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source: XIOS/dev/dev_olga/src/io/nc4_data_output.cpp @ 1589

Last change on this file since 1589 was 1589, checked in by oabramkina, 6 years ago
Backporting r1578 and r1586 to dev, cleaning the code before merging it to XIOS 2.5.
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: 132.0 KB

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1	#include "nc4_data_output.hpp"
2
3	#include "attribute_template.hpp"
4	#include "group_template.hpp"
5
6	#include "file.hpp"
7	#include "calendar.hpp"
8	#include "context.hpp"
9	#include "context_server.hpp"
10	#include "netCdfException.hpp"
11	#include "exception.hpp"
12	#include "timer.hpp"
13	#include "uuid.hpp"
14	namespace xios
15	{
16	/// ////////////////////// Dfinitions ////////////////////// ///
17	CNc4DataOutput::CNc4DataOutput
18	(CFile* file, const StdString & filename, bool exist)
19	: SuperClass()
20	, SuperClassWriter(filename, exist)
21	, filename(filename)
22	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
23	{
24	SuperClass::type = MULTI_FILE;
25	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
26	}
27
28	CNc4DataOutput::CNc4DataOutput
29	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
30	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
31	: SuperClass()
32	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
33	, comm_file(comm_file)
34	, filename(filename)
35	, isCollective(isCollective)
36	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
37	{
38	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
39	if (file==NULL) compressionLevel = 0 ;
40	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
41	}
42
43	CNc4DataOutput::~CNc4DataOutput(void)
44	{ /* Ne rien faire de plus */ }
45
46	///--------------------------------------------------------------
47
48	const StdString & CNc4DataOutput::getFileName(void) const
49	{
50	return (this->filename);
51	}
52
53	//---------------------------------------------------------------
54
55	void CNc4DataOutput::writeDomain_(CDomain* domain)
56	{
57	StdString lonName,latName ;
58
59	domain->computeWrittenIndex();
60	domain->computeWrittenCompressedIndex(comm_file);
61
62	if (domain->type == CDomain::type_attr::unstructured)
63	{
64	if (SuperClassWriter::useCFConvention)
65	writeUnstructuredDomain(domain) ;
66	else
67	writeUnstructuredDomainUgrid(domain) ;
68	return ;
69	}
70
71	CContext* context = CContext::getCurrent() ;
72	CContextServer* server=context->server ;
73
74	if (domain->IsWritten(this->filename)) return;
75	domain->checkAttributes();
76
77	if (domain->isEmpty())
78	if (SuperClass::type==MULTI_FILE) return;
79
80	std::vector<StdString> dim0, dim1;
81	StdString domid = domain->getDomainOutputName();
82	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
83	if (isWrittenDomain(domid)) return ;
84	else setWrittenDomain(domid);
85
86	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
87
88
89	StdString dimXid, dimYid ;
90
91	nc_type typePrec ;
92	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
93	else if (domain->prec==4) typePrec = NC_FLOAT ;
94	else if (domain->prec==8) typePrec = NC_DOUBLE ;
95
96	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
97	switch (domain->type)
98	{
99	case CDomain::type_attr::curvilinear :
100
101	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
102	else lonName = domain->lon_name;
103
104	if (domain->lat_name.isEmpty()) latName = "nav_lat";
105	else latName = domain->lat_name;
106
107	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
108	else dimXid=domain->dim_i_name.getValue() + appendDomid;
109
110	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
111	else dimYid=domain->dim_j_name.getValue() + appendDomid;
112
113	break ;
114
115	case CDomain::type_attr::rectilinear :
116
117	if (domain->lon_name.isEmpty())
118	{
119	if (domain->dim_i_name.isEmpty())
120	lonName = "lon";
121	else
122	lonName = domain->dim_i_name.getValue();
123	}
124	else lonName = domain->lon_name;
125
126	if (domain->lat_name.isEmpty())
127	{
128	if (domain->dim_j_name.isEmpty())
129	latName = "lat";
130	else
131	latName = domain->dim_j_name.getValue();
132	}
133	else latName = domain->lat_name;
134
135	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
136	else dimXid = domain->dim_i_name.getValue()+appendDomid;
137
138	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
139	else dimYid = domain->dim_j_name.getValue()+appendDomid;
140	break;
141	}
142
143	StdString dimVertId = StdString("nvertex").append(appendDomid);
144
145	string lonid,latid,bounds_lonid,bounds_latid ;
146	string areaId = "area" + appendDomid;
147	/*
148	StdString lonid_loc = (server->intraCommSize > 1)
149	? StdString("lon").append(appendDomid).append("_local")
150	: lonid;
151	StdString latid_loc = (server->intraCommSize > 1)
152	? StdString("lat").append(appendDomid).append("_local")
153	: latid;
154	*/
155
156	CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
157	int nbWritten = indexToWrite.numElements();
158	CArray<double,1> writtenLat, writtenLon;
159	CArray<double,2> writtenBndsLat, writtenBndsLon;
160	CArray<double,1> writtenArea;
161
162	if (domain->hasLonLat)
163	{
164	writtenLat.resize(nbWritten);
165	writtenLon.resize(nbWritten);
166	for (int idx = 0; idx < nbWritten; ++idx)
167	{
168	if (indexToWrite(idx) < 0)
169	{
170	writtenLat(idx) = -1.; // hole
171	writtenLon(idx) = -1.;
172	}
173	else
174	{
175	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
176	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
177	}
178	}
179
180	if (domain->hasBounds)
181	{
182	int nvertex = domain->nvertex, idx;
183	writtenBndsLat.resize(nvertex, nbWritten);
184	writtenBndsLon.resize(nvertex, nbWritten);
185	CArray<double,2>& boundslat = domain->bounds_latvalue;
186	CArray<double,2>& boundslon = domain->bounds_lonvalue;
187	for (idx = 0; idx < nbWritten; ++idx)
188	for (int nv = 0; nv < nvertex; ++nv)
189	{
190	if (indexToWrite(idx) < 0)
191	{
192	writtenBndsLat(nv, idx) = -1.; // hole
193	writtenBndsLon(nv, idx) = -1.;
194	}
195	else
196	{
197	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
198	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
199	}
200	}
201	}
202	}
203
204	if (domain->hasArea)
205	{
206	writtenArea.resize(nbWritten);
207	for (int idx = 0; idx < nbWritten; ++idx)
208	{
209	if (indexToWrite(idx) < 0)
210	writtenArea(idx) = -1.;
211	else
212	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
213	}
214	}
215
216	try
217	{
218	switch (SuperClass::type)
219	{
220	case (MULTI_FILE) :
221	{
222	switch (domain->type)
223	{
224	case CDomain::type_attr::curvilinear :
225	dim0.push_back(dimYid); dim0.push_back(dimXid);
226	lonid = lonName+appendDomid;
227	latid = latName+appendDomid;
228	break ;
229	case CDomain::type_attr::rectilinear :
230	lonid = lonName+appendDomid;
231	latid = latName+appendDomid;
232	dim0.push_back(dimYid);
233	dim1.push_back(dimXid);
234	break;
235	}
236	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
237	else bounds_lonid = "bounds_"+lonName+appendDomid;
238	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
239	else bounds_latid = "bounds_"+latName+appendDomid;
240
241	SuperClassWriter::addDimension(dimXid, domain->ni);
242	SuperClassWriter::addDimension(dimYid, domain->nj);
243
244	if (domain->hasBounds)
245	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
246
247	if (server->intraCommSize > 1)
248	{
249	this->writeLocalAttributes(domain->ibegin,
250	domain->ni,
251	domain->jbegin,
252	domain->nj,
253	appendDomid);
254
255	if (singleDomain)
256	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
257	domain->ibegin,
258	domain->ni,
259	domain->jbegin,
260	domain->nj,
261	domain->ni_glo,domain->nj_glo,
262	server->intraCommRank,server->intraCommSize);
263	}
264
265	if (domain->hasLonLat)
266	{
267	switch (domain->type)
268	{
269	case CDomain::type_attr::curvilinear :
270	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
271	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
272	break ;
273	case CDomain::type_attr::rectilinear :
274	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
275	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
276	break ;
277	}
278
279	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
280	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
281
282	if (domain->hasBounds)
283	{
284	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
285	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
286
287	dim0.clear();
288	dim0.push_back(dimYid);
289	dim0.push_back(dimXid);
290	dim0.push_back(dimVertId);
291	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
292	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
293	}
294	}
295
296	dim0.clear();
297	dim0.push_back(dimYid);
298	dim0.push_back(dimXid);
299
300
301	// supress mask if (server->intraCommSize > 1)
302	// supress mask {
303	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
304	// supress mask
305	// supress mask this->writeMaskAttributes(maskid,
306	// supress mask domain->data_dim.getValue()/*,
307	// supress mask domain->data_ni.getValue(),
308	// supress mask domain->data_nj.getValue(),
309	// supress mask domain->data_ibegin.getValue(),
310	// supress mask domain->data_jbegin.getValue()*/);
311	// supress mask }
312
313	//SuperClassWriter::setDefaultValue(maskid, &dvm);
314
315	if (domain->hasArea)
316	{
317	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
318	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
319	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
320	}
321
322	SuperClassWriter::definition_end();
323
324	if (domain->hasLonLat)
325	{
326	switch (domain->type)
327	{
328	case CDomain::type_attr::curvilinear :
329	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
330	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
331	break;
332	case CDomain::type_attr::rectilinear :
333	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->ni)) ;
334	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
335	CArray<double,1> lon = writtenLon(Range(0,domain->ni-1)) ;
336	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
337	break;
338	}
339
340	if (domain->hasBounds)
341	{
342	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
343	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
344	}
345	}
346
347	if (domain->hasArea)
348	{
349	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
350	}
351
352	SuperClassWriter::definition_start();
353
354	break;
355	}
356	case (ONE_FILE) :
357	{
358	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
359	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
360
361	if (domain->hasBounds)
362	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
363
364	if (domain->hasLonLat)
365	{
366	switch (domain->type)
367	{
368	case CDomain::type_attr::curvilinear :
369	dim0.push_back(dimYid); dim0.push_back(dimXid);
370	lonid = lonName+appendDomid;
371	latid = latName+appendDomid;
372	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
373	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
374	break;
375
376	case CDomain::type_attr::rectilinear :
377	dim0.push_back(dimYid);
378	dim1.push_back(dimXid);
379	lonid = lonName+appendDomid;
380	latid = latName+appendDomid;
381	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
382	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
383	break;
384	}
385	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
386	else bounds_lonid = "bounds_"+lonName+appendDomid;
387	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
388	else bounds_latid = "bounds_"+latName+appendDomid;
389
390	this->writeAxisAttributes
391	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
392	this->writeAxisAttributes
393	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
394
395	if (domain->hasBounds)
396	{
397	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
398	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
399
400	dim0.clear();
401	dim0.push_back(dimYid);
402	dim0.push_back(dimXid);
403	dim0.push_back(dimVertId);
404	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
405	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
406	}
407	}
408
409	if (domain->hasArea)
410	{
411	dim0.clear();
412	dim0.push_back(dimYid); dim0.push_back(dimXid);
413	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
414	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
415	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
416	dim0.clear();
417	}
418
419	SuperClassWriter::definition_end();
420
421	switch (domain->type)
422	{
423	case CDomain::type_attr::curvilinear :
424	{
425	std::vector<StdSize> start(2) ;
426	std::vector<StdSize> count(2) ;
427	// Comment out for a moment because it is not working for a hole
428	// if (domain->isEmpty())
429	// {
430	// start[0]=0 ; start[1]=0 ;
431	// count[0]=0 ; count[1]=0 ;
432	// }
433	// else
434	{
435	start[1]=domain->ibegin;
436	start[0]=domain->jbegin;
437	count[1]=domain->ni ; count[0]=domain->nj ;
438	}
439
440	if (domain->hasLonLat)
441	{
442	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
443	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
444	}
445	break;
446	}
447	case CDomain::type_attr::rectilinear :
448	{
449	if (domain->hasLonLat)
450	{
451	std::vector<StdSize> start(1) ;
452	std::vector<StdSize> count(1) ;
453	if (domain->isEmpty())
454	{
455	start[0]=0 ;
456	count[0]=0 ;
457	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
458	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
459	}
460	else
461	{
462	start[0]=domain->jbegin;
463	count[0]=domain->nj;
464	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->ni));
465	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
466
467	start[0]=domain->ibegin;
468	count[0]=domain->ni;
469	CArray<double,1> lon = writtenLon(Range(0,domain->ni-1));
470	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
471	}
472	}
473	break;
474	}
475	}
476
477	if (domain->hasBounds)
478	{
479	std::vector<StdSize> start(3);
480	std::vector<StdSize> count(3);
481	if (domain->isEmpty())
482	{
483	start[2] = start[1] = start[0] = 0;
484	count[2] = count[1] = count[0] = 0;
485	}
486	else
487	{
488	start[2] = 0;
489	start[1] = domain->ibegin;
490	start[0] = domain->jbegin;
491	count[2] = domain->nvertex;
492	count[1] = domain->ni;
493	count[0] = domain->nj;
494	}
495
496	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0, &start, &count);
497	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0, &start, &count);
498	}
499
500	if (domain->hasArea)
501	{
502	std::vector<StdSize> start(2);
503	std::vector<StdSize> count(2);
504
505	if (domain->isEmpty())
506	{
507	start[0] = 0; start[1] = 0;
508	count[0] = 0; count[1] = 0;
509	}
510	else
511	{
512	start[1] = domain->ibegin;
513	start[0] = domain->jbegin;
514	count[1] = domain->ni;
515	count[0] = domain->nj;
516	}
517
518	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
519	}
520
521	SuperClassWriter::definition_start();
522	break;
523	}
524	default :
525	ERROR("CNc4DataOutput::writeDomain(domain)",
526	<< "[ type = " << SuperClass::type << "]"
527	<< " not implemented yet !");
528	}
529	}
530	catch (CNetCdfException& e)
531	{
532	StdString msg("On writing the domain : ");
533	msg.append(domid); msg.append("\n");
534	msg.append("In the context : ");
535	msg.append(context->getId()); msg.append("\n");
536	msg.append(e.what());
537	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
538	}
539
540	domain->addRelFile(this->filename);
541	}
542
543	//--------------------------------------------------------------
544
545	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
546	{
547	CContext* context = CContext::getCurrent() ;
548	CContextServer* server=context->server ;
549
550	if (domain->IsWritten(this->filename)) return;
551
552	StdString domid = domain->getDomainOutputName();
553
554	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
555	// Thus the entire mesh connectivity will be generated at once.
556	if (isWrittenDomain(domid)) return ;
557	else setWrittenDomain(domid);
558
559	domain->checkAttributes();
560	if (domain->isEmpty())
561	if (SuperClass::type==MULTI_FILE) return ;
562
563	nc_type typePrec ;
564	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
565	else if (domain->prec==4) typePrec = NC_FLOAT ;
566	else if (domain->prec==8) typePrec = NC_DOUBLE ;
567
568	std::vector<StdString> dim0;
569	StdString domainName = domain->name;
570	domain->assignMesh(domainName, domain->nvertex);
571	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
572
573	StdString node_x = domainName + "_node_x";
574	StdString node_y = domainName + "_node_y";
575
576	StdString edge_x = domainName + "_edge_x";
577	StdString edge_y = domainName + "_edge_y";
578	StdString edge_nodes = domainName + "_edge_nodes";
579
580	StdString face_x = domainName + "_face_x";
581	StdString face_y = domainName + "_face_y";
582	StdString face_nodes = domainName + "_face_nodes";
583	StdString face_edges = domainName + "_face_edges";
584	StdString edge_faces = domainName + "_edge_face_links";
585	StdString face_faces = domainName + "_face_links";
586
587	StdString dimNode = "n" + domainName + "_node";
588	StdString dimEdge = "n" + domainName + "_edge";
589	StdString dimFace = "n" + domainName + "_face";
590	StdString dimVertex = "n" + domainName + "_vertex";
591	StdString dimTwo = "Two";
592
593	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
594	dim0.clear();
595	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
596	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
597	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
598	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
599	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
600
601	try
602	{
603	switch (SuperClass::type)
604	{
605	case (ONE_FILE) :
606	{
607	// Adding nodes
608	if (domain->nvertex == 1)
609	{
610	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
611	{
612	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
613	dim0.clear();
614	dim0.push_back(dimNode);
615	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
616	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
617	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
618	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
619	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
620	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
621	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
622	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
623	}
624	} // domain->nvertex == 1
625
626	// Adding edges and nodes, if nodes have not been defined previously
627	if (domain->nvertex == 2)
628	{
629	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
630	{
631	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
632	dim0.clear();
633	dim0.push_back(dimNode);
634	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
635	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
636	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
637	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
638	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
639	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
640	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
641	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
642	}
643	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
644	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
645	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
646	dim0.clear();
647	dim0.push_back(dimEdge);
648	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
649	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
650	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
651	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
652	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
653	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
654	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
655	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
656	dim0.clear();
657	dim0.push_back(dimEdge);
658	dim0.push_back(dimTwo);
659	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
660	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
661	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
662	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
663	} // domain->nvertex == 2
664
665	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
666	if (domain->nvertex > 2)
667	{
668	// Nodes
669	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
670	{
671	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
672	dim0.clear();
673	dim0.push_back(dimNode);
674	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
675	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
676	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
677	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
678	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
679	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
680	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
681	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
682	}
683	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
684	{
685	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
686	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
687	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
688	dim0.clear();
689	dim0.push_back(dimEdge);
690	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
691	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
692	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
693	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
694	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
695	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
696	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
697	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
698	dim0.clear();
699	dim0.push_back(dimEdge);
700	dim0.push_back(dimTwo);
701	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
702	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
703	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
704	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
705	}
706	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
707	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
708	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
709	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
710	dim0.clear();
711	dim0.push_back(dimFace);
712	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
713	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
714	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
715	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
716	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
717	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
718	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
719	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
720	dim0.clear();
721	dim0.push_back(dimFace);
722	dim0.push_back(dimVertex);
723	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
724	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
725	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
726	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
727	dim0.clear();
728	dim0.push_back(dimFace);
729	dim0.push_back(dimVertex);
730	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
731	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
732	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
733	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
734	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
735	dim0.clear();
736	dim0.push_back(dimEdge);
737	dim0.push_back(dimTwo);
738	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
739	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
740	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
741	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
742	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
743	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
744	dim0.clear();
745	dim0.push_back(dimFace);
746	dim0.push_back(dimVertex);
747	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
748	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
749	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
750	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
751	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
752	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
753	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
754	} // domain->nvertex > 2
755
756	SuperClassWriter::definition_end();
757
758	std::vector<StdSize> startEdges(1) ;
759	std::vector<StdSize> countEdges(1) ;
760	std::vector<StdSize> startNodes(1) ;
761	std::vector<StdSize> countNodes(1) ;
762	std::vector<StdSize> startFaces(1) ;
763	std::vector<StdSize> countFaces(1) ;
764	std::vector<StdSize> startEdgeNodes(2) ;
765	std::vector<StdSize> countEdgeNodes(2) ;
766	std::vector<StdSize> startEdgeFaces(2) ;
767	std::vector<StdSize> countEdgeFaces(2) ;
768	std::vector<StdSize> startFaceConctv(2) ;
769	std::vector<StdSize> countFaceConctv(2) ;
770
771	if (domain->nvertex == 1)
772	{
773	if (domain->isEmpty())
774	{
775	startNodes[0]=0 ;
776	countNodes[0]=0 ;
777	}
778	else
779	{
780	startNodes[0] = domain->ibegin;
781	countNodes[0] = domain->ni ;
782	}
783
784	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
785	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
786	}
787	else if (domain->nvertex == 2)
788	{
789	if (domain->isEmpty())
790	{
791	startEdges[0]=0 ;
792	countEdges[0]=0 ;
793	startNodes[0]=0 ;
794	countNodes[0]=0 ;
795	startEdgeNodes[0]=0;
796	startEdgeNodes[1]=0;
797	countEdgeNodes[0]=0;
798	countEdgeNodes[1]=0;
799
800	}
801	else
802	{
803	startEdges[0] = domain->ibegin;
804	countEdges[0] = domain->ni;
805	startNodes[0] = domain->mesh->node_start;
806	countNodes[0] = domain->mesh->node_count;
807	startEdgeNodes[0] = domain->ibegin;
808	startEdgeNodes[1] = 0;
809	countEdgeNodes[0] = domain->ni;
810	countEdgeNodes[1] = 2;
811	}
812	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
813	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
814	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
815	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
816	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
817	}
818	else
819	{
820	if (domain->isEmpty())
821	{
822	startFaces[0] = 0 ;
823	countFaces[0] = 0 ;
824	startNodes[0] = 0;
825	countNodes[0] = 0;
826	startEdges[0] = 0;
827	countEdges[0] = 0;
828	startEdgeFaces[0] = 0;
829	startEdgeFaces[1] = 0;
830	countEdgeFaces[0] = 0;
831	countEdgeFaces[1] = 0;
832	startFaceConctv[0] = 0;
833	startFaceConctv[1] = 0;
834	countFaceConctv[0] = 0;
835	countFaceConctv[1] = 0;
836	}
837	else
838	{
839	startFaces[0] = domain->ibegin;
840	countFaces[0] = domain->ni ;
841	startNodes[0] = domain->mesh->node_start;
842	countNodes[0] = domain->mesh->node_count;
843	startEdges[0] = domain->mesh->edge_start;
844	countEdges[0] = domain->mesh->edge_count;
845	startEdgeNodes[0] = domain->mesh->edge_start;
846	startEdgeNodes[1] = 0;
847	countEdgeNodes[0] = domain->mesh->edge_count;
848	countEdgeNodes[1]= 2;
849	startEdgeFaces[0] = domain->mesh->edge_start;
850	startEdgeFaces[1]= 0;
851	countEdgeFaces[0] = domain->mesh->edge_count;
852	countEdgeFaces[1]= 2;
853	startFaceConctv[0] = domain->ibegin;
854	startFaceConctv[1] = 0;
855	countFaceConctv[0] = domain->ni;
856	countFaceConctv[1] = domain->nvertex;
857	}
858	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
859	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
860	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
861	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
862	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
863	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
864	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
865	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
866	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
867	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
868	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
869	}
870	SuperClassWriter::definition_start();
871
872	break;
873	} // ONE_FILE
874
875	case (MULTI_FILE) :
876	{
877	ERROR("CNc4DataOutput::writeDomain(domain)",
878	<< "[ type = multiple_file ]"
879	<< " is not yet implemented for UGRID files !");
880	break;
881	}
882
883	default :
884	ERROR("CNc4DataOutput::writeDomain(domain)",
885	<< "[ type = " << SuperClass::type << "]"
886	<< " not implemented yet !");
887	} // switch
888	} // try
889
890	catch (CNetCdfException& e)
891	{
892	StdString msg("On writing the domain : ");
893	msg.append(domid); msg.append("\n");
894	msg.append("In the context : ");
895	msg.append(context->getId()); msg.append("\n");
896	msg.append(e.what());
897	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
898	}
899
900	domain->addRelFile(this->filename);
901	}
902
903	//--------------------------------------------------------------
904
905	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
906	{
907	CContext* context = CContext::getCurrent() ;
908	CContextServer* server=context->server ;
909
910	if (domain->IsWritten(this->filename)) return;
911	domain->checkAttributes();
912
913	if (domain->isEmpty())
914	if (SuperClass::type==MULTI_FILE) return ;
915
916	std::vector<StdString> dim0, dim1;
917	StdString domid = domain->getDomainOutputName();
918	if (isWrittenDomain(domid)) return ;
919	else setWrittenDomain(domid);
920
921	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
922
923	StdString lonName,latName, cellName ;
924	if (domain->lon_name.isEmpty()) lonName = "lon";
925	else lonName = domain->lon_name;
926
927	if (domain->lat_name.isEmpty()) latName = "lat";
928	else latName = domain->lat_name;
929
930	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
931	else cellName="cell";
932	StdString dimXid = cellName+appendDomid;
933	StdString dimVertId = StdString("nvertex").append(appendDomid);
934
935	string lonid,latid,bounds_lonid,bounds_latid ;
936	string areaId = "area" + appendDomid;
937
938	nc_type typePrec ;
939	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
940	else if (domain->prec==4) typePrec = NC_FLOAT ;
941	else if (domain->prec==8) typePrec = NC_DOUBLE ;
942
943	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
944
945	CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
946	int nbWritten = indexToWrite.numElements();
947	CArray<double,1> writtenLat, writtenLon;
948	CArray<double,2> writtenBndsLat, writtenBndsLon;
949	CArray<double,1> writtenArea;
950
951	if (domain->hasLonLat)
952	{
953	writtenLat.resize(nbWritten);
954	writtenLon.resize(nbWritten);
955	for (int idx = 0; idx < nbWritten; ++idx)
956	{
957	if (indexToWrite(idx) < 0)
958	{
959	writtenLat(idx) = -1.;
960	writtenLon(idx) = -1.;
961	}
962	else
963	{
964	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
965	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
966	}
967	}
968	}
969
970	if (domain->hasBounds)
971	{
972	int nvertex = domain->nvertex, idx;
973	writtenBndsLat.resize(nvertex, nbWritten);
974	writtenBndsLon.resize(nvertex, nbWritten);
975	CArray<double,2>& boundslat = domain->bounds_latvalue;
976	CArray<double,2>& boundslon = domain->bounds_lonvalue;
977	for (idx = 0; idx < nbWritten; ++idx)
978	{
979	for (int nv = 0; nv < nvertex; ++nv)
980	{
981	if (indexToWrite(idx) < 0)
982	{
983	writtenBndsLat(nv, idx) = -1.;
984	writtenBndsLon(nv, idx) = -1.;
985	}
986	else
987	{
988	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
989	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
990	}
991	}
992	}
993	}
994
995	if (domain->hasArea)
996	{
997	writtenArea.resize(nbWritten);
998	for (int idx = 0; idx < nbWritten; ++idx)
999	{
1000	if (indexToWrite(idx) < 0)
1001	writtenArea(idx) = -1.;
1002	else
1003	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
1004	}
1005	}
1006
1007	try
1008	{
1009	switch (SuperClass::type)
1010	{
1011	case (MULTI_FILE) :
1012	{
1013	dim0.push_back(dimXid);
1014	SuperClassWriter::addDimension(dimXid, domain->ni);
1015
1016	lonid = lonName+appendDomid;
1017	latid = latName+appendDomid;
1018	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1019	else bounds_lonid = "bounds_"+lonName+appendDomid;
1020	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1021	else bounds_latid = "bounds_"+latName+appendDomid;
1022
1023	if (domain->hasLonLat)
1024	{
1025	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1026	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1027	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1028	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1029	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1030	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1031	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
1032	}
1033	dim0.clear();
1034	if (domain->hasBounds)
1035	{
1036	dim0.push_back(dimXid);
1037	dim0.push_back(dimVertId);
1038	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1039	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1040	}
1041
1042	dim0.clear();
1043	dim0.push_back(dimXid);
1044	if (domain->hasArea)
1045	{
1046	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1047	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1048	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1049	}
1050
1051	SuperClassWriter::definition_end();
1052
1053	if (domain->hasLonLat)
1054	{
1055	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
1056	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
1057	if (domain->hasBounds)
1058	{
1059	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
1060	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
1061	}
1062	}
1063
1064	if (domain->hasArea)
1065	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
1066
1067	SuperClassWriter::definition_start();
1068	break ;
1069	}
1070
1071	case (ONE_FILE) :
1072	{
1073	lonid = lonName+appendDomid;
1074	latid = latName+appendDomid;
1075	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1076	else bounds_lonid = "bounds_"+lonName+appendDomid;
1077	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1078	else bounds_latid = "bounds_"+latName+appendDomid;
1079
1080	dim0.push_back(dimXid);
1081	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
1082	if (domain->hasLonLat)
1083	{
1084	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1085	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1086
1087	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1088	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1089	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1090	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1091	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
1092	}
1093	dim0.clear();
1094
1095	if (domain->hasBounds)
1096	{
1097	dim0.push_back(dimXid);
1098	dim0.push_back(dimVertId);
1099	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1100	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1101	}
1102
1103	if (domain->hasArea)
1104	{
1105	dim0.clear();
1106	dim0.push_back(dimXid);
1107	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1108	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1109	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1110	}
1111
1112	SuperClassWriter::definition_end();
1113
1114	std::vector<StdSize> start(1), startBounds(2) ;
1115	std::vector<StdSize> count(1), countBounds(2) ;
1116	if (domain->isEmpty())
1117	{
1118	start[0]=0 ;
1119	count[0]=0 ;
1120	startBounds[1]=0 ;
1121	countBounds[1]=nvertex ;
1122	startBounds[0]=0 ;
1123	countBounds[0]=0 ;
1124	}
1125	else
1126	{
1127	start[0]=domain->ibegin;
1128	count[0]=domain->ni;
1129	startBounds[0]=domain->ibegin;
1130	startBounds[1]=0 ;
1131	countBounds[0]=domain->ni;
1132	countBounds[1]=nvertex ;
1133	}
1134
1135	if (domain->hasLonLat)
1136	{
1137	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
1138	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
1139	if (domain->hasBounds)
1140	{
1141	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1142	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1143	}
1144	}
1145
1146	if (domain->hasArea)
1147	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
1148
1149	SuperClassWriter::definition_start();
1150
1151	break;
1152	}
1153	default :
1154	ERROR("CNc4DataOutput::writeDomain(domain)",
1155	<< "[ type = " << SuperClass::type << "]"
1156	<< " not implemented yet !");
1157	}
1158	}
1159	catch (CNetCdfException& e)
1160	{
1161	StdString msg("On writing the domain : ");
1162	msg.append(domid); msg.append("\n");
1163	msg.append("In the context : ");
1164	msg.append(context->getId()); msg.append("\n");
1165	msg.append(e.what());
1166	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1167	}
1168	domain->addRelFile(this->filename);
1169	}
1170	//--------------------------------------------------------------
1171
1172	void CNc4DataOutput::writeAxis_(CAxis* axis)
1173	{
1174	if (axis->IsWritten(this->filename)) return;
1175	axis->checkAttributes();
1176
1177	axis->computeWrittenIndex();
1178	axis->computeWrittenCompressedIndex(comm_file);
1179
1180	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
1181	: axis->n_glo.getValue();
1182
1183	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
1184
1185	std::vector<StdString> dims;
1186	StdString axisid = axis->getAxisOutputName();
1187	StdString axisDim, axisBoundsId;
1188	if (isWrittenAxis(axisid)) return ;
1189	else setWrittenAxis(axisid);
1190
1191	nc_type typePrec ;
1192	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1193	else if (axis->prec==4) typePrec = NC_FLOAT ;
1194	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1195
1196	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1197	string strId="str_len" ;
1198	try
1199	{
1200	if (axis->dim_name.isEmpty()) axisDim = axisid;
1201	else axisDim=axis->dim_name.getValue();
1202	SuperClassWriter::addDimension(axisDim, size);
1203	dims.push_back(axisDim);
1204
1205	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1206
1207	if (axis->hasValue \|\| !axis->label.isEmpty())
1208	{
1209	if (!axis->label.isEmpty()) dims.push_back(strId);
1210
1211	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1212
1213	if (!axis->name.isEmpty())
1214	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1215
1216	if (!axis->standard_name.isEmpty())
1217	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1218
1219	if (!axis->long_name.isEmpty())
1220	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1221
1222	if (!axis->unit.isEmpty())
1223	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1224
1225	if (!axis->axis_type.isEmpty())
1226	{
1227	switch(axis->axis_type)
1228	{
1229	case CAxis::axis_type_attr::X :
1230	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1231	break;
1232	case CAxis::axis_type_attr::Y :
1233	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1234	break;
1235	case CAxis::axis_type_attr::Z :
1236	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1237	break;
1238	case CAxis::axis_type_attr::T :
1239	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1240	break;
1241	}
1242	}
1243
1244	if (!axis->positive.isEmpty())
1245	{
1246	SuperClassWriter::addAttribute("positive",
1247	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1248	&axisid);
1249	}
1250
1251	if (!axis->formula.isEmpty())
1252	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1253
1254	if (!axis->formula_term.isEmpty())
1255	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
1256
1257	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1258	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1259	{
1260	dims.push_back("axis_nbounds");
1261	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1262	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1263
1264	if (!axis->standard_name.isEmpty())
1265	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1266
1267	if (!axis->unit.isEmpty())
1268	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1269
1270	if (!axis->formula_bounds.isEmpty())
1271	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1272
1273	if (!axis->formula_term_bounds.isEmpty())
1274	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
1275	}
1276	}
1277
1278	SuperClassWriter::definition_end();
1279
1280	CArray<int, 1>& indexToWrite = axis->localIndexToWriteOnServer;
1281	int nbWritten = indexToWrite.numElements();
1282	CArray<double,1> axis_value(indexToWrite.numElements());
1283	if (!axis->value.isEmpty())
1284	{
1285	for (int i = 0; i < nbWritten; i++)
1286	{
1287	if (indexToWrite(i) < 0)
1288	axis_value(i) = -1; // Some value in case of a hole
1289	else
1290	axis_value(i) = axis->value(indexToWrite(i));
1291	}
1292	}
1293	CArray<double,2> axis_bounds;
1294	CArray<string,1> axis_label;
1295	if (!axis->label.isEmpty())
1296	{
1297	axis_label.resize(indexToWrite.numElements());
1298	for (int i = 0; i < nbWritten; i++)
1299	{
1300	if (indexToWrite(i) < 0)
1301	axis_label(i) = boost::lexical_cast<string>(-1); // Some value in case of a hole
1302	else
1303	axis_label(i) = axis->label(indexToWrite(i));
1304	}
1305	}
1306
1307	switch (SuperClass::type)
1308	{
1309	case MULTI_FILE:
1310	{
1311	if (axis->label.isEmpty())
1312	{
1313	if (!axis->value.isEmpty())
1314	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1315
1316	if (!axis->bounds.isEmpty())
1317	{
1318	axis_bounds.resize(2, indexToWrite.numElements());
1319	for (int i = 0; i < nbWritten; ++i)
1320	{
1321	if (indexToWrite(i) < 0)
1322	{
1323	axis_bounds(0, i) = -1.; // Some value in case of a hole
1324	axis_bounds(1, i) = -1.;
1325	}
1326	else
1327	{
1328	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1329	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1330	}
1331	}
1332	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0);
1333	}
1334	}
1335	else
1336	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0);
1337
1338	SuperClassWriter::definition_start();
1339	break;
1340	}
1341	case ONE_FILE:
1342	{
1343	std::vector<StdSize> start(1), startBounds(2) ;
1344	std::vector<StdSize> count(1), countBounds(2) ;
1345	start[0] = startBounds[0] = axis->begin;
1346	count[0] = countBounds[0] = axis->n;
1347	startBounds[1] = 0;
1348	countBounds[1] = 2;
1349
1350	if (axis->label.isEmpty())
1351	{
1352	if (!axis->value.isEmpty())
1353	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1354
1355	if (!axis->bounds.isEmpty())
1356	{
1357	axis_bounds.resize(2, indexToWrite.numElements());
1358	for (int i = 0; i < nbWritten; ++i)
1359	{
1360	if (indexToWrite(i) < 0)
1361	{
1362	axis_bounds(0, i) = -1.;
1363	axis_bounds(1, i) = -1.;
1364	}
1365	else
1366	{
1367	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1368	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1369	}
1370	}
1371	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1372	}
1373	}
1374	else
1375	{
1376	std::vector<StdSize> startLabel(2), countLabel(2);
1377	startLabel[0] = start[0]; startLabel[1] = 0;
1378	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1379	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0, &startLabel, &countLabel);
1380	}
1381
1382	SuperClassWriter::definition_start();
1383
1384	break;
1385	}
1386	default :
1387	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1388	<< "[ type = " << SuperClass::type << "]"
1389	<< " not implemented yet !");
1390	}
1391	}
1392	catch (CNetCdfException& e)
1393	{
1394	StdString msg("On writing the axis : ");
1395	msg.append(axisid); msg.append("\n");
1396	msg.append("In the context : ");
1397	CContext* context = CContext::getCurrent() ;
1398	msg.append(context->getId()); msg.append("\n");
1399	msg.append(e.what());
1400	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1401	}
1402	axis->addRelFile(this->filename);
1403	}
1404
1405	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1406	{
1407	if (scalar->IsWritten(this->filename)) return;
1408	scalar->checkAttributes();
1409	int scalarSize = 1;
1410
1411	StdString scalaId = scalar->getScalarOutputName();
1412	StdString boundsId;
1413	if (isWrittenAxis(scalaId)) return ;
1414	else setWrittenAxis(scalaId);
1415
1416	nc_type typePrec ;
1417	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1418	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1419	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1420
1421	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1422	string strId="str_len" ;
1423
1424	try
1425	{
1426	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1427
1428	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1429	{
1430	std::vector<StdString> dims;
1431	StdString scalarDim = scalaId;
1432
1433	if (!scalar->label.isEmpty()) dims.push_back(strId);
1434
1435	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1436
1437	if (!scalar->name.isEmpty())
1438	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1439
1440	if (!scalar->standard_name.isEmpty())
1441	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1442
1443	if (!scalar->long_name.isEmpty())
1444	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1445
1446	if (!scalar->unit.isEmpty())
1447	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1448
1449	if (!scalar->axis_type.isEmpty())
1450	{
1451	switch(scalar->axis_type)
1452	{
1453	case CScalar::axis_type_attr::X :
1454	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1455	break;
1456	case CScalar::axis_type_attr::Y :
1457	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1458	break;
1459	case CScalar::axis_type_attr::Z :
1460	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1461	break;
1462	case CScalar::axis_type_attr::T :
1463	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1464	break;
1465	}
1466	}
1467
1468	if (!scalar->positive.isEmpty())
1469	{
1470	SuperClassWriter::addAttribute("positive",
1471	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1472	&scalaId);
1473	}
1474
1475	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1476	{
1477	dims.clear();
1478	dims.push_back("axis_nbounds");
1479	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1480	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1481	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1482	}
1483
1484	SuperClassWriter::definition_end();
1485
1486	switch (SuperClass::type)
1487	{
1488	case MULTI_FILE:
1489	{
1490	CArray<double,1> scalarValue(scalarSize);
1491	CArray<string,1> scalarLabel(scalarSize);
1492	CArray<double,1> scalarBounds(scalarSize*2);
1493
1494	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1495	{
1496	scalarValue(0) = scalar->value;
1497	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1498	}
1499
1500	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1501	{
1502	scalarBounds(0) = scalar->bounds(0);
1503	scalarBounds(1) = scalar->bounds(1);
1504	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1505	}
1506
1507	if (!scalar->label.isEmpty())
1508	{
1509	scalarLabel(0) = scalar->label;
1510	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1511	}
1512
1513	SuperClassWriter::definition_start();
1514
1515	break;
1516	}
1517	case ONE_FILE:
1518	{
1519	CArray<double,1> scalarValue(scalarSize);
1520	CArray<string,1> scalarLabel(scalarSize);
1521	CArray<double,1> scalarBounds(scalarSize*2);
1522
1523	std::vector<StdSize> start(1);
1524	std::vector<StdSize> count(1);
1525	start[0] = 0;
1526	count[0] = 1;
1527	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1528	{
1529	scalarValue(0) = scalar->value;
1530	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1531	}
1532	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1533	{
1534	scalarBounds(0) = scalar->bounds(0);
1535	scalarBounds(1) = scalar->bounds(1);
1536	count[0] = 2;
1537	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1538	}
1539	if (!scalar->label.isEmpty())
1540	{
1541	scalarLabel(0) = scalar->label;
1542	count[0] = stringArrayLen;
1543	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1544	}
1545
1546	SuperClassWriter::definition_start();
1547
1548	break;
1549	}
1550	default :
1551	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1552	<< "[ type = " << SuperClass::type << "]"
1553	<< " not implemented yet !");
1554	}
1555	}
1556	}
1557	catch (CNetCdfException& e)
1558	{
1559	StdString msg("On writing the scalar : ");
1560	msg.append(scalaId); msg.append("\n");
1561	msg.append("In the context : ");
1562	CContext* context = CContext::getCurrent() ;
1563	msg.append(context->getId()); msg.append("\n");
1564	msg.append(e.what());
1565	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1566	}
1567	scalar->addRelFile(this->filename);
1568	}
1569
1570	//--------------------------------------------------------------
1571
1572	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1573	{
1574	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1575
1576	try
1577	{
1578	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1579	std::vector<StdString> domainList = grid->getDomainList();
1580	std::vector<StdString> axisList = grid->getAxisList();
1581	std::vector<StdString> scalarList = grid->getScalarList();
1582	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1583
1584	std::vector<StdString> dims;
1585
1586	if (grid->isCompressible())
1587	{
1588	StdString varId = grid->getId() + "_points";
1589
1590	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1591	SuperClassWriter::addDimension(varId, nbIndexes);
1592
1593	dims.push_back(varId);
1594	SuperClassWriter::addVariable(varId, NC_INT, dims);
1595
1596	StdOStringStream compress;
1597	for (int i = numElement - 1; i >= 0; --i)
1598	{
1599	if (2 == axisDomainOrder(i))
1600	{
1601	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1602	StdString domId = domain->getDomainOutputName();
1603	StdString appendDomId = singleDomain ? "" : "_" + domId;
1604
1605	switch (domain->type)
1606	{
1607	case CDomain::type_attr::curvilinear:
1608	compress << "y" << appendDomId << " x" << appendDomId;
1609	break;
1610	case CDomain::type_attr::rectilinear:
1611	compress << "lat" << appendDomId << " lon" << appendDomId;
1612	break;
1613	case CDomain::type_attr::unstructured:
1614	StdString cellName = (!domain->dim_i_name.isEmpty()) ? cellName=domain->dim_i_name : "cell";
1615	compress << cellName << appendDomId;
1616	// compress << "cell" << appendDomId;
1617	break;
1618	}
1619	++idxDomain;
1620	}
1621	else if (1 == axisDomainOrder(i))
1622	{
1623	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1624	compress << axis->getAxisOutputName();
1625	++idxAxis;
1626	}
1627	else
1628	{
1629	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1630	compress << scalar->getScalarOutputName();
1631	++idxScalar;
1632	}
1633
1634	if (i != 0) compress << ' ';
1635	}
1636	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1637
1638	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1639	indexes = grid->localIndexToWriteOnServer;
1640
1641	switch (SuperClass::type)
1642	{
1643	case (MULTI_FILE):
1644	{
1645	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1646	break;
1647	}
1648	case (ONE_FILE):
1649	{
1650	if (grid->doGridHaveDataDistributed())
1651	grid->getDistributionServer()->computeGlobalIndex(indexes);
1652
1653	std::vector<StdSize> start, count;
1654	start.push_back(grid->getOffsetWrittenIndexes());
1655	count.push_back(grid->getNumberWrittenIndexes());
1656
1657	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1658	break;
1659	}
1660	}
1661	}
1662	else
1663	{
1664	for (int i = 0; i < numElement; ++i)
1665	{
1666	StdString varId, compress;
1667	CArray<int, 1> indexes;
1668	bool isDistributed;
1669	StdSize nbIndexes, totalNbIndexes, offset;
1670	int firstGlobalIndex;
1671
1672	if (2 == axisDomainOrder(i))
1673	{
1674	CDomain* domain = CDomain::get(domainList[idxDomain]);
1675	StdString domId = domain->getDomainOutputName();
1676
1677	if (!domain->isCompressible()
1678	\|\| domain->type == CDomain::type_attr::unstructured
1679	\|\| domain->isWrittenCompressed(this->filename)
1680	\|\| isWrittenCompressedDomain(domId))
1681	continue;
1682
1683	StdString appendDomId = singleDomain ? "" : "_" + domId;
1684
1685	varId = domId + "_points";
1686	switch (domain->type)
1687	{
1688	case CDomain::type_attr::curvilinear:
1689	compress = "y" + appendDomId + " x" + appendDomId;
1690	break;
1691	case CDomain::type_attr::rectilinear:
1692	compress = "lat" + appendDomId + " lon" + appendDomId;
1693	break;
1694	}
1695
1696	// indexes.resize(domain->compressedIndexToWriteOnServer[comm_file].numElements());
1697	// indexes = domain->compressedIndexToWriteOnServer[com_file];
1698	indexes.resize(domain->getCompressedIndexToWriteOnServer(comm_file).numElements());
1699	indexes = domain->getCompressedIndexToWriteOnServer(comm_file);
1700
1701	isDistributed = domain->isDistributed();
1702	nbIndexes = domain->getNumberWrittenIndexes(comm_file);
1703	totalNbIndexes = domain->getTotalNumberWrittenIndexes(comm_file);
1704	offset = domain->getOffsetWrittenIndexes(comm_file);
1705	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1706
1707	domain->addRelFileCompressed(this->filename);
1708	setWrittenCompressedDomain(domId);
1709	++idxDomain;
1710	}
1711	else if (1 == axisDomainOrder(i))
1712	{
1713	CAxis* axis = CAxis::get(axisList[idxAxis]);
1714	StdString axisId = axis->getAxisOutputName();
1715
1716	if (!axis->isCompressible()
1717	\|\| axis->isWrittenCompressed(this->filename)
1718	\|\| isWrittenCompressedAxis(axisId))
1719	continue;
1720
1721	varId = axisId + "_points";
1722	compress = axisId;
1723
1724	// indexes.resize(axis->compressedIndexToWriteOnServer.numElements());
1725	// indexes = axis->compressedIndexToWriteOnServer;
1726
1727	indexes.resize(axis->getCompressedIndexToWriteOnServer(comm_file).numElements());
1728	indexes = axis->getCompressedIndexToWriteOnServer(comm_file);
1729
1730	isDistributed = axis->isDistributed();
1731	nbIndexes = axis->getNumberWrittenIndexes(comm_file);
1732	totalNbIndexes = axis->getTotalNumberWrittenIndexes(comm_file);
1733	offset = axis->getOffsetWrittenIndexes(comm_file);
1734	firstGlobalIndex = axis->begin;
1735
1736	axis->addRelFileCompressed(this->filename);
1737	setWrittenCompressedAxis(axisId);
1738	++idxAxis;
1739	}
1740	else
1741	{
1742	}
1743
1744	if (!varId.empty())
1745	{
1746	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1747
1748	dims.clear();
1749	dims.push_back(varId);
1750	SuperClassWriter::addVariable(varId, NC_INT, dims);
1751
1752	SuperClassWriter::addAttribute("compress", compress, &varId);
1753
1754	switch (SuperClass::type)
1755	{
1756	case (MULTI_FILE):
1757	{
1758	indexes -= firstGlobalIndex;
1759	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1760	break;
1761	}
1762	case (ONE_FILE):
1763	{
1764	std::vector<StdSize> start, count;
1765	start.push_back(offset);
1766	count.push_back(nbIndexes);
1767
1768	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1769	break;
1770	}
1771	}
1772	}
1773	}
1774	}
1775
1776	grid->addRelFileCompressed(this->filename);
1777	}
1778	catch (CNetCdfException& e)
1779	{
1780	StdString msg("On writing compressed grid : ");
1781	msg.append(grid->getId()); msg.append("\n");
1782	msg.append("In the context : ");
1783	CContext* context = CContext::getCurrent();
1784	msg.append(context->getId()); msg.append("\n");
1785	msg.append(e.what());
1786	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1787	}
1788	}
1789
1790	//--------------------------------------------------------------
1791
1792	void CNc4DataOutput::writeTimeDimension_(void)
1793	{
1794	try
1795	{
1796	SuperClassWriter::addDimension(getTimeCounterName());
1797	}
1798	catch (CNetCdfException& e)
1799	{
1800	StdString msg("On writing time dimension : time_couter\n");
1801	msg.append("In the context : ");
1802	CContext* context = CContext::getCurrent() ;
1803	msg.append(context->getId()); msg.append("\n");
1804	msg.append(e.what());
1805	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1806	}
1807	}
1808
1809	//--------------------------------------------------------------
1810
1811	void CNc4DataOutput::writeField_(CField* field)
1812	{
1813	CContext* context = CContext::getCurrent() ;
1814	CContextServer* server=context->server ;
1815
1816	std::vector<StdString> dims, coodinates;
1817	CGrid* grid = field->grid;
1818	if (!grid->doGridHaveDataToWrite())
1819	if (SuperClass::type==MULTI_FILE) return ;
1820
1821	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1822	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1823	std::vector<StdString> domainList = grid->getDomainList();
1824	std::vector<StdString> axisList = grid->getAxisList();
1825	std::vector<StdString> scalarList = grid->getScalarList();
1826
1827	StdString timeid = getTimeCounterName();
1828	StdString dimXid,dimYid;
1829	std::deque<StdString> dimIdList, dimCoordList;
1830	bool hasArea = false;
1831	StdString cellMeasures = "area:";
1832	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1833
1834	for (int i = 0; i < numElement; ++i)
1835	{
1836	if (2 == axisDomainOrder(i))
1837	{
1838	CDomain* domain = CDomain::get(domainList[idxDomain]);
1839	StdString domId = domain->getDomainOutputName();
1840	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1841	StdString lonName,latName ;
1842	StdString dimIname,dimJname ;
1843
1844	if (domain->lon_name.isEmpty())
1845	{
1846	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1847	else lonName = "lon";
1848	}
1849	else lonName = domain->lon_name;
1850
1851	if (domain->lat_name.isEmpty())
1852	{
1853	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1854	else latName = "lat";
1855	}
1856	else latName = domain->lat_name;
1857
1858	if (domain->dim_i_name.isEmpty())
1859	{
1860	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1861	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1862	else dimIname = lonName;
1863	}
1864	else dimIname = domain->dim_i_name;
1865
1866	if (domain->dim_j_name.isEmpty())
1867	{
1868	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1869	else dimJname = latName;
1870	}
1871	else dimJname = domain->dim_j_name;
1872
1873	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1874	{
1875	dimIdList.push_back(domId + "_points");
1876	field->setUseCompressedOutput();
1877	}
1878
1879	switch (domain->type)
1880	{
1881	case CDomain::type_attr::curvilinear:
1882	if (!compressedOutput \|\| !domain->isCompressible())
1883	{
1884	dimXid=dimIname+appendDomId;
1885	dimYid=dimJname+appendDomId;
1886	dimIdList.push_back(dimXid);
1887	dimIdList.push_back(dimYid);
1888	}
1889	dimCoordList.push_back(lonName+appendDomId);
1890	dimCoordList.push_back(latName+appendDomId);
1891	break ;
1892	case CDomain::type_attr::rectilinear:
1893	if (!compressedOutput \|\| !domain->isCompressible())
1894	{
1895	dimXid = dimIname+appendDomId;
1896	dimYid = dimJname+appendDomId;
1897	dimIdList.push_back(dimXid);
1898	dimIdList.push_back(dimYid);
1899	}
1900	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1901	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1902
1903	break ;
1904	case CDomain::type_attr::unstructured:
1905	{
1906	if (SuperClassWriter::useCFConvention)
1907	{
1908	dimXid = dimIname + appendDomId;
1909	dimIdList.push_back(dimXid);
1910	dimCoordList.push_back(lonName+appendDomId);
1911	dimCoordList.push_back(latName+appendDomId);
1912	}
1913	else
1914	{
1915	StdString domainName = domain->name;
1916	if (domain->nvertex == 1)
1917	{
1918	dimXid = "n" + domainName + "_node";
1919	dimIdList.push_back(dimXid);
1920	dimCoordList.push_back(StdString(domainName + "_node_x"));
1921	dimCoordList.push_back(StdString(domainName + "_node_y"));
1922	}
1923	else if (domain->nvertex == 2)
1924	{
1925	dimXid = "n" + domainName + "_edge";
1926	dimIdList.push_back(dimXid);
1927	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1928	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1929	}
1930	else
1931	{
1932	dimXid = "n" + domainName + "_face";
1933	dimIdList.push_back(dimXid);
1934	dimCoordList.push_back(StdString(domainName + "_face_x"));
1935	dimCoordList.push_back(StdString(domainName + "_face_y"));
1936	}
1937	} // ugrid convention
1938	} // case unstructured domain
1939	}
1940
1941	if (domain->hasArea)
1942	{
1943	hasArea = true;
1944	cellMeasures += " area" + appendDomId;
1945	}
1946	++idxDomain;
1947	}
1948	else if (1 == axisDomainOrder(i))
1949	{
1950	CAxis* axis = CAxis::get(axisList[idxAxis]);
1951	StdString axisId = axis->getAxisOutputName();
1952	StdString axisDim;
1953
1954	if (axis->dim_name.isEmpty()) axisDim = axisId;
1955	else axisDim=axis->dim_name.getValue();
1956
1957	if (compressedOutput && axis->isCompressible())
1958	{
1959	dimIdList.push_back(axisDim + "_points");
1960	field->setUseCompressedOutput();
1961	}
1962	else
1963	dimIdList.push_back(axisDim);
1964
1965	if (axisDim != axisId) dimCoordList.push_back(axisId);
1966	++idxAxis;
1967	}
1968	else
1969	{
1970	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1971	StdString scalarId = scalar->getScalarOutputName();
1972	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1973	dimCoordList.push_back(scalarId);
1974	++idxScalar;
1975	}
1976	}
1977
1978	StdString fieldid = field->getFieldOutputName();
1979
1980	nc_type type ;
1981	if (field->prec.isEmpty()) type = NC_FLOAT ;
1982	else
1983	{
1984	if (field->prec==2) type = NC_SHORT ;
1985	else if (field->prec==4) type = NC_FLOAT ;
1986	else if (field->prec==8) type = NC_DOUBLE ;
1987	}
1988
1989	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1990
1991	if (wtime)
1992	{
1993	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1994	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
1995	dims.push_back(timeid);
1996	}
1997
1998	if (compressedOutput && grid->isCompressible())
1999	{
2000	dims.push_back(grid->getId() + "_points");
2001	field->setUseCompressedOutput();
2002	}
2003	else
2004	{
2005	while (!dimIdList.empty())
2006	{
2007	dims.push_back(dimIdList.back());
2008	dimIdList.pop_back();
2009	}
2010	}
2011
2012	while (!dimCoordList.empty())
2013	{
2014	coodinates.push_back(dimCoordList.back());
2015	dimCoordList.pop_back();
2016	}
2017
2018	try
2019	{
2020	SuperClassWriter::addVariable(fieldid, type, dims);
2021
2022	if (!field->standard_name.isEmpty())
2023	SuperClassWriter::addAttribute
2024	("standard_name", field->standard_name.getValue(), &fieldid);
2025
2026	if (!field->long_name.isEmpty())
2027	SuperClassWriter::addAttribute
2028	("long_name", field->long_name.getValue(), &fieldid);
2029
2030	if (!field->unit.isEmpty())
2031	SuperClassWriter::addAttribute
2032	("units", field->unit.getValue(), &fieldid);
2033
2034	// Ugrid field attributes "mesh" and "location"
2035	if (!SuperClassWriter::useCFConvention)
2036	{
2037	if (!domainList.empty())
2038	{
2039	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
2040	StdString mesh = domain->name;
2041	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
2042	StdString location;
2043	if (domain->nvertex == 1)
2044	location = "node";
2045	else if (domain->nvertex == 2)
2046	location = "edge";
2047	else if (domain->nvertex > 2)
2048	location = "face";
2049	SuperClassWriter::addAttribute("location", location, &fieldid);
2050	}
2051
2052	}
2053
2054	if (!field->valid_min.isEmpty())
2055	SuperClassWriter::addAttribute
2056	("valid_min", field->valid_min.getValue(), &fieldid);
2057
2058	if (!field->valid_max.isEmpty())
2059	SuperClassWriter::addAttribute
2060	("valid_max", field->valid_max.getValue(), &fieldid);
2061
2062	if (!field->scale_factor.isEmpty())
2063	SuperClassWriter::addAttribute
2064	("scale_factor", field->scale_factor.getValue(), &fieldid);
2065
2066	if (!field->add_offset.isEmpty())
2067	SuperClassWriter::addAttribute
2068	("add_offset", field->add_offset.getValue(), &fieldid);
2069
2070	SuperClassWriter::addAttribute
2071	("online_operation", field->operation.getValue(), &fieldid);
2072
2073	// write child variables as attributes
2074
2075
2076	bool alreadyAddCellMethod = false;
2077	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
2078	if (!field->cell_methods.isEmpty())
2079	{
2080	StdString cellMethodString = field->cell_methods;
2081	if (field->cell_methods_mode.isEmpty() \|\|
2082	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
2083	{
2084	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
2085	alreadyAddCellMethod = true;
2086	}
2087	else
2088	{
2089	switch (field->cell_methods_mode)
2090	{
2091	case (CField::cell_methods_mode_attr::prefix):
2092	cellMethodsPrefix = cellMethodString;
2093	cellMethodsPrefix += " ";
2094	break;
2095	case (CField::cell_methods_mode_attr::suffix):
2096	cellMethodsSuffix = " ";
2097	cellMethodsSuffix += cellMethodString;
2098	break;
2099	case (CField::cell_methods_mode_attr::none):
2100	break;
2101	default:
2102	break;
2103	}
2104	}
2105	}
2106
2107
2108	if (wtime)
2109	{
2110	CDuration freqOp = field->freq_op.getValue();
2111	freqOp.solveTimeStep(*context->calendar);
2112	StdString freqOpStr = freqOp.toStringUDUnits();
2113	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
2114
2115	CDuration freqOut = field->getRelFile()->output_freq.getValue();
2116	freqOut.solveTimeStep(*context->calendar);
2117	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
2118
2119	StdString cellMethods(cellMethodsPrefix + "time: ");
2120	if (field->operation.getValue() == "instant") cellMethods += "point";
2121	else if (field->operation.getValue() == "average") cellMethods += "mean";
2122	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
2123	else cellMethods += field->operation;
2124	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
2125	cellMethods += " (interval: " + freqOpStr + ")";
2126	cellMethods += cellMethodsSuffix;
2127	if (!alreadyAddCellMethod)
2128	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
2129	}
2130
2131	if (hasArea)
2132	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
2133
2134	if (!field->default_value.isEmpty())
2135	{
2136	double default_value = field->default_value.getValue();
2137	if (type == NC_DOUBLE)
2138	{
2139	SuperClassWriter::setDefaultValue(fieldid, &default_value);
2140	}
2141	else if (type == NC_SHORT)
2142	{
2143	short sdefault_value = (short)default_value;
2144	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
2145	}
2146	else
2147	{
2148	float fdefault_value = (float)default_value;
2149	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
2150	}
2151	}
2152	else
2153	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
2154
2155	if (field->compression_level.isEmpty())
2156	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
2157	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
2158
2159	{ // Ecriture des coordonnes
2160
2161	StdString coordstr; //boost::algorithm::join(coodinates, " ")
2162	std::vector<StdString>::iterator
2163	itc = coodinates.begin(), endc = coodinates.end();
2164
2165	for (; itc!= endc; itc++)
2166	{
2167	StdString & coord = *itc;
2168	if (itc+1 != endc)
2169	coordstr.append(coord).append(" ");
2170	else coordstr.append(coord);
2171	}
2172
2173	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
2174
2175	}
2176
2177	vector<CVariable*> listVars = field->getAllVariables() ;
2178	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
2179
2180	}
2181	catch (CNetCdfException& e)
2182	{
2183	StdString msg("On writing field : ");
2184	msg.append(fieldid); msg.append("\n");
2185	msg.append("In the context : ");
2186	msg.append(context->getId()); msg.append("\n");
2187	msg.append(e.what());
2188	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2189	}
2190	} // writeField_()
2191
2192	//--------------------------------------------------------------
2193
2194	void CNc4DataOutput::writeFile_ (CFile* file)
2195	{
2196	StdString filename = file->getFileOutputName();
2197	StdString description = (!file->description.isEmpty())
2198	? file->description.getValue()
2199	: StdString("Created by xios");
2200
2201	singleDomain = (file->nbDomains == 1);
2202
2203	StdString conv_str ;
2204	if (file->convention_str.isEmpty())
2205	{
2206	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2207	else conv_str="UGRID" ;
2208	}
2209	else conv_str=file->convention_str ;
2210
2211	try
2212	{
2213	if (!appendMode) this->writeFileAttributes(filename, description,
2214	conv_str,
2215	StdString("An IPSL model"),
2216	this->getTimeStamp());
2217
2218	if (!appendMode)
2219	SuperClassWriter::addDimension("axis_nbounds", 2);
2220	}
2221	catch (CNetCdfException& e)
2222	{
2223	StdString msg("On writing file : ");
2224	msg.append(filename); msg.append("\n");
2225	msg.append("In the context : ");
2226	CContext* context = CContext::getCurrent() ;
2227	msg.append(context->getId()); msg.append("\n");
2228	msg.append(e.what());
2229	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2230	}
2231	}
2232
2233	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2234	{
2235	StdString name = var->getVariableOutputName();
2236
2237	try
2238	{
2239	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2240	addAttribute(name, var->getData<int>(), &fieldId);
2241	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2242	addAttribute(name, var->getData<short int>(), &fieldId);
2243	else if (var->type.getValue() == CVariable::type_attr::t_float)
2244	addAttribute(name, var->getData<float>(), &fieldId);
2245	else if (var->type.getValue() == CVariable::type_attr::t_double)
2246	addAttribute(name, var->getData<double>(), &fieldId);
2247	else if (var->type.getValue() == CVariable::type_attr::t_string)
2248	addAttribute(name, var->getData<string>(), &fieldId);
2249	else
2250	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2251	<< "Unsupported variable of type " << var->type.getStringValue());
2252	}
2253	catch (CNetCdfException& e)
2254	{
2255	StdString msg("On writing attributes of variable with name : ");
2256	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2257	msg.append("In the context : ");
2258	CContext* context = CContext::getCurrent() ;
2259	msg.append(context->getId()); msg.append("\n");
2260	msg.append(e.what());
2261	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2262	}
2263	}
2264
2265	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2266	{
2267	StdString name = var->getVariableOutputName();
2268
2269	try
2270	{
2271	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2272	addAttribute(name, var->getData<int>());
2273	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2274	addAttribute(name, var->getData<short int>());
2275	else if (var->type.getValue() == CVariable::type_attr::t_float)
2276	addAttribute(name, var->getData<float>());
2277	else if (var->type.getValue() == CVariable::type_attr::t_double)
2278	addAttribute(name, var->getData<double>());
2279	else if (var->type.getValue() == CVariable::type_attr::t_string)
2280	addAttribute(name, var->getData<string>());
2281	else
2282	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2283	<< "Unsupported variable of type " << var->type.getStringValue());
2284	}
2285	catch (CNetCdfException& e)
2286	{
2287	StdString msg("On writing attributes of variable with name : ");
2288	msg.append(name); msg.append("\n");
2289	msg.append("In the context : ");
2290	CContext* context = CContext::getCurrent() ;
2291	msg.append(context->getId()); msg.append("\n");
2292	msg.append(e.what());
2293	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2294	}
2295	}
2296
2297	void CNc4DataOutput::syncFile_ (void)
2298	{
2299	try
2300	{
2301	SuperClassWriter::sync() ;
2302	}
2303	catch (CNetCdfException& e)
2304	{
2305	StdString msg("On synchronizing the write among processes");
2306	msg.append("In the context : ");
2307	CContext* context = CContext::getCurrent() ;
2308	msg.append(context->getId()); msg.append("\n");
2309	msg.append(e.what());
2310	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2311	}
2312	}
2313
2314	void CNc4DataOutput::closeFile_ (void)
2315	{
2316	try
2317	{
2318	SuperClassWriter::close() ;
2319	}
2320	catch (CNetCdfException& e)
2321	{
2322	StdString msg("On closing file");
2323	msg.append("In the context : ");
2324	CContext* context = CContext::getCurrent() ;
2325	msg.append(context->getId()); msg.append("\n");
2326	msg.append(e.what());
2327	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2328	}
2329
2330	}
2331
2332	//---------------------------------------------------------------
2333
2334	StdString CNc4DataOutput::getTimeStamp(void) const
2335	{
2336	const int buffer_size = 100;
2337	time_t rawtime;
2338	struct tm * timeinfo = NULL;
2339	char buffer [buffer_size];
2340	StdString formatStr;
2341	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2342	else formatStr=file->time_stamp_format;
2343
2344	// time ( &rawtime );
2345	// timeinfo = localtime ( &rawtime );
2346	time ( &rawtime );
2347	timeinfo = gmtime ( &rawtime );
2348	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2349
2350	return (StdString(buffer));
2351	}
2352
2353	//---------------------------------------------------------------
2354
2355	void CNc4DataOutput::writeFieldData_ (CField* field)
2356	{
2357	CContext* context = CContext::getCurrent();
2358	CContextServer* server = context->server;
2359	CGrid* grid = field->grid;
2360
2361	if (field->getNStep()<1)
2362	{
2363	return;
2364	}
2365
2366	if (!grid->doGridHaveDataToWrite())
2367	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2368	{
2369	return;
2370	}
2371
2372	StdString fieldid = field->getFieldOutputName();
2373
2374	StdOStringStream oss;
2375	string timeAxisId;
2376	if (field->hasTimeInstant) timeAxisId = "time_instant";
2377	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2378
2379	StdString timeBoundId = getTimeCounterName() + "_bounds";
2380
2381	StdString timeAxisBoundId;
2382	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2383	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2384
2385	if (!field->wasWritten())
2386	{
2387	if (appendMode && field->file->record_offset.isEmpty() &&
2388	field->getOperationTimeType() != func::CFunctor::once)
2389	{
2390	double factorUnit;
2391	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2392	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2393	else factorUnit=1 ;
2394	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2395	}
2396
2397	field->setWritten();
2398	}
2399
2400
2401	CArray<double,1> time_data(1);
2402	CArray<double,1> time_data_bound(2);
2403	CArray<double,1> time_counter(1);
2404	CArray<double,1> time_counter_bound(2);
2405
2406	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2407	bool wtimeCounter =false ;
2408	bool wtimeData =false ;
2409
2410
2411	if (wtime)
2412	{
2413	Time lastWrite = field->last_Write_srv;
2414	Time lastLastWrite = field->lastlast_Write_srv;
2415
2416
2417	if (field->hasTimeInstant)
2418	{
2419	time_data(0) = time_data_bound(1) = lastWrite;
2420	time_data_bound(0) = time_data_bound(1) = lastWrite;
2421	if (timeCounterType==instant)
2422	{
2423	time_counter(0) = time_data(0);
2424	time_counter_bound(0) = time_data_bound(0);
2425	time_counter_bound(1) = time_data_bound(1);
2426	wtimeCounter=true ;
2427	}
2428	if (hasTimeInstant) wtimeData=true ;
2429	}
2430	else if (field->hasTimeCentered)
2431	{
2432	time_data(0) = (lastWrite + lastLastWrite) / 2;
2433	time_data_bound(0) = lastLastWrite;
2434	time_data_bound(1) = lastWrite;
2435	if (timeCounterType==centered)
2436	{
2437	time_counter(0) = time_data(0) ;
2438	time_counter_bound(0) = time_data_bound(0) ;
2439	time_counter_bound(1) = time_data_bound(1) ;
2440	wtimeCounter=true ;
2441	}
2442	if (hasTimeCentered) wtimeData=true ;
2443	}
2444
2445	if (timeCounterType==record)
2446	{
2447	time_counter(0) = field->getNStep() - 1;
2448	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2449	wtimeCounter=true ;
2450	}
2451
2452	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2453	{
2454	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2455	time_data/=secByDay;
2456	time_data_bound/=secByDay;
2457	time_counter/=secByDay;
2458	time_counter_bound/=secByDay;
2459	}
2460	}
2461
2462	bool isRoot = (server->intraCommRank == 0);
2463
2464	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2465	{
2466	double scaleFactor = 1.0;
2467	double addOffset = 0.0;
2468	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2469	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2470	field->scaleFactorAddOffset(scaleFactor, addOffset);
2471	}
2472
2473	try
2474	{
2475	size_t writtenSize;
2476	if (field->getUseCompressedOutput())
2477	writtenSize = grid->getNumberWrittenIndexes();
2478	else
2479	writtenSize = grid->getWrittenDataSize();
2480
2481	CArray<double,1> fieldData(writtenSize);
2482	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2483
2484	if (field->getUseCompressedOutput())
2485	field->outputCompressedField(fieldData);
2486	else
2487	field->outputField(fieldData);
2488
2489	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2490
2491	switch (SuperClass::type)
2492	{
2493	case (MULTI_FILE) :
2494	{
2495	CTimer::get("Files : writing data").resume();
2496	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2497	CTimer::get("Files : writing data").suspend();
2498	if (wtime)
2499	{
2500	CTimer::get("Files : writing time axis").resume();
2501	if ( wtimeData)
2502	{
2503	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2504	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2505	}
2506	if (wtimeCounter)
2507	{
2508	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2509	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2510	}
2511	CTimer::get("Files : writing time axis").suspend();
2512	}
2513	break;
2514	}
2515	case (ONE_FILE) :
2516	{
2517
2518	std::vector<StdSize> start, count;
2519
2520	if (field->getUseCompressedOutput())
2521	{
2522	if (grid->isCompressible())
2523	{
2524	start.push_back(grid->getOffsetWrittenIndexes());
2525	count.push_back(grid->getNumberWrittenIndexes());
2526	}
2527	else
2528	{
2529	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2530	std::vector<StdString> domainList = grid->getDomainList();
2531	std::vector<StdString> axisList = grid->getAxisList();
2532	int numElement = axisDomainOrder.numElements();
2533	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2534	int idx = domainList.size() * 2 + axisList.size() - 1;
2535
2536	start.reserve(idx+1);
2537	count.reserve(idx+1);
2538
2539	for (int i = numElement - 1; i >= 0; --i)
2540	{
2541	if (2 == axisDomainOrder(i))
2542	{
2543	CDomain* domain = CDomain::get(domainList[idxDomain]);
2544
2545	if (domain->isCompressible())
2546	{
2547	start.push_back(domain->getOffsetWrittenIndexes(comm_file));
2548	count.push_back(domain->getNumberWrittenIndexes(comm_file));
2549	idx -= 2;
2550	}
2551	else
2552	{
2553	if ((domain->type) != CDomain::type_attr::unstructured)
2554	{
2555	start.push_back(domain->jbegin);
2556	count.push_back(domain->nj);
2557	}
2558	--idx;
2559	start.push_back(domain->ibegin);
2560	count.push_back(domain->ni);
2561	--idx;
2562	}
2563	--idxDomain;
2564	}
2565	else if (1 == axisDomainOrder(i))
2566	{
2567	CAxis* axis = CAxis::get(axisList[idxAxis]);
2568
2569	if (axis->isCompressible())
2570	{
2571	start.push_back(axis->getOffsetWrittenIndexes(comm_file));
2572	count.push_back(axis->getNumberWrittenIndexes(comm_file));
2573	}
2574	else
2575	{
2576	start.push_back(axis->begin);
2577	count.push_back(axis->n);
2578	}
2579	--idxAxis;
2580	--idx;
2581	}
2582	}
2583	}
2584	}
2585	else
2586	{
2587	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2588	std::vector<StdString> domainList = grid->getDomainList();
2589	std::vector<StdString> axisList = grid->getAxisList();
2590	int numElement = axisDomainOrder.numElements();
2591	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2592	int idx = domainList.size() * 2 + axisList.size() - 1;
2593
2594	start.reserve(idx+1);
2595	count.reserve(idx+1);
2596
2597	for (int i = numElement - 1; i >= 0; --i)
2598	{
2599	if (2 == axisDomainOrder(i))
2600	{
2601	CDomain* domain = CDomain::get(domainList[idxDomain]);
2602	if ((domain->type) != CDomain::type_attr::unstructured)
2603	{
2604	start.push_back(domain->jbegin);
2605	count.push_back(domain->nj);
2606	}
2607	--idx ;
2608
2609	start.push_back(domain->ibegin);
2610	count.push_back(domain->ni);
2611	--idx ;
2612	--idxDomain;
2613	}
2614	else if (1 == axisDomainOrder(i))
2615	{
2616	CAxis* axis = CAxis::get(axisList[idxAxis]);
2617	start.push_back(axis->begin);
2618	count.push_back(axis->n);
2619	--idx;
2620	--idxAxis;
2621	}
2622	else
2623	{
2624	if (1 == axisDomainOrder.numElements())
2625	{
2626	start.push_back(0);
2627	count.push_back(1);
2628	}
2629	--idx;
2630	}
2631	}
2632	}
2633
2634
2635	CTimer::get("Files : writing data").resume();
2636	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2637	CTimer::get("Files : writing data").suspend();
2638
2639	if (wtime)
2640	{
2641	CTimer::get("Files : writing time axis").resume();
2642	if ( wtimeData)
2643	{
2644	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2645	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2646	}
2647	if (wtimeCounter)
2648	{
2649	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2650	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2651
2652	}
2653	CTimer::get("Files : writing time axis").suspend();
2654	}
2655
2656	break;
2657	}
2658	}
2659	}
2660	catch (CNetCdfException& e)
2661	{
2662	StdString msg("On writing field data: ");
2663	msg.append(fieldid); msg.append("\n");
2664	msg.append("In the context : ");
2665	msg.append(context->getId()); msg.append("\n");
2666	msg.append(e.what());
2667	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2668	}
2669	}
2670
2671	//---------------------------------------------------------------
2672
2673	void CNc4DataOutput::writeTimeAxis_
2674	(CField* field,
2675	const std::shared_ptr<CCalendar> cal)
2676	{
2677	StdOStringStream oss;
2678	bool createInstantAxis=false ;
2679	bool createCenteredAxis=false ;
2680	bool createTimeCounterAxis=false ;
2681
2682	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2683
2684
2685	StdString axisId ;
2686	StdString axisBoundId;
2687	StdString timeid(getTimeCounterName());
2688	StdString timeBoundId("axis_nbounds");
2689
2690	StdString strTimeUnits ;
2691	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2692	else strTimeUnits="seconds since " ;
2693
2694	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2695	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2696
2697
2698	if (field->file->time_counter.isEmpty())
2699	{
2700	if (timeCounterType==none) createTimeCounterAxis=true ;
2701	if (field->hasTimeCentered)
2702	{
2703	timeCounterType=centered ;
2704	if (!hasTimeCentered) createCenteredAxis=true ;
2705	}
2706	if (field->hasTimeInstant)
2707	{
2708	if (timeCounterType==none) timeCounterType=instant ;
2709	if (!hasTimeInstant) createInstantAxis=true ;
2710	}
2711	}
2712	else if (field->file->time_counter==CFile::time_counter_attr::instant)
2713	{
2714	if (field->hasTimeCentered)
2715	{
2716	if (!hasTimeCentered) createCenteredAxis=true ;
2717	}
2718	if (field->hasTimeInstant)
2719	{
2720	if (timeCounterType==none) createTimeCounterAxis=true ;
2721	timeCounterType=instant ;
2722	if (!hasTimeInstant) createInstantAxis=true ;
2723	}
2724	}
2725	else if (field->file->time_counter==CFile::time_counter_attr::centered)
2726	{
2727	if (field->hasTimeCentered)
2728	{
2729	if (timeCounterType==none) createTimeCounterAxis=true ;
2730	timeCounterType=centered ;
2731	if (!hasTimeCentered) createCenteredAxis=true ;
2732	}
2733	if (field->hasTimeInstant)
2734	{
2735	if (!hasTimeInstant) createInstantAxis=true ;
2736	}
2737	}
2738	else if (field->file->time_counter==CFile::time_counter_attr::instant_exclusive)
2739	{
2740	if (field->hasTimeCentered)
2741	{
2742	if (!hasTimeCentered) createCenteredAxis=true ;
2743	}
2744	if (field->hasTimeInstant)
2745	{
2746	if (timeCounterType==none) createTimeCounterAxis=true ;
2747	timeCounterType=instant ;
2748	}
2749	}
2750	else if (field->file->time_counter==CFile::time_counter_attr::centered_exclusive)
2751	{
2752	if (field->hasTimeCentered)
2753	{
2754	if (timeCounterType==none) createTimeCounterAxis=true ;
2755	timeCounterType=centered ;
2756	}
2757	if (field->hasTimeInstant)
2758	{
2759	if (!hasTimeInstant) createInstantAxis=true ;
2760	}
2761	}
2762	else if (field->file->time_counter==CFile::time_counter_attr::exclusive)
2763	{
2764	if (field->hasTimeCentered)
2765	{
2766	if (timeCounterType==none) createTimeCounterAxis=true ;
2767	if (timeCounterType==instant) createInstantAxis=true ;
2768	timeCounterType=centered ;
2769	}
2770	if (field->hasTimeInstant)
2771	{
2772	if (timeCounterType==none)
2773	{
2774	createTimeCounterAxis=true ;
2775	timeCounterType=instant ;
2776	}
2777	if (timeCounterType==centered)
2778	{
2779	if (!hasTimeInstant) createInstantAxis=true ;
2780	}
2781	}
2782	}
2783	else if (field->file->time_counter==CFile::time_counter_attr::none)
2784	{
2785	if (field->hasTimeCentered)
2786	{
2787	if (!hasTimeCentered) createCenteredAxis=true ;
2788	}
2789	if (field->hasTimeInstant)
2790	{
2791	if (!hasTimeInstant) createInstantAxis=true ;
2792	}
2793	}
2794	else if (field->file->time_counter==CFile::time_counter_attr::record)
2795	{
2796	if (timeCounterType==none) createTimeCounterAxis=true ;
2797	timeCounterType=record ;
2798	if (field->hasTimeCentered)
2799	{
2800	if (!hasTimeCentered) createCenteredAxis=true ;
2801	}
2802	if (field->hasTimeInstant)
2803	{
2804	if (!hasTimeInstant) createInstantAxis=true ;
2805	}
2806	}
2807
2808	if (createInstantAxis)
2809	{
2810	axisId="time_instant" ;
2811	axisBoundId="time_instant_bounds";
2812	hasTimeInstant=true ;
2813	}
2814
2815	if (createCenteredAxis)
2816	{
2817	axisId="time_centered" ;
2818	axisBoundId="time_centered_bounds";
2819	hasTimeCentered=true ;
2820	}
2821
2822
2823	try
2824	{
2825	std::vector<StdString> dims;
2826
2827	if (createInstantAxis \|\| createCenteredAxis)
2828	{
2829	// Adding time_instant or time_centered
2830	dims.push_back(timeid);
2831	if (!SuperClassWriter::varExist(axisId))
2832	{
2833	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2834
2835	CDate timeOrigin=cal->getTimeOrigin() ;
2836	StdOStringStream oss2;
2837	StdString strInitdate=oss2.str() ;
2838	StdString strTimeOrigin=timeOrigin.toString() ;
2839	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2840	strTimeOrigin, axisBoundId);
2841	}
2842
2843	// Adding time_instant_bounds or time_centered_bounds variables
2844	if (!SuperClassWriter::varExist(axisBoundId))
2845	{
2846	dims.clear() ;
2847	dims.push_back(timeid);
2848	dims.push_back(timeBoundId);
2849	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2850	}
2851	}
2852
2853	if (createTimeCounterAxis)
2854	{
2855	// Adding time_counter
2856	axisId = getTimeCounterName();
2857	axisBoundId = getTimeCounterName() + "_bounds";
2858	dims.clear();
2859	dims.push_back(timeid);
2860	if (!SuperClassWriter::varExist(axisId))
2861	{
2862	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2863	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2864
2865	if (field->file->time_counter.isEmpty() \|\|
2866	(field->file->time_counter != CFile::time_counter_attr::record))
2867	{
2868	CDate timeOrigin = cal->getTimeOrigin();
2869	StdString strTimeOrigin = timeOrigin.toString();
2870
2871	this->writeTimeAxisAttributes(axisId, cal->getType(),
2872	strTimeUnits+strTimeOrigin,
2873	strTimeOrigin, axisBoundId);
2874	}
2875	}
2876
2877	// Adding time_counter_bound dimension
2878	if (field->file->time_counter.isEmpty() \|\| (field->file->time_counter != CFile::time_counter_attr::record))
2879	{
2880	if (!SuperClassWriter::varExist(axisBoundId))
2881	{
2882	dims.clear();
2883	dims.push_back(timeid);
2884	dims.push_back(timeBoundId);
2885	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2886	}
2887	}
2888	}
2889	}
2890	catch (CNetCdfException& e)
2891	{
2892	StdString msg("On writing time axis data: ");
2893	msg.append("In the context : ");
2894	CContext* context = CContext::getCurrent() ;
2895	msg.append(context->getId()); msg.append("\n");
2896	msg.append(e.what());
2897	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2898	const std::shared_ptr<CCalendar> cal)", << msg);
2899	}
2900	}
2901
2902	//---------------------------------------------------------------
2903
2904	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2905	const StdString & calendar,
2906	const StdString & units,
2907	const StdString & time_origin,
2908	const StdString & time_bounds,
2909	const StdString & standard_name,
2910	const StdString & long_name)
2911	{
2912	try
2913	{
2914	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2915	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2916	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2917	SuperClassWriter::addAttribute("units", units , &axis_name);
2918	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2919	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2920	}
2921	catch (CNetCdfException& e)
2922	{
2923	StdString msg("On writing time axis Attribute: ");
2924	msg.append("In the context : ");
2925	CContext* context = CContext::getCurrent() ;
2926	msg.append(context->getId()); msg.append("\n");
2927	msg.append(e.what());
2928	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2929	const StdString & calendar,\
2930	const StdString & units, \
2931	const StdString & time_origin, \
2932	const StdString & time_bounds, \
2933	const StdString & standard_name, \
2934	const StdString & long_name)", << msg);
2935	}
2936	}
2937
2938	//---------------------------------------------------------------
2939
2940	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2941	const StdString & axis,
2942	const StdString & standard_name,
2943	const StdString & long_name,
2944	const StdString & units,
2945	const StdString & nav_model)
2946	{
2947	try
2948	{
2949	if (!axis.empty())
2950	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2951
2952	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2953	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2954	SuperClassWriter::addAttribute("units" , units , &axis_name);
2955	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2956	}
2957	catch (CNetCdfException& e)
2958	{
2959	StdString msg("On writing Axis Attribute: ");
2960	msg.append("In the context : ");
2961	CContext* context = CContext::getCurrent() ;
2962	msg.append(context->getId()); msg.append("\n");
2963	msg.append(e.what());
2964	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2965	const StdString & axis, \
2966	const StdString & standard_name, \
2967	const StdString & long_name, \
2968	const StdString & units, \
2969	const StdString & nav_model)", << msg);
2970	}
2971	}
2972
2973	//---------------------------------------------------------------
2974
2975	void CNc4DataOutput::writeLocalAttributes
2976	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2977	{
2978	try
2979	{
2980	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2981	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2982	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2983	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2984	}
2985	catch (CNetCdfException& e)
2986	{
2987	StdString msg("On writing Local Attributes: ");
2988	msg.append("In the context : ");
2989	CContext* context = CContext::getCurrent() ;
2990	msg.append(context->getId()); msg.append("\n");
2991	msg.append(e.what());
2992	ERROR("CNc4DataOutput::writeLocalAttributes \
2993	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2994	}
2995
2996	}
2997
2998	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2999	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
3000	{
3001	CArray<int,1> array(2) ;
3002
3003	try
3004	{
3005	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
3006	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
3007	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
3008	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
3009	array=ni_glo,nj_glo ;
3010	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
3011	array=ni,nj ;
3012	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
3013	array=ibegin+1,jbegin+1 ;
3014	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
3015	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
3016	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
3017	array=0,0 ;
3018	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
3019	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
3020	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
3021	/*
3022	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
3023	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
3024	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
3025	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
3026	*/
3027	}
3028	catch (CNetCdfException& e)
3029	{
3030	StdString msg("On writing Local Attributes IOIPSL \n");
3031	msg.append("In the context : ");
3032	CContext* context = CContext::getCurrent() ;
3033	msg.append(context->getId()); msg.append("\n");
3034	msg.append(e.what());
3035	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
3036	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
3037	}
3038	}
3039	//---------------------------------------------------------------
3040
3041	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
3042	const StdString & description,
3043	const StdString & conventions,
3044	const StdString & production,
3045	const StdString & timeStamp)
3046	{
3047	try
3048	{
3049	SuperClassWriter::addAttribute("name" , name);
3050	SuperClassWriter::addAttribute("description", description);
3051	SuperClassWriter::addAttribute("title" , description);
3052	SuperClassWriter::addAttribute("Conventions", conventions);
3053	// SuperClassWriter::addAttribute("production" , production);
3054
3055	StdString timeStampStr ;
3056	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
3057	else timeStampStr=file->time_stamp_name ;
3058	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
3059
3060	StdString uuidName ;
3061	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
3062	else uuidName=file->uuid_name ;
3063
3064	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
3065	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
3066
3067	}
3068	catch (CNetCdfException& e)
3069	{
3070	StdString msg("On writing File Attributes \n ");
3071	msg.append("In the context : ");
3072	CContext* context = CContext::getCurrent() ;
3073	msg.append(context->getId()); msg.append("\n");
3074	msg.append(e.what());
3075	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
3076	const StdString & description, \
3077	const StdString & conventions, \
3078	const StdString & production, \
3079	const StdString & timeStamp)", << msg);
3080	}
3081	}
3082
3083	//---------------------------------------------------------------
3084
3085	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
3086	int data_dim,
3087	int data_ni,
3088	int data_nj,
3089	int data_ibegin,
3090	int data_jbegin)
3091	{
3092	try
3093	{
3094	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
3095	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
3096	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
3097	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
3098	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
3099	}
3100	catch (CNetCdfException& e)
3101	{
3102	StdString msg("On writing Mask Attributes \n ");
3103	msg.append("In the context : ");
3104	CContext* context = CContext::getCurrent() ;
3105	msg.append(context->getId()); msg.append("\n");
3106	msg.append(e.what());
3107	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
3108	int data_dim, \
3109	int data_ni, \
3110	int data_nj, \
3111	int data_ibegin, \
3112	int data_jbegin)", << msg);
3113	}
3114	}
3115
3116	///--------------------------------------------------------------
3117
3118	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
3119	{
3120	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
3121	if (it == timeToRecordCache.end())
3122	{
3123	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
3124	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
3125	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
3126
3127	CArray<double,2> timeAxisBounds;
3128	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
3129
3130	StdSize record = 0;
3131	double dtime(time);
3132	for (int n = dimSize[0] - 1; n >= 0; n--)
3133	{
3134	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3135	timeAxisBounds*=factorUnit ;
3136	if (timeAxisBounds(1, 0) < dtime)
3137	{
3138	record = n + 1;
3139	break;
3140	}
3141	}
3142	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3143	}
3144	return it->second;
3145	}
3146
3147	///--------------------------------------------------------------
3148
3149	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3150	{
3151	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3152	}
3153
3154	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3155	{
3156	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3157	}
3158
3159	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3160	{
3161	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3162	}
3163
3164	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3165	{
3166	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3167	}
3168
3169	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3170	{
3171	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3172	}
3173
3174	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3175	{
3176	this->writtenDomains.insert(domainName);
3177	}
3178
3179	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3180	{
3181	this->writtenCompressedDomains.insert(domainName);
3182	}
3183
3184	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3185	{
3186	this->writtenAxis.insert(axisName);
3187	}
3188
3189	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3190	{
3191	this->writtenCompressedAxis.insert(axisName);
3192	}
3193
3194	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3195	{
3196	this->writtenScalar.insert(scalarName);
3197	}
3198	} // namespace xios

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