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source: XIOS/branchs/xios-2.5/src/io/nc4_data_output.cpp @ 1855

Last change on this file since 1855 was 1624, checked in by oabramkina, 6 years ago

Bugfix for NEMO-like land processes elimination.

Values describing a domain (latitude, longitude, bounds,...) are set to -1 on land processes.

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: 133.6 KB

Line
1	#include "nc4_data_output.hpp"
2
3	#include "attribute_template.hpp"
4	#include "group_template.hpp"
5
6	#include "file.hpp"
7	#include "calendar.hpp"
8	#include "context.hpp"
9	#include "context_server.hpp"
10	#include "netCdfException.hpp"
11	#include "exception.hpp"
12	#include "timer.hpp"
13	#include "uuid.hpp"
14	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->zoom_ni);
242	SuperClassWriter::addDimension(dimYid, domain->zoom_nj);
243
244	if (domain->hasBounds)
245	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
246
247	if (server->intraCommSize > 1)
248	{
249	this->writeLocalAttributes(domain->zoom_ibegin,
250	domain->zoom_ni,
251	domain->zoom_jbegin,
252	domain->zoom_nj,
253	appendDomid);
254
255	if (singleDomain)
256	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
257	domain->zoom_ibegin,
258	domain->zoom_ni,
259	domain->zoom_jbegin,
260	domain->zoom_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->zoom_ni)) ;
334	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
335	CArray<double,1> lon = writtenLon(Range(0,domain->zoom_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->global_zoom_ni);
359	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
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 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->zoom_ibegin-domain->global_zoom_ibegin;
436	start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
437	count[1]=domain->zoom_ni ; count[0]=domain->zoom_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->zoom_jbegin-domain->global_zoom_jbegin;
463	count[0]=domain->zoom_nj;
464	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni));
465	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
466
467	start[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
468	count[0]=domain->zoom_ni;
469	CArray<double,1> lon = writtenLon(Range(0,domain->zoom_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->zoom_ibegin - domain->global_zoom_ibegin;
490	start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
491	count[2] = domain->nvertex;
492	count[1] = domain->zoom_ni;
493	count[0] = domain->zoom_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->zoom_ibegin - domain->global_zoom_ibegin;
513	start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
514	count[1] = domain->zoom_ni;
515	count[0] = domain->zoom_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->zoom_ibegin-domain->global_zoom_ibegin;
781	countNodes[0] = domain->zoom_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->zoom_ibegin-domain->global_zoom_ibegin;
804	countEdges[0] = domain->zoom_ni;
805	startNodes[0] = domain->mesh->node_start;
806	countNodes[0] = domain->mesh->node_count;
807	startEdgeNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
808	startEdgeNodes[1] = 0;
809	countEdgeNodes[0] = domain->zoom_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->zoom_ibegin-domain->global_zoom_ibegin;
840	countFaces[0] = domain->zoom_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->zoom_ibegin-domain->global_zoom_ibegin;
854	startFaceConctv[1] = 0;
855	countFaceConctv[0] = domain->zoom_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->zoom_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->zoom_ibegin - domain->global_zoom_ibegin;
1128	count[0]=domain->zoom_ni;
1129	startBounds[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
1130	startBounds[1]=0 ;
1131	countBounds[0]=domain->zoom_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 zoom_size = (MULTI_FILE == SuperClass::type) ? axis->zoom_n.getValue()
1181	: axis->global_zoom_n.getValue();
1182
1183	int zoom_count = axis->zoom_n;
1184	int zoom_begin = axis->zoom_begin;
1185	// int zoom_begin = (MULTI_FILE == SuperClass::type) ? axis->global_zoom_begin
1186	// : axis->zoom_begin;
1187
1188	if ((0 == axis->zoom_n) && (MULTI_FILE == SuperClass::type)) return;
1189
1190	std::vector<StdString> dims;
1191	StdString axisid = axis->getAxisOutputName();
1192	StdString axisDim, axisBoundsId;
1193	if (isWrittenAxis(axisid)) return ;
1194	else setWrittenAxis(axisid);
1195
1196	nc_type typePrec ;
1197	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1198	else if (axis->prec==4) typePrec = NC_FLOAT ;
1199	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1200
1201	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1202	string strId="str_len" ;
1203	try
1204	{
1205	if (axis->dim_name.isEmpty()) axisDim = axisid;
1206	else axisDim=axis->dim_name.getValue();
1207	SuperClassWriter::addDimension(axisDim, zoom_size);
1208	dims.push_back(axisDim);
1209
1210	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1211
1212	if (axis->hasValue \|\| !axis->label.isEmpty())
1213	{
1214	if (!axis->label.isEmpty()) dims.push_back(strId);
1215
1216	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1217
1218	if (!axis->name.isEmpty())
1219	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1220
1221	if (!axis->standard_name.isEmpty())
1222	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1223
1224	if (!axis->long_name.isEmpty())
1225	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1226
1227	if (!axis->unit.isEmpty())
1228	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1229
1230	if (!axis->axis_type.isEmpty())
1231	{
1232	switch(axis->axis_type)
1233	{
1234	case CAxis::axis_type_attr::X :
1235	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1236	break;
1237	case CAxis::axis_type_attr::Y :
1238	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1239	break;
1240	case CAxis::axis_type_attr::Z :
1241	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1242	break;
1243	case CAxis::axis_type_attr::T :
1244	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1245	break;
1246	}
1247	}
1248
1249	if (!axis->positive.isEmpty())
1250	{
1251	SuperClassWriter::addAttribute("positive",
1252	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1253	&axisid);
1254	}
1255
1256	if (!axis->formula.isEmpty())
1257	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1258
1259	if (!axis->formula_term.isEmpty())
1260	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
1261
1262	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1263	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1264	{
1265	dims.push_back("axis_nbounds");
1266	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1267	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1268
1269	if (!axis->standard_name.isEmpty())
1270	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1271
1272	if (!axis->unit.isEmpty())
1273	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1274
1275	if (!axis->formula_bounds.isEmpty())
1276	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1277
1278	if (!axis->formula_term_bounds.isEmpty())
1279	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
1280	}
1281	}
1282
1283	SuperClassWriter::definition_end();
1284
1285	CArray<int, 1>& indexToWrite = axis->localIndexToWriteOnServer;
1286	int nbWritten = indexToWrite.numElements();
1287	CArray<double,1> axis_value(indexToWrite.numElements());
1288	if (!axis->value.isEmpty())
1289	{
1290	for (int i = 0; i < nbWritten; i++)
1291	{
1292	if (indexToWrite(i) < 0)
1293	axis_value(i) = -1; // Some value in case of a hole
1294	else
1295	axis_value(i) = axis->value(indexToWrite(i));
1296	}
1297	}
1298	CArray<double,2> axis_bounds;
1299	CArray<string,1> axis_label;
1300	if (!axis->label.isEmpty())
1301	{
1302	axis_label.resize(indexToWrite.numElements());
1303	for (int i = 0; i < nbWritten; i++)
1304	{
1305	if (indexToWrite(i) < 0)
1306	axis_label(i) = boost::lexical_cast<string>(-1); // Some value in case of a hole
1307	else
1308	axis_label(i) = axis->label(indexToWrite(i));
1309	}
1310	}
1311
1312	switch (SuperClass::type)
1313	{
1314	case MULTI_FILE:
1315	{
1316	if (axis->label.isEmpty())
1317	{
1318	if (!axis->value.isEmpty())
1319	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1320
1321	if (!axis->bounds.isEmpty())
1322	{
1323	axis_bounds.resize(2, indexToWrite.numElements());
1324	for (int i = 0; i < nbWritten; ++i)
1325	{
1326	if (indexToWrite(i) < 0)
1327	{
1328	axis_bounds(0, i) = -1.; // Some value in case of a hole
1329	axis_bounds(1, i) = -1.;
1330	}
1331	else
1332	{
1333	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1334	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1335	}
1336	}
1337	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0);
1338	}
1339	}
1340	else
1341	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0);
1342
1343	SuperClassWriter::definition_start();
1344	break;
1345	}
1346	case ONE_FILE:
1347	{
1348	std::vector<StdSize> start(1), startBounds(2) ;
1349	std::vector<StdSize> count(1), countBounds(2) ;
1350	start[0] = startBounds[0] = zoom_begin - axis->global_zoom_begin;
1351	count[0] = countBounds[0] = zoom_count; // zoom_size
1352	startBounds[1] = 0;
1353	countBounds[1] = 2;
1354
1355	if (axis->label.isEmpty())
1356	{
1357	if (!axis->value.isEmpty())
1358	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1359
1360	if (!axis->bounds.isEmpty())
1361	{
1362	axis_bounds.resize(2, indexToWrite.numElements());
1363	for (int i = 0; i < nbWritten; ++i)
1364	{
1365	if (indexToWrite(i) < 0)
1366	{
1367	axis_bounds(0, i) = -1.;
1368	axis_bounds(1, i) = -1.;
1369	}
1370	else
1371	{
1372	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1373	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1374	}
1375	}
1376	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1377	}
1378	}
1379	else
1380	{
1381	std::vector<StdSize> startLabel(2), countLabel(2);
1382	startLabel[0] = start[0]; startLabel[1] = 0;
1383	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1384	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0, &startLabel, &countLabel);
1385	}
1386
1387	SuperClassWriter::definition_start();
1388
1389	break;
1390	}
1391	default :
1392	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1393	<< "[ type = " << SuperClass::type << "]"
1394	<< " not implemented yet !");
1395	}
1396	}
1397	catch (CNetCdfException& e)
1398	{
1399	StdString msg("On writing the axis : ");
1400	msg.append(axisid); msg.append("\n");
1401	msg.append("In the context : ");
1402	CContext* context = CContext::getCurrent() ;
1403	msg.append(context->getId()); msg.append("\n");
1404	msg.append(e.what());
1405	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1406	}
1407	axis->addRelFile(this->filename);
1408	}
1409
1410	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1411	{
1412	if (scalar->IsWritten(this->filename)) return;
1413	scalar->checkAttributes();
1414	int scalarSize = 1;
1415
1416	StdString scalaId = scalar->getScalarOutputName();
1417	StdString boundsId;
1418	if (isWrittenAxis(scalaId)) return ;
1419	else setWrittenAxis(scalaId);
1420
1421	nc_type typePrec ;
1422	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1423	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1424	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1425
1426	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1427	string strId="str_len" ;
1428
1429	try
1430	{
1431	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1432
1433	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1434	{
1435	std::vector<StdString> dims;
1436	StdString scalarDim = scalaId;
1437
1438	if (!scalar->label.isEmpty()) dims.push_back(strId);
1439
1440	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1441
1442	if (!scalar->name.isEmpty())
1443	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1444
1445	if (!scalar->standard_name.isEmpty())
1446	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1447
1448	if (!scalar->long_name.isEmpty())
1449	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1450
1451	if (!scalar->unit.isEmpty())
1452	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1453
1454	if (!scalar->axis_type.isEmpty())
1455	{
1456	switch(scalar->axis_type)
1457	{
1458	case CScalar::axis_type_attr::X :
1459	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1460	break;
1461	case CScalar::axis_type_attr::Y :
1462	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1463	break;
1464	case CScalar::axis_type_attr::Z :
1465	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1466	break;
1467	case CScalar::axis_type_attr::T :
1468	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1469	break;
1470	}
1471	}
1472
1473	if (!scalar->positive.isEmpty())
1474	{
1475	SuperClassWriter::addAttribute("positive",
1476	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1477	&scalaId);
1478	}
1479
1480	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1481	{
1482	dims.clear();
1483	dims.push_back("axis_nbounds");
1484	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1485	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1486	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1487	}
1488
1489	SuperClassWriter::definition_end();
1490
1491	switch (SuperClass::type)
1492	{
1493	case MULTI_FILE:
1494	{
1495	CArray<double,1> scalarValue(scalarSize);
1496	CArray<string,1> scalarLabel(scalarSize);
1497	CArray<double,1> scalarBounds(scalarSize*2);
1498
1499	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1500	{
1501	scalarValue(0) = scalar->value;
1502	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1503	}
1504
1505	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1506	{
1507	scalarBounds(0) = scalar->bounds(0);
1508	scalarBounds(1) = scalar->bounds(1);
1509	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1510	}
1511
1512	if (!scalar->label.isEmpty())
1513	{
1514	scalarLabel(0) = scalar->label;
1515	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1516	}
1517
1518	SuperClassWriter::definition_start();
1519
1520	break;
1521	}
1522	case ONE_FILE:
1523	{
1524	CArray<double,1> scalarValue(scalarSize);
1525	CArray<string,1> scalarLabel(scalarSize);
1526	CArray<double,1> scalarBounds(scalarSize*2);
1527
1528	std::vector<StdSize> start(1);
1529	std::vector<StdSize> count(1);
1530	start[0] = 0;
1531	count[0] = 1;
1532	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1533	{
1534	scalarValue(0) = scalar->value;
1535	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1536	}
1537	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1538	{
1539	scalarBounds(0) = scalar->bounds(0);
1540	scalarBounds(1) = scalar->bounds(1);
1541	count[0] = 2;
1542	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1543	}
1544	if (!scalar->label.isEmpty())
1545	{
1546	scalarLabel(0) = scalar->label;
1547	count[0] = stringArrayLen;
1548	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1549	}
1550
1551	SuperClassWriter::definition_start();
1552
1553	break;
1554	}
1555	default :
1556	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1557	<< "[ type = " << SuperClass::type << "]"
1558	<< " not implemented yet !");
1559	}
1560	}
1561	}
1562	catch (CNetCdfException& e)
1563	{
1564	StdString msg("On writing the scalar : ");
1565	msg.append(scalaId); msg.append("\n");
1566	msg.append("In the context : ");
1567	CContext* context = CContext::getCurrent() ;
1568	msg.append(context->getId()); msg.append("\n");
1569	msg.append(e.what());
1570	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1571	}
1572	scalar->addRelFile(this->filename);
1573	}
1574
1575	//--------------------------------------------------------------
1576
1577	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1578	{
1579	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1580
1581	try
1582	{
1583	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1584	std::vector<StdString> domainList = grid->getDomainList();
1585	std::vector<StdString> axisList = grid->getAxisList();
1586	std::vector<StdString> scalarList = grid->getScalarList();
1587	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1588
1589	std::vector<StdString> dims;
1590
1591	if (grid->isCompressible())
1592	{
1593	StdString varId = grid->getId() + "_points";
1594
1595	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1596	SuperClassWriter::addDimension(varId, nbIndexes);
1597
1598	dims.push_back(varId);
1599	SuperClassWriter::addVariable(varId, NC_INT, dims);
1600
1601	StdOStringStream compress;
1602	for (int i = numElement - 1; i >= 0; --i)
1603	{
1604	if (2 == axisDomainOrder(i))
1605	{
1606	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1607	StdString domId = domain->getDomainOutputName();
1608	StdString appendDomId = singleDomain ? "" : "_" + domId;
1609
1610	switch (domain->type)
1611	{
1612	case CDomain::type_attr::curvilinear:
1613	compress << "y" << appendDomId << " x" << appendDomId;
1614	break;
1615	case CDomain::type_attr::rectilinear:
1616	compress << "lat" << appendDomId << " lon" << appendDomId;
1617	break;
1618	case CDomain::type_attr::unstructured:
1619	StdString cellName = (!domain->dim_i_name.isEmpty()) ? cellName=domain->dim_i_name : "cell";
1620	compress << cellName << appendDomId;
1621	// compress << "cell" << appendDomId;
1622	break;
1623	}
1624	++idxDomain;
1625	}
1626	else if (1 == axisDomainOrder(i))
1627	{
1628	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1629	compress << axis->getAxisOutputName();
1630	++idxAxis;
1631	}
1632	else
1633	{
1634	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1635	compress << scalar->getScalarOutputName();
1636	++idxScalar;
1637	}
1638
1639	if (i != 0) compress << ' ';
1640	}
1641	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1642
1643	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1644	indexes = grid->localIndexToWriteOnServer;
1645
1646	switch (SuperClass::type)
1647	{
1648	case (MULTI_FILE):
1649	{
1650	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1651	break;
1652	}
1653	case (ONE_FILE):
1654	{
1655	if (grid->doGridHaveDataDistributed())
1656	grid->getDistributionServer()->computeGlobalIndex(indexes);
1657
1658	std::vector<StdSize> start, count;
1659	start.push_back(grid->getOffsetWrittenIndexes());
1660	count.push_back(grid->getNumberWrittenIndexes());
1661
1662	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1663	break;
1664	}
1665	}
1666	}
1667	else
1668	{
1669	for (int i = 0; i < numElement; ++i)
1670	{
1671	StdString varId, compress;
1672	CArray<int, 1> indexes;
1673	bool isDistributed;
1674	StdSize nbIndexes, totalNbIndexes, offset;
1675	int firstGlobalIndex;
1676
1677	if (2 == axisDomainOrder(i))
1678	{
1679	CDomain* domain = CDomain::get(domainList[idxDomain]);
1680	StdString domId = domain->getDomainOutputName();
1681
1682	if (!domain->isCompressible()
1683	\|\| domain->type == CDomain::type_attr::unstructured
1684	\|\| domain->isWrittenCompressed(this->filename)
1685	\|\| isWrittenCompressedDomain(domId))
1686	continue;
1687
1688	StdString appendDomId = singleDomain ? "" : "_" + domId;
1689
1690	varId = domId + "_points";
1691	switch (domain->type)
1692	{
1693	case CDomain::type_attr::curvilinear:
1694	compress = "y" + appendDomId + " x" + appendDomId;
1695	break;
1696	case CDomain::type_attr::rectilinear:
1697	compress = "lat" + appendDomId + " lon" + appendDomId;
1698	break;
1699	}
1700
1701	// indexes.resize(domain->compressedIndexToWriteOnServer[comm_file].numElements());
1702	// indexes = domain->compressedIndexToWriteOnServer[com_file];
1703	indexes.resize(domain->getCompressedIndexToWriteOnServer(comm_file).numElements());
1704	indexes = domain->getCompressedIndexToWriteOnServer(comm_file);
1705
1706	isDistributed = domain->isDistributed();
1707	nbIndexes = domain->getNumberWrittenIndexes(comm_file);
1708	totalNbIndexes = domain->getTotalNumberWrittenIndexes(comm_file);
1709	offset = domain->getOffsetWrittenIndexes(comm_file);
1710	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1711
1712	domain->addRelFileCompressed(this->filename);
1713	setWrittenCompressedDomain(domId);
1714	++idxDomain;
1715	}
1716	else if (1 == axisDomainOrder(i))
1717	{
1718	CAxis* axis = CAxis::get(axisList[idxAxis]);
1719	StdString axisId = axis->getAxisOutputName();
1720
1721	if (!axis->isCompressible()
1722	\|\| axis->isWrittenCompressed(this->filename)
1723	\|\| isWrittenCompressedAxis(axisId))
1724	continue;
1725
1726	varId = axisId + "_points";
1727	compress = axisId;
1728
1729	// indexes.resize(axis->compressedIndexToWriteOnServer.numElements());
1730	// indexes = axis->compressedIndexToWriteOnServer;
1731
1732	indexes.resize(axis->getCompressedIndexToWriteOnServer(comm_file).numElements());
1733	indexes = axis->getCompressedIndexToWriteOnServer(comm_file);
1734
1735	isDistributed = axis->isDistributed();
1736	nbIndexes = axis->getNumberWrittenIndexes(comm_file);
1737	totalNbIndexes = axis->getTotalNumberWrittenIndexes(comm_file);
1738	offset = axis->getOffsetWrittenIndexes(comm_file);
1739	firstGlobalIndex = axis->begin;
1740
1741	axis->addRelFileCompressed(this->filename);
1742	setWrittenCompressedAxis(axisId);
1743	++idxAxis;
1744	}
1745	else
1746	{
1747	}
1748
1749	if (!varId.empty())
1750	{
1751	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1752
1753	dims.clear();
1754	dims.push_back(varId);
1755	SuperClassWriter::addVariable(varId, NC_INT, dims);
1756
1757	SuperClassWriter::addAttribute("compress", compress, &varId);
1758
1759	switch (SuperClass::type)
1760	{
1761	case (MULTI_FILE):
1762	{
1763	indexes -= firstGlobalIndex;
1764	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1765	break;
1766	}
1767	case (ONE_FILE):
1768	{
1769	std::vector<StdSize> start, count;
1770	start.push_back(offset);
1771	count.push_back(nbIndexes);
1772
1773	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1774	break;
1775	}
1776	}
1777	}
1778	}
1779	}
1780
1781	grid->addRelFileCompressed(this->filename);
1782	}
1783	catch (CNetCdfException& e)
1784	{
1785	StdString msg("On writing compressed grid : ");
1786	msg.append(grid->getId()); msg.append("\n");
1787	msg.append("In the context : ");
1788	CContext* context = CContext::getCurrent();
1789	msg.append(context->getId()); msg.append("\n");
1790	msg.append(e.what());
1791	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1792	}
1793	}
1794
1795	//--------------------------------------------------------------
1796
1797	void CNc4DataOutput::writeTimeDimension_(void)
1798	{
1799	try
1800	{
1801	SuperClassWriter::addDimension(getTimeCounterName());
1802	}
1803	catch (CNetCdfException& e)
1804	{
1805	StdString msg("On writing time dimension : time_couter\n");
1806	msg.append("In the context : ");
1807	CContext* context = CContext::getCurrent() ;
1808	msg.append(context->getId()); msg.append("\n");
1809	msg.append(e.what());
1810	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1811	}
1812	}
1813
1814	//--------------------------------------------------------------
1815
1816	void CNc4DataOutput::writeField_(CField* field)
1817	{
1818	CContext* context = CContext::getCurrent() ;
1819	CContextServer* server=context->server ;
1820
1821	std::vector<StdString> dims, coodinates;
1822	CGrid* grid = field->grid;
1823	if (!grid->doGridHaveDataToWrite())
1824	if (SuperClass::type==MULTI_FILE) return ;
1825
1826	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1827	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1828	std::vector<StdString> domainList = grid->getDomainList();
1829	std::vector<StdString> axisList = grid->getAxisList();
1830	std::vector<StdString> scalarList = grid->getScalarList();
1831
1832	StdString timeid = getTimeCounterName();
1833	StdString dimXid,dimYid;
1834	std::deque<StdString> dimIdList, dimCoordList;
1835	bool hasArea = false;
1836	StdString cellMeasures = "area:";
1837	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1838
1839	for (int i = 0; i < numElement; ++i)
1840	{
1841	if (2 == axisDomainOrder(i))
1842	{
1843	CDomain* domain = CDomain::get(domainList[idxDomain]);
1844	StdString domId = domain->getDomainOutputName();
1845	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1846	StdString lonName,latName ;
1847	StdString dimIname,dimJname ;
1848
1849	if (domain->lon_name.isEmpty())
1850	{
1851	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1852	else lonName = "lon";
1853	}
1854	else lonName = domain->lon_name;
1855
1856	if (domain->lat_name.isEmpty())
1857	{
1858	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1859	else latName = "lat";
1860	}
1861	else latName = domain->lat_name;
1862
1863	if (domain->dim_i_name.isEmpty())
1864	{
1865	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1866	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1867	else dimIname = lonName;
1868	}
1869	else dimIname = domain->dim_i_name;
1870
1871	if (domain->dim_j_name.isEmpty())
1872	{
1873	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1874	else dimJname = latName;
1875	}
1876	else dimJname = domain->dim_j_name;
1877
1878	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1879	{
1880	dimIdList.push_back(domId + "_points");
1881	field->setUseCompressedOutput();
1882	}
1883
1884	switch (domain->type)
1885	{
1886	case CDomain::type_attr::curvilinear:
1887	if (!compressedOutput \|\| !domain->isCompressible())
1888	{
1889	dimXid=dimIname+appendDomId;
1890	dimYid=dimJname+appendDomId;
1891	dimIdList.push_back(dimXid);
1892	dimIdList.push_back(dimYid);
1893	}
1894	dimCoordList.push_back(lonName+appendDomId);
1895	dimCoordList.push_back(latName+appendDomId);
1896	break ;
1897	case CDomain::type_attr::rectilinear:
1898	if (!compressedOutput \|\| !domain->isCompressible())
1899	{
1900	dimXid = dimIname+appendDomId;
1901	dimYid = dimJname+appendDomId;
1902	dimIdList.push_back(dimXid);
1903	dimIdList.push_back(dimYid);
1904	}
1905	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1906	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1907
1908	break ;
1909	case CDomain::type_attr::unstructured:
1910	{
1911	if (SuperClassWriter::useCFConvention)
1912	{
1913	dimXid = dimIname + appendDomId;
1914	dimIdList.push_back(dimXid);
1915	dimCoordList.push_back(lonName+appendDomId);
1916	dimCoordList.push_back(latName+appendDomId);
1917	}
1918	else
1919	{
1920	StdString domainName = domain->name;
1921	if (domain->nvertex == 1)
1922	{
1923	dimXid = "n" + domainName + "_node";
1924	dimIdList.push_back(dimXid);
1925	dimCoordList.push_back(StdString(domainName + "_node_x"));
1926	dimCoordList.push_back(StdString(domainName + "_node_y"));
1927	}
1928	else if (domain->nvertex == 2)
1929	{
1930	dimXid = "n" + domainName + "_edge";
1931	dimIdList.push_back(dimXid);
1932	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1933	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1934	}
1935	else
1936	{
1937	dimXid = "n" + domainName + "_face";
1938	dimIdList.push_back(dimXid);
1939	dimCoordList.push_back(StdString(domainName + "_face_x"));
1940	dimCoordList.push_back(StdString(domainName + "_face_y"));
1941	}
1942	} // ugrid convention
1943	} // case unstructured domain
1944	}
1945
1946	if (domain->hasArea)
1947	{
1948	hasArea = true;
1949	cellMeasures += " area" + appendDomId;
1950	}
1951	++idxDomain;
1952	}
1953	else if (1 == axisDomainOrder(i))
1954	{
1955	CAxis* axis = CAxis::get(axisList[idxAxis]);
1956	StdString axisId = axis->getAxisOutputName();
1957	StdString axisDim;
1958
1959	if (axis->dim_name.isEmpty()) axisDim = axisId;
1960	else axisDim=axis->dim_name.getValue();
1961
1962	if (compressedOutput && axis->isCompressible())
1963	{
1964	dimIdList.push_back(axisDim + "_points");
1965	field->setUseCompressedOutput();
1966	}
1967	else
1968	dimIdList.push_back(axisDim);
1969
1970	if (axisDim != axisId) dimCoordList.push_back(axisId);
1971	++idxAxis;
1972	}
1973	else
1974	{
1975	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1976	StdString scalarId = scalar->getScalarOutputName();
1977	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1978	dimCoordList.push_back(scalarId);
1979	++idxScalar;
1980	}
1981	}
1982
1983	StdString fieldid = field->getFieldOutputName();
1984
1985	nc_type type ;
1986	if (field->prec.isEmpty()) type = NC_FLOAT ;
1987	else
1988	{
1989	if (field->prec==2) type = NC_SHORT ;
1990	else if (field->prec==4) type = NC_FLOAT ;
1991	else if (field->prec==8) type = NC_DOUBLE ;
1992	}
1993
1994	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1995
1996	if (wtime)
1997	{
1998	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1999	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
2000	dims.push_back(timeid);
2001	}
2002
2003	if (compressedOutput && grid->isCompressible())
2004	{
2005	dims.push_back(grid->getId() + "_points");
2006	field->setUseCompressedOutput();
2007	}
2008	else
2009	{
2010	while (!dimIdList.empty())
2011	{
2012	dims.push_back(dimIdList.back());
2013	dimIdList.pop_back();
2014	}
2015	}
2016
2017	while (!dimCoordList.empty())
2018	{
2019	coodinates.push_back(dimCoordList.back());
2020	dimCoordList.pop_back();
2021	}
2022
2023	try
2024	{
2025	SuperClassWriter::addVariable(fieldid, type, dims);
2026
2027	if (!field->standard_name.isEmpty())
2028	SuperClassWriter::addAttribute
2029	("standard_name", field->standard_name.getValue(), &fieldid);
2030
2031	if (!field->long_name.isEmpty())
2032	SuperClassWriter::addAttribute
2033	("long_name", field->long_name.getValue(), &fieldid);
2034
2035	if (!field->unit.isEmpty())
2036	SuperClassWriter::addAttribute
2037	("units", field->unit.getValue(), &fieldid);
2038
2039	// Ugrid field attributes "mesh" and "location"
2040	if (!SuperClassWriter::useCFConvention)
2041	{
2042	if (!domainList.empty())
2043	{
2044	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
2045	StdString mesh = domain->name;
2046	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
2047	StdString location;
2048	if (domain->nvertex == 1)
2049	location = "node";
2050	else if (domain->nvertex == 2)
2051	location = "edge";
2052	else if (domain->nvertex > 2)
2053	location = "face";
2054	SuperClassWriter::addAttribute("location", location, &fieldid);
2055	}
2056
2057	}
2058
2059	if (!field->valid_min.isEmpty())
2060	SuperClassWriter::addAttribute
2061	("valid_min", field->valid_min.getValue(), &fieldid);
2062
2063	if (!field->valid_max.isEmpty())
2064	SuperClassWriter::addAttribute
2065	("valid_max", field->valid_max.getValue(), &fieldid);
2066
2067	if (!field->scale_factor.isEmpty())
2068	SuperClassWriter::addAttribute
2069	("scale_factor", field->scale_factor.getValue(), &fieldid);
2070
2071	if (!field->add_offset.isEmpty())
2072	SuperClassWriter::addAttribute
2073	("add_offset", field->add_offset.getValue(), &fieldid);
2074
2075	SuperClassWriter::addAttribute
2076	("online_operation", field->operation.getValue(), &fieldid);
2077
2078	// write child variables as attributes
2079
2080
2081	bool alreadyAddCellMethod = false;
2082	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
2083	if (!field->cell_methods.isEmpty())
2084	{
2085	StdString cellMethodString = field->cell_methods;
2086	if (field->cell_methods_mode.isEmpty() \|\|
2087	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
2088	{
2089	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
2090	alreadyAddCellMethod = true;
2091	}
2092	else
2093	{
2094	switch (field->cell_methods_mode)
2095	{
2096	case (CField::cell_methods_mode_attr::prefix):
2097	cellMethodsPrefix = cellMethodString;
2098	cellMethodsPrefix += " ";
2099	break;
2100	case (CField::cell_methods_mode_attr::suffix):
2101	cellMethodsSuffix = " ";
2102	cellMethodsSuffix += cellMethodString;
2103	break;
2104	case (CField::cell_methods_mode_attr::none):
2105	break;
2106	default:
2107	break;
2108	}
2109	}
2110	}
2111
2112
2113	if (wtime)
2114	{
2115	CDuration freqOp = field->freq_op.getValue();
2116	freqOp.solveTimeStep(*context->calendar);
2117	StdString freqOpStr = freqOp.toStringUDUnits();
2118	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
2119
2120	CDuration freqOut = field->getRelFile()->output_freq.getValue();
2121	freqOut.solveTimeStep(*context->calendar);
2122	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
2123
2124	StdString cellMethods(cellMethodsPrefix + "time: ");
2125	if (field->operation.getValue() == "instant") cellMethods += "point";
2126	else if (field->operation.getValue() == "average") cellMethods += "mean";
2127	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
2128	else cellMethods += field->operation;
2129	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
2130	cellMethods += " (interval: " + freqOpStr + ")";
2131	cellMethods += cellMethodsSuffix;
2132	if (!alreadyAddCellMethod)
2133	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
2134	}
2135
2136	if (hasArea)
2137	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
2138
2139	if (!field->default_value.isEmpty())
2140	{
2141	double default_value = field->default_value.getValue();
2142	if (type == NC_DOUBLE)
2143	{
2144	SuperClassWriter::setDefaultValue(fieldid, &default_value);
2145	}
2146	else if (type == NC_SHORT)
2147	{
2148	short sdefault_value = (short)default_value;
2149	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
2150	}
2151	else
2152	{
2153	float fdefault_value = (float)default_value;
2154	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
2155	}
2156	}
2157	else
2158	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
2159
2160	if (field->compression_level.isEmpty())
2161	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
2162	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
2163
2164	{ // Ecriture des coordonnes
2165
2166	StdString coordstr; //boost::algorithm::join(coodinates, " ")
2167	std::vector<StdString>::iterator
2168	itc = coodinates.begin(), endc = coodinates.end();
2169
2170	for (; itc!= endc; itc++)
2171	{
2172	StdString & coord = *itc;
2173	if (itc+1 != endc)
2174	coordstr.append(coord).append(" ");
2175	else coordstr.append(coord);
2176	}
2177
2178	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
2179
2180	}
2181
2182	vector<CVariable*> listVars = field->getAllVariables() ;
2183	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
2184
2185	}
2186	catch (CNetCdfException& e)
2187	{
2188	StdString msg("On writing field : ");
2189	msg.append(fieldid); msg.append("\n");
2190	msg.append("In the context : ");
2191	msg.append(context->getId()); msg.append("\n");
2192	msg.append(e.what());
2193	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2194	}
2195	} // writeField_()
2196
2197	//--------------------------------------------------------------
2198
2199	void CNc4DataOutput::writeFile_ (CFile* file)
2200	{
2201	StdString filename = file->getFileOutputName();
2202	StdString description = (!file->description.isEmpty())
2203	? file->description.getValue()
2204	: StdString("Created by xios");
2205
2206	singleDomain = (file->nbDomains == 1);
2207
2208	StdString conv_str ;
2209	if (file->convention_str.isEmpty())
2210	{
2211	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2212	else conv_str="UGRID" ;
2213	}
2214	else conv_str=file->convention_str ;
2215
2216	try
2217	{
2218	if (!appendMode) this->writeFileAttributes(filename, description,
2219	conv_str,
2220	StdString("An IPSL model"),
2221	this->getTimeStamp());
2222
2223	if (!appendMode)
2224	SuperClassWriter::addDimension("axis_nbounds", 2);
2225	}
2226	catch (CNetCdfException& e)
2227	{
2228	StdString msg("On writing file : ");
2229	msg.append(filename); msg.append("\n");
2230	msg.append("In the context : ");
2231	CContext* context = CContext::getCurrent() ;
2232	msg.append(context->getId()); msg.append("\n");
2233	msg.append(e.what());
2234	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2235	}
2236	}
2237
2238	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2239	{
2240	StdString name = var->getVariableOutputName();
2241
2242	try
2243	{
2244	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2245	addAttribute(name, var->getData<int>(), &fieldId);
2246	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2247	addAttribute(name, var->getData<short int>(), &fieldId);
2248	else if (var->type.getValue() == CVariable::type_attr::t_float)
2249	addAttribute(name, var->getData<float>(), &fieldId);
2250	else if (var->type.getValue() == CVariable::type_attr::t_double)
2251	addAttribute(name, var->getData<double>(), &fieldId);
2252	else if (var->type.getValue() == CVariable::type_attr::t_string)
2253	addAttribute(name, var->getData<string>(), &fieldId);
2254	else
2255	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2256	<< "Unsupported variable of type " << var->type.getStringValue());
2257	}
2258	catch (CNetCdfException& e)
2259	{
2260	StdString msg("On writing attributes of variable with name : ");
2261	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2262	msg.append("In the context : ");
2263	CContext* context = CContext::getCurrent() ;
2264	msg.append(context->getId()); msg.append("\n");
2265	msg.append(e.what());
2266	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2267	}
2268	}
2269
2270	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2271	{
2272	StdString name = var->getVariableOutputName();
2273
2274	try
2275	{
2276	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2277	addAttribute(name, var->getData<int>());
2278	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2279	addAttribute(name, var->getData<short int>());
2280	else if (var->type.getValue() == CVariable::type_attr::t_float)
2281	addAttribute(name, var->getData<float>());
2282	else if (var->type.getValue() == CVariable::type_attr::t_double)
2283	addAttribute(name, var->getData<double>());
2284	else if (var->type.getValue() == CVariable::type_attr::t_string)
2285	addAttribute(name, var->getData<string>());
2286	else
2287	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2288	<< "Unsupported variable of type " << var->type.getStringValue());
2289	}
2290	catch (CNetCdfException& e)
2291	{
2292	StdString msg("On writing attributes of variable with name : ");
2293	msg.append(name); msg.append("\n");
2294	msg.append("In the context : ");
2295	CContext* context = CContext::getCurrent() ;
2296	msg.append(context->getId()); msg.append("\n");
2297	msg.append(e.what());
2298	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2299	}
2300	}
2301
2302	void CNc4DataOutput::syncFile_ (void)
2303	{
2304	try
2305	{
2306	SuperClassWriter::sync() ;
2307	}
2308	catch (CNetCdfException& e)
2309	{
2310	StdString msg("On synchronizing the write among processes");
2311	msg.append("In the context : ");
2312	CContext* context = CContext::getCurrent() ;
2313	msg.append(context->getId()); msg.append("\n");
2314	msg.append(e.what());
2315	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2316	}
2317	}
2318
2319	void CNc4DataOutput::closeFile_ (void)
2320	{
2321	try
2322	{
2323	SuperClassWriter::close() ;
2324	}
2325	catch (CNetCdfException& e)
2326	{
2327	StdString msg("On closing file");
2328	msg.append("In the context : ");
2329	CContext* context = CContext::getCurrent() ;
2330	msg.append(context->getId()); msg.append("\n");
2331	msg.append(e.what());
2332	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2333	}
2334
2335	}
2336
2337	//---------------------------------------------------------------
2338
2339	StdString CNc4DataOutput::getTimeStamp(void) const
2340	{
2341	const int buffer_size = 100;
2342	time_t rawtime;
2343	struct tm * timeinfo = NULL;
2344	char buffer [buffer_size];
2345	StdString formatStr;
2346	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2347	else formatStr=file->time_stamp_format;
2348
2349	// time ( &rawtime );
2350	// timeinfo = localtime ( &rawtime );
2351	time ( &rawtime );
2352	timeinfo = gmtime ( &rawtime );
2353	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2354
2355	return (StdString(buffer));
2356	}
2357
2358	//---------------------------------------------------------------
2359
2360	void CNc4DataOutput::writeFieldData_ (CField* field)
2361	{
2362	CContext* context = CContext::getCurrent();
2363	CContextServer* server = context->server;
2364	CGrid* grid = field->grid;
2365
2366	if (field->getNStep()<1)
2367	{
2368	return;
2369	}
2370
2371	if (!grid->doGridHaveDataToWrite())
2372	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2373	{
2374	return;
2375	}
2376
2377	StdString fieldid = field->getFieldOutputName();
2378
2379	StdOStringStream oss;
2380	string timeAxisId;
2381	if (field->hasTimeInstant) timeAxisId = "time_instant";
2382	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2383
2384	StdString timeBoundId = getTimeCounterName() + "_bounds";
2385
2386	StdString timeAxisBoundId;
2387	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2388	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2389
2390	if (!field->wasWritten())
2391	{
2392	if (appendMode && field->file->record_offset.isEmpty() &&
2393	field->getOperationTimeType() != func::CFunctor::once)
2394	{
2395	double factorUnit;
2396	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2397	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2398	else factorUnit=1 ;
2399	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2400	}
2401
2402	field->setWritten();
2403	}
2404
2405
2406	CArray<double,1> time_data(1);
2407	CArray<double,1> time_data_bound(2);
2408	CArray<double,1> time_counter(1);
2409	CArray<double,1> time_counter_bound(2);
2410
2411	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2412	bool wtimeCounter =false ;
2413	bool wtimeData =false ;
2414
2415
2416	if (wtime)
2417	{
2418	Time lastWrite = field->last_Write_srv;
2419	Time lastLastWrite = field->lastlast_Write_srv;
2420
2421
2422	if (field->hasTimeInstant)
2423	{
2424	time_data(0) = time_data_bound(1) = lastWrite;
2425	time_data_bound(0) = time_data_bound(1) = lastWrite;
2426	if (timeCounterType==instant)
2427	{
2428	time_counter(0) = time_data(0);
2429	time_counter_bound(0) = time_data_bound(0);
2430	time_counter_bound(1) = time_data_bound(1);
2431	wtimeCounter=true ;
2432	}
2433	if (hasTimeInstant) wtimeData=true ;
2434	}
2435	else if (field->hasTimeCentered)
2436	{
2437	time_data(0) = (lastWrite + lastLastWrite) / 2;
2438	time_data_bound(0) = lastLastWrite;
2439	time_data_bound(1) = lastWrite;
2440	if (timeCounterType==centered)
2441	{
2442	time_counter(0) = time_data(0) ;
2443	time_counter_bound(0) = time_data_bound(0) ;
2444	time_counter_bound(1) = time_data_bound(1) ;
2445	wtimeCounter=true ;
2446	}
2447	if (hasTimeCentered) wtimeData=true ;
2448	}
2449
2450	if (timeCounterType==record)
2451	{
2452	time_counter(0) = field->getNStep() - 1;
2453	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2454	wtimeCounter=true ;
2455	}
2456
2457	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2458	{
2459	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2460	time_data/=secByDay;
2461	time_data_bound/=secByDay;
2462	time_counter/=secByDay;
2463	time_counter_bound/=secByDay;
2464	}
2465	}
2466
2467	bool isRoot = (server->intraCommRank == 0);
2468
2469	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2470	{
2471	double scaleFactor = 1.0;
2472	double addOffset = 0.0;
2473	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2474	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2475	field->scaleFactorAddOffset(scaleFactor, addOffset);
2476	}
2477
2478	try
2479	{
2480	size_t writtenSize;
2481	if (field->getUseCompressedOutput())
2482	writtenSize = grid->getNumberWrittenIndexes();
2483	else
2484	writtenSize = grid->getWrittenDataSize();
2485
2486	CArray<double,1> fieldData(writtenSize);
2487	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2488
2489	if (field->getUseCompressedOutput())
2490	field->outputCompressedField(fieldData);
2491	else
2492	field->outputField(fieldData);
2493
2494	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2495
2496	switch (SuperClass::type)
2497	{
2498	case (MULTI_FILE) :
2499	{
2500	CTimer::get("Files : writing data").resume();
2501	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2502	CTimer::get("Files : writing data").suspend();
2503	if (wtime)
2504	{
2505	CTimer::get("Files : writing time axis").resume();
2506	if ( wtimeData)
2507	{
2508	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2509	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2510	}
2511	if (wtimeCounter)
2512	{
2513	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2514	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2515	}
2516	CTimer::get("Files : writing time axis").suspend();
2517	}
2518	break;
2519	}
2520	case (ONE_FILE) :
2521	{
2522	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2523	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2524	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2525
2526	std::vector<StdSize> start, count;
2527
2528	if (field->getUseCompressedOutput())
2529	{
2530	if (grid->isCompressible())
2531	{
2532	start.push_back(grid->getOffsetWrittenIndexes());
2533	count.push_back(grid->getNumberWrittenIndexes());
2534	}
2535	else
2536	{
2537	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2538	std::vector<StdString> domainList = grid->getDomainList();
2539	std::vector<StdString> axisList = grid->getAxisList();
2540	int numElement = axisDomainOrder.numElements();
2541	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2542	int idx = nZoomBeginGlobal.size() - 1;
2543
2544	start.reserve(nZoomBeginGlobal.size());
2545	count.reserve(nZoomBeginGlobal.size());
2546
2547
2548	for (int i = numElement - 1; i >= 0; --i)
2549	{
2550	if (2 == axisDomainOrder(i))
2551	{
2552	CDomain* domain = CDomain::get(domainList[idxDomain]);
2553
2554	if (domain->isCompressible())
2555	{
2556	start.push_back(domain->getOffsetWrittenIndexes(comm_file));
2557	count.push_back(domain->getNumberWrittenIndexes(comm_file));
2558	idx -= 2;
2559	}
2560	else
2561	{
2562	if ((domain->type) != CDomain::type_attr::unstructured)
2563	{
2564	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2565	count.push_back(nZoomSizeServer[idx]);
2566	}
2567	--idx;
2568	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2569	count.push_back(nZoomSizeServer[idx]);
2570	--idx;
2571	}
2572	--idxDomain;
2573	}
2574	else if (1 == axisDomainOrder(i))
2575	{
2576	CAxis* axis = CAxis::get(axisList[idxAxis]);
2577
2578	if (axis->isCompressible())
2579	{
2580	start.push_back(axis->getOffsetWrittenIndexes(comm_file));
2581	count.push_back(axis->getNumberWrittenIndexes(comm_file));
2582	}
2583	else
2584	{
2585	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2586	count.push_back(nZoomSizeServer[idx]);
2587	}
2588	--idxAxis;
2589	--idx;
2590	}
2591	}
2592	}
2593	}
2594	else
2595	{
2596	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2597	std::vector<StdString> domainList = grid->getDomainList();
2598	std::vector<StdString> axisList = grid->getAxisList();
2599	int numElement = axisDomainOrder.numElements();
2600	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2601	int idx = domainList.size() * 2 + axisList.size() - 1;
2602
2603	start.reserve(nZoomBeginGlobal.size());
2604	count.reserve(nZoomBeginGlobal.size());
2605
2606	for (int i = numElement - 1; i >= 0; --i)
2607	{
2608	if (2 == axisDomainOrder(i))
2609	{
2610	CDomain* domain = CDomain::get(domainList[idxDomain]);
2611	if ((domain->type) != CDomain::type_attr::unstructured)
2612	{
2613	start.push_back(domain->zoom_jbegin - domain->global_zoom_jbegin);
2614	count.push_back(domain->zoom_nj);
2615	}
2616	--idx ;
2617
2618	start.push_back(domain->zoom_ibegin - domain->global_zoom_ibegin);
2619	count.push_back(domain->zoom_ni);
2620	--idx ;
2621	--idxDomain;
2622	}
2623	else if (1 == axisDomainOrder(i))
2624	{
2625	CAxis* axis = CAxis::get(axisList[idxAxis]);
2626	start.push_back(axis->zoom_begin - axis->global_zoom_begin);
2627	count.push_back(axis->zoom_n);
2628	--idx;
2629	--idxAxis;
2630	}
2631	else
2632	{
2633	if (1 == axisDomainOrder.numElements())
2634	{
2635	start.push_back(0);
2636	count.push_back(1);
2637	}
2638	--idx;
2639	}
2640	}
2641	}
2642
2643
2644	CTimer::get("Files : writing data").resume();
2645	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2646	CTimer::get("Files : writing data").suspend();
2647
2648	if (wtime)
2649	{
2650	CTimer::get("Files : writing time axis").resume();
2651	if ( wtimeData)
2652	{
2653	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2654	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2655	}
2656	if (wtimeCounter)
2657	{
2658	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2659	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2660
2661	}
2662	CTimer::get("Files : writing time axis").suspend();
2663	}
2664
2665	break;
2666	}
2667	}
2668	}
2669	catch (CNetCdfException& e)
2670	{
2671	StdString msg("On writing field data: ");
2672	msg.append(fieldid); msg.append("\n");
2673	msg.append("In the context : ");
2674	msg.append(context->getId()); msg.append("\n");
2675	msg.append(e.what());
2676	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2677	}
2678	}
2679
2680	//---------------------------------------------------------------
2681
2682	void CNc4DataOutput::writeTimeAxis_
2683	(CField* field,
2684	const boost::shared_ptr<CCalendar> cal)
2685	{
2686	StdOStringStream oss;
2687	bool createInstantAxis=false ;
2688	bool createCenteredAxis=false ;
2689	bool createTimeCounterAxis=false ;
2690
2691	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2692
2693
2694	StdString axisId ;
2695	StdString axisBoundId;
2696	StdString timeid(getTimeCounterName());
2697	StdString timeBoundId("axis_nbounds");
2698
2699	StdString strTimeUnits ;
2700	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2701	else strTimeUnits="seconds since " ;
2702
2703	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2704	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2705
2706
2707	if (field->file->time_counter.isEmpty())
2708	{
2709	if (timeCounterType==none) createTimeCounterAxis=true ;
2710	if (field->hasTimeCentered)
2711	{
2712	timeCounterType=centered ;
2713	if (!hasTimeCentered) createCenteredAxis=true ;
2714	}
2715	if (field->hasTimeInstant)
2716	{
2717	if (timeCounterType==none) timeCounterType=instant ;
2718	if (!hasTimeInstant) createInstantAxis=true ;
2719	}
2720	}
2721	else if (field->file->time_counter==CFile::time_counter_attr::instant)
2722	{
2723	if (field->hasTimeCentered)
2724	{
2725	if (!hasTimeCentered) createCenteredAxis=true ;
2726	}
2727	if (field->hasTimeInstant)
2728	{
2729	if (timeCounterType==none) createTimeCounterAxis=true ;
2730	timeCounterType=instant ;
2731	if (!hasTimeInstant) createInstantAxis=true ;
2732	}
2733	}
2734	else if (field->file->time_counter==CFile::time_counter_attr::centered)
2735	{
2736	if (field->hasTimeCentered)
2737	{
2738	if (timeCounterType==none) createTimeCounterAxis=true ;
2739	timeCounterType=centered ;
2740	if (!hasTimeCentered) createCenteredAxis=true ;
2741	}
2742	if (field->hasTimeInstant)
2743	{
2744	if (!hasTimeInstant) createInstantAxis=true ;
2745	}
2746	}
2747	else if (field->file->time_counter==CFile::time_counter_attr::instant_exclusive)
2748	{
2749	if (field->hasTimeCentered)
2750	{
2751	if (!hasTimeCentered) createCenteredAxis=true ;
2752	}
2753	if (field->hasTimeInstant)
2754	{
2755	if (timeCounterType==none) createTimeCounterAxis=true ;
2756	timeCounterType=instant ;
2757	}
2758	}
2759	else if (field->file->time_counter==CFile::time_counter_attr::centered_exclusive)
2760	{
2761	if (field->hasTimeCentered)
2762	{
2763	if (timeCounterType==none) createTimeCounterAxis=true ;
2764	timeCounterType=centered ;
2765	}
2766	if (field->hasTimeInstant)
2767	{
2768	if (!hasTimeInstant) createInstantAxis=true ;
2769	}
2770	}
2771	else if (field->file->time_counter==CFile::time_counter_attr::exclusive)
2772	{
2773	if (field->hasTimeCentered)
2774	{
2775	if (timeCounterType==none) createTimeCounterAxis=true ;
2776	if (timeCounterType==instant) createInstantAxis=true ;
2777	timeCounterType=centered ;
2778	}
2779	if (field->hasTimeInstant)
2780	{
2781	if (timeCounterType==none)
2782	{
2783	createTimeCounterAxis=true ;
2784	timeCounterType=instant ;
2785	}
2786	if (timeCounterType==centered)
2787	{
2788	if (!hasTimeInstant) createInstantAxis=true ;
2789	}
2790	}
2791	}
2792	else if (field->file->time_counter==CFile::time_counter_attr::none)
2793	{
2794	if (field->hasTimeCentered)
2795	{
2796	if (!hasTimeCentered) createCenteredAxis=true ;
2797	}
2798	if (field->hasTimeInstant)
2799	{
2800	if (!hasTimeInstant) createInstantAxis=true ;
2801	}
2802	}
2803	else if (field->file->time_counter==CFile::time_counter_attr::record)
2804	{
2805	if (timeCounterType==none) createTimeCounterAxis=true ;
2806	timeCounterType=record ;
2807	if (field->hasTimeCentered)
2808	{
2809	if (!hasTimeCentered) createCenteredAxis=true ;
2810	}
2811	if (field->hasTimeInstant)
2812	{
2813	if (!hasTimeInstant) createInstantAxis=true ;
2814	}
2815	}
2816
2817	if (createInstantAxis)
2818	{
2819	axisId="time_instant" ;
2820	axisBoundId="time_instant_bounds";
2821	hasTimeInstant=true ;
2822	}
2823
2824	if (createCenteredAxis)
2825	{
2826	axisId="time_centered" ;
2827	axisBoundId="time_centered_bounds";
2828	hasTimeCentered=true ;
2829	}
2830
2831
2832	try
2833	{
2834	std::vector<StdString> dims;
2835
2836	if (createInstantAxis \|\| createCenteredAxis)
2837	{
2838	// Adding time_instant or time_centered
2839	dims.push_back(timeid);
2840	if (!SuperClassWriter::varExist(axisId))
2841	{
2842	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2843
2844	CDate timeOrigin=cal->getTimeOrigin() ;
2845	StdOStringStream oss2;
2846	StdString strInitdate=oss2.str() ;
2847	StdString strTimeOrigin=timeOrigin.toString() ;
2848	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2849	strTimeOrigin, axisBoundId);
2850	}
2851
2852	// Adding time_instant_bounds or time_centered_bounds variables
2853	if (!SuperClassWriter::varExist(axisBoundId))
2854	{
2855	dims.clear() ;
2856	dims.push_back(timeid);
2857	dims.push_back(timeBoundId);
2858	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2859	}
2860	}
2861
2862	if (createTimeCounterAxis)
2863	{
2864	// Adding time_counter
2865	axisId = getTimeCounterName();
2866	axisBoundId = getTimeCounterName() + "_bounds";
2867	dims.clear();
2868	dims.push_back(timeid);
2869	if (!SuperClassWriter::varExist(axisId))
2870	{
2871	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2872	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2873
2874	if (field->file->time_counter.isEmpty() \|\|
2875	(field->file->time_counter != CFile::time_counter_attr::record))
2876	{
2877	CDate timeOrigin = cal->getTimeOrigin();
2878	StdString strTimeOrigin = timeOrigin.toString();
2879
2880	this->writeTimeAxisAttributes(axisId, cal->getType(),
2881	strTimeUnits+strTimeOrigin,
2882	strTimeOrigin, axisBoundId);
2883	}
2884	}
2885
2886	// Adding time_counter_bound dimension
2887	if (field->file->time_counter.isEmpty() \|\| (field->file->time_counter != CFile::time_counter_attr::record))
2888	{
2889	if (!SuperClassWriter::varExist(axisBoundId))
2890	{
2891	dims.clear();
2892	dims.push_back(timeid);
2893	dims.push_back(timeBoundId);
2894	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2895	}
2896	}
2897	}
2898	}
2899	catch (CNetCdfException& e)
2900	{
2901	StdString msg("On writing time axis data: ");
2902	msg.append("In the context : ");
2903	CContext* context = CContext::getCurrent() ;
2904	msg.append(context->getId()); msg.append("\n");
2905	msg.append(e.what());
2906	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2907	const boost::shared_ptr<CCalendar> cal)", << msg);
2908	}
2909	}
2910
2911	//---------------------------------------------------------------
2912
2913	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2914	const StdString & calendar,
2915	const StdString & units,
2916	const StdString & time_origin,
2917	const StdString & time_bounds,
2918	const StdString & standard_name,
2919	const StdString & long_name)
2920	{
2921	try
2922	{
2923	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2924	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2925	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2926	SuperClassWriter::addAttribute("units", units , &axis_name);
2927	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2928	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2929	}
2930	catch (CNetCdfException& e)
2931	{
2932	StdString msg("On writing time axis Attribute: ");
2933	msg.append("In the context : ");
2934	CContext* context = CContext::getCurrent() ;
2935	msg.append(context->getId()); msg.append("\n");
2936	msg.append(e.what());
2937	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2938	const StdString & calendar,\
2939	const StdString & units, \
2940	const StdString & time_origin, \
2941	const StdString & time_bounds, \
2942	const StdString & standard_name, \
2943	const StdString & long_name)", << msg);
2944	}
2945	}
2946
2947	//---------------------------------------------------------------
2948
2949	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2950	const StdString & axis,
2951	const StdString & standard_name,
2952	const StdString & long_name,
2953	const StdString & units,
2954	const StdString & nav_model)
2955	{
2956	try
2957	{
2958	if (!axis.empty())
2959	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2960
2961	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2962	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2963	SuperClassWriter::addAttribute("units" , units , &axis_name);
2964	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2965	}
2966	catch (CNetCdfException& e)
2967	{
2968	StdString msg("On writing Axis Attribute: ");
2969	msg.append("In the context : ");
2970	CContext* context = CContext::getCurrent() ;
2971	msg.append(context->getId()); msg.append("\n");
2972	msg.append(e.what());
2973	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2974	const StdString & axis, \
2975	const StdString & standard_name, \
2976	const StdString & long_name, \
2977	const StdString & units, \
2978	const StdString & nav_model)", << msg);
2979	}
2980	}
2981
2982	//---------------------------------------------------------------
2983
2984	void CNc4DataOutput::writeLocalAttributes
2985	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2986	{
2987	try
2988	{
2989	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2990	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2991	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2992	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2993	}
2994	catch (CNetCdfException& e)
2995	{
2996	StdString msg("On writing Local Attributes: ");
2997	msg.append("In the context : ");
2998	CContext* context = CContext::getCurrent() ;
2999	msg.append(context->getId()); msg.append("\n");
3000	msg.append(e.what());
3001	ERROR("CNc4DataOutput::writeLocalAttributes \
3002	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
3003	}
3004
3005	}
3006
3007	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
3008	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
3009	{
3010	CArray<int,1> array(2) ;
3011
3012	try
3013	{
3014	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
3015	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
3016	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
3017	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
3018	array=ni_glo,nj_glo ;
3019	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
3020	array=ni,nj ;
3021	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
3022	array=ibegin+1,jbegin+1 ;
3023	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
3024	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
3025	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
3026	array=0,0 ;
3027	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
3028	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
3029	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
3030	/*
3031	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
3032	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
3033	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
3034	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
3035	*/
3036	}
3037	catch (CNetCdfException& e)
3038	{
3039	StdString msg("On writing Local Attributes IOIPSL \n");
3040	msg.append("In the context : ");
3041	CContext* context = CContext::getCurrent() ;
3042	msg.append(context->getId()); msg.append("\n");
3043	msg.append(e.what());
3044	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
3045	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
3046	}
3047	}
3048	//---------------------------------------------------------------
3049
3050	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
3051	const StdString & description,
3052	const StdString & conventions,
3053	const StdString & production,
3054	const StdString & timeStamp)
3055	{
3056	try
3057	{
3058	SuperClassWriter::addAttribute("name" , name);
3059	SuperClassWriter::addAttribute("description", description);
3060	SuperClassWriter::addAttribute("title" , description);
3061	SuperClassWriter::addAttribute("Conventions", conventions);
3062	// SuperClassWriter::addAttribute("production" , production);
3063
3064	StdString timeStampStr ;
3065	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
3066	else timeStampStr=file->time_stamp_name ;
3067	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
3068
3069	StdString uuidName ;
3070	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
3071	else uuidName=file->uuid_name ;
3072
3073	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
3074	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
3075
3076	}
3077	catch (CNetCdfException& e)
3078	{
3079	StdString msg("On writing File Attributes \n ");
3080	msg.append("In the context : ");
3081	CContext* context = CContext::getCurrent() ;
3082	msg.append(context->getId()); msg.append("\n");
3083	msg.append(e.what());
3084	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
3085	const StdString & description, \
3086	const StdString & conventions, \
3087	const StdString & production, \
3088	const StdString & timeStamp)", << msg);
3089	}
3090	}
3091
3092	//---------------------------------------------------------------
3093
3094	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
3095	int data_dim,
3096	int data_ni,
3097	int data_nj,
3098	int data_ibegin,
3099	int data_jbegin)
3100	{
3101	try
3102	{
3103	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
3104	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
3105	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
3106	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
3107	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
3108	}
3109	catch (CNetCdfException& e)
3110	{
3111	StdString msg("On writing Mask Attributes \n ");
3112	msg.append("In the context : ");
3113	CContext* context = CContext::getCurrent() ;
3114	msg.append(context->getId()); msg.append("\n");
3115	msg.append(e.what());
3116	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
3117	int data_dim, \
3118	int data_ni, \
3119	int data_nj, \
3120	int data_ibegin, \
3121	int data_jbegin)", << msg);
3122	}
3123	}
3124
3125	///--------------------------------------------------------------
3126
3127	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
3128	{
3129	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
3130	if (it == timeToRecordCache.end())
3131	{
3132	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
3133	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
3134	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
3135
3136	CArray<double,2> timeAxisBounds;
3137	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
3138
3139	StdSize record = 0;
3140	double dtime(time);
3141	for (int n = dimSize[0] - 1; n >= 0; n--)
3142	{
3143	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3144	timeAxisBounds*=factorUnit ;
3145	if (timeAxisBounds(1, 0) < dtime)
3146	{
3147	record = n + 1;
3148	break;
3149	}
3150	}
3151	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3152	}
3153	return it->second;
3154	}
3155
3156	///--------------------------------------------------------------
3157
3158	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3159	{
3160	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3161	}
3162
3163	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3164	{
3165	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3166	}
3167
3168	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3169	{
3170	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3171	}
3172
3173	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3174	{
3175	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3176	}
3177
3178	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3179	{
3180	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3181	}
3182
3183	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3184	{
3185	this->writtenDomains.insert(domainName);
3186	}
3187
3188	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3189	{
3190	this->writtenCompressedDomains.insert(domainName);
3191	}
3192
3193	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3194	{
3195	this->writtenAxis.insert(axisName);
3196	}
3197
3198	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3199	{
3200	this->writtenCompressedAxis.insert(axisName);
3201	}
3202
3203	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3204	{
3205	this->writtenScalar.insert(scalarName);
3206	}
3207	} // namespace xios

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