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source: XIOS/dev/XIOS_DEV_CMIP6/src/io/nc4_data_output.cpp @ 1436

Last change on this file since 1436 was 1436, checked in by oabramkina, 6 years ago
Corrections for scalar bounds.
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: 136.7 KB

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1	#include "nc4_data_output.hpp"
2
3	#include <boost/lexical_cast.hpp>
4	#include "attribute_template.hpp"
5	#include "group_template.hpp"
6
7	#include "file.hpp"
8	#include "calendar.hpp"
9	#include "context.hpp"
10	#include "context_server.hpp"
11	#include "netCdfException.hpp"
12	#include "exception.hpp"
13	#include "timer.hpp"
14	#include "uuid.hpp"
15	namespace xios
16	{
17	/// ////////////////////// Dfinitions ////////////////////// ///
18	CNc4DataOutput::CNc4DataOutput
19	(CFile* file, const StdString & filename, bool exist)
20	: SuperClass()
21	, SuperClassWriter(filename, exist)
22	, filename(filename)
23	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
24	{
25	SuperClass::type = MULTI_FILE;
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	}
40
41	CNc4DataOutput::~CNc4DataOutput(void)
42	{ /* Ne rien faire de plus */ }
43
44	///--------------------------------------------------------------
45
46	const StdString & CNc4DataOutput::getFileName(void) const
47	{
48	return (this->filename);
49	}
50
51	//---------------------------------------------------------------
52
53	void CNc4DataOutput::writeDomain_(CDomain* domain)
54	{
55	StdString lonName,latName ;
56
57	domain->computeWrittenIndex();
58	domain->computeWrittenCompressedIndex(comm_file);
59
60	if (domain->type == CDomain::type_attr::unstructured)
61	{
62	if (SuperClassWriter::useCFConvention)
63	writeUnstructuredDomain(domain) ;
64	else
65	writeUnstructuredDomainUgrid(domain) ;
66	return ;
67	}
68
69	CContext* context = CContext::getCurrent() ;
70	CContextServer* server=context->server ;
71
72	if (domain->IsWritten(this->filename)) return;
73	domain->checkAttributes();
74
75	if (domain->isEmpty())
76	if (SuperClass::type==MULTI_FILE) return;
77
78	std::vector<StdString> dim0, dim1;
79	StdString domid = domain->getDomainOutputName();
80	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
81	if (isWrittenDomain(domid)) return ;
82	else setWrittenDomain(domid);
83
84	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
85
86
87	StdString dimXid, dimYid ;
88
89	nc_type typePrec ;
90	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
91	else if (domain->prec==4) typePrec = NC_FLOAT ;
92	else if (domain->prec==8) typePrec = NC_DOUBLE ;
93
94	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
95	switch (domain->type)
96	{
97	case CDomain::type_attr::curvilinear :
98
99	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
100	else lonName = domain->lon_name;
101
102	if (domain->lat_name.isEmpty()) latName = "nav_lat";
103	else latName = domain->lat_name;
104
105	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
106	else dimXid=domain->dim_i_name.getValue() + appendDomid;
107
108	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
109	else dimYid=domain->dim_j_name.getValue() + appendDomid;
110
111	break ;
112
113	case CDomain::type_attr::rectilinear :
114
115	if (domain->lon_name.isEmpty())
116	{
117	if (domain->dim_i_name.isEmpty())
118	lonName = "lon";
119	else
120	lonName = domain->dim_i_name.getValue();
121	}
122	else lonName = domain->lon_name;
123
124	if (domain->lat_name.isEmpty())
125	{
126	if (domain->dim_j_name.isEmpty())
127	latName = "lat";
128	else
129	latName = domain->dim_j_name.getValue();
130	}
131	else latName = domain->lat_name;
132
133	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
134	else dimXid = domain->dim_i_name.getValue()+appendDomid;
135
136	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
137	else dimYid = domain->dim_j_name.getValue()+appendDomid;
138	break;
139	}
140
141	StdString dimVertId = StdString("nvertex").append(appendDomid);
142
143	string lonid,latid,bounds_lonid,bounds_latid ;
144	string areaId = "area" + appendDomid;
145	/*
146	StdString lonid_loc = (server->intraCommSize > 1)
147	? StdString("lon").append(appendDomid).append("_local")
148	: lonid;
149	StdString latid_loc = (server->intraCommSize > 1)
150	? StdString("lat").append(appendDomid).append("_local")
151	: latid;
152	*/
153
154	CArray<size_t, 1>& indexToWrite = domain->localIndexToWriteOnServer;
155	int nbWritten = indexToWrite.numElements();
156	CArray<double,1> writtenLat, writtenLon;
157	CArray<double,2> writtenBndsLat, writtenBndsLon;
158	CArray<double,1> writtenArea;
159
160	if (domain->hasLonLat)
161	{
162	writtenLat.resize(nbWritten);
163	writtenLon.resize(nbWritten);
164	for (int idx = 0; idx < nbWritten; ++idx)
165	{
166	if (idx < domain->latvalue.numElements())
167	{
168	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
169	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
170	}
171	else
172	{
173	writtenLat(idx) = 0.;
174	writtenLon(idx) = 0.;
175	}
176	}
177
178
179	if (domain->hasBounds)
180	{
181	int nvertex = domain->nvertex, idx;
182	writtenBndsLat.resize(nvertex, nbWritten);
183	writtenBndsLon.resize(nvertex, nbWritten);
184	CArray<double,2>& boundslat = domain->bounds_latvalue;
185	CArray<double,2>& boundslon = domain->bounds_lonvalue;
186	for (idx = 0; idx < nbWritten; ++idx)
187	for (int nv = 0; nv < nvertex; ++nv)
188	{
189	if (idx < boundslat.columns())
190	{
191	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
192	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
193	}
194	else
195	{
196	writtenBndsLat(nv, idx) = 0.;
197	writtenBndsLon(nv, idx) = 0.;
198	}
199	}
200	}
201	}
202
203	if (domain->hasArea)
204	{
205	writtenArea.resize(nbWritten);
206	for (int idx = 0; idx < nbWritten; ++idx)
207	{
208	if (idx < domain->areavalue.numElements())
209	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
210	else
211	writtenArea(idx) = 0.;
212	}
213	}
214
215	try
216	{
217	switch (SuperClass::type)
218	{
219	case (MULTI_FILE) :
220	{
221	// if (domain->isEmpty()) return;
222
223	if (server->intraCommSize > 1)
224	{
225	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
226	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
227	}
228
229	switch (domain->type)
230	{
231	case CDomain::type_attr::curvilinear :
232	dim0.push_back(dimYid); dim0.push_back(dimXid);
233	lonid = lonName+appendDomid;
234	latid = latName+appendDomid;
235	break ;
236	case CDomain::type_attr::rectilinear :
237	lonid = lonName+appendDomid;
238	latid = latName+appendDomid;
239	dim0.push_back(dimYid);
240	dim1.push_back(dimXid);
241	break;
242	}
243	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
244	else bounds_lonid = "bounds_"+lonName+appendDomid;
245	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
246	else bounds_latid = "bounds_"+latName+appendDomid;
247
248	SuperClassWriter::addDimension(dimXid, domain->zoom_ni);
249	SuperClassWriter::addDimension(dimYid, domain->zoom_nj);
250
251	if (domain->hasBounds)
252	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
253
254	if (server->intraCommSize > 1)
255	{
256	this->writeLocalAttributes(domain->zoom_ibegin,
257	domain->zoom_ni,
258	domain->zoom_jbegin,
259	domain->zoom_nj,
260	appendDomid);
261
262	if (singleDomain)
263	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
264	domain->zoom_ibegin,
265	domain->zoom_ni,
266	domain->zoom_jbegin,
267	domain->zoom_nj,
268	domain->ni_glo,domain->nj_glo,
269	server->intraCommRank,server->intraCommSize);
270	}
271
272	if (domain->hasLonLat)
273	{
274	switch (domain->type)
275	{
276	case CDomain::type_attr::curvilinear :
277	SuperClassWriter::addVariable(latid, typePrec, dim0);
278	SuperClassWriter::addVariable(lonid, typePrec, dim0);
279	break ;
280	case CDomain::type_attr::rectilinear :
281	SuperClassWriter::addVariable(latid, typePrec, dim0);
282	SuperClassWriter::addVariable(lonid, typePrec, dim1);
283	break ;
284	}
285
286	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
287	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
288
289	if (domain->hasBounds)
290	{
291	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
292	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
293
294	dim0.clear();
295	dim0.push_back(dimYid);
296	dim0.push_back(dimXid);
297	dim0.push_back(dimVertId);
298	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
299	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
300	}
301	}
302
303	dim0.clear();
304	dim0.push_back(dimYid);
305	dim0.push_back(dimXid);
306
307
308	// supress mask if (server->intraCommSize > 1)
309	// supress mask {
310	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
311	// supress mask
312	// supress mask this->writeMaskAttributes(maskid,
313	// supress mask domain->data_dim.getValue()/*,
314	// supress mask domain->data_ni.getValue(),
315	// supress mask domain->data_nj.getValue(),
316	// supress mask domain->data_ibegin.getValue(),
317	// supress mask domain->data_jbegin.getValue()*/);
318	// supress mask }
319
320	//SuperClassWriter::setDefaultValue(maskid, &dvm);
321
322	if (domain->hasArea)
323	{
324	SuperClassWriter::addVariable(areaId, typePrec, dim0);
325	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
326	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
327	}
328
329	SuperClassWriter::definition_end();
330
331	if (domain->hasLonLat)
332	{
333	switch (domain->type)
334	{
335	case CDomain::type_attr::curvilinear :
336	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
337	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
338	break;
339	case CDomain::type_attr::rectilinear :
340	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni)) ;
341	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
342	CArray<double,1> lon = writtenLon(Range(0,domain->zoom_ni-1)) ;
343	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
344	break;
345	}
346
347	if (domain->hasBounds)
348	{
349	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
350	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
351	}
352	}
353
354	if (domain->hasArea)
355	{
356	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
357	}
358
359	SuperClassWriter::definition_start();
360
361	break;
362	}
363	case (ONE_FILE) :
364	{
365	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
366	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
367
368	if (domain->hasBounds)
369	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
370
371	if (domain->hasLonLat)
372	{
373	switch (domain->type)
374	{
375	case CDomain::type_attr::curvilinear :
376	dim0.push_back(dimYid); dim0.push_back(dimXid);
377	lonid = lonName+appendDomid;
378	latid = latName+appendDomid;
379	SuperClassWriter::addVariable(latid, typePrec, dim0);
380	SuperClassWriter::addVariable(lonid, typePrec, dim0);
381	break;
382
383	case CDomain::type_attr::rectilinear :
384	dim0.push_back(dimYid);
385	dim1.push_back(dimXid);
386	lonid = lonName+appendDomid;
387	latid = latName+appendDomid;
388	SuperClassWriter::addVariable(latid, typePrec, dim0);
389	SuperClassWriter::addVariable(lonid, typePrec, dim1);
390	break;
391	}
392	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
393	else bounds_lonid = "bounds_"+lonName+appendDomid;
394	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
395	else bounds_latid = "bounds_"+latName+appendDomid;
396
397	this->writeAxisAttributes
398	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
399	this->writeAxisAttributes
400	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
401
402	if (domain->hasBounds)
403	{
404	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
405	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
406
407	dim0.clear();
408	dim0.push_back(dimYid);
409	dim0.push_back(dimXid);
410	dim0.push_back(dimVertId);
411	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
412	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
413	}
414	}
415
416	if (domain->hasArea)
417	{
418	dim0.clear();
419	dim0.push_back(dimYid); dim0.push_back(dimXid);
420	SuperClassWriter::addVariable(areaId, typePrec, dim0);
421	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
422	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
423	dim0.clear();
424	}
425
426	SuperClassWriter::definition_end();
427
428	switch (domain->type)
429	{
430	case CDomain::type_attr::curvilinear :
431	{
432	std::vector<StdSize> start(2) ;
433	std::vector<StdSize> count(2) ;
434	if (domain->isEmpty())
435	{
436	start[0]=0 ; start[1]=0 ;
437	count[0]=0 ; count[1]=0 ;
438	}
439	else
440	{
441	start[1]=domain->zoom_ibegin-domain->global_zoom_ibegin;
442	start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
443	count[1]=domain->zoom_ni ; count[0]=domain->zoom_nj ;
444	}
445
446	if (domain->hasLonLat)
447	{
448	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
449	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
450	}
451	break;
452	}
453	case CDomain::type_attr::rectilinear :
454	{
455	if (domain->hasLonLat)
456	{
457	std::vector<StdSize> start(1) ;
458	std::vector<StdSize> count(1) ;
459	if (domain->isEmpty())
460	{
461	start[0]=0 ;
462	count[0]=0 ;
463	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
464	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
465	}
466	else
467	{
468	start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
469	count[0]=domain->zoom_nj;
470	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni));
471	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
472
473	start[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
474	count[0]=domain->zoom_ni;
475	CArray<double,1> lon = writtenLon(Range(0,domain->zoom_ni-1));
476	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
477	}
478	}
479	break;
480	}
481	}
482
483	if (domain->hasBounds)
484	{
485	std::vector<StdSize> start(3);
486	std::vector<StdSize> count(3);
487	if (domain->isEmpty())
488	{
489	start[2] = start[1] = start[0] = 0;
490	count[2] = count[1] = count[0] = 0;
491	}
492	else
493	{
494	start[2] = 0;
495	start[1] = domain->zoom_ibegin - domain->global_zoom_ibegin;
496	start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
497	count[2] = domain->nvertex;
498	count[1] = domain->zoom_ni;
499	count[0] = domain->zoom_nj;
500	}
501
502	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0, &start, &count);
503	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0, &start, &count);
504	}
505
506	if (domain->hasArea)
507	{
508	std::vector<StdSize> start(2);
509	std::vector<StdSize> count(2);
510
511	if (domain->isEmpty())
512	{
513	start[0] = 0; start[1] = 0;
514	count[0] = 0; count[1] = 0;
515	}
516	else
517	{
518	start[1] = domain->zoom_ibegin - domain->global_zoom_ibegin;
519	start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
520	count[1] = domain->zoom_ni;
521	count[0] = domain->zoom_nj;
522	}
523
524	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
525	}
526
527	SuperClassWriter::definition_start();
528	break;
529	}
530	default :
531	ERROR("CNc4DataOutput::writeDomain(domain)",
532	<< "[ type = " << SuperClass::type << "]"
533	<< " not implemented yet !");
534	}
535	}
536	catch (CNetCdfException& e)
537	{
538	StdString msg("On writing the domain : ");
539	msg.append(domid); msg.append("\n");
540	msg.append("In the context : ");
541	msg.append(context->getId()); msg.append("\n");
542	msg.append(e.what());
543	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
544	}
545
546	domain->addRelFile(this->filename);
547	}
548
549	//--------------------------------------------------------------
550
551	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
552	{
553	CContext* context = CContext::getCurrent() ;
554	CContextServer* server=context->server ;
555
556	if (domain->IsWritten(this->filename)) return;
557	domain->checkAttributes();
558	if (domain->isEmpty())
559	if (SuperClass::type==MULTI_FILE) return ;
560
561	nc_type typePrec ;
562	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
563	else if (domain->prec==4) typePrec = NC_FLOAT ;
564	else if (domain->prec==8) typePrec = NC_DOUBLE ;
565
566	std::vector<StdString> dim0;
567	StdString domid = domain->getDomainOutputName();
568	StdString domainName = domain->name;
569	domain->assignMesh(domainName, domain->nvertex);
570	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
571
572	StdString node_x = domainName + "_node_x";
573	StdString node_y = domainName + "_node_y";
574
575	StdString edge_x = domainName + "_edge_x";
576	StdString edge_y = domainName + "_edge_y";
577	StdString edge_nodes = domainName + "_edge_nodes";
578
579	StdString face_x = domainName + "_face_x";
580	StdString face_y = domainName + "_face_y";
581	StdString face_nodes = domainName + "_face_nodes";
582	StdString face_edges = domainName + "_face_edges";
583	StdString edge_faces = domainName + "_edge_face_links";
584	StdString face_faces = domainName + "_face_links";
585
586	StdString dimNode = "n" + domainName + "_node";
587	StdString dimEdge = "n" + domainName + "_edge";
588	StdString dimFace = "n" + domainName + "_face";
589	StdString dimVertex = "n" + domainName + "_vertex";
590	StdString dimTwo = "Two";
591
592	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
593	if (!isWrittenDomain(domid))
594	{
595	dim0.clear();
596	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
597	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
598	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
599	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
600	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
601	}
602
603	try
604	{
605	switch (SuperClass::type)
606	{
607	case (ONE_FILE) :
608	{
609	// Adding nodes
610	if (domain->nvertex == 1)
611	{
612	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
613	{
614	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
615	dim0.clear();
616	dim0.push_back(dimNode);
617	SuperClassWriter::addVariable(node_x, typePrec, dim0);
618	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
619	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
620	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
621	SuperClassWriter::addVariable(node_y, typePrec, dim0);
622	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
623	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
624	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
625	}
626	} // domain->nvertex == 1
627
628	// Adding edges and nodes, if nodes have not been defined previously
629	if (domain->nvertex == 2)
630	{
631	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
632	{
633	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
634	dim0.clear();
635	dim0.push_back(dimNode);
636	SuperClassWriter::addVariable(node_x, typePrec, dim0);
637	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
638	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
639	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
640	SuperClassWriter::addVariable(node_y, typePrec, dim0);
641	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
642	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
643	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
644	}
645	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
646	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
647	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
648	dim0.clear();
649	dim0.push_back(dimEdge);
650	SuperClassWriter::addVariable(edge_x, typePrec, dim0);
651	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
652	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
653	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
654	SuperClassWriter::addVariable(edge_y, typePrec, dim0);
655	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
656	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
657	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
658	dim0.clear();
659	dim0.push_back(dimEdge);
660	dim0.push_back(dimTwo);
661	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
662	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
663	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
664	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
665	} // domain->nvertex == 2
666
667	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
668	if (domain->nvertex > 2)
669	{
670	// Nodes
671	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
672	{
673	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
674	dim0.clear();
675	dim0.push_back(dimNode);
676	SuperClassWriter::addVariable(node_x, typePrec, dim0);
677	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
678	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
679	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
680	SuperClassWriter::addVariable(node_y, typePrec, dim0);
681	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
682	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
683	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
684	}
685	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
686	{
687	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
688	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
689	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
690	dim0.clear();
691	dim0.push_back(dimEdge);
692	SuperClassWriter::addVariable(edge_x, typePrec, dim0);
693	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
694	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
695	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
696	SuperClassWriter::addVariable(edge_y, typePrec, dim0);
697	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
698	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
699	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
700	dim0.clear();
701	dim0.push_back(dimEdge);
702	dim0.push_back(dimTwo);
703	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
704	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
705	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
706	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
707	}
708	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
709	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
710	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
711	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
712	dim0.clear();
713	dim0.push_back(dimFace);
714	SuperClassWriter::addVariable(face_x, typePrec, dim0);
715	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
716	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
717	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
718	SuperClassWriter::addVariable(face_y, typePrec, dim0);
719	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
720	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
721	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
722	dim0.clear();
723	dim0.push_back(dimFace);
724	dim0.push_back(dimVertex);
725	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
726	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
727	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
728	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
729	dim0.clear();
730	dim0.push_back(dimFace);
731	dim0.push_back(dimVertex);
732	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
733	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
734	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
735	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
736	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
737	dim0.clear();
738	dim0.push_back(dimEdge);
739	dim0.push_back(dimTwo);
740	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
741	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
742	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
743	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
744	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
745	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
746	dim0.clear();
747	dim0.push_back(dimFace);
748	dim0.push_back(dimVertex);
749	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
750	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
751	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
752	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
753	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
754	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
755	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
756	} // domain->nvertex > 2
757
758	SuperClassWriter::definition_end();
759
760	std::vector<StdSize> startEdges(1) ;
761	std::vector<StdSize> countEdges(1) ;
762	std::vector<StdSize> startNodes(1) ;
763	std::vector<StdSize> countNodes(1) ;
764	std::vector<StdSize> startFaces(1) ;
765	std::vector<StdSize> countFaces(1) ;
766	std::vector<StdSize> startEdgeNodes(2) ;
767	std::vector<StdSize> countEdgeNodes(2) ;
768	std::vector<StdSize> startEdgeFaces(2) ;
769	std::vector<StdSize> countEdgeFaces(2) ;
770	std::vector<StdSize> startFaceConctv(2) ;
771	std::vector<StdSize> countFaceConctv(2) ;
772
773	if (!isWrittenDomain(domid))
774	{
775	if (domain->nvertex == 1)
776	{
777	if (domain->isEmpty())
778	{
779	startNodes[0]=0 ;
780	countNodes[0]=0 ;
781	}
782	else
783	{
784	startNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
785	countNodes[0] = domain->zoom_ni ;
786	}
787
788	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
789	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
790	}
791	else if (domain->nvertex == 2)
792	{
793	if (domain->isEmpty())
794	{
795	startEdges[0]=0 ;
796	countEdges[0]=0 ;
797	startNodes[0]=0 ;
798	countNodes[0]=0 ;
799	startEdgeNodes[0]=0;
800	startEdgeNodes[1]=0;
801	countEdgeNodes[0]=0;
802	countEdgeNodes[1]=0;
803
804	}
805	else
806	{
807	startEdges[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
808	countEdges[0] = domain->zoom_ni;
809	startNodes[0] = domain->mesh->node_start;
810	countNodes[0] = domain->mesh->node_count;
811	startEdgeNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
812	startEdgeNodes[1] = 0;
813	countEdgeNodes[0] = domain->zoom_ni;
814	countEdgeNodes[1] = 2;
815	}
816	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
817	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
818	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
819	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
820	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
821	}
822	else
823	{
824	if (domain->isEmpty())
825	{
826	startFaces[0] = 0 ;
827	countFaces[0] = 0 ;
828	startNodes[0] = 0;
829	countNodes[0] = 0;
830	startEdges[0] = 0;
831	countEdges[0] = 0;
832	startEdgeFaces[0] = 0;
833	startEdgeFaces[1] = 0;
834	countEdgeFaces[0] = 0;
835	countEdgeFaces[1] = 0;
836	startFaceConctv[0] = 0;
837	startFaceConctv[1] = 0;
838	countFaceConctv[0] = 0;
839	countFaceConctv[1] = 0;
840	}
841	else
842	{
843	startFaces[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
844	countFaces[0] = domain->zoom_ni ;
845	startNodes[0] = domain->mesh->node_start;
846	countNodes[0] = domain->mesh->node_count;
847	startEdges[0] = domain->mesh->edge_start;
848	countEdges[0] = domain->mesh->edge_count;
849	startEdgeNodes[0] = domain->mesh->edge_start;
850	startEdgeNodes[1] = 0;
851	countEdgeNodes[0] = domain->mesh->edge_count;
852	countEdgeNodes[1]= 2;
853	startEdgeFaces[0] = domain->mesh->edge_start;
854	startEdgeFaces[1]= 0;
855	countEdgeFaces[0] = domain->mesh->edge_count;
856	countEdgeFaces[1]= 2;
857	startFaceConctv[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
858	startFaceConctv[1] = 0;
859	countFaceConctv[0] = domain->zoom_ni;
860	countFaceConctv[1] = domain->nvertex;
861	}
862	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
863	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
864	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
865	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
866	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
867	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
868	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
869	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
870	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
871	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
872	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
873	}
874	setWrittenDomain(domid);
875	} // !isWrittenDomain
876	else
877	{
878	if (domain->nvertex == 2)
879	{
880	startEdges[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
881	countEdges[0] = domain->zoom_ni;
882	startEdgeNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
883	startEdgeNodes[1] = 0;
884	countEdgeNodes[0] = domain->zoom_ni;
885	countEdgeNodes[1]= 2;
886	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
887	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
888	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
889	}
890	if (domain->nvertex > 2)
891	{
892
893	if (!domain->mesh->edgesAreWritten)
894	{
895	startEdges[0] = domain->mesh->edge_start;
896	countEdges[0] = domain->mesh->edge_count;
897	startEdgeNodes[0] = domain->mesh->edge_start;
898	startEdgeNodes[1] = 0;
899	countEdgeNodes[0] = domain->mesh->edge_count;
900	countEdgeNodes[1]= 2;
901	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
902	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
903	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
904	}
905	startFaces[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
906	countFaces[0] = domain->zoom_ni;
907	startEdgeFaces[0] = domain->mesh->edge_start;
908	startEdgeFaces[1]= 0;
909	countEdgeFaces[0] = domain->mesh->edge_count;
910	countEdgeFaces[1]= 2;
911	startFaceConctv[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
912	startFaceConctv[1] = 0;
913	countFaceConctv[0] = domain->zoom_ni;
914	countFaceConctv[1] = domain->nvertex;
915	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
916	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
917	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
918	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
919	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
920	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
921	}
922	}// isWrittenDomain
923
924	SuperClassWriter::definition_start();
925
926	break;
927	} // ONE_FILE
928
929	case (MULTI_FILE) :
930	{
931	break;
932	}
933
934	default :
935	ERROR("CNc4DataOutput::writeDomain(domain)",
936	<< "[ type = " << SuperClass::type << "]"
937	<< " not implemented yet !");
938	} // switch
939	} // try
940
941	catch (CNetCdfException& e)
942	{
943	StdString msg("On writing the domain : ");
944	msg.append(domid); msg.append("\n");
945	msg.append("In the context : ");
946	msg.append(context->getId()); msg.append("\n");
947	msg.append(e.what());
948	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
949	}
950
951	domain->addRelFile(this->filename);
952	}
953
954	//--------------------------------------------------------------
955
956	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
957	{
958	CContext* context = CContext::getCurrent() ;
959	CContextServer* server=context->server ;
960
961	if (domain->IsWritten(this->filename)) return;
962	domain->checkAttributes();
963
964	if (domain->isEmpty())
965	if (SuperClass::type==MULTI_FILE) return ;
966
967	std::vector<StdString> dim0, dim1;
968	StdString domid = domain->getDomainOutputName();
969	if (isWrittenDomain(domid)) return ;
970	else setWrittenDomain(domid);
971
972	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
973
974	StdString lonName,latName, cellName ;
975	if (domain->lon_name.isEmpty()) lonName = "lon";
976	else lonName = domain->lon_name;
977
978	if (domain->lat_name.isEmpty()) latName = "lat";
979	else latName = domain->lat_name;
980
981	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
982	else cellName="cell";
983	StdString dimXid = cellName+appendDomid;
984	StdString dimVertId = StdString("nvertex").append(appendDomid);
985
986	string lonid,latid,bounds_lonid,bounds_latid ;
987	string areaId = "area" + appendDomid;
988
989	nc_type typePrec ;
990	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
991	else if (domain->prec==4) typePrec = NC_FLOAT ;
992	else if (domain->prec==8) typePrec = NC_DOUBLE ;
993
994	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
995
996	CArray<size_t, 1>& indexToWrite = domain->localIndexToWriteOnServer;
997	int nbWritten = indexToWrite.numElements();
998	CArray<double,1> writtenLat, writtenLon;
999	CArray<double,2> writtenBndsLat, writtenBndsLon;
1000	CArray<double,1> writtenArea;
1001
1002	if (domain->hasLonLat)
1003	{
1004	writtenLat.resize(nbWritten);
1005	writtenLon.resize(nbWritten);
1006	for (int idx = 0; idx < nbWritten; ++idx)
1007	{
1008	if (idx < domain->latvalue.numElements())
1009	{
1010	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
1011	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
1012	}
1013	else
1014	{
1015	writtenLat(idx) = 0.;
1016	writtenLon(idx) = 0.;
1017	}
1018	}
1019	}
1020
1021	if (domain->hasBounds)
1022	{
1023	int nvertex = domain->nvertex, idx;
1024	writtenBndsLat.resize(nvertex, nbWritten);
1025	writtenBndsLon.resize(nvertex, nbWritten);
1026	CArray<double,2>& boundslat = domain->bounds_latvalue;
1027	CArray<double,2>& boundslon = domain->bounds_lonvalue;
1028	for (idx = 0; idx < nbWritten; ++idx)
1029	{
1030	for (int nv = 0; nv < nvertex; ++nv)
1031	{
1032	if (idx < boundslat.columns())
1033	{
1034	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
1035	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
1036	}
1037	else
1038	{
1039	writtenBndsLat(nv, idx) = 0.;
1040	writtenBndsLon(nv, idx) = 0.;
1041	}
1042	}
1043	}
1044	}
1045
1046	if (domain->hasArea)
1047	{
1048	writtenArea.resize(nbWritten);
1049	for (int idx = 0; idx < nbWritten; ++idx)
1050	{
1051	if (idx < domain->areavalue.numElements())
1052	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
1053	else
1054	writtenArea(idx) = 0.;
1055	}
1056	}
1057
1058	try
1059	{
1060	switch (SuperClass::type)
1061	{
1062	case (MULTI_FILE) :
1063	{
1064	dim0.push_back(dimXid);
1065	SuperClassWriter::addDimension(dimXid, domain->zoom_ni);
1066
1067	lonid = lonName+appendDomid;
1068	latid = latName+appendDomid;
1069	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1070	else bounds_lonid = "bounds_"+lonName+appendDomid;
1071	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1072	else bounds_latid = "bounds_"+latName+appendDomid;
1073
1074	if (domain->hasLonLat)
1075	{
1076	SuperClassWriter::addVariable(latid, typePrec, dim0);
1077	SuperClassWriter::addVariable(lonid, typePrec, dim0);
1078	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1079	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1080	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1081	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1082	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
1083	}
1084	dim0.clear();
1085	if (domain->hasBounds)
1086	{
1087	dim0.push_back(dimXid);
1088	dim0.push_back(dimVertId);
1089	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
1090	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
1091	}
1092
1093	dim0.clear();
1094	dim0.push_back(dimXid);
1095	if (domain->hasArea)
1096	{
1097	SuperClassWriter::addVariable(areaId, typePrec, dim0);
1098	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1099	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1100	}
1101
1102	SuperClassWriter::definition_end();
1103
1104	if (domain->hasLonLat)
1105	{
1106	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
1107	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
1108	if (domain->hasBounds)
1109	{
1110	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
1111	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
1112	}
1113	}
1114
1115	if (domain->hasArea)
1116	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
1117
1118	SuperClassWriter::definition_start();
1119	break ;
1120	}
1121
1122	case (ONE_FILE) :
1123	{
1124	lonid = lonName+appendDomid;
1125	latid = latName+appendDomid;
1126	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1127	else bounds_lonid = "bounds_"+lonName+appendDomid;
1128	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1129	else bounds_latid = "bounds_"+latName+appendDomid;
1130
1131	dim0.push_back(dimXid);
1132	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
1133	if (domain->hasLonLat)
1134	{
1135	SuperClassWriter::addVariable(latid, typePrec, dim0);
1136	SuperClassWriter::addVariable(lonid, typePrec, dim0);
1137
1138	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1139	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1140	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1141	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1142	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
1143	}
1144	dim0.clear();
1145
1146	if (domain->hasBounds)
1147	{
1148	dim0.push_back(dimXid);
1149	dim0.push_back(dimVertId);
1150	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
1151	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
1152	}
1153
1154	if (domain->hasArea)
1155	{
1156	dim0.clear();
1157	dim0.push_back(dimXid);
1158	SuperClassWriter::addVariable(areaId, typePrec, dim0);
1159	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1160	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1161	}
1162
1163	SuperClassWriter::definition_end();
1164
1165	std::vector<StdSize> start(1), startBounds(2) ;
1166	std::vector<StdSize> count(1), countBounds(2) ;
1167	if (domain->isEmpty())
1168	{
1169	start[0]=0 ;
1170	count[0]=0 ;
1171	startBounds[1]=0 ;
1172	countBounds[1]=nvertex ;
1173	startBounds[0]=0 ;
1174	countBounds[0]=0 ;
1175	}
1176	else
1177	{
1178	start[0]=domain->zoom_ibegin - domain->global_zoom_ibegin;
1179	count[0]=domain->zoom_ni;
1180	startBounds[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
1181	startBounds[1]=0 ;
1182	countBounds[0]=domain->zoom_ni;
1183	countBounds[1]=nvertex ;
1184	}
1185
1186	if (domain->hasLonLat)
1187	{
1188	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
1189	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
1190	if (domain->hasBounds)
1191	{
1192	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1193	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1194	}
1195	}
1196
1197	if (domain->hasArea)
1198	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
1199
1200	SuperClassWriter::definition_start();
1201
1202	break;
1203	}
1204	default :
1205	ERROR("CNc4DataOutput::writeDomain(domain)",
1206	<< "[ type = " << SuperClass::type << "]"
1207	<< " not implemented yet !");
1208	}
1209	}
1210	catch (CNetCdfException& e)
1211	{
1212	StdString msg("On writing the domain : ");
1213	msg.append(domid); msg.append("\n");
1214	msg.append("In the context : ");
1215	msg.append(context->getId()); msg.append("\n");
1216	msg.append(e.what());
1217	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1218	}
1219	domain->addRelFile(this->filename);
1220	}
1221	//--------------------------------------------------------------
1222
1223	void CNc4DataOutput::writeAxis_(CAxis* axis)
1224	{
1225	if (axis->IsWritten(this->filename)) return;
1226	axis->checkAttributes();
1227
1228	axis->computeWrittenIndex();
1229	axis->computeWrittenCompressedIndex(comm_file);
1230
1231	int zoom_size = (MULTI_FILE == SuperClass::type) ? axis->zoom_n
1232	: axis->global_zoom_n;
1233
1234	int zoom_count = axis->zoom_n;
1235	int zoom_begin = axis->zoom_begin;
1236	// int zoom_begin = (MULTI_FILE == SuperClass::type) ? axis->global_zoom_begin
1237	// : axis->zoom_begin;
1238
1239	if ((0 == axis->zoom_n) && (MULTI_FILE == SuperClass::type)) return;
1240
1241	std::vector<StdString> dims;
1242	StdString axisid = axis->getAxisOutputName();
1243	StdString axisDim, axisBoundsId;
1244	if (isWrittenAxis(axisid)) return ;
1245	else setWrittenAxis(axisid);
1246
1247	nc_type typePrec ;
1248	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1249	else if (axis->prec==4) typePrec = NC_FLOAT ;
1250	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1251
1252	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1253	string strId="str_len" ;
1254	try
1255	{
1256	if (axis->dim_name.isEmpty()) axisDim = axisid;
1257	else axisDim=axis->dim_name.getValue();
1258	SuperClassWriter::addDimension(axisDim, zoom_size);
1259	dims.push_back(axisDim);
1260
1261	if (!axis->label.isEmpty()) SuperClassWriter::addDimension(strId, stringArrayLen);
1262
1263	if (axis->hasValue \|\| !axis->label.isEmpty())
1264	{
1265	if (!axis->label.isEmpty()) dims.push_back(strId);
1266
1267	SuperClassWriter::addVariable(axisid, typePrec, dims);
1268
1269	if (!axis->name.isEmpty())
1270	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1271
1272	if (!axis->standard_name.isEmpty())
1273	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1274
1275	if (!axis->long_name.isEmpty())
1276	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1277
1278	if (!axis->unit.isEmpty())
1279	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1280
1281	if (!axis->axis_type.isEmpty())
1282	{
1283	switch(axis->axis_type)
1284	{
1285	case CAxis::axis_type_attr::X :
1286	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1287	break;
1288	case CAxis::axis_type_attr::Y :
1289	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1290	break;
1291	case CAxis::axis_type_attr::Z :
1292	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1293	break;
1294	case CAxis::axis_type_attr::T :
1295	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1296	break;
1297	}
1298	}
1299
1300	if (!axis->positive.isEmpty())
1301	{
1302	SuperClassWriter::addAttribute("positive",
1303	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1304	&axisid);
1305	}
1306
1307	if (!axis->formula.isEmpty())
1308	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1309
1310	if (!axis->formula_term.isEmpty())
1311	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
1312
1313	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1314	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1315	{
1316	dims.push_back("axis_nbounds");
1317	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims);
1318	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1319
1320	if (!axis->standard_name.isEmpty())
1321	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1322
1323	if (!axis->unit.isEmpty())
1324	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1325
1326	if (!axis->formula_bounds.isEmpty())
1327	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1328
1329	if (!axis->formula_term_bounds.isEmpty())
1330	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
1331	}
1332	}
1333
1334	SuperClassWriter::definition_end();
1335
1336	CArray<size_t, 1>& indexToWrite = axis->localIndexToWriteOnServer;
1337	int nbWritten = indexToWrite.numElements();
1338	CArray<double,1> axis_value(indexToWrite.numElements());
1339	if (!axis->value.isEmpty())
1340	{
1341	for (int i = 0; i < nbWritten; i++)
1342	{
1343	if (i < axis->value.numElements())
1344	axis_value(i) = axis->value(indexToWrite(i));
1345	else
1346	axis_value(i) = 0.;
1347	}
1348	}
1349	CArray<double,2> axis_bounds;
1350	CArray<string,1> axis_label;
1351	if (!axis->label.isEmpty())
1352	{
1353	axis_label.resize(indexToWrite.numElements());
1354	for (int i = 0; i < nbWritten; i++)
1355	{
1356	if (i < axis->label.numElements())
1357	axis_label(i) = axis->label(indexToWrite(i));
1358	else
1359	axis_label(i) = boost::lexical_cast<string>(0); // Write 0 as a label
1360	}
1361	}
1362
1363	switch (SuperClass::type)
1364	{
1365	case MULTI_FILE:
1366	{
1367	if (axis->label.isEmpty())
1368	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1369
1370	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1371	{
1372	axis_bounds.resize(2, indexToWrite.numElements());
1373	for (int i = 0; i < nbWritten; ++i)
1374	{
1375	if (i < axis->bounds.columns())
1376	{
1377	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1378	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1379	}
1380	else
1381	{
1382	axis_bounds(0, i) = 0.;
1383	axis_bounds(1, i) = 0.;
1384
1385	}
1386	}
1387
1388	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0);
1389	}
1390
1391	// Need to check after
1392	if (!axis->label.isEmpty())
1393	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0);
1394
1395	SuperClassWriter::definition_start();
1396	break;
1397	}
1398	case ONE_FILE:
1399	{
1400	std::vector<StdSize> start(1), startBounds(2) ;
1401	std::vector<StdSize> count(1), countBounds(2) ;
1402	start[0] = startBounds[0] = zoom_begin - axis->global_zoom_begin;
1403	count[0] = countBounds[0] = zoom_count; // zoom_size
1404	startBounds[1] = 0;
1405	countBounds[1] = 2;
1406
1407	if (axis->label.isEmpty())
1408	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1409
1410	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1411	{
1412	axis_bounds.resize(2, indexToWrite.numElements());
1413	for (int i = 0; i < nbWritten; ++i)
1414	{
1415	if (i < axis->bounds.columns())
1416	{
1417	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1418	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1419	}
1420	else
1421	{
1422	axis_bounds(0, i) = 0.;
1423	axis_bounds(1, i) = 0.;
1424	}
1425	}
1426	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1427	}
1428
1429	// Need to check after
1430	if (!axis->label.isEmpty())
1431	{
1432	std::vector<StdSize> startLabel(2), countLabel(2);
1433	startLabel[0] = start[0]; startLabel[1] = 0;
1434	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1435	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0, &startLabel, &countLabel);
1436	}
1437
1438	SuperClassWriter::definition_start();
1439
1440	break;
1441	}
1442	default :
1443	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1444	<< "[ type = " << SuperClass::type << "]"
1445	<< " not implemented yet !");
1446	}
1447	}
1448	catch (CNetCdfException& e)
1449	{
1450	StdString msg("On writing the axis : ");
1451	msg.append(axisid); msg.append("\n");
1452	msg.append("In the context : ");
1453	CContext* context = CContext::getCurrent() ;
1454	msg.append(context->getId()); msg.append("\n");
1455	msg.append(e.what());
1456	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1457	}
1458	axis->addRelFile(this->filename);
1459	}
1460
1461	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1462	{
1463	if (scalar->IsWritten(this->filename)) return;
1464	scalar->checkAttributes();
1465	int scalarSize = 1;
1466
1467	StdString scalaId = scalar->getScalarOutputName();
1468	StdString boundsId;
1469	if (isWrittenAxis(scalaId)) return ;
1470	else setWrittenAxis(scalaId);
1471
1472	nc_type typePrec ;
1473	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1474	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1475	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1476
1477	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1478	string strId="str_len" ;
1479
1480	try
1481	{
1482	if (!scalar->label.isEmpty()) SuperClassWriter::addDimension(strId, stringArrayLen);
1483
1484	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1485	{
1486	std::vector<StdString> dims;
1487	StdString scalarDim = scalaId;
1488
1489	if (!scalar->label.isEmpty()) dims.push_back(strId);
1490
1491	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1492
1493	if (!scalar->name.isEmpty())
1494	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1495
1496	if (!scalar->standard_name.isEmpty())
1497	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1498
1499	if (!scalar->long_name.isEmpty())
1500	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1501
1502	if (!scalar->unit.isEmpty())
1503	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1504
1505	if (!scalar->axis_type.isEmpty())
1506	{
1507	switch(scalar->axis_type)
1508	{
1509	case CScalar::axis_type_attr::X :
1510	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1511	break;
1512	case CScalar::axis_type_attr::Y :
1513	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1514	break;
1515	case CScalar::axis_type_attr::Z :
1516	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1517	break;
1518	case CScalar::axis_type_attr::T :
1519	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1520	break;
1521	}
1522	}
1523
1524	if (!scalar->positive.isEmpty())
1525	{
1526	SuperClassWriter::addAttribute("positive",
1527	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1528	&scalaId);
1529	}
1530
1531	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1532	{
1533	dims.clear();
1534	dims.push_back("axis_nbounds");
1535	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1536	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1537	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1538	}
1539
1540	SuperClassWriter::definition_end();
1541
1542	switch (SuperClass::type)
1543	{
1544	case MULTI_FILE:
1545	{
1546	CArray<double,1> scalarValue(scalarSize);
1547	CArray<string,1> scalarLabel(scalarSize);
1548	CArray<double,1> scalarBounds(scalarSize*2);
1549
1550	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1551	{
1552	scalarValue(0) = scalar->value;
1553	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1554	}
1555
1556	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1557	{
1558	scalarBounds(0) = scalar->bounds(0);
1559	scalarBounds(1) = scalar->bounds(1);
1560	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1561	}
1562
1563	if (!scalar->label.isEmpty())
1564	{
1565	scalarLabel(0) = scalar->label;
1566	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1567	}
1568
1569	SuperClassWriter::definition_start();
1570
1571	break;
1572	}
1573	case ONE_FILE:
1574	{
1575	CArray<double,1> scalarValue(scalarSize);
1576	CArray<string,1> scalarLabel(scalarSize);
1577	CArray<double,1> scalarBounds(scalarSize*2);
1578
1579	std::vector<StdSize> start(1);
1580	std::vector<StdSize> count(1);
1581	start[0] = 0;
1582	count[0] = 1;
1583	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1584	{
1585	scalarValue(0) = scalar->value;
1586	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1587	}
1588	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1589	{
1590	scalarBounds(0) = scalar->bounds(0);
1591	scalarBounds(1) = scalar->bounds(1);
1592	count[0] = 2;
1593	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1594	}
1595	if (!scalar->label.isEmpty())
1596	{
1597	scalarLabel(0) = scalar->label;
1598	count[0] = stringArrayLen;
1599	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1600	}
1601
1602	SuperClassWriter::definition_start();
1603
1604	break;
1605	}
1606	default :
1607	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1608	<< "[ type = " << SuperClass::type << "]"
1609	<< " not implemented yet !");
1610	}
1611	}
1612	}
1613	catch (CNetCdfException& e)
1614	{
1615	StdString msg("On writing the scalar : ");
1616	msg.append(scalaId); msg.append("\n");
1617	msg.append("In the context : ");
1618	CContext* context = CContext::getCurrent() ;
1619	msg.append(context->getId()); msg.append("\n");
1620	msg.append(e.what());
1621	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1622	}
1623	scalar->addRelFile(this->filename);
1624	}
1625
1626	//--------------------------------------------------------------
1627
1628	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1629	{
1630	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1631
1632	try
1633	{
1634	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1635	std::vector<StdString> domainList = grid->getDomainList();
1636	std::vector<StdString> axisList = grid->getAxisList();
1637	std::vector<StdString> scalarList = grid->getScalarList();
1638	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1639
1640	std::vector<StdString> dims;
1641
1642	if (grid->isCompressible())
1643	{
1644	StdString varId = grid->getId() + "_points";
1645
1646	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1647	SuperClassWriter::addDimension(varId, nbIndexes);
1648
1649	dims.push_back(varId);
1650	SuperClassWriter::addVariable(varId, NC_INT, dims);
1651
1652	StdOStringStream compress;
1653	for (int i = numElement - 1; i >= 0; --i)
1654	{
1655	if (2 == axisDomainOrder(i))
1656	{
1657	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1658	StdString domId = domain->getDomainOutputName();
1659	StdString appendDomId = singleDomain ? "" : "_" + domId;
1660
1661	switch (domain->type)
1662	{
1663	case CDomain::type_attr::curvilinear:
1664	compress << "y" << appendDomId << " x" << appendDomId;
1665	break;
1666	case CDomain::type_attr::rectilinear:
1667	compress << "lat" << appendDomId << " lon" << appendDomId;
1668	break;
1669	case CDomain::type_attr::unstructured:
1670	StdString cellName = (!domain->dim_i_name.isEmpty()) ? cellName=domain->dim_i_name : "cell";
1671	compress << cellName << appendDomId;
1672	// compress << "cell" << appendDomId;
1673	break;
1674	}
1675	++idxDomain;
1676	}
1677	else if (1 == axisDomainOrder(i))
1678	{
1679	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1680	compress << axis->getAxisOutputName();
1681	++idxAxis;
1682	}
1683	else
1684	{
1685	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1686	compress << scalar->getScalarOutputName();
1687	++idxScalar;
1688	}
1689
1690	if (i != 0) compress << ' ';
1691	}
1692	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1693
1694	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1695	indexes = grid->localIndexToWriteOnServer;
1696
1697	switch (SuperClass::type)
1698	{
1699	case (MULTI_FILE):
1700	{
1701	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1702	break;
1703	}
1704	case (ONE_FILE):
1705	{
1706	if (grid->doGridHaveDataDistributed())
1707	grid->getDistributionServer()->computeGlobalIndex(indexes);
1708
1709	std::vector<StdSize> start, count;
1710	start.push_back(grid->getOffsetWrittenIndexes());
1711	count.push_back(grid->getNumberWrittenIndexes());
1712
1713	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1714	break;
1715	}
1716	}
1717	}
1718	else
1719	{
1720	for (int i = 0; i < numElement; ++i)
1721	{
1722	StdString varId, compress;
1723	CArray<int, 1> indexes;
1724	bool isDistributed;
1725	StdSize nbIndexes, totalNbIndexes, offset;
1726	int firstGlobalIndex;
1727
1728	if (2 == axisDomainOrder(i))
1729	{
1730	CDomain* domain = CDomain::get(domainList[idxDomain]);
1731	StdString domId = domain->getDomainOutputName();
1732
1733	if (!domain->isCompressible()
1734	\|\| domain->type == CDomain::type_attr::unstructured
1735	\|\| domain->isWrittenCompressed(this->filename)
1736	\|\| isWrittenCompressedDomain(domId))
1737	continue;
1738
1739	StdString appendDomId = singleDomain ? "" : "_" + domId;
1740
1741	varId = domId + "_points";
1742	switch (domain->type)
1743	{
1744	case CDomain::type_attr::curvilinear:
1745	compress = "y" + appendDomId + " x" + appendDomId;
1746	break;
1747	case CDomain::type_attr::rectilinear:
1748	compress = "lat" + appendDomId + " lon" + appendDomId;
1749	break;
1750	}
1751
1752	// indexes.resize(domain->compressedIndexToWriteOnServer[comm_file].numElements());
1753	// indexes = domain->compressedIndexToWriteOnServer[com_file];
1754	indexes.resize(domain->getCompressedIndexToWriteOnServer(comm_file).numElements());
1755	indexes = domain->getCompressedIndexToWriteOnServer(comm_file);
1756
1757	isDistributed = domain->isDistributed();
1758	nbIndexes = domain->getNumberWrittenIndexes(comm_file);
1759	totalNbIndexes = domain->getTotalNumberWrittenIndexes(comm_file);
1760	offset = domain->getOffsetWrittenIndexes(comm_file);
1761	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1762
1763	domain->addRelFileCompressed(this->filename);
1764	setWrittenCompressedDomain(domId);
1765	++idxDomain;
1766	}
1767	else if (1 == axisDomainOrder(i))
1768	{
1769	CAxis* axis = CAxis::get(axisList[idxAxis]);
1770	StdString axisId = axis->getAxisOutputName();
1771
1772	if (!axis->isCompressible()
1773	\|\| axis->isWrittenCompressed(this->filename)
1774	\|\| isWrittenCompressedAxis(axisId))
1775	continue;
1776
1777	varId = axisId + "_points";
1778	compress = axisId;
1779
1780	// indexes.resize(axis->compressedIndexToWriteOnServer.numElements());
1781	// indexes = axis->compressedIndexToWriteOnServer;
1782
1783	indexes.resize(axis->getCompressedIndexToWriteOnServer(comm_file).numElements());
1784	indexes = axis->getCompressedIndexToWriteOnServer(comm_file);
1785
1786	isDistributed = axis->isDistributed();
1787	nbIndexes = axis->getNumberWrittenIndexes(comm_file);
1788	totalNbIndexes = axis->getTotalNumberWrittenIndexes(comm_file);
1789	offset = axis->getOffsetWrittenIndexes(comm_file);
1790	firstGlobalIndex = axis->begin;
1791
1792	axis->addRelFileCompressed(this->filename);
1793	setWrittenCompressedAxis(axisId);
1794	++idxAxis;
1795	}
1796	else
1797	{
1798	}
1799
1800	if (!varId.empty())
1801	{
1802	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1803
1804	dims.clear();
1805	dims.push_back(varId);
1806	SuperClassWriter::addVariable(varId, NC_INT, dims);
1807
1808	SuperClassWriter::addAttribute("compress", compress, &varId);
1809
1810	switch (SuperClass::type)
1811	{
1812	case (MULTI_FILE):
1813	{
1814	indexes -= firstGlobalIndex;
1815	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1816	break;
1817	}
1818	case (ONE_FILE):
1819	{
1820	std::vector<StdSize> start, count;
1821	start.push_back(offset);
1822	count.push_back(nbIndexes);
1823
1824	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1825	break;
1826	}
1827	}
1828	}
1829	}
1830	}
1831
1832	grid->addRelFileCompressed(this->filename);
1833	}
1834	catch (CNetCdfException& e)
1835	{
1836	StdString msg("On writing compressed grid : ");
1837	msg.append(grid->getId()); msg.append("\n");
1838	msg.append("In the context : ");
1839	CContext* context = CContext::getCurrent();
1840	msg.append(context->getId()); msg.append("\n");
1841	msg.append(e.what());
1842	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1843	}
1844	}
1845
1846	//--------------------------------------------------------------
1847
1848	void CNc4DataOutput::writeTimeDimension_(void)
1849	{
1850	try
1851	{
1852	SuperClassWriter::addDimension(getTimeCounterName());
1853	}
1854	catch (CNetCdfException& e)
1855	{
1856	StdString msg("On writing time dimension : time_couter\n");
1857	msg.append("In the context : ");
1858	CContext* context = CContext::getCurrent() ;
1859	msg.append(context->getId()); msg.append("\n");
1860	msg.append(e.what());
1861	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1862	}
1863	}
1864
1865	//--------------------------------------------------------------
1866
1867	void CNc4DataOutput::writeField_(CField* field)
1868	{
1869	CContext* context = CContext::getCurrent() ;
1870	CContextServer* server=context->server ;
1871
1872	std::vector<StdString> dims, coodinates;
1873	CGrid* grid = field->grid;
1874	if (!grid->doGridHaveDataToWrite())
1875	if (SuperClass::type==MULTI_FILE) return ;
1876
1877	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1878	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1879	std::vector<StdString> domainList = grid->getDomainList();
1880	std::vector<StdString> axisList = grid->getAxisList();
1881	std::vector<StdString> scalarList = grid->getScalarList();
1882
1883	StdString timeid = getTimeCounterName();
1884	StdString dimXid,dimYid;
1885	std::deque<StdString> dimIdList, dimCoordList;
1886	bool hasArea = false;
1887	StdString cellMeasures = "area:";
1888	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1889
1890	for (int i = 0; i < numElement; ++i)
1891	{
1892	if (2 == axisDomainOrder(i))
1893	{
1894	CDomain* domain = CDomain::get(domainList[idxDomain]);
1895	StdString domId = domain->getDomainOutputName();
1896	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1897	StdString lonName,latName ;
1898	StdString dimIname,dimJname ;
1899
1900	if (domain->lon_name.isEmpty())
1901	{
1902	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1903	else lonName = "lon";
1904	}
1905	else lonName = domain->lon_name;
1906
1907	if (domain->lat_name.isEmpty())
1908	{
1909	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1910	else latName = "lat";
1911	}
1912	else latName = domain->lat_name;
1913
1914	if (domain->dim_i_name.isEmpty())
1915	{
1916	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1917	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1918	else dimIname = lonName;
1919	}
1920	else dimIname = domain->dim_i_name;
1921
1922	if (domain->dim_j_name.isEmpty())
1923	{
1924	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1925	else dimJname = latName;
1926	}
1927	else dimJname = domain->dim_j_name;
1928
1929	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1930	{
1931	dimIdList.push_back(domId + "_points");
1932	field->setUseCompressedOutput();
1933	}
1934
1935	switch (domain->type)
1936	{
1937	case CDomain::type_attr::curvilinear:
1938	if (!compressedOutput \|\| !domain->isCompressible())
1939	{
1940	dimXid=dimIname+appendDomId;
1941	dimYid=dimJname+appendDomId;
1942	dimIdList.push_back(dimXid);
1943	dimIdList.push_back(dimYid);
1944	}
1945	dimCoordList.push_back(lonName+appendDomId);
1946	dimCoordList.push_back(latName+appendDomId);
1947	break ;
1948	case CDomain::type_attr::rectilinear:
1949	if (!compressedOutput \|\| !domain->isCompressible())
1950	{
1951	dimXid = dimIname+appendDomId;
1952	dimYid = dimJname+appendDomId;
1953	dimIdList.push_back(dimXid);
1954	dimIdList.push_back(dimYid);
1955	}
1956	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1957	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1958
1959	break ;
1960	case CDomain::type_attr::unstructured:
1961	{
1962	if (SuperClassWriter::useCFConvention)
1963	{
1964	dimXid = dimIname + appendDomId;
1965	dimIdList.push_back(dimXid);
1966	dimCoordList.push_back(lonName+appendDomId);
1967	dimCoordList.push_back(latName+appendDomId);
1968	}
1969	else
1970	{
1971	StdString domainName = domain->name;
1972	if (domain->nvertex == 1)
1973	{
1974	dimXid = "n" + domainName + "_node";
1975	dimIdList.push_back(dimXid);
1976	dimCoordList.push_back(StdString(domainName + "_node_x"));
1977	dimCoordList.push_back(StdString(domainName + "_node_y"));
1978	}
1979	else if (domain->nvertex == 2)
1980	{
1981	dimXid = "n" + domainName + "_edge";
1982	dimIdList.push_back(dimXid);
1983	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1984	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1985	}
1986	else
1987	{
1988	dimXid = "n" + domainName + "_face";
1989	dimIdList.push_back(dimXid);
1990	dimCoordList.push_back(StdString(domainName + "_face_x"));
1991	dimCoordList.push_back(StdString(domainName + "_face_y"));
1992	}
1993	} // ugrid convention
1994	} // case unstructured domain
1995	}
1996
1997	if (domain->hasArea)
1998	{
1999	hasArea = true;
2000	cellMeasures += " area" + appendDomId;
2001	}
2002	++idxDomain;
2003	}
2004	else if (1 == axisDomainOrder(i))
2005	{
2006	CAxis* axis = CAxis::get(axisList[idxAxis]);
2007	StdString axisId = axis->getAxisOutputName();
2008	StdString axisDim;
2009
2010	if (axis->dim_name.isEmpty()) axisDim = axisId;
2011	else axisDim=axis->dim_name.getValue();
2012
2013	if (compressedOutput && axis->isCompressible())
2014	{
2015	dimIdList.push_back(axisDim + "_points");
2016	field->setUseCompressedOutput();
2017	}
2018	else
2019	dimIdList.push_back(axisDim);
2020
2021	if (axisDim != axisId) dimCoordList.push_back(axisId);
2022	++idxAxis;
2023	}
2024	else
2025	{
2026	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
2027	StdString scalarId = scalar->getScalarOutputName();
2028	dimCoordList.push_back(scalarId);
2029	++idxScalar;
2030	}
2031	}
2032
2033	StdString fieldid = field->getFieldOutputName();
2034
2035	nc_type type ;
2036	if (field->prec.isEmpty()) type = NC_FLOAT ;
2037	else
2038	{
2039	if (field->prec==2) type = NC_SHORT ;
2040	else if (field->prec==4) type = NC_FLOAT ;
2041	else if (field->prec==8) type = NC_DOUBLE ;
2042	}
2043
2044	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
2045
2046	if (wtime)
2047	{
2048	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
2049	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
2050	dims.push_back(timeid);
2051	}
2052
2053	if (compressedOutput && grid->isCompressible())
2054	{
2055	dims.push_back(grid->getId() + "_points");
2056	field->setUseCompressedOutput();
2057	}
2058	else
2059	{
2060	while (!dimIdList.empty())
2061	{
2062	dims.push_back(dimIdList.back());
2063	dimIdList.pop_back();
2064	}
2065	}
2066
2067	while (!dimCoordList.empty())
2068	{
2069	coodinates.push_back(dimCoordList.back());
2070	dimCoordList.pop_back();
2071	}
2072
2073	try
2074	{
2075	SuperClassWriter::addVariable(fieldid, type, dims);
2076
2077	if (!field->standard_name.isEmpty())
2078	SuperClassWriter::addAttribute
2079	("standard_name", field->standard_name.getValue(), &fieldid);
2080
2081	if (!field->long_name.isEmpty())
2082	SuperClassWriter::addAttribute
2083	("long_name", field->long_name.getValue(), &fieldid);
2084
2085	if (!field->unit.isEmpty())
2086	SuperClassWriter::addAttribute
2087	("units", field->unit.getValue(), &fieldid);
2088
2089	// Ugrid field attributes "mesh" and "location"
2090	if (!SuperClassWriter::useCFConvention)
2091	{
2092	if (!domainList.empty())
2093	{
2094	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
2095	StdString mesh = domain->name;
2096	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
2097	StdString location;
2098	if (domain->nvertex == 1)
2099	location = "node";
2100	else if (domain->nvertex == 2)
2101	location = "edge";
2102	else if (domain->nvertex > 2)
2103	location = "face";
2104	SuperClassWriter::addAttribute("location", location, &fieldid);
2105	}
2106
2107	}
2108
2109	if (!field->valid_min.isEmpty())
2110	SuperClassWriter::addAttribute
2111	("valid_min", field->valid_min.getValue(), &fieldid);
2112
2113	if (!field->valid_max.isEmpty())
2114	SuperClassWriter::addAttribute
2115	("valid_max", field->valid_max.getValue(), &fieldid);
2116
2117	if (!field->scale_factor.isEmpty())
2118	SuperClassWriter::addAttribute
2119	("scale_factor", field->scale_factor.getValue(), &fieldid);
2120
2121	if (!field->add_offset.isEmpty())
2122	SuperClassWriter::addAttribute
2123	("add_offset", field->add_offset.getValue(), &fieldid);
2124
2125	SuperClassWriter::addAttribute
2126	("online_operation", field->operation.getValue(), &fieldid);
2127
2128	// write child variables as attributes
2129
2130
2131	bool alreadyAddCellMethod = false;
2132	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
2133	if (!field->cell_methods.isEmpty())
2134	{
2135	StdString cellMethodString = field->cell_methods;
2136	if (field->cell_methods_mode.isEmpty() \|\|
2137	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
2138	{
2139	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
2140	alreadyAddCellMethod = true;
2141	}
2142	else
2143	{
2144	switch (field->cell_methods_mode)
2145	{
2146	case (CField::cell_methods_mode_attr::prefix):
2147	cellMethodsPrefix = cellMethodString;
2148	cellMethodsPrefix += " ";
2149	break;
2150	case (CField::cell_methods_mode_attr::suffix):
2151	cellMethodsSuffix = " ";
2152	cellMethodsSuffix += cellMethodString;
2153	break;
2154	case (CField::cell_methods_mode_attr::none):
2155	break;
2156	default:
2157	break;
2158	}
2159	}
2160	}
2161
2162
2163	if (wtime)
2164	{
2165	CDuration freqOp = field->freq_op.getValue();
2166	freqOp.solveTimeStep(*context->calendar);
2167	StdString freqOpStr = freqOp.toStringUDUnits();
2168	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
2169
2170	CDuration freqOut = field->getRelFile()->output_freq.getValue();
2171	freqOut.solveTimeStep(*context->calendar);
2172	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
2173
2174	StdString cellMethods(cellMethodsPrefix + "time: ");
2175	if (field->operation.getValue() == "instant") cellMethods += "point";
2176	else if (field->operation.getValue() == "average") cellMethods += "mean";
2177	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
2178	else cellMethods += field->operation;
2179	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
2180	cellMethods += " (interval: " + freqOpStr + ")";
2181	cellMethods += cellMethodsSuffix;
2182	if (!alreadyAddCellMethod)
2183	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
2184	}
2185
2186	if (hasArea)
2187	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
2188
2189	if (!field->default_value.isEmpty())
2190	{
2191	double default_value = field->default_value.getValue();
2192	if (type == NC_DOUBLE)
2193	{
2194	SuperClassWriter::setDefaultValue(fieldid, &default_value);
2195	}
2196	else if (type == NC_SHORT)
2197	{
2198	short sdefault_value = (short)default_value;
2199	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
2200	}
2201	else
2202	{
2203	float fdefault_value = (float)default_value;
2204	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
2205	}
2206	}
2207	else
2208	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
2209
2210	if (field->compression_level.isEmpty())
2211	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
2212	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
2213
2214	{ // Ecriture des coordonnes
2215
2216	StdString coordstr; //boost::algorithm::join(coodinates, " ")
2217	std::vector<StdString>::iterator
2218	itc = coodinates.begin(), endc = coodinates.end();
2219
2220	for (; itc!= endc; itc++)
2221	{
2222	StdString & coord = *itc;
2223	if (itc+1 != endc)
2224	coordstr.append(coord).append(" ");
2225	else coordstr.append(coord);
2226	}
2227
2228	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
2229
2230	}
2231
2232	vector<CVariable*> listVars = field->getAllVariables() ;
2233	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
2234
2235	}
2236	catch (CNetCdfException& e)
2237	{
2238	StdString msg("On writing field : ");
2239	msg.append(fieldid); msg.append("\n");
2240	msg.append("In the context : ");
2241	msg.append(context->getId()); msg.append("\n");
2242	msg.append(e.what());
2243	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2244	}
2245	} // writeField_()
2246
2247	//--------------------------------------------------------------
2248
2249	void CNc4DataOutput::writeFile_ (CFile* file)
2250	{
2251	StdString filename = file->getFileOutputName();
2252	StdString description = (!file->description.isEmpty())
2253	? file->description.getValue()
2254	: StdString("Created by xios");
2255
2256	singleDomain = (file->nbDomains == 1);
2257
2258	StdString conv_str ;
2259	if (file->convention_str.isEmpty())
2260	{
2261	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2262	else conv_str="UGRID" ;
2263	}
2264	else conv_str=file->convention_str ;
2265
2266	try
2267	{
2268	if (!appendMode) this->writeFileAttributes(filename, description,
2269	conv_str,
2270	StdString("An IPSL model"),
2271	this->getTimeStamp());
2272
2273	if (!appendMode)
2274	SuperClassWriter::addDimension("axis_nbounds", 2);
2275	}
2276	catch (CNetCdfException& e)
2277	{
2278	StdString msg("On writing file : ");
2279	msg.append(filename); msg.append("\n");
2280	msg.append("In the context : ");
2281	CContext* context = CContext::getCurrent() ;
2282	msg.append(context->getId()); msg.append("\n");
2283	msg.append(e.what());
2284	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2285	}
2286	}
2287
2288	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2289	{
2290	StdString name = var->getVariableOutputName();
2291
2292	try
2293	{
2294	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2295	addAttribute(name, var->getData<int>(), &fieldId);
2296	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2297	addAttribute(name, var->getData<short int>(), &fieldId);
2298	else if (var->type.getValue() == CVariable::type_attr::t_float)
2299	addAttribute(name, var->getData<float>(), &fieldId);
2300	else if (var->type.getValue() == CVariable::type_attr::t_double)
2301	addAttribute(name, var->getData<double>(), &fieldId);
2302	else if (var->type.getValue() == CVariable::type_attr::t_string)
2303	addAttribute(name, var->getData<string>(), &fieldId);
2304	else
2305	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2306	<< "Unsupported variable of type " << var->type.getStringValue());
2307	}
2308	catch (CNetCdfException& e)
2309	{
2310	StdString msg("On writing attributes of variable with name : ");
2311	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2312	msg.append("In the context : ");
2313	CContext* context = CContext::getCurrent() ;
2314	msg.append(context->getId()); msg.append("\n");
2315	msg.append(e.what());
2316	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2317	}
2318	}
2319
2320	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2321	{
2322	StdString name = var->getVariableOutputName();
2323
2324	try
2325	{
2326	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2327	addAttribute(name, var->getData<int>());
2328	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2329	addAttribute(name, var->getData<short int>());
2330	else if (var->type.getValue() == CVariable::type_attr::t_float)
2331	addAttribute(name, var->getData<float>());
2332	else if (var->type.getValue() == CVariable::type_attr::t_double)
2333	addAttribute(name, var->getData<double>());
2334	else if (var->type.getValue() == CVariable::type_attr::t_string)
2335	addAttribute(name, var->getData<string>());
2336	else
2337	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2338	<< "Unsupported variable of type " << var->type.getStringValue());
2339	}
2340	catch (CNetCdfException& e)
2341	{
2342	StdString msg("On writing attributes of variable with name : ");
2343	msg.append(name); msg.append("\n");
2344	msg.append("In the context : ");
2345	CContext* context = CContext::getCurrent() ;
2346	msg.append(context->getId()); msg.append("\n");
2347	msg.append(e.what());
2348	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2349	}
2350	}
2351
2352	void CNc4DataOutput::syncFile_ (void)
2353	{
2354	try
2355	{
2356	SuperClassWriter::sync() ;
2357	}
2358	catch (CNetCdfException& e)
2359	{
2360	StdString msg("On synchronizing the write among processes");
2361	msg.append("In the context : ");
2362	CContext* context = CContext::getCurrent() ;
2363	msg.append(context->getId()); msg.append("\n");
2364	msg.append(e.what());
2365	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2366	}
2367	}
2368
2369	void CNc4DataOutput::closeFile_ (void)
2370	{
2371	try
2372	{
2373	SuperClassWriter::close() ;
2374	}
2375	catch (CNetCdfException& e)
2376	{
2377	StdString msg("On closing file");
2378	msg.append("In the context : ");
2379	CContext* context = CContext::getCurrent() ;
2380	msg.append(context->getId()); msg.append("\n");
2381	msg.append(e.what());
2382	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2383	}
2384
2385	}
2386
2387	//---------------------------------------------------------------
2388
2389	StdString CNc4DataOutput::getTimeStamp(void) const
2390	{
2391	const int buffer_size = 100;
2392	time_t rawtime;
2393	struct tm * timeinfo = NULL;
2394	char buffer [buffer_size];
2395	StdString formatStr;
2396	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2397	else formatStr=file->time_stamp_format;
2398
2399	// time ( &rawtime );
2400	// timeinfo = localtime ( &rawtime );
2401	time ( &rawtime );
2402	timeinfo = gmtime ( &rawtime );
2403	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2404
2405	return (StdString(buffer));
2406	}
2407
2408	//---------------------------------------------------------------
2409
2410	void CNc4DataOutput::writeFieldData_ (CField* field)
2411	{
2412	CContext* context = CContext::getCurrent();
2413	CContextServer* server = context->server;
2414	CGrid* grid = field->grid;
2415
2416	if (field->getNStep()<1)
2417	{
2418	return;
2419	}
2420
2421	if (!grid->doGridHaveDataToWrite())
2422	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2423	{
2424	return;
2425	}
2426
2427	StdString fieldid = field->getFieldOutputName();
2428
2429	StdOStringStream oss;
2430	string timeAxisId;
2431	if (field->hasTimeInstant) timeAxisId = "time_instant";
2432	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2433
2434	StdString timeBoundId = getTimeCounterName() + "_bounds";
2435
2436	StdString timeAxisBoundId;
2437	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2438	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2439
2440	if (!field->wasWritten())
2441	{
2442	if (appendMode && field->file->record_offset.isEmpty() &&
2443	field->getOperationTimeType() != func::CFunctor::once)
2444	{
2445	double factorUnit;
2446	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2447	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2448	else factorUnit=1 ;
2449	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2450	}
2451
2452	field->setWritten();
2453	}
2454
2455
2456	CArray<double,1> time_data(1);
2457	CArray<double,1> time_data_bound(2);
2458	CArray<double,1> time_counter(1);
2459	CArray<double,1> time_counter_bound(2);
2460
2461	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2462	bool wtimeCounter =false ;
2463	bool wtimeData =false ;
2464
2465
2466	if (wtime)
2467	{
2468	Time lastWrite = field->last_Write_srv;
2469	Time lastLastWrite = field->lastlast_Write_srv;
2470
2471
2472	if (field->hasTimeInstant)
2473	{
2474	time_data(0) = time_data_bound(1) = lastWrite;
2475	time_data_bound(0) = time_data_bound(1) = lastWrite;
2476	if (timeCounterType==instant)
2477	{
2478	time_counter(0) = time_data(0);
2479	time_counter_bound(0) = time_data_bound(0);
2480	time_counter_bound(1) = time_data_bound(1);
2481	wtimeCounter=true ;
2482	}
2483	if (hasTimeInstant) wtimeData=true ;
2484	}
2485	else if (field->hasTimeCentered)
2486	{
2487	time_data(0) = (lastWrite + lastLastWrite) / 2;
2488	time_data_bound(0) = lastLastWrite;
2489	time_data_bound(1) = lastWrite;
2490	if (timeCounterType==centered)
2491	{
2492	time_counter(0) = time_data(0) ;
2493	time_counter_bound(0) = time_data_bound(0) ;
2494	time_counter_bound(1) = time_data_bound(1) ;
2495	wtimeCounter=true ;
2496	}
2497	if (hasTimeCentered) wtimeData=true ;
2498	}
2499
2500	if (timeCounterType==record)
2501	{
2502	time_counter(0) = field->getNStep() - 1;
2503	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2504	wtimeCounter=true ;
2505	}
2506
2507	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2508	{
2509	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2510	time_data/=secByDay;
2511	time_data_bound/=secByDay;
2512	time_counter/=secByDay;
2513	time_counter_bound/=secByDay;
2514	}
2515	}
2516
2517	bool isRoot = (server->intraCommRank == 0);
2518
2519	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2520	{
2521	double scaleFactor = 1.0;
2522	double addOffset = 0.0;
2523	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2524	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2525	field->scaleFactorAddOffset(scaleFactor, addOffset);
2526	}
2527
2528	try
2529	{
2530	size_t writtenSize;
2531	if (field->getUseCompressedOutput())
2532	writtenSize = grid->getNumberWrittenIndexes();
2533	else
2534	writtenSize = grid->getWrittenDataSize();
2535
2536	CArray<double,1> fieldData(writtenSize);
2537	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2538
2539	if (field->getUseCompressedOutput())
2540	field->outputCompressedField(fieldData);
2541	else
2542	field->outputField(fieldData);
2543
2544	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2545
2546	switch (SuperClass::type)
2547	{
2548	case (MULTI_FILE) :
2549	{
2550	CTimer::get("Files : writing data").resume();
2551	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2552	CTimer::get("Files : writing data").suspend();
2553	if (wtime)
2554	{
2555	CTimer::get("Files : writing time axis").resume();
2556	if ( wtimeData)
2557	{
2558	// SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2559	// SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2560	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2561	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2562	}
2563	if (wtimeCounter)
2564	{
2565	// SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2566	// if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2567	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2568	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2569	}
2570	CTimer::get("Files : writing time axis").suspend();
2571	}
2572	break;
2573	}
2574	case (ONE_FILE) :
2575	{
2576	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2577	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2578	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2579
2580	std::vector<StdSize> start, count;
2581
2582	if (field->getUseCompressedOutput())
2583	{
2584	if (grid->isCompressible())
2585	{
2586	start.push_back(grid->getOffsetWrittenIndexes());
2587	count.push_back(grid->getNumberWrittenIndexes());
2588	}
2589	else
2590	{
2591	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2592	std::vector<StdString> domainList = grid->getDomainList();
2593	std::vector<StdString> axisList = grid->getAxisList();
2594	int numElement = axisDomainOrder.numElements();
2595	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2596	int idx = nZoomBeginGlobal.size() - 1;
2597
2598	start.reserve(nZoomBeginGlobal.size());
2599	count.reserve(nZoomBeginGlobal.size());
2600
2601
2602	for (int i = numElement - 1; i >= 0; --i)
2603	{
2604	if (2 == axisDomainOrder(i))
2605	{
2606	CDomain* domain = CDomain::get(domainList[idxDomain]);
2607
2608	if (domain->isCompressible())
2609	{
2610	start.push_back(domain->getOffsetWrittenIndexes(comm_file));
2611	count.push_back(domain->getNumberWrittenIndexes(comm_file));
2612	idx -= 2;
2613	}
2614	else
2615	{
2616	if ((domain->type) != CDomain::type_attr::unstructured)
2617	{
2618	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2619	count.push_back(nZoomSizeServer[idx]);
2620	}
2621	--idx;
2622	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2623	count.push_back(nZoomSizeServer[idx]);
2624	--idx;
2625	}
2626	--idxDomain;
2627	}
2628	else if (1 == axisDomainOrder(i))
2629	{
2630	CAxis* axis = CAxis::get(axisList[idxAxis]);
2631
2632	if (axis->isCompressible())
2633	{
2634	start.push_back(axis->getOffsetWrittenIndexes(comm_file));
2635	count.push_back(axis->getNumberWrittenIndexes(comm_file));
2636	}
2637	else
2638	{
2639	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2640	count.push_back(nZoomSizeServer[idx]);
2641	}
2642
2643	--idxAxis;
2644	--idx;
2645	}
2646	}
2647	}
2648	}
2649	else
2650	{
2651	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2652	std::vector<StdString> domainList = grid->getDomainList();
2653	std::vector<StdString> axisList = grid->getAxisList();
2654	int numElement = axisDomainOrder.numElements();
2655	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2656	int idx = domainList.size() * 2 + axisList.size() - 1;// nZoomBeginGlobal.size() - 1;
2657
2658	start.reserve(nZoomBeginGlobal.size());
2659	count.reserve(nZoomBeginGlobal.size());
2660
2661	for (int i = numElement - 1; i >= 0; --i)
2662	{
2663	if (2 == axisDomainOrder(i))
2664	{
2665	CDomain* domain = CDomain::get(domainList[idxDomain]);
2666	if ((domain->type) != CDomain::type_attr::unstructured)
2667	{
2668	start.push_back(domain->zoom_jbegin - domain->global_zoom_jbegin);
2669	count.push_back(domain->zoom_nj);
2670	}
2671	--idx ;
2672
2673	start.push_back(domain->zoom_ibegin - domain->global_zoom_ibegin);
2674	count.push_back(domain->zoom_ni);
2675	--idx ;
2676	--idxDomain;
2677	}
2678	else if (1 == axisDomainOrder(i))
2679	{
2680	CAxis* axis = CAxis::get(axisList[idxAxis]);
2681	start.push_back(axis->zoom_begin - axis->global_zoom_begin);
2682	count.push_back(axis->zoom_n);
2683	--idx;
2684	--idxAxis;
2685	}
2686	else
2687	{
2688	if (1 == axisDomainOrder.numElements())
2689	{
2690	start.push_back(0);
2691	count.push_back(1);
2692	}
2693	--idx;
2694	}
2695	}
2696	}
2697
2698
2699	CTimer::get("Files : writing data").resume();
2700	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2701	CTimer::get("Files : writing data").suspend();
2702
2703	if (wtime)
2704	{
2705	CTimer::get("Files : writing time axis").resume();
2706	if ( wtimeData)
2707	{
2708	// SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2709	// SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2710	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2711	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2712	}
2713	if (wtimeCounter)
2714	{
2715	// SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2716	// if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2717	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2718	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2719
2720	}
2721	CTimer::get("Files : writing time axis").suspend();
2722	}
2723
2724	break;
2725	}
2726	}
2727	}
2728	catch (CNetCdfException& e)
2729	{
2730	StdString msg("On writing field data: ");
2731	msg.append(fieldid); msg.append("\n");
2732	msg.append("In the context : ");
2733	msg.append(context->getId()); msg.append("\n");
2734	msg.append(e.what());
2735	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2736	}
2737	}
2738
2739	//---------------------------------------------------------------
2740
2741	void CNc4DataOutput::writeTimeAxis_
2742	(CField* field,
2743	const boost::shared_ptr<CCalendar> cal)
2744	{
2745	StdOStringStream oss;
2746	bool createInstantAxis=false ;
2747	bool createCenteredAxis=false ;
2748	bool createTimeCounterAxis=false ;
2749
2750	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2751
2752
2753	StdString axisId ;
2754	StdString axisBoundId;
2755	StdString timeid(getTimeCounterName());
2756	StdString timeBoundId("axis_nbounds");
2757
2758	StdString strTimeUnits ;
2759	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2760	else strTimeUnits="seconds since " ;
2761
2762	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2763	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2764
2765
2766	if (field->file->time_counter.isEmpty())
2767	{
2768	if (timeCounterType==none) createTimeCounterAxis=true ;
2769	if (field->hasTimeCentered)
2770	{
2771	timeCounterType=centered ;
2772	if (!hasTimeCentered) createCenteredAxis=true ;
2773	}
2774	if (field->hasTimeInstant)
2775	{
2776	if (timeCounterType==none) timeCounterType=instant ;
2777	if (!hasTimeInstant) createInstantAxis=true ;
2778	}
2779	}
2780	else if (field->file->time_counter==CFile::time_counter_attr::instant)
2781	{
2782	if (field->hasTimeCentered)
2783	{
2784	if (!hasTimeCentered) createCenteredAxis=true ;
2785	}
2786	if (field->hasTimeInstant)
2787	{
2788	if (timeCounterType==none) createTimeCounterAxis=true ;
2789	timeCounterType=instant ;
2790	if (!hasTimeInstant) createInstantAxis=true ;
2791	}
2792	}
2793	else if (field->file->time_counter==CFile::time_counter_attr::centered)
2794	{
2795	if (field->hasTimeCentered)
2796	{
2797	if (timeCounterType==none) createTimeCounterAxis=true ;
2798	timeCounterType=centered ;
2799	if (!hasTimeCentered) createCenteredAxis=true ;
2800	}
2801	if (field->hasTimeInstant)
2802	{
2803	if (!hasTimeInstant) createInstantAxis=true ;
2804	}
2805	}
2806	else if (field->file->time_counter==CFile::time_counter_attr::instant_exclusive)
2807	{
2808	if (field->hasTimeCentered)
2809	{
2810	if (!hasTimeCentered) createCenteredAxis=true ;
2811	}
2812	if (field->hasTimeInstant)
2813	{
2814	if (timeCounterType==none) createTimeCounterAxis=true ;
2815	timeCounterType=instant ;
2816	}
2817	}
2818	else if (field->file->time_counter==CFile::time_counter_attr::centered_exclusive)
2819	{
2820	if (field->hasTimeCentered)
2821	{
2822	if (timeCounterType==none) createTimeCounterAxis=true ;
2823	timeCounterType=centered ;
2824	}
2825	if (field->hasTimeInstant)
2826	{
2827	if (!hasTimeInstant) createInstantAxis=true ;
2828	}
2829	}
2830	else if (field->file->time_counter==CFile::time_counter_attr::exclusive)
2831	{
2832	if (field->hasTimeCentered)
2833	{
2834	if (timeCounterType==none) createTimeCounterAxis=true ;
2835	if (timeCounterType==instant) createInstantAxis=true ;
2836	timeCounterType=centered ;
2837	}
2838	if (field->hasTimeInstant)
2839	{
2840	if (timeCounterType==none)
2841	{
2842	createTimeCounterAxis=true ;
2843	timeCounterType=instant ;
2844	}
2845	if (timeCounterType==centered)
2846	{
2847	if (!hasTimeInstant) createInstantAxis=true ;
2848	}
2849	}
2850	}
2851	else if (field->file->time_counter==CFile::time_counter_attr::none)
2852	{
2853	if (field->hasTimeCentered)
2854	{
2855	if (!hasTimeCentered) createCenteredAxis=true ;
2856	}
2857	if (field->hasTimeInstant)
2858	{
2859	if (!hasTimeInstant) createInstantAxis=true ;
2860	}
2861	}
2862	else if (field->file->time_counter==CFile::time_counter_attr::record)
2863	{
2864	if (timeCounterType==none) createTimeCounterAxis=true ;
2865	timeCounterType=record ;
2866	if (field->hasTimeCentered)
2867	{
2868	if (!hasTimeCentered) createCenteredAxis=true ;
2869	}
2870	if (field->hasTimeInstant)
2871	{
2872	if (!hasTimeInstant) createInstantAxis=true ;
2873	}
2874	}
2875
2876	if (createInstantAxis)
2877	{
2878	axisId="time_instant" ;
2879	axisBoundId="time_instant_bounds";
2880	hasTimeInstant=true ;
2881	}
2882
2883	if (createCenteredAxis)
2884	{
2885	axisId="time_centered" ;
2886	axisBoundId="time_centered_bounds";
2887	hasTimeCentered=true ;
2888	}
2889
2890
2891	try
2892	{
2893	std::vector<StdString> dims;
2894
2895	if (createInstantAxis \|\| createCenteredAxis)
2896	{
2897	// Adding time_instant or time_centered
2898	dims.push_back(timeid);
2899	if (!SuperClassWriter::varExist(axisId))
2900	{
2901	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2902
2903	CDate timeOrigin=cal->getTimeOrigin() ;
2904	StdOStringStream oss2;
2905	StdString strInitdate=oss2.str() ;
2906	StdString strTimeOrigin=timeOrigin.toString() ;
2907	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2908	strTimeOrigin, axisBoundId);
2909	}
2910
2911	// Adding time_instant_bounds or time_centered_bounds variables
2912	if (!SuperClassWriter::varExist(axisBoundId))
2913	{
2914	dims.clear() ;
2915	dims.push_back(timeid);
2916	dims.push_back(timeBoundId);
2917	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2918	}
2919	}
2920
2921	if (createTimeCounterAxis)
2922	{
2923	// Adding time_counter
2924	axisId = getTimeCounterName();
2925	axisBoundId = getTimeCounterName() + "_bounds";
2926	dims.clear();
2927	dims.push_back(timeid);
2928	if (!SuperClassWriter::varExist(axisId))
2929	{
2930	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2931	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2932
2933	if (field->file->time_counter.isEmpty() \|\|
2934	(field->file->time_counter != CFile::time_counter_attr::record))
2935	{
2936	CDate timeOrigin = cal->getTimeOrigin();
2937	StdString strTimeOrigin = timeOrigin.toString();
2938
2939	this->writeTimeAxisAttributes(axisId, cal->getType(),
2940	strTimeUnits+strTimeOrigin,
2941	strTimeOrigin, axisBoundId);
2942	}
2943	}
2944
2945	// Adding time_counter_bound dimension
2946	if (field->file->time_counter.isEmpty() \|\| (field->file->time_counter != CFile::time_counter_attr::record))
2947	{
2948	if (!SuperClassWriter::varExist(axisBoundId))
2949	{
2950	dims.clear();
2951	dims.push_back(timeid);
2952	dims.push_back(timeBoundId);
2953	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2954	}
2955	}
2956	}
2957	}
2958	catch (CNetCdfException& e)
2959	{
2960	StdString msg("On writing time axis data: ");
2961	msg.append("In the context : ");
2962	CContext* context = CContext::getCurrent() ;
2963	msg.append(context->getId()); msg.append("\n");
2964	msg.append(e.what());
2965	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2966	const boost::shared_ptr<CCalendar> cal)", << msg);
2967	}
2968	}
2969
2970	//---------------------------------------------------------------
2971
2972	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2973	const StdString & calendar,
2974	const StdString & units,
2975	const StdString & time_origin,
2976	const StdString & time_bounds,
2977	const StdString & standard_name,
2978	const StdString & long_name)
2979	{
2980	try
2981	{
2982	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2983	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2984	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2985	SuperClassWriter::addAttribute("units", units , &axis_name);
2986	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2987	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2988	}
2989	catch (CNetCdfException& e)
2990	{
2991	StdString msg("On writing time axis Attribute: ");
2992	msg.append("In the context : ");
2993	CContext* context = CContext::getCurrent() ;
2994	msg.append(context->getId()); msg.append("\n");
2995	msg.append(e.what());
2996	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2997	const StdString & calendar,\
2998	const StdString & units, \
2999	const StdString & time_origin, \
3000	const StdString & time_bounds, \
3001	const StdString & standard_name, \
3002	const StdString & long_name)", << msg);
3003	}
3004	}
3005
3006	//---------------------------------------------------------------
3007
3008	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
3009	const StdString & axis,
3010	const StdString & standard_name,
3011	const StdString & long_name,
3012	const StdString & units,
3013	const StdString & nav_model)
3014	{
3015	try
3016	{
3017	if (!axis.empty())
3018	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
3019
3020	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
3021	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
3022	SuperClassWriter::addAttribute("units" , units , &axis_name);
3023	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
3024	}
3025	catch (CNetCdfException& e)
3026	{
3027	StdString msg("On writing Axis Attribute: ");
3028	msg.append("In the context : ");
3029	CContext* context = CContext::getCurrent() ;
3030	msg.append(context->getId()); msg.append("\n");
3031	msg.append(e.what());
3032	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
3033	const StdString & axis, \
3034	const StdString & standard_name, \
3035	const StdString & long_name, \
3036	const StdString & units, \
3037	const StdString & nav_model)", << msg);
3038	}
3039	}
3040
3041	//---------------------------------------------------------------
3042
3043	void CNc4DataOutput::writeLocalAttributes
3044	(int ibegin, int ni, int jbegin, int nj, StdString domid)
3045	{
3046	try
3047	{
3048	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
3049	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
3050	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
3051	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
3052	}
3053	catch (CNetCdfException& e)
3054	{
3055	StdString msg("On writing Local Attributes: ");
3056	msg.append("In the context : ");
3057	CContext* context = CContext::getCurrent() ;
3058	msg.append(context->getId()); msg.append("\n");
3059	msg.append(e.what());
3060	ERROR("CNc4DataOutput::writeLocalAttributes \
3061	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
3062	}
3063
3064	}
3065
3066	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
3067	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
3068	{
3069	CArray<int,1> array(2) ;
3070
3071	try
3072	{
3073	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
3074	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
3075	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
3076	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
3077	array=ni_glo,nj_glo ;
3078	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
3079	array=ni,nj ;
3080	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
3081	array=ibegin+1,jbegin+1 ;
3082	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
3083	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
3084	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
3085	array=0,0 ;
3086	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
3087	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
3088	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
3089	/*
3090	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
3091	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
3092	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
3093	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
3094	*/
3095	}
3096	catch (CNetCdfException& e)
3097	{
3098	StdString msg("On writing Local Attributes IOIPSL \n");
3099	msg.append("In the context : ");
3100	CContext* context = CContext::getCurrent() ;
3101	msg.append(context->getId()); msg.append("\n");
3102	msg.append(e.what());
3103	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
3104	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
3105	}
3106	}
3107	//---------------------------------------------------------------
3108
3109	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
3110	const StdString & description,
3111	const StdString & conventions,
3112	const StdString & production,
3113	const StdString & timeStamp)
3114	{
3115	try
3116	{
3117	SuperClassWriter::addAttribute("name" , name);
3118	SuperClassWriter::addAttribute("description", description);
3119	SuperClassWriter::addAttribute("title" , description);
3120	SuperClassWriter::addAttribute("Conventions", conventions);
3121	// SuperClassWriter::addAttribute("production" , production);
3122
3123	StdString timeStampStr ;
3124	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
3125	else timeStampStr=file->time_stamp_name ;
3126	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
3127
3128	StdString uuidName ;
3129	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
3130	else uuidName=file->uuid_name ;
3131
3132	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
3133	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
3134
3135	}
3136	catch (CNetCdfException& e)
3137	{
3138	StdString msg("On writing File Attributes \n ");
3139	msg.append("In the context : ");
3140	CContext* context = CContext::getCurrent() ;
3141	msg.append(context->getId()); msg.append("\n");
3142	msg.append(e.what());
3143	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
3144	const StdString & description, \
3145	const StdString & conventions, \
3146	const StdString & production, \
3147	const StdString & timeStamp)", << msg);
3148	}
3149	}
3150
3151	//---------------------------------------------------------------
3152
3153	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
3154	int data_dim,
3155	int data_ni,
3156	int data_nj,
3157	int data_ibegin,
3158	int data_jbegin)
3159	{
3160	try
3161	{
3162	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
3163	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
3164	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
3165	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
3166	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
3167	}
3168	catch (CNetCdfException& e)
3169	{
3170	StdString msg("On writing Mask Attributes \n ");
3171	msg.append("In the context : ");
3172	CContext* context = CContext::getCurrent() ;
3173	msg.append(context->getId()); msg.append("\n");
3174	msg.append(e.what());
3175	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
3176	int data_dim, \
3177	int data_ni, \
3178	int data_nj, \
3179	int data_ibegin, \
3180	int data_jbegin)", << msg);
3181	}
3182	}
3183
3184	///--------------------------------------------------------------
3185
3186	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
3187	{
3188	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
3189	if (it == timeToRecordCache.end())
3190	{
3191	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
3192	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
3193	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
3194
3195	CArray<double,2> timeAxisBounds;
3196	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
3197
3198	StdSize record = 0;
3199	double dtime(time);
3200	for (int n = dimSize[0] - 1; n >= 0; n--)
3201	{
3202	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3203	timeAxisBounds*=factorUnit ;
3204	if (timeAxisBounds(1, 0) < dtime)
3205	{
3206	record = n + 1;
3207	break;
3208	}
3209	}
3210	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3211	}
3212	return it->second;
3213	}
3214
3215	///--------------------------------------------------------------
3216
3217	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3218	{
3219	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3220	}
3221
3222	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3223	{
3224	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3225	}
3226
3227	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3228	{
3229	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3230	}
3231
3232	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3233	{
3234	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3235	}
3236
3237	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3238	{
3239	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3240	}
3241
3242	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3243	{
3244	this->writtenDomains.insert(domainName);
3245	}
3246
3247	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3248	{
3249	this->writtenCompressedDomains.insert(domainName);
3250	}
3251
3252	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3253	{
3254	this->writtenAxis.insert(axisName);
3255	}
3256
3257	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3258	{
3259	this->writtenCompressedAxis.insert(axisName);
3260	}
3261
3262	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3263	{
3264	this->writtenScalar.insert(scalarName);
3265	}
3266	} // namespace xios

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