

Note: See TracBrowser for help on using the repository browser.

Context Navigation

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

Download in other formats: