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nc4_data_output.cpp @ 2181

Last change on this file since 2181 was 2181, checked in by ymipsl, 3 years ago

Add missing metadata in mesh when using ugrid convention writing :

face_edge_connectivity
edge_face_connectivity
face_face_connectivity

Property copyright set to
Software name : XIOS (Xml I/O Server)
http://forge.ipsl.jussieu.fr/ioserver
Creation date : January 2009
Licence : CeCCIL version2
see license file in root directory : Licence_CeCILL_V2-en.txt
or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement)
CNRS/IPSL (Institut Pierre Simon Laplace)
Project Manager : Yann Meurdesoif
yann.meurdesoif@cea.fr
Property svn:executable set to *

File size: 132.3 KB

Line
1	#include "nc4_data_output.hpp"
2
3	#include "attribute_template.hpp"
4	#include "group_template.hpp"
5
6	#include "file.hpp"
7	#include "calendar.hpp"
8	#include "context.hpp"
9	#include "context_server.hpp"
10	#include "netCdfException.hpp"
11	#include "exception.hpp"
12	#include "timer.hpp"
13	#include "uuid.hpp"
14	namespace xios
15	{
16	/// ////////////////////// Dfinitions ////////////////////// ///
17	CNc4DataOutput::CNc4DataOutput
18	(CFile* file, const StdString & filename, bool exist)
19	: SuperClass()
20	, SuperClassWriter(filename, exist)
21	, filename(filename)
22	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
23	{
24	SuperClass::type = MULTI_FILE;
25	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
26	}
27
28	CNc4DataOutput::CNc4DataOutput
29	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
30	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
31	: SuperClass()
32	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
33	, comm_file(comm_file)
34	, filename(filename)
35	, isCollective(isCollective)
36	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
37	{
38	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
39	if (file==NULL) compressionLevel = 0 ;
40	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
41	}
42
43	CNc4DataOutput::~CNc4DataOutput(void)
44	{ /* Ne rien faire de plus */ }
45
46	///--------------------------------------------------------------
47
48	const StdString & CNc4DataOutput::getFileName(void) const
49	{
50	return (this->filename);
51	}
52
53	//---------------------------------------------------------------
54
55	void CNc4DataOutput::writeDomain_(CDomain* domain)
56	TRY
57	{
58	StdString lonName,latName ;
59
60	domain->computeWrittenIndex();
61	domain->computeWrittenCompressedIndex(comm_file);
62
63	if (domain->type == CDomain::type_attr::unstructured)
64	{
65	if (SuperClassWriter::useCFConvention)
66	writeUnstructuredDomain(domain) ;
67	else
68	writeUnstructuredDomainUgrid(domain) ;
69	return ;
70	}
71
72	CContext* context = CContext::getCurrent() ;
73	CContextServer* server=context->server ;
74
75	if (domain->IsWritten(this->filename)) return;
76	domain->checkAttributes();
77
78	if (domain->isEmpty())
79	if (SuperClass::type==MULTI_FILE) return;
80
81	std::vector<StdString> dim0, dim1;
82	StdString domid = domain->getDomainOutputName();
83	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
84	if (isWrittenDomain(domid)) return ;
85	else setWrittenDomain(domid);
86
87	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
88
89
90	StdString dimXid, dimYid ;
91
92	nc_type typePrec ;
93	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
94	else if (domain->prec==4) typePrec = NC_FLOAT ;
95	else if (domain->prec==8) typePrec = NC_DOUBLE ;
96
97	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
98	switch (domain->type)
99	{
100	case CDomain::type_attr::curvilinear :
101
102	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
103	else lonName = domain->lon_name;
104
105	if (domain->lat_name.isEmpty()) latName = "nav_lat";
106	else latName = domain->lat_name;
107
108	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
109	else dimXid=domain->dim_i_name.getValue() + appendDomid;
110
111	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
112	else dimYid=domain->dim_j_name.getValue() + appendDomid;
113
114	break ;
115
116	case CDomain::type_attr::rectilinear :
117
118	if (domain->lon_name.isEmpty())
119	{
120	if (domain->dim_i_name.isEmpty())
121	lonName = "lon";
122	else
123	lonName = domain->dim_i_name.getValue();
124	}
125	else lonName = domain->lon_name;
126
127	if (domain->lat_name.isEmpty())
128	{
129	if (domain->dim_j_name.isEmpty())
130	latName = "lat";
131	else
132	latName = domain->dim_j_name.getValue();
133	}
134	else latName = domain->lat_name;
135
136	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
137	else dimXid = domain->dim_i_name.getValue()+appendDomid;
138
139	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
140	else dimYid = domain->dim_j_name.getValue()+appendDomid;
141	break;
142	}
143
144	StdString dimVertId = StdString("nvertex").append(appendDomid);
145
146	string lonid,latid,bounds_lonid,bounds_latid ;
147	string areaId = "area" + appendDomid;
148	/*
149	StdString lonid_loc = (server->intraCommSize > 1)
150	? StdString("lon").append(appendDomid).append("_local")
151	: lonid;
152	StdString latid_loc = (server->intraCommSize > 1)
153	? StdString("lat").append(appendDomid).append("_local")
154	: latid;
155	*/
156
157	CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
158	int nbWritten = indexToWrite.numElements();
159	CArray<double,1> writtenLat, writtenLon;
160	CArray<double,2> writtenBndsLat, writtenBndsLon;
161	CArray<double,1> writtenArea;
162
163	if (domain->hasLonLat)
164	{
165	writtenLat.resize(nbWritten);
166	writtenLon.resize(nbWritten);
167	for (int idx = 0; idx < nbWritten; ++idx)
168	{
169	if (indexToWrite(idx) < 0)
170	{
171	writtenLat(idx) = -1.; // hole
172	writtenLon(idx) = -1.;
173	}
174	else
175	{
176	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
177	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
178	}
179	}
180
181	if (domain->hasBounds)
182	{
183	int nvertex = domain->nvertex, idx;
184	writtenBndsLat.resize(nvertex, nbWritten);
185	writtenBndsLon.resize(nvertex, nbWritten);
186	CArray<double,2>& boundslat = domain->bounds_latvalue;
187	CArray<double,2>& boundslon = domain->bounds_lonvalue;
188	for (idx = 0; idx < nbWritten; ++idx)
189	for (int nv = 0; nv < nvertex; ++nv)
190	{
191	if (indexToWrite(idx) < 0)
192	{
193	writtenBndsLat(nv, idx) = -1.; // hole
194	writtenBndsLon(nv, idx) = -1.;
195	}
196	else
197	{
198	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
199	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
200	}
201	}
202	}
203	}
204
205	if (domain->hasArea)
206	{
207	writtenArea.resize(nbWritten);
208	for (int idx = 0; idx < nbWritten; ++idx)
209	{
210	if (indexToWrite(idx) < 0)
211	writtenArea(idx) = -1.;
212	else
213	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
214	}
215	}
216
217	try
218	{
219	switch (SuperClass::type)
220	{
221	case (MULTI_FILE) :
222	{
223	switch (domain->type)
224	{
225	case CDomain::type_attr::curvilinear :
226	dim0.push_back(dimYid); dim0.push_back(dimXid);
227	lonid = lonName+appendDomid;
228	latid = latName+appendDomid;
229	break ;
230	case CDomain::type_attr::rectilinear :
231	lonid = lonName+appendDomid;
232	latid = latName+appendDomid;
233	dim0.push_back(dimYid);
234	dim1.push_back(dimXid);
235	break;
236	}
237	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
238	else bounds_lonid = "bounds_"+lonName+appendDomid;
239	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
240	else bounds_latid = "bounds_"+latName+appendDomid;
241
242	SuperClassWriter::addDimension(dimXid, domain->ni);
243	SuperClassWriter::addDimension(dimYid, domain->nj);
244
245	if (domain->hasBounds)
246	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
247
248	if (server->intraCommSize > 1)
249	{
250	this->writeLocalAttributes(domain->ibegin,
251	domain->ni,
252	domain->jbegin,
253	domain->nj,
254	appendDomid);
255
256	if (singleDomain)
257	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
258	domain->ibegin,
259	domain->ni,
260	domain->jbegin,
261	domain->nj,
262	domain->ni_glo,domain->nj_glo,
263	server->intraCommRank,server->intraCommSize);
264	}
265
266	if (domain->hasLonLat)
267	{
268	switch (domain->type)
269	{
270	case CDomain::type_attr::curvilinear :
271	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
272	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
273	break ;
274	case CDomain::type_attr::rectilinear :
275	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
276	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
277	break ;
278	}
279
280	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
281	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
282
283	if (domain->hasBounds)
284	{
285	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
286	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
287
288	dim0.clear();
289	dim0.push_back(dimYid);
290	dim0.push_back(dimXid);
291	dim0.push_back(dimVertId);
292	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
293	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
294	}
295	}
296
297	dim0.clear();
298	dim0.push_back(dimYid);
299	dim0.push_back(dimXid);
300
301
302	// supress mask if (server->intraCommSize > 1)
303	// supress mask {
304	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
305	// supress mask
306	// supress mask this->writeMaskAttributes(maskid,
307	// supress mask domain->data_dim.getValue()/*,
308	// supress mask domain->data_ni.getValue(),
309	// supress mask domain->data_nj.getValue(),
310	// supress mask domain->data_ibegin.getValue(),
311	// supress mask domain->data_jbegin.getValue()*/);
312	// supress mask }
313
314	//SuperClassWriter::setDefaultValue(maskid, &dvm);
315
316	if (domain->hasArea)
317	{
318	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
319	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
320	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
321	}
322
323	SuperClassWriter::definition_end();
324
325	if (domain->hasLonLat)
326	{
327	switch (domain->type)
328	{
329	case CDomain::type_attr::curvilinear :
330	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
331	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
332	break;
333	case CDomain::type_attr::rectilinear :
334	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->ni)) ;
335	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
336	CArray<double,1> lon = writtenLon(Range(0,domain->ni-1)) ;
337	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
338	break;
339	}
340
341	if (domain->hasBounds)
342	{
343	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
344	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
345	}
346	}
347
348	if (domain->hasArea)
349	{
350	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
351	}
352
353	SuperClassWriter::definition_start();
354
355	break;
356	}
357	case (ONE_FILE) :
358	{
359	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
360	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
361
362	if (domain->hasBounds)
363	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
364
365	if (domain->hasLonLat)
366	{
367	switch (domain->type)
368	{
369	case CDomain::type_attr::curvilinear :
370	dim0.push_back(dimYid); dim0.push_back(dimXid);
371	lonid = lonName+appendDomid;
372	latid = latName+appendDomid;
373	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
374	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
375	break;
376
377	case CDomain::type_attr::rectilinear :
378	dim0.push_back(dimYid);
379	dim1.push_back(dimXid);
380	lonid = lonName+appendDomid;
381	latid = latName+appendDomid;
382	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
383	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
384	break;
385	}
386	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
387	else bounds_lonid = "bounds_"+lonName+appendDomid;
388	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
389	else bounds_latid = "bounds_"+latName+appendDomid;
390
391	this->writeAxisAttributes
392	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
393	this->writeAxisAttributes
394	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
395
396	if (domain->hasBounds)
397	{
398	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
399	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
400
401	dim0.clear();
402	dim0.push_back(dimYid);
403	dim0.push_back(dimXid);
404	dim0.push_back(dimVertId);
405	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
406	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
407	}
408	}
409
410	if (domain->hasArea)
411	{
412	dim0.clear();
413	dim0.push_back(dimYid); dim0.push_back(dimXid);
414	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
415	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
416	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
417	dim0.clear();
418	}
419
420	SuperClassWriter::definition_end();
421
422	switch (domain->type)
423	{
424	case CDomain::type_attr::curvilinear :
425	{
426	std::vector<StdSize> start(2) ;
427	std::vector<StdSize> count(2) ;
428	// Comment out: it is not working for a hole
429	// if (domain->isEmpty())
430	// {
431	// start[0]=0 ; start[1]=0 ;
432	// count[0]=0 ; count[1]=0 ;
433	// }
434	// else
435	{
436	start[1]=domain->ibegin;
437	start[0]=domain->jbegin;
438	count[1]=domain->ni ; count[0]=domain->nj ;
439	}
440
441	if (domain->hasLonLat)
442	{
443	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
444	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
445	}
446	break;
447	}
448	case CDomain::type_attr::rectilinear :
449	{
450	if (domain->hasLonLat)
451	{
452	std::vector<StdSize> start(1) ;
453	std::vector<StdSize> count(1) ;
454	if (domain->isEmpty())
455	{
456	start[0]=0 ;
457	count[0]=0 ;
458	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
459	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
460	}
461	else
462	{
463	start[0]=domain->jbegin;
464	count[0]=domain->nj;
465	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->ni));
466	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
467
468	start[0]=domain->ibegin;
469	count[0]=domain->ni;
470	CArray<double,1> lon = writtenLon(Range(0,domain->ni-1));
471	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
472	}
473	}
474	break;
475	}
476	}
477
478	if (domain->hasBounds)
479	{
480	std::vector<StdSize> start(3);
481	std::vector<StdSize> count(3);
482	if (domain->isEmpty())
483	{
484	start[2] = start[1] = start[0] = 0;
485	count[2] = count[1] = count[0] = 0;
486	}
487	else
488	{
489	start[2] = 0;
490	start[1] = domain->ibegin;
491	start[0] = domain->jbegin;
492	count[2] = domain->nvertex;
493	count[1] = domain->ni;
494	count[0] = domain->nj;
495	}
496
497	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0, &start, &count);
498	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0, &start, &count);
499	}
500
501	if (domain->hasArea)
502	{
503	std::vector<StdSize> start(2);
504	std::vector<StdSize> count(2);
505
506	if (domain->isEmpty())
507	{
508	start[0] = 0; start[1] = 0;
509	count[0] = 0; count[1] = 0;
510	}
511	else
512	{
513	start[1] = domain->ibegin;
514	start[0] = domain->jbegin;
515	count[1] = domain->ni;
516	count[0] = domain->nj;
517	}
518
519	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
520	}
521
522	SuperClassWriter::definition_start();
523	break;
524	}
525	default :
526	ERROR("CNc4DataOutput::writeDomain(domain)",
527	<< "[ type = " << SuperClass::type << "]"
528	<< " not implemented yet !");
529	}
530	}
531	catch (CNetCdfException& e)
532	{
533	StdString msg("On writing the domain : ");
534	msg.append(domid); msg.append("\n");
535	msg.append("In the context : ");
536	msg.append(context->getId()); msg.append("\n");
537	msg.append(e.what());
538	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
539	}
540
541	domain->addRelFile(this->filename);
542	}
543	CATCH
544
545	//--------------------------------------------------------------
546
547	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
548	{
549	CContext* context = CContext::getCurrent() ;
550	CContextServer* server=context->server ;
551
552	if (domain->IsWritten(this->filename)) return;
553
554	StdString domid = domain->getDomainOutputName();
555
556	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
557	// Thus the entire mesh connectivity will be generated at once.
558	if (isWrittenDomain(domid)) return ;
559	else setWrittenDomain(domid);
560
561	domain->checkAttributes();
562	if (domain->isEmpty())
563	if (SuperClass::type==MULTI_FILE) return ;
564
565	nc_type typePrec ;
566	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
567	else if (domain->prec==4) typePrec = NC_FLOAT ;
568	else if (domain->prec==8) typePrec = NC_DOUBLE ;
569
570	std::vector<StdString> dim0;
571	StdString domainName = domain->name;
572	domain->assignMesh(domainName, domain->nvertex);
573	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
574
575	StdString node_x = domainName + "_node_x";
576	StdString node_y = domainName + "_node_y";
577
578	StdString edge_x = domainName + "_edge_x";
579	StdString edge_y = domainName + "_edge_y";
580	StdString edge_nodes = domainName + "_edge_nodes";
581
582	StdString face_x = domainName + "_face_x";
583	StdString face_y = domainName + "_face_y";
584	StdString face_nodes = domainName + "_face_nodes";
585	StdString face_edges = domainName + "_face_edges";
586	StdString edge_faces = domainName + "_edge_face_links";
587	StdString face_faces = domainName + "_face_links";
588
589	StdString dimNode = "n" + domainName + "_node";
590	StdString dimEdge = "n" + domainName + "_edge";
591	StdString dimFace = "n" + domainName + "_face";
592	StdString dimVertex = "n" + domainName + "_vertex";
593	StdString dimTwo = "Two";
594
595	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
596	dim0.clear();
597	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
598	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
599	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
600	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
601	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
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, compressionLevel);
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, compressionLevel);
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, compressionLevel);
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, compressionLevel);
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, compressionLevel);
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, compressionLevel);
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, compressionLevel);
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, compressionLevel);
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, compressionLevel);
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::addAttribute("face_edge_connectivity", face_edges, &domainName);
690	SuperClassWriter::addAttribute("edge_face_connectivity", edge_faces, &domainName);
691	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
692	dim0.clear();
693	dim0.push_back(dimEdge);
694	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
695	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
696	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
697	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
698	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
699	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
700	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
701	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
702	dim0.clear();
703	dim0.push_back(dimEdge);
704	dim0.push_back(dimTwo);
705	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
706	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
707	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
708	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
709	}
710	SuperClassWriter::addAttribute("face_face_connectivity", face_faces, &domainName);
711	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
712	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
713	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
714	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
715	dim0.clear();
716	dim0.push_back(dimFace);
717	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
718	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
719	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
720	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
721	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
722	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
723	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
724	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
725	dim0.clear();
726	dim0.push_back(dimFace);
727	dim0.push_back(dimVertex);
728	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
729	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
730	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
731	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
732	dim0.clear();
733	dim0.push_back(dimFace);
734	dim0.push_back(dimVertex);
735	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
736	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
737	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
738	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
739	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
740	dim0.clear();
741	dim0.push_back(dimEdge);
742	dim0.push_back(dimTwo);
743	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
744	SuperClassWriter::addAttribute("cf_role", StdString("edge_face_connectivity"), &edge_faces);
745	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
746	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
747	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
748	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
749	dim0.clear();
750	dim0.push_back(dimFace);
751	dim0.push_back(dimVertex);
752	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
753	SuperClassWriter::addAttribute("cf_role", StdString("face_face_connectivity"), &face_faces);
754	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
755	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
756	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
757	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
758	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
759	} // domain->nvertex > 2
760
761	SuperClassWriter::definition_end();
762
763	std::vector<StdSize> startEdges(1) ;
764	std::vector<StdSize> countEdges(1) ;
765	std::vector<StdSize> startNodes(1) ;
766	std::vector<StdSize> countNodes(1) ;
767	std::vector<StdSize> startFaces(1) ;
768	std::vector<StdSize> countFaces(1) ;
769	std::vector<StdSize> startEdgeNodes(2) ;
770	std::vector<StdSize> countEdgeNodes(2) ;
771	std::vector<StdSize> startEdgeFaces(2) ;
772	std::vector<StdSize> countEdgeFaces(2) ;
773	std::vector<StdSize> startFaceConctv(2) ;
774	std::vector<StdSize> countFaceConctv(2) ;
775
776	if (domain->nvertex == 1)
777	{
778	if (domain->isEmpty())
779	{
780	startNodes[0]=0 ;
781	countNodes[0]=0 ;
782	}
783	else
784	{
785	startNodes[0] = domain->ibegin;
786	countNodes[0] = domain->ni ;
787	}
788
789	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
790	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
791	}
792	else if (domain->nvertex == 2)
793	{
794	if (domain->isEmpty())
795	{
796	startEdges[0]=0 ;
797	countEdges[0]=0 ;
798	startNodes[0]=0 ;
799	countNodes[0]=0 ;
800	startEdgeNodes[0]=0;
801	startEdgeNodes[1]=0;
802	countEdgeNodes[0]=0;
803	countEdgeNodes[1]=0;
804
805	}
806	else
807	{
808	startEdges[0] = domain->ibegin;
809	countEdges[0] = domain->ni;
810	startNodes[0] = domain->mesh->node_start;
811	countNodes[0] = domain->mesh->node_count;
812	startEdgeNodes[0] = domain->ibegin;
813	startEdgeNodes[1] = 0;
814	countEdgeNodes[0] = domain->ni;
815	countEdgeNodes[1] = 2;
816	}
817	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
818	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
819	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
820	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
821	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
822	}
823	else
824	{
825	if (domain->isEmpty())
826	{
827	startFaces[0] = 0 ;
828	countFaces[0] = 0 ;
829	startNodes[0] = 0;
830	countNodes[0] = 0;
831	startEdges[0] = 0;
832	countEdges[0] = 0;
833	startEdgeFaces[0] = 0;
834	startEdgeFaces[1] = 0;
835	countEdgeFaces[0] = 0;
836	countEdgeFaces[1] = 0;
837	startFaceConctv[0] = 0;
838	startFaceConctv[1] = 0;
839	countFaceConctv[0] = 0;
840	countFaceConctv[1] = 0;
841	}
842	else
843	{
844	startFaces[0] = domain->ibegin;
845	countFaces[0] = domain->ni ;
846	startNodes[0] = domain->mesh->node_start;
847	countNodes[0] = domain->mesh->node_count;
848	startEdges[0] = domain->mesh->edge_start;
849	countEdges[0] = domain->mesh->edge_count;
850	startEdgeNodes[0] = domain->mesh->edge_start;
851	startEdgeNodes[1] = 0;
852	countEdgeNodes[0] = domain->mesh->edge_count;
853	countEdgeNodes[1]= 2;
854	startEdgeFaces[0] = domain->mesh->edge_start;
855	startEdgeFaces[1]= 0;
856	countEdgeFaces[0] = domain->mesh->edge_count;
857	countEdgeFaces[1]= 2;
858	startFaceConctv[0] = domain->ibegin;
859	startFaceConctv[1] = 0;
860	countFaceConctv[0] = domain->ni;
861	countFaceConctv[1] = domain->nvertex;
862	}
863	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
864	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
865	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
866	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
867	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
868	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
869	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
870	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
871	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
872	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
873	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
874	}
875	SuperClassWriter::definition_start();
876
877	break;
878	} // ONE_FILE
879
880	case (MULTI_FILE) :
881	{
882	ERROR("CNc4DataOutput::writeDomain(domain)",
883	<< "[ type = multiple_file ]"
884	<< " is not yet implemented for UGRID files !");
885	break;
886	}
887
888	default :
889	ERROR("CNc4DataOutput::writeDomain(domain)",
890	<< "[ type = " << SuperClass::type << "]"
891	<< " not implemented yet !");
892	} // switch
893	} // try
894
895	catch (CNetCdfException& e)
896	{
897	StdString msg("On writing the domain : ");
898	msg.append(domid); msg.append("\n");
899	msg.append("In the context : ");
900	msg.append(context->getId()); msg.append("\n");
901	msg.append(e.what());
902	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
903	}
904
905	domain->addRelFile(this->filename);
906	}
907
908	//--------------------------------------------------------------
909
910	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
911	{
912	CContext* context = CContext::getCurrent() ;
913	CContextServer* server=context->server ;
914
915	if (domain->IsWritten(this->filename)) return;
916	domain->checkAttributes();
917
918	if (domain->isEmpty())
919	if (SuperClass::type==MULTI_FILE) return ;
920
921	std::vector<StdString> dim0, dim1;
922	StdString domid = domain->getDomainOutputName();
923	if (isWrittenDomain(domid)) return ;
924	else setWrittenDomain(domid);
925
926	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
927
928	StdString lonName,latName, cellName ;
929	if (domain->lon_name.isEmpty()) lonName = "lon";
930	else lonName = domain->lon_name;
931
932	if (domain->lat_name.isEmpty()) latName = "lat";
933	else latName = domain->lat_name;
934
935	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
936	else cellName="cell";
937	StdString dimXid = cellName+appendDomid;
938	StdString dimVertId = StdString("nvertex").append(appendDomid);
939
940	string lonid,latid,bounds_lonid,bounds_latid ;
941	string areaId = "area" + appendDomid;
942
943	nc_type typePrec ;
944	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
945	else if (domain->prec==4) typePrec = NC_FLOAT ;
946	else if (domain->prec==8) typePrec = NC_DOUBLE ;
947
948	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
949
950	CArray<int, 1>& indexToWrite = domain->localIndexToWriteOnServer;
951	int nbWritten = indexToWrite.numElements();
952	CArray<double,1> writtenLat, writtenLon;
953	CArray<double,2> writtenBndsLat, writtenBndsLon;
954	CArray<double,1> writtenArea;
955
956	if (domain->hasLonLat)
957	{
958	writtenLat.resize(nbWritten);
959	writtenLon.resize(nbWritten);
960	for (int idx = 0; idx < nbWritten; ++idx)
961	{
962	if (indexToWrite(idx) < 0)
963	{
964	writtenLat(idx) = -1.;
965	writtenLon(idx) = -1.;
966	}
967	else
968	{
969	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
970	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
971	}
972	}
973	}
974
975	if (domain->hasBounds)
976	{
977	int nvertex = domain->nvertex, idx;
978	writtenBndsLat.resize(nvertex, nbWritten);
979	writtenBndsLon.resize(nvertex, nbWritten);
980	CArray<double,2>& boundslat = domain->bounds_latvalue;
981	CArray<double,2>& boundslon = domain->bounds_lonvalue;
982	for (idx = 0; idx < nbWritten; ++idx)
983	{
984	for (int nv = 0; nv < nvertex; ++nv)
985	{
986	if (indexToWrite(idx) < 0)
987	{
988	writtenBndsLat(nv, idx) = -1.;
989	writtenBndsLon(nv, idx) = -1.;
990	}
991	else
992	{
993	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
994	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
995	}
996	}
997	}
998	}
999
1000	if (domain->hasArea)
1001	{
1002	writtenArea.resize(nbWritten);
1003	for (int idx = 0; idx < nbWritten; ++idx)
1004	{
1005	if (indexToWrite(idx) < 0)
1006	writtenArea(idx) = -1.;
1007	else
1008	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
1009	}
1010	}
1011
1012	try
1013	{
1014	switch (SuperClass::type)
1015	{
1016	case (MULTI_FILE) :
1017	{
1018	dim0.push_back(dimXid);
1019	SuperClassWriter::addDimension(dimXid, domain->ni);
1020
1021	lonid = lonName+appendDomid;
1022	latid = latName+appendDomid;
1023	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1024	else bounds_lonid = "bounds_"+lonName+appendDomid;
1025	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1026	else bounds_latid = "bounds_"+latName+appendDomid;
1027
1028	if (domain->hasLonLat)
1029	{
1030	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1031	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1032	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1033	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1034	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1035	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1036	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
1037	}
1038	dim0.clear();
1039	if (domain->hasBounds)
1040	{
1041	dim0.push_back(dimXid);
1042	dim0.push_back(dimVertId);
1043	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1044	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1045	}
1046
1047	dim0.clear();
1048	dim0.push_back(dimXid);
1049	if (domain->hasArea)
1050	{
1051	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1052	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1053	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1054	}
1055
1056	SuperClassWriter::definition_end();
1057
1058	if (domain->hasLonLat)
1059	{
1060	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
1061	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
1062	if (domain->hasBounds)
1063	{
1064	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
1065	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
1066	}
1067	}
1068
1069	if (domain->hasArea)
1070	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
1071
1072	SuperClassWriter::definition_start();
1073	break ;
1074	}
1075
1076	case (ONE_FILE) :
1077	{
1078	lonid = lonName+appendDomid;
1079	latid = latName+appendDomid;
1080	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1081	else bounds_lonid = "bounds_"+lonName+appendDomid;
1082	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1083	else bounds_latid = "bounds_"+latName+appendDomid;
1084
1085	dim0.push_back(dimXid);
1086	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
1087	if (domain->hasLonLat)
1088	{
1089	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1090	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1091
1092	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1093	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1094	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1095	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1096	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
1097	}
1098	dim0.clear();
1099
1100	if (domain->hasBounds)
1101	{
1102	dim0.push_back(dimXid);
1103	dim0.push_back(dimVertId);
1104	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1105	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1106	}
1107
1108	if (domain->hasArea)
1109	{
1110	dim0.clear();
1111	dim0.push_back(dimXid);
1112	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1113	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1114	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1115	}
1116
1117	SuperClassWriter::definition_end();
1118
1119	std::vector<StdSize> start(1), startBounds(2) ;
1120	std::vector<StdSize> count(1), countBounds(2) ;
1121	if (domain->isEmpty())
1122	{
1123	start[0]=0 ;
1124	count[0]=0 ;
1125	startBounds[1]=0 ;
1126	countBounds[1]=nvertex ;
1127	startBounds[0]=0 ;
1128	countBounds[0]=0 ;
1129	}
1130	else
1131	{
1132	start[0]=domain->ibegin;
1133	count[0]=domain->ni;
1134	startBounds[0]=domain->ibegin;
1135	startBounds[1]=0 ;
1136	countBounds[0]=domain->ni;
1137	countBounds[1]=nvertex ;
1138	}
1139
1140	if (domain->hasLonLat)
1141	{
1142	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
1143	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
1144	if (domain->hasBounds)
1145	{
1146	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1147	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1148	}
1149	}
1150
1151	if (domain->hasArea)
1152	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
1153
1154	SuperClassWriter::definition_start();
1155
1156	break;
1157	}
1158	default :
1159	ERROR("CNc4DataOutput::writeDomain(domain)",
1160	<< "[ type = " << SuperClass::type << "]"
1161	<< " not implemented yet !");
1162	}
1163	}
1164	catch (CNetCdfException& e)
1165	{
1166	StdString msg("On writing the domain : ");
1167	msg.append(domid); msg.append("\n");
1168	msg.append("In the context : ");
1169	msg.append(context->getId()); msg.append("\n");
1170	msg.append(e.what());
1171	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1172	}
1173	domain->addRelFile(this->filename);
1174	}
1175	//--------------------------------------------------------------
1176
1177	void CNc4DataOutput::writeAxis_(CAxis* axis)
1178	{
1179	if (axis->IsWritten(this->filename)) return;
1180	axis->checkAttributes();
1181
1182	axis->computeWrittenIndex();
1183	axis->computeWrittenCompressedIndex(comm_file);
1184
1185	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
1186	: axis->n_glo.getValue();
1187
1188	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
1189
1190	std::vector<StdString> dims;
1191	StdString axisid = axis->getAxisOutputName();
1192	StdString axisDim, axisBoundsId;
1193	if (isWrittenAxis(axisid)) return ;
1194	else setWrittenAxis(axisid);
1195
1196	nc_type typePrec ;
1197	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1198	else if (axis->prec==4) typePrec = NC_FLOAT ;
1199	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1200
1201	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1202	string strId="str_len" ;
1203	try
1204	{
1205	if (axis->dim_name.isEmpty()) axisDim = axisid;
1206	else axisDim=axis->dim_name.getValue();
1207	SuperClassWriter::addDimension(axisDim, size);
1208	dims.push_back(axisDim);
1209
1210	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1211
1212	if (axis->hasValue \|\| !axis->label.isEmpty())
1213	{
1214	if (!axis->label.isEmpty()) dims.push_back(strId);
1215
1216	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1217
1218	if (!axis->name.isEmpty())
1219	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1220
1221	if (!axis->standard_name.isEmpty())
1222	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1223
1224	if (!axis->long_name.isEmpty())
1225	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1226
1227	if (!axis->unit.isEmpty())
1228	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1229
1230	if (!axis->axis_type.isEmpty())
1231	{
1232	switch(axis->axis_type)
1233	{
1234	case CAxis::axis_type_attr::X :
1235	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1236	break;
1237	case CAxis::axis_type_attr::Y :
1238	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1239	break;
1240	case CAxis::axis_type_attr::Z :
1241	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1242	break;
1243	case CAxis::axis_type_attr::T :
1244	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1245	break;
1246	}
1247	}
1248
1249	if (!axis->positive.isEmpty())
1250	{
1251	SuperClassWriter::addAttribute("positive",
1252	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1253	&axisid);
1254	}
1255
1256	if (!axis->formula.isEmpty())
1257	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1258
1259	if (!axis->formula_term.isEmpty())
1260	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
1261
1262	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1263	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1264	{
1265	dims.push_back("axis_nbounds");
1266	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1267	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1268
1269	if (!axis->standard_name.isEmpty())
1270	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1271
1272	if (!axis->unit.isEmpty())
1273	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1274
1275	if (!axis->formula_bounds.isEmpty())
1276	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1277
1278	if (!axis->formula_term_bounds.isEmpty())
1279	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
1280	}
1281	}
1282
1283	SuperClassWriter::definition_end();
1284
1285	CArray<int, 1>& indexToWrite = axis->localIndexToWriteOnServer;
1286	int nbWritten = indexToWrite.numElements();
1287	CArray<double,1> axis_value(indexToWrite.numElements());
1288	if (!axis->value.isEmpty())
1289	{
1290	for (int i = 0; i < nbWritten; i++)
1291	{
1292	if (indexToWrite(i) < 0)
1293	axis_value(i) = -1; // Some value in case of a hole
1294	else
1295	axis_value(i) = axis->value(indexToWrite(i));
1296	}
1297	}
1298	CArray<double,2> axis_bounds;
1299	CArray<string,1> axis_label;
1300	if (!axis->label.isEmpty())
1301	{
1302	axis_label.resize(indexToWrite.numElements());
1303	for (int i = 0; i < nbWritten; i++)
1304	{
1305	if (indexToWrite(i) < 0)
1306	axis_label(i) = boost::lexical_cast<string>(-1); // Some value in case of a hole
1307	else
1308	axis_label(i) = axis->label(indexToWrite(i));
1309	}
1310	}
1311
1312	switch (SuperClass::type)
1313	{
1314	case MULTI_FILE:
1315	{
1316	if (axis->label.isEmpty())
1317	{
1318	if (!axis->value.isEmpty())
1319	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1320
1321	if (!axis->bounds.isEmpty())
1322	{
1323	axis_bounds.resize(2, indexToWrite.numElements());
1324	for (int i = 0; i < nbWritten; ++i)
1325	{
1326	if (indexToWrite(i) < 0)
1327	{
1328	axis_bounds(0, i) = -1.; // Some value in case of a hole
1329	axis_bounds(1, i) = -1.;
1330	}
1331	else
1332	{
1333	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1334	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1335	}
1336	}
1337	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0);
1338	}
1339	}
1340	else
1341	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0);
1342
1343	SuperClassWriter::definition_start();
1344	break;
1345	}
1346	case ONE_FILE:
1347	{
1348	std::vector<StdSize> start(1), startBounds(2) ;
1349	std::vector<StdSize> count(1), countBounds(2) ;
1350	start[0] = startBounds[0] = axis->begin;
1351	count[0] = countBounds[0] = axis->n;
1352	startBounds[1] = 0;
1353	countBounds[1] = 2;
1354
1355	if (axis->label.isEmpty())
1356	{
1357	if (!axis->value.isEmpty())
1358	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1359
1360	if (!axis->bounds.isEmpty())
1361	{
1362	axis_bounds.resize(2, indexToWrite.numElements());
1363	for (int i = 0; i < nbWritten; ++i)
1364	{
1365	if (indexToWrite(i) < 0)
1366	{
1367	axis_bounds(0, i) = -1.;
1368	axis_bounds(1, i) = -1.;
1369	}
1370	else
1371	{
1372	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1373	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1374	}
1375	}
1376	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1377	}
1378	}
1379	else
1380	{
1381	std::vector<StdSize> startLabel(2), countLabel(2);
1382	startLabel[0] = start[0]; startLabel[1] = 0;
1383	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1384	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0, &startLabel, &countLabel);
1385	}
1386
1387	SuperClassWriter::definition_start();
1388
1389	break;
1390	}
1391	default :
1392	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1393	<< "[ type = " << SuperClass::type << "]"
1394	<< " not implemented yet !");
1395	}
1396	}
1397	catch (CNetCdfException& e)
1398	{
1399	StdString msg("On writing the axis : ");
1400	msg.append(axisid); msg.append("\n");
1401	msg.append("In the context : ");
1402	CContext* context = CContext::getCurrent() ;
1403	msg.append(context->getId()); msg.append("\n");
1404	msg.append(e.what());
1405	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1406	}
1407	axis->addRelFile(this->filename);
1408	}
1409
1410	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1411	{
1412	if (scalar->IsWritten(this->filename)) return;
1413	scalar->checkAttributes();
1414	int scalarSize = 1;
1415
1416	StdString scalaId = scalar->getScalarOutputName();
1417	StdString boundsId;
1418	if (isWrittenAxis(scalaId)) return ;
1419	else setWrittenAxis(scalaId);
1420
1421	nc_type typePrec ;
1422	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1423	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1424	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1425
1426	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1427	string strId="str_len" ;
1428
1429	try
1430	{
1431	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1432
1433	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1434	{
1435	std::vector<StdString> dims;
1436	StdString scalarDim = scalaId;
1437
1438	if (!scalar->label.isEmpty()) dims.push_back(strId);
1439
1440	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1441
1442	if (!scalar->name.isEmpty())
1443	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1444
1445	if (!scalar->standard_name.isEmpty())
1446	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1447
1448	if (!scalar->long_name.isEmpty())
1449	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1450
1451	if (!scalar->unit.isEmpty())
1452	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1453
1454	if (!scalar->axis_type.isEmpty())
1455	{
1456	switch(scalar->axis_type)
1457	{
1458	case CScalar::axis_type_attr::X :
1459	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1460	break;
1461	case CScalar::axis_type_attr::Y :
1462	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1463	break;
1464	case CScalar::axis_type_attr::Z :
1465	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1466	break;
1467	case CScalar::axis_type_attr::T :
1468	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1469	break;
1470	}
1471	}
1472
1473	if (!scalar->positive.isEmpty())
1474	{
1475	SuperClassWriter::addAttribute("positive",
1476	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1477	&scalaId);
1478	}
1479
1480	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1481	{
1482	dims.clear();
1483	dims.push_back("axis_nbounds");
1484	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1485	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1486	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1487	}
1488
1489	SuperClassWriter::definition_end();
1490
1491	switch (SuperClass::type)
1492	{
1493	case MULTI_FILE:
1494	{
1495	CArray<double,1> scalarValue(scalarSize);
1496	CArray<string,1> scalarLabel(scalarSize);
1497	CArray<double,1> scalarBounds(scalarSize*2);
1498
1499	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1500	{
1501	scalarValue(0) = scalar->value;
1502	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1503	}
1504
1505	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1506	{
1507	scalarBounds(0) = scalar->bounds(0);
1508	scalarBounds(1) = scalar->bounds(1);
1509	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1510	}
1511
1512	if (!scalar->label.isEmpty())
1513	{
1514	scalarLabel(0) = scalar->label;
1515	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1516	}
1517
1518	SuperClassWriter::definition_start();
1519
1520	break;
1521	}
1522	case ONE_FILE:
1523	{
1524	CArray<double,1> scalarValue(scalarSize);
1525	CArray<string,1> scalarLabel(scalarSize);
1526	CArray<double,1> scalarBounds(scalarSize*2);
1527
1528	std::vector<StdSize> start(1);
1529	std::vector<StdSize> count(1);
1530	start[0] = 0;
1531	count[0] = 1;
1532	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1533	{
1534	scalarValue(0) = scalar->value;
1535	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1536	}
1537	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1538	{
1539	scalarBounds(0) = scalar->bounds(0);
1540	scalarBounds(1) = scalar->bounds(1);
1541	count[0] = 2;
1542	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1543	}
1544	if (!scalar->label.isEmpty())
1545	{
1546	scalarLabel(0) = scalar->label;
1547	count[0] = stringArrayLen;
1548	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1549	}
1550
1551	SuperClassWriter::definition_start();
1552
1553	break;
1554	}
1555	default :
1556	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1557	<< "[ type = " << SuperClass::type << "]"
1558	<< " not implemented yet !");
1559	}
1560	}
1561	}
1562	catch (CNetCdfException& e)
1563	{
1564	StdString msg("On writing the scalar : ");
1565	msg.append(scalaId); msg.append("\n");
1566	msg.append("In the context : ");
1567	CContext* context = CContext::getCurrent() ;
1568	msg.append(context->getId()); msg.append("\n");
1569	msg.append(e.what());
1570	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1571	}
1572	scalar->addRelFile(this->filename);
1573	}
1574
1575	//--------------------------------------------------------------
1576
1577	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1578	{
1579	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1580
1581	try
1582	{
1583	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1584	std::vector<StdString> domainList = grid->getDomainList();
1585	std::vector<StdString> axisList = grid->getAxisList();
1586	std::vector<StdString> scalarList = grid->getScalarList();
1587	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1588
1589	std::vector<StdString> dims;
1590
1591	if (grid->isCompressible())
1592	{
1593	StdString varId = grid->getId() + "_points";
1594
1595	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1596	SuperClassWriter::addDimension(varId, nbIndexes);
1597
1598	dims.push_back(varId);
1599	SuperClassWriter::addVariable(varId, NC_INT, dims);
1600
1601	StdOStringStream compress;
1602	for (int i = numElement - 1; i >= 0; --i)
1603	{
1604	if (2 == axisDomainOrder(i))
1605	{
1606	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1607	StdString domId = domain->getDomainOutputName();
1608	StdString appendDomId = singleDomain ? "" : "_" + domId;
1609
1610	switch (domain->type)
1611	{
1612	case CDomain::type_attr::curvilinear:
1613	compress << "y" << appendDomId << " x" << appendDomId;
1614	break;
1615	case CDomain::type_attr::rectilinear:
1616	compress << "lat" << appendDomId << " lon" << appendDomId;
1617	break;
1618	case CDomain::type_attr::unstructured:
1619	StdString cellName = (!domain->dim_i_name.isEmpty()) ? cellName=domain->dim_i_name : "cell";
1620	compress << cellName << appendDomId;
1621	// compress << "cell" << appendDomId;
1622	break;
1623	}
1624	++idxDomain;
1625	}
1626	else if (1 == axisDomainOrder(i))
1627	{
1628	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1629	compress << axis->getAxisOutputName();
1630	++idxAxis;
1631	}
1632	else
1633	{
1634	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1635	compress << scalar->getScalarOutputName();
1636	++idxScalar;
1637	}
1638
1639	if (i != 0) compress << ' ';
1640	}
1641	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1642
1643	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1644	indexes = grid->localIndexToWriteOnServer;
1645
1646	switch (SuperClass::type)
1647	{
1648	case (MULTI_FILE):
1649	{
1650	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1651	break;
1652	}
1653	case (ONE_FILE):
1654	{
1655	if (grid->doGridHaveDataDistributed())
1656	grid->getDistributionServer()->computeGlobalIndex(indexes);
1657
1658	std::vector<StdSize> start, count;
1659	start.push_back(grid->getOffsetWrittenIndexes());
1660	count.push_back(grid->getNumberWrittenIndexes());
1661
1662	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1663	break;
1664	}
1665	}
1666	}
1667	else
1668	{
1669	for (int i = 0; i < numElement; ++i)
1670	{
1671	StdString varId, compress;
1672	CArray<int, 1> indexes;
1673	bool isDistributed;
1674	StdSize nbIndexes, totalNbIndexes, offset;
1675	int firstGlobalIndex;
1676
1677	if (2 == axisDomainOrder(i))
1678	{
1679	CDomain* domain = CDomain::get(domainList[idxDomain]);
1680	StdString domId = domain->getDomainOutputName();
1681
1682	if (!domain->isCompressible()
1683	\|\| domain->type == CDomain::type_attr::unstructured
1684	\|\| domain->isWrittenCompressed(this->filename)
1685	\|\| isWrittenCompressedDomain(domId))
1686	continue;
1687
1688	StdString appendDomId = singleDomain ? "" : "_" + domId;
1689
1690	varId = domId + "_points";
1691	switch (domain->type)
1692	{
1693	case CDomain::type_attr::curvilinear:
1694	compress = "y" + appendDomId + " x" + appendDomId;
1695	break;
1696	case CDomain::type_attr::rectilinear:
1697	compress = "lat" + appendDomId + " lon" + appendDomId;
1698	break;
1699	}
1700
1701	// indexes.resize(domain->compressedIndexToWriteOnServer[comm_file].numElements());
1702	// indexes = domain->compressedIndexToWriteOnServer[com_file];
1703	indexes.resize(domain->getCompressedIndexToWriteOnServer(comm_file).numElements());
1704	indexes = domain->getCompressedIndexToWriteOnServer(comm_file);
1705
1706	isDistributed = domain->isDistributed();
1707	nbIndexes = domain->getNumberWrittenIndexes(comm_file);
1708	totalNbIndexes = domain->getTotalNumberWrittenIndexes(comm_file);
1709	offset = domain->getOffsetWrittenIndexes(comm_file);
1710	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1711
1712	domain->addRelFileCompressed(this->filename);
1713	setWrittenCompressedDomain(domId);
1714	++idxDomain;
1715	}
1716	else if (1 == axisDomainOrder(i))
1717	{
1718	CAxis* axis = CAxis::get(axisList[idxAxis]);
1719	StdString axisId = axis->getAxisOutputName();
1720
1721	if (!axis->isCompressible()
1722	\|\| axis->isWrittenCompressed(this->filename)
1723	\|\| isWrittenCompressedAxis(axisId))
1724	continue;
1725
1726	varId = axisId + "_points";
1727	compress = axisId;
1728
1729	// indexes.resize(axis->compressedIndexToWriteOnServer.numElements());
1730	// indexes = axis->compressedIndexToWriteOnServer;
1731
1732	indexes.resize(axis->getCompressedIndexToWriteOnServer(comm_file).numElements());
1733	indexes = axis->getCompressedIndexToWriteOnServer(comm_file);
1734
1735	isDistributed = axis->isDistributed();
1736	nbIndexes = axis->getNumberWrittenIndexes(comm_file);
1737	totalNbIndexes = axis->getTotalNumberWrittenIndexes(comm_file);
1738	offset = axis->getOffsetWrittenIndexes(comm_file);
1739	firstGlobalIndex = axis->begin;
1740
1741	axis->addRelFileCompressed(this->filename);
1742	setWrittenCompressedAxis(axisId);
1743	++idxAxis;
1744	}
1745	else
1746	{
1747	}
1748
1749	if (!varId.empty())
1750	{
1751	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1752
1753	dims.clear();
1754	dims.push_back(varId);
1755	SuperClassWriter::addVariable(varId, NC_INT, dims);
1756
1757	SuperClassWriter::addAttribute("compress", compress, &varId);
1758
1759	switch (SuperClass::type)
1760	{
1761	case (MULTI_FILE):
1762	{
1763	indexes -= firstGlobalIndex;
1764	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1765	break;
1766	}
1767	case (ONE_FILE):
1768	{
1769	std::vector<StdSize> start, count;
1770	start.push_back(offset);
1771	count.push_back(nbIndexes);
1772
1773	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1774	break;
1775	}
1776	}
1777	}
1778	}
1779	}
1780
1781	grid->addRelFileCompressed(this->filename);
1782	}
1783	catch (CNetCdfException& e)
1784	{
1785	StdString msg("On writing compressed grid : ");
1786	msg.append(grid->getId()); msg.append("\n");
1787	msg.append("In the context : ");
1788	CContext* context = CContext::getCurrent();
1789	msg.append(context->getId()); msg.append("\n");
1790	msg.append(e.what());
1791	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1792	}
1793	}
1794
1795	//--------------------------------------------------------------
1796
1797	void CNc4DataOutput::writeTimeDimension_(void)
1798	{
1799	try
1800	{
1801	SuperClassWriter::addDimension(getTimeCounterName());
1802	}
1803	catch (CNetCdfException& e)
1804	{
1805	StdString msg("On writing time dimension : time_couter\n");
1806	msg.append("In the context : ");
1807	CContext* context = CContext::getCurrent() ;
1808	msg.append(context->getId()); msg.append("\n");
1809	msg.append(e.what());
1810	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1811	}
1812	}
1813
1814	//--------------------------------------------------------------
1815
1816	void CNc4DataOutput::writeField_(CField* field)
1817	{
1818	CContext* context = CContext::getCurrent() ;
1819	CContextServer* server=context->server ;
1820
1821	std::vector<StdString> dims, coodinates;
1822	CGrid* grid = field->grid;
1823	if (!grid->doGridHaveDataToWrite())
1824	if (SuperClass::type==MULTI_FILE) return ;
1825
1826	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1827	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1828	std::vector<StdString> domainList = grid->getDomainList();
1829	std::vector<StdString> axisList = grid->getAxisList();
1830	std::vector<StdString> scalarList = grid->getScalarList();
1831
1832	StdString timeid = getTimeCounterName();
1833	StdString dimXid,dimYid;
1834	std::deque<StdString> dimIdList, dimCoordList;
1835	bool hasArea = false;
1836	StdString cellMeasures = "area:";
1837	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1838
1839	for (int i = 0; i < numElement; ++i)
1840	{
1841	if (2 == axisDomainOrder(i))
1842	{
1843	CDomain* domain = CDomain::get(domainList[idxDomain]);
1844	StdString domId = domain->getDomainOutputName();
1845	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1846	StdString lonName,latName ;
1847	StdString dimIname,dimJname ;
1848
1849	if (domain->lon_name.isEmpty())
1850	{
1851	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1852	else lonName = "lon";
1853	}
1854	else lonName = domain->lon_name;
1855
1856	if (domain->lat_name.isEmpty())
1857	{
1858	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1859	else latName = "lat";
1860	}
1861	else latName = domain->lat_name;
1862
1863	if (domain->dim_i_name.isEmpty())
1864	{
1865	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1866	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1867	else dimIname = lonName;
1868	}
1869	else dimIname = domain->dim_i_name;
1870
1871	if (domain->dim_j_name.isEmpty())
1872	{
1873	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1874	else dimJname = latName;
1875	}
1876	else dimJname = domain->dim_j_name;
1877
1878	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1879	{
1880	dimIdList.push_back(domId + "_points");
1881	field->setUseCompressedOutput();
1882	}
1883
1884	switch (domain->type)
1885	{
1886	case CDomain::type_attr::curvilinear:
1887	if (!compressedOutput \|\| !domain->isCompressible())
1888	{
1889	dimXid=dimIname+appendDomId;
1890	dimYid=dimJname+appendDomId;
1891	dimIdList.push_back(dimXid);
1892	dimIdList.push_back(dimYid);
1893	}
1894	dimCoordList.push_back(lonName+appendDomId);
1895	dimCoordList.push_back(latName+appendDomId);
1896	break ;
1897	case CDomain::type_attr::rectilinear:
1898	if (!compressedOutput \|\| !domain->isCompressible())
1899	{
1900	dimXid = dimIname+appendDomId;
1901	dimYid = dimJname+appendDomId;
1902	dimIdList.push_back(dimXid);
1903	dimIdList.push_back(dimYid);
1904	}
1905	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1906	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1907
1908	break ;
1909	case CDomain::type_attr::unstructured:
1910	{
1911	if (SuperClassWriter::useCFConvention)
1912	{
1913	dimXid = dimIname + appendDomId;
1914	dimIdList.push_back(dimXid);
1915	dimCoordList.push_back(lonName+appendDomId);
1916	dimCoordList.push_back(latName+appendDomId);
1917	}
1918	else
1919	{
1920	StdString domainName = domain->name;
1921	if (domain->nvertex == 1)
1922	{
1923	dimXid = "n" + domainName + "_node";
1924	dimIdList.push_back(dimXid);
1925	dimCoordList.push_back(StdString(domainName + "_node_x"));
1926	dimCoordList.push_back(StdString(domainName + "_node_y"));
1927	}
1928	else if (domain->nvertex == 2)
1929	{
1930	dimXid = "n" + domainName + "_edge";
1931	dimIdList.push_back(dimXid);
1932	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1933	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1934	}
1935	else
1936	{
1937	dimXid = "n" + domainName + "_face";
1938	dimIdList.push_back(dimXid);
1939	dimCoordList.push_back(StdString(domainName + "_face_x"));
1940	dimCoordList.push_back(StdString(domainName + "_face_y"));
1941	}
1942	} // ugrid convention
1943	} // case unstructured domain
1944	}
1945
1946	if (domain->hasArea)
1947	{
1948	hasArea = true;
1949	cellMeasures += " area" + appendDomId;
1950	}
1951	++idxDomain;
1952	}
1953	else if (1 == axisDomainOrder(i))
1954	{
1955	CAxis* axis = CAxis::get(axisList[idxAxis]);
1956	StdString axisId = axis->getAxisOutputName();
1957	StdString axisDim;
1958
1959	if (axis->dim_name.isEmpty()) axisDim = axisId;
1960	else axisDim=axis->dim_name.getValue();
1961
1962	if (compressedOutput && axis->isCompressible())
1963	{
1964	dimIdList.push_back(axisDim + "_points");
1965	field->setUseCompressedOutput();
1966	}
1967	else
1968	dimIdList.push_back(axisDim);
1969
1970	if (axisDim != axisId) dimCoordList.push_back(axisId);
1971	++idxAxis;
1972	}
1973	else
1974	{
1975	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
1976	StdString scalarId = scalar->getScalarOutputName();
1977	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1978	dimCoordList.push_back(scalarId);
1979	++idxScalar;
1980	}
1981	}
1982
1983	StdString fieldid = field->getFieldOutputName();
1984
1985	nc_type type ;
1986	if (field->prec.isEmpty()) type = NC_FLOAT ;
1987	else
1988	{
1989	if (field->prec==2) type = NC_SHORT ;
1990	else if (field->prec==4) type = NC_FLOAT ;
1991	else if (field->prec==8) type = NC_DOUBLE ;
1992	}
1993
1994	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1995
1996	if (wtime)
1997	{
1998	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1999	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
2000	dims.push_back(timeid);
2001	}
2002
2003	if (compressedOutput && grid->isCompressible())
2004	{
2005	dims.push_back(grid->getId() + "_points");
2006	field->setUseCompressedOutput();
2007	}
2008	else
2009	{
2010	while (!dimIdList.empty())
2011	{
2012	dims.push_back(dimIdList.back());
2013	dimIdList.pop_back();
2014	}
2015	}
2016
2017	while (!dimCoordList.empty())
2018	{
2019	coodinates.push_back(dimCoordList.back());
2020	dimCoordList.pop_back();
2021	}
2022
2023	try
2024	{
2025	SuperClassWriter::addVariable(fieldid, type, dims);
2026
2027	if (!field->standard_name.isEmpty())
2028	SuperClassWriter::addAttribute
2029	("standard_name", field->standard_name.getValue(), &fieldid);
2030
2031	if (!field->long_name.isEmpty())
2032	SuperClassWriter::addAttribute
2033	("long_name", field->long_name.getValue(), &fieldid);
2034
2035	if (!field->unit.isEmpty())
2036	SuperClassWriter::addAttribute
2037	("units", field->unit.getValue(), &fieldid);
2038
2039	// Ugrid field attributes "mesh" and "location"
2040	if (!SuperClassWriter::useCFConvention)
2041	{
2042	if (!domainList.empty())
2043	{
2044	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
2045	StdString mesh = domain->name;
2046	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
2047	StdString location;
2048	if (domain->nvertex == 1)
2049	location = "node";
2050	else if (domain->nvertex == 2)
2051	location = "edge";
2052	else if (domain->nvertex > 2)
2053	location = "face";
2054	SuperClassWriter::addAttribute("location", location, &fieldid);
2055	}
2056
2057	}
2058
2059	if (!field->valid_min.isEmpty())
2060	SuperClassWriter::addAttribute
2061	("valid_min", field->valid_min.getValue(), &fieldid);
2062
2063	if (!field->valid_max.isEmpty())
2064	SuperClassWriter::addAttribute
2065	("valid_max", field->valid_max.getValue(), &fieldid);
2066
2067	if (!field->scale_factor.isEmpty())
2068	SuperClassWriter::addAttribute
2069	("scale_factor", field->scale_factor.getValue(), &fieldid);
2070
2071	if (!field->add_offset.isEmpty())
2072	SuperClassWriter::addAttribute
2073	("add_offset", field->add_offset.getValue(), &fieldid);
2074
2075	SuperClassWriter::addAttribute
2076	("online_operation", field->operation.getValue(), &fieldid);
2077
2078	// write child variables as attributes
2079
2080
2081	bool alreadyAddCellMethod = false;
2082	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
2083	if (!field->cell_methods.isEmpty())
2084	{
2085	StdString cellMethodString = field->cell_methods;
2086	if (field->cell_methods_mode.isEmpty() \|\|
2087	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
2088	{
2089	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
2090	alreadyAddCellMethod = true;
2091	}
2092	else
2093	{
2094	switch (field->cell_methods_mode)
2095	{
2096	case (CField::cell_methods_mode_attr::prefix):
2097	cellMethodsPrefix = cellMethodString;
2098	cellMethodsPrefix += " ";
2099	break;
2100	case (CField::cell_methods_mode_attr::suffix):
2101	cellMethodsSuffix = " ";
2102	cellMethodsSuffix += cellMethodString;
2103	break;
2104	case (CField::cell_methods_mode_attr::none):
2105	break;
2106	default:
2107	break;
2108	}
2109	}
2110	}
2111
2112
2113	if (wtime)
2114	{
2115	CDuration freqOp = field->freq_op.getValue();
2116	freqOp.solveTimeStep(*context->calendar);
2117	StdString freqOpStr = freqOp.toStringUDUnits();
2118	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
2119
2120	CDuration freqOut = field->getRelFile()->output_freq.getValue();
2121	freqOut.solveTimeStep(*context->calendar);
2122	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
2123
2124	StdString cellMethods(cellMethodsPrefix + "time: ");
2125	if (field->operation.getValue() == "instant") cellMethods += "point";
2126	else if (field->operation.getValue() == "average") cellMethods += "mean";
2127	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
2128	else cellMethods += field->operation;
2129	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
2130	cellMethods += " (interval: " + freqOpStr + ")";
2131	cellMethods += cellMethodsSuffix;
2132	if (!alreadyAddCellMethod)
2133	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
2134	}
2135
2136	if (hasArea)
2137	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
2138
2139	if (!field->default_value.isEmpty())
2140	{
2141	double default_value = field->default_value.getValue();
2142	if (type == NC_DOUBLE)
2143	{
2144	SuperClassWriter::setDefaultValue(fieldid, &default_value);
2145	}
2146	else if (type == NC_SHORT)
2147	{
2148	short sdefault_value = (short)default_value;
2149	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
2150	}
2151	else
2152	{
2153	float fdefault_value = (float)default_value;
2154	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
2155	}
2156	}
2157	else
2158	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
2159
2160	if (field->compression_level.isEmpty())
2161	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
2162	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
2163
2164	{ // Ecriture des coordonnes
2165
2166	StdString coordstr; //boost::algorithm::join(coodinates, " ")
2167	std::vector<StdString>::iterator
2168	itc = coodinates.begin(), endc = coodinates.end();
2169
2170	for (; itc!= endc; itc++)
2171	{
2172	StdString & coord = *itc;
2173	if (itc+1 != endc)
2174	coordstr.append(coord).append(" ");
2175	else coordstr.append(coord);
2176	}
2177
2178	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
2179
2180	}
2181
2182	vector<CVariable*> listVars = field->getAllVariables() ;
2183	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
2184
2185	}
2186	catch (CNetCdfException& e)
2187	{
2188	StdString msg("On writing field : ");
2189	msg.append(fieldid); msg.append("\n");
2190	msg.append("In the context : ");
2191	msg.append(context->getId()); msg.append("\n");
2192	msg.append(e.what());
2193	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2194	}
2195	} // writeField_()
2196
2197	//--------------------------------------------------------------
2198
2199	void CNc4DataOutput::writeFile_ (CFile* file)
2200	{
2201	StdString filename = file->getFileOutputName();
2202	StdString description = (!file->description.isEmpty())
2203	? file->description.getValue()
2204	: StdString("Created by xios");
2205
2206	singleDomain = (file->nbDomains == 1);
2207
2208	StdString conv_str ;
2209	if (file->convention_str.isEmpty())
2210	{
2211	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2212	else conv_str="UGRID" ;
2213	}
2214	else conv_str=file->convention_str ;
2215
2216	try
2217	{
2218	if (!appendMode) this->writeFileAttributes(filename, description,
2219	conv_str,
2220	StdString("An IPSL model"),
2221	this->getTimeStamp());
2222
2223	if (!appendMode)
2224	SuperClassWriter::addDimension("axis_nbounds", 2);
2225	}
2226	catch (CNetCdfException& e)
2227	{
2228	StdString msg("On writing file : ");
2229	msg.append(filename); msg.append("\n");
2230	msg.append("In the context : ");
2231	CContext* context = CContext::getCurrent() ;
2232	msg.append(context->getId()); msg.append("\n");
2233	msg.append(e.what());
2234	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2235	}
2236	}
2237
2238	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2239	{
2240	StdString name = var->getVariableOutputName();
2241
2242	try
2243	{
2244	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2245	addAttribute(name, var->getData<int>(), &fieldId);
2246	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2247	addAttribute(name, var->getData<short int>(), &fieldId);
2248	else if (var->type.getValue() == CVariable::type_attr::t_float)
2249	addAttribute(name, var->getData<float>(), &fieldId);
2250	else if (var->type.getValue() == CVariable::type_attr::t_double)
2251	addAttribute(name, var->getData<double>(), &fieldId);
2252	else if (var->type.getValue() == CVariable::type_attr::t_string)
2253	addAttribute(name, var->getData<string>(), &fieldId);
2254	else
2255	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2256	<< "Unsupported variable of type " << var->type.getStringValue());
2257	}
2258	catch (CNetCdfException& e)
2259	{
2260	StdString msg("On writing attributes of variable with name : ");
2261	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2262	msg.append("In the context : ");
2263	CContext* context = CContext::getCurrent() ;
2264	msg.append(context->getId()); msg.append("\n");
2265	msg.append(e.what());
2266	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2267	}
2268	}
2269
2270	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2271	{
2272	StdString name = var->getVariableOutputName();
2273
2274	try
2275	{
2276	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2277	addAttribute(name, var->getData<int>());
2278	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2279	addAttribute(name, var->getData<short int>());
2280	else if (var->type.getValue() == CVariable::type_attr::t_float)
2281	addAttribute(name, var->getData<float>());
2282	else if (var->type.getValue() == CVariable::type_attr::t_double)
2283	addAttribute(name, var->getData<double>());
2284	else if (var->type.getValue() == CVariable::type_attr::t_string)
2285	addAttribute(name, var->getData<string>());
2286	else
2287	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2288	<< "Unsupported variable of type " << var->type.getStringValue());
2289	}
2290	catch (CNetCdfException& e)
2291	{
2292	StdString msg("On writing attributes of variable with name : ");
2293	msg.append(name); msg.append("\n");
2294	msg.append("In the context : ");
2295	CContext* context = CContext::getCurrent() ;
2296	msg.append(context->getId()); msg.append("\n");
2297	msg.append(e.what());
2298	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2299	}
2300	}
2301
2302	void CNc4DataOutput::syncFile_ (void)
2303	{
2304	try
2305	{
2306	SuperClassWriter::sync() ;
2307	}
2308	catch (CNetCdfException& e)
2309	{
2310	StdString msg("On synchronizing the write among processes");
2311	msg.append("In the context : ");
2312	CContext* context = CContext::getCurrent() ;
2313	msg.append(context->getId()); msg.append("\n");
2314	msg.append(e.what());
2315	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2316	}
2317	}
2318
2319	void CNc4DataOutput::closeFile_ (void)
2320	{
2321	try
2322	{
2323	SuperClassWriter::close() ;
2324	}
2325	catch (CNetCdfException& e)
2326	{
2327	StdString msg("On closing file");
2328	msg.append("In the context : ");
2329	CContext* context = CContext::getCurrent() ;
2330	msg.append(context->getId()); msg.append("\n");
2331	msg.append(e.what());
2332	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2333	}
2334
2335	}
2336
2337	//---------------------------------------------------------------
2338
2339	StdString CNc4DataOutput::getTimeStamp(void) const
2340	{
2341	const int buffer_size = 100;
2342	time_t rawtime;
2343	struct tm * timeinfo = NULL;
2344	char buffer [buffer_size];
2345	StdString formatStr;
2346	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2347	else formatStr=file->time_stamp_format;
2348
2349	// time ( &rawtime );
2350	// timeinfo = localtime ( &rawtime );
2351	time ( &rawtime );
2352	timeinfo = gmtime ( &rawtime );
2353	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2354
2355	return (StdString(buffer));
2356	}
2357
2358	//---------------------------------------------------------------
2359
2360	void CNc4DataOutput::writeFieldData_ (CField* field)
2361	{
2362	CContext* context = CContext::getCurrent();
2363	CContextServer* server = context->server;
2364	CGrid* grid = field->grid;
2365
2366	if (field->getNStep()<1)
2367	{
2368	return;
2369	}
2370
2371	if (!grid->doGridHaveDataToWrite())
2372	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2373	{
2374	return;
2375	}
2376
2377	StdString fieldid = field->getFieldOutputName();
2378
2379	StdOStringStream oss;
2380	string timeAxisId;
2381	if (field->hasTimeInstant) timeAxisId = "time_instant";
2382	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2383
2384	StdString timeBoundId = getTimeCounterName() + "_bounds";
2385
2386	StdString timeAxisBoundId;
2387	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2388	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2389
2390	if (!field->wasWritten())
2391	{
2392	if (appendMode && field->file->record_offset.isEmpty() &&
2393	field->getOperationTimeType() != func::CFunctor::once)
2394	{
2395	double factorUnit;
2396	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2397	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2398	else factorUnit=1 ;
2399	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2400	}
2401
2402	field->setWritten();
2403	}
2404
2405
2406	CArray<double,1> time_data(1);
2407	CArray<double,1> time_data_bound(2);
2408	CArray<double,1> time_counter(1);
2409	CArray<double,1> time_counter_bound(2);
2410
2411	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2412	bool wtimeCounter =false ;
2413	bool wtimeData =false ;
2414
2415
2416	if (wtime)
2417	{
2418	Time lastWrite = field->last_Write_srv;
2419	Time lastLastWrite = field->lastlast_Write_srv;
2420
2421
2422	if (field->hasTimeInstant)
2423	{
2424	time_data(0) = time_data_bound(1) = lastWrite;
2425	time_data_bound(0) = time_data_bound(1) = lastWrite;
2426	if (timeCounterType==instant)
2427	{
2428	time_counter(0) = time_data(0);
2429	time_counter_bound(0) = time_data_bound(0);
2430	time_counter_bound(1) = time_data_bound(1);
2431	wtimeCounter=true ;
2432	}
2433	if (hasTimeInstant) wtimeData=true ;
2434	}
2435	else if (field->hasTimeCentered)
2436	{
2437	time_data(0) = (lastWrite + lastLastWrite) / 2;
2438	time_data_bound(0) = lastLastWrite;
2439	time_data_bound(1) = lastWrite;
2440	if (timeCounterType==centered)
2441	{
2442	time_counter(0) = time_data(0) ;
2443	time_counter_bound(0) = time_data_bound(0) ;
2444	time_counter_bound(1) = time_data_bound(1) ;
2445	wtimeCounter=true ;
2446	}
2447	if (hasTimeCentered) wtimeData=true ;
2448	}
2449
2450	if (timeCounterType==record)
2451	{
2452	time_counter(0) = field->getNStep() - 1;
2453	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2454	wtimeCounter=true ;
2455	}
2456
2457	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2458	{
2459	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2460	time_data/=secByDay;
2461	time_data_bound/=secByDay;
2462	time_counter/=secByDay;
2463	time_counter_bound/=secByDay;
2464	}
2465	}
2466
2467	bool isRoot = (server->intraCommRank == 0);
2468
2469	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2470	{
2471	double scaleFactor = 1.0;
2472	double addOffset = 0.0;
2473	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2474	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2475	field->scaleFactorAddOffset(scaleFactor, addOffset);
2476	}
2477
2478	try
2479	{
2480	size_t writtenSize;
2481	if (field->getUseCompressedOutput())
2482	writtenSize = grid->getNumberWrittenIndexes();
2483	else
2484	writtenSize = grid->getWrittenDataSize();
2485
2486	CArray<double,1> fieldData(writtenSize);
2487	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2488
2489	if (field->getUseCompressedOutput())
2490	field->outputCompressedField(fieldData);
2491	else
2492	field->outputField(fieldData);
2493
2494	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2495
2496	switch (SuperClass::type)
2497	{
2498	case (MULTI_FILE) :
2499	{
2500	CTimer::get("Files : writing data").resume();
2501	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2502	CTimer::get("Files : writing data").suspend();
2503	if (wtime)
2504	{
2505	CTimer::get("Files : writing time axis").resume();
2506	if ( wtimeData)
2507	{
2508	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2509	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2510	}
2511	if (wtimeCounter)
2512	{
2513	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2514	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2515	}
2516	CTimer::get("Files : writing time axis").suspend();
2517	}
2518	break;
2519	}
2520	case (ONE_FILE) :
2521	{
2522
2523	std::vector<StdSize> start, count;
2524
2525	if (field->getUseCompressedOutput())
2526	{
2527	if (grid->isCompressible())
2528	{
2529	start.push_back(grid->getOffsetWrittenIndexes());
2530	count.push_back(grid->getNumberWrittenIndexes());
2531	}
2532	else
2533	{
2534	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2535	std::vector<StdString> domainList = grid->getDomainList();
2536	std::vector<StdString> axisList = grid->getAxisList();
2537	int numElement = axisDomainOrder.numElements();
2538	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2539	int idx = domainList.size() * 2 + axisList.size() - 1;
2540
2541	start.reserve(idx+1);
2542	count.reserve(idx+1);
2543
2544	for (int i = numElement - 1; i >= 0; --i)
2545	{
2546	if (2 == axisDomainOrder(i))
2547	{
2548	CDomain* domain = CDomain::get(domainList[idxDomain]);
2549
2550	if (domain->isCompressible())
2551	{
2552	start.push_back(domain->getOffsetWrittenIndexes(comm_file));
2553	count.push_back(domain->getNumberWrittenIndexes(comm_file));
2554	idx -= 2;
2555	}
2556	else
2557	{
2558	if ((domain->type) != CDomain::type_attr::unstructured)
2559	{
2560	start.push_back(domain->jbegin);
2561	count.push_back(domain->nj);
2562	}
2563	--idx;
2564	start.push_back(domain->ibegin);
2565	count.push_back(domain->ni);
2566	--idx;
2567	}
2568	--idxDomain;
2569	}
2570	else if (1 == axisDomainOrder(i))
2571	{
2572	CAxis* axis = CAxis::get(axisList[idxAxis]);
2573
2574	if (axis->isCompressible())
2575	{
2576	start.push_back(axis->getOffsetWrittenIndexes(comm_file));
2577	count.push_back(axis->getNumberWrittenIndexes(comm_file));
2578	}
2579	else
2580	{
2581	start.push_back(axis->begin);
2582	count.push_back(axis->n);
2583	}
2584	--idxAxis;
2585	--idx;
2586	}
2587	}
2588	}
2589	}
2590	else
2591	{
2592	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2593	std::vector<StdString> domainList = grid->getDomainList();
2594	std::vector<StdString> axisList = grid->getAxisList();
2595	int numElement = axisDomainOrder.numElements();
2596	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2597	int idx = domainList.size() * 2 + axisList.size() - 1;
2598
2599	start.reserve(idx+1);
2600	count.reserve(idx+1);
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	if ((domain->type) != CDomain::type_attr::unstructured)
2608	{
2609	start.push_back(domain->jbegin);
2610	count.push_back(domain->nj);
2611	}
2612	--idx ;
2613
2614	start.push_back(domain->ibegin);
2615	count.push_back(domain->ni);
2616	--idx ;
2617	--idxDomain;
2618	}
2619	else if (1 == axisDomainOrder(i))
2620	{
2621	CAxis* axis = CAxis::get(axisList[idxAxis]);
2622	start.push_back(axis->begin);
2623	count.push_back(axis->n);
2624	--idx;
2625	--idxAxis;
2626	}
2627	else
2628	{
2629	if (1 == axisDomainOrder.numElements())
2630	{
2631	start.push_back(0);
2632	count.push_back(1);
2633	}
2634	--idx;
2635	}
2636	}
2637	}
2638
2639
2640	CTimer::get("Files : writing data").resume();
2641	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2642	CTimer::get("Files : writing data").suspend();
2643
2644	if (wtime)
2645	{
2646	CTimer::get("Files : writing time axis").resume();
2647	if ( wtimeData)
2648	{
2649	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2650	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2651	}
2652	if (wtimeCounter)
2653	{
2654	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2655	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2656
2657	}
2658	CTimer::get("Files : writing time axis").suspend();
2659	}
2660
2661	break;
2662	}
2663	}
2664	}
2665	catch (CNetCdfException& e)
2666	{
2667	StdString msg("On writing field data: ");
2668	msg.append(fieldid); msg.append("\n");
2669	msg.append("In the context : ");
2670	msg.append(context->getId()); msg.append("\n");
2671	msg.append(e.what());
2672	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2673	}
2674	}
2675
2676	//---------------------------------------------------------------
2677
2678	void CNc4DataOutput::writeTimeAxis_
2679	(CField* field,
2680	const std::shared_ptr<CCalendar> cal)
2681	{
2682	StdOStringStream oss;
2683	bool createInstantAxis=false ;
2684	bool createCenteredAxis=false ;
2685	bool createTimeCounterAxis=false ;
2686
2687	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2688
2689
2690	StdString axisId ;
2691	StdString axisBoundId;
2692	StdString timeid(getTimeCounterName());
2693	StdString timeBoundId("axis_nbounds");
2694
2695	StdString strTimeUnits ;
2696	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2697	else strTimeUnits="seconds since " ;
2698
2699	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2700	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2701
2702
2703	if (field->file->time_counter.isEmpty())
2704	{
2705	if (timeCounterType==none) createTimeCounterAxis=true ;
2706	if (field->hasTimeCentered)
2707	{
2708	timeCounterType=centered ;
2709	if (!hasTimeCentered) createCenteredAxis=true ;
2710	}
2711	if (field->hasTimeInstant)
2712	{
2713	if (timeCounterType==none) timeCounterType=instant ;
2714	if (!hasTimeInstant) createInstantAxis=true ;
2715	}
2716	}
2717	else if (field->file->time_counter==CFile::time_counter_attr::instant)
2718	{
2719	if (field->hasTimeCentered)
2720	{
2721	if (!hasTimeCentered) createCenteredAxis=true ;
2722	}
2723	if (field->hasTimeInstant)
2724	{
2725	if (timeCounterType==none) createTimeCounterAxis=true ;
2726	timeCounterType=instant ;
2727	if (!hasTimeInstant) createInstantAxis=true ;
2728	}
2729	}
2730	else if (field->file->time_counter==CFile::time_counter_attr::centered)
2731	{
2732	if (field->hasTimeCentered)
2733	{
2734	if (timeCounterType==none) createTimeCounterAxis=true ;
2735	timeCounterType=centered ;
2736	if (!hasTimeCentered) createCenteredAxis=true ;
2737	}
2738	if (field->hasTimeInstant)
2739	{
2740	if (!hasTimeInstant) createInstantAxis=true ;
2741	}
2742	}
2743	else if (field->file->time_counter==CFile::time_counter_attr::instant_exclusive)
2744	{
2745	if (field->hasTimeCentered)
2746	{
2747	if (!hasTimeCentered) createCenteredAxis=true ;
2748	}
2749	if (field->hasTimeInstant)
2750	{
2751	if (timeCounterType==none) createTimeCounterAxis=true ;
2752	timeCounterType=instant ;
2753	}
2754	}
2755	else if (field->file->time_counter==CFile::time_counter_attr::centered_exclusive)
2756	{
2757	if (field->hasTimeCentered)
2758	{
2759	if (timeCounterType==none) createTimeCounterAxis=true ;
2760	timeCounterType=centered ;
2761	}
2762	if (field->hasTimeInstant)
2763	{
2764	if (!hasTimeInstant) createInstantAxis=true ;
2765	}
2766	}
2767	else if (field->file->time_counter==CFile::time_counter_attr::exclusive)
2768	{
2769	if (field->hasTimeCentered)
2770	{
2771	if (timeCounterType==none) createTimeCounterAxis=true ;
2772	if (timeCounterType==instant) createInstantAxis=true ;
2773	timeCounterType=centered ;
2774	}
2775	if (field->hasTimeInstant)
2776	{
2777	if (timeCounterType==none)
2778	{
2779	createTimeCounterAxis=true ;
2780	timeCounterType=instant ;
2781	}
2782	if (timeCounterType==centered)
2783	{
2784	if (!hasTimeInstant) createInstantAxis=true ;
2785	}
2786	}
2787	}
2788	else if (field->file->time_counter==CFile::time_counter_attr::none)
2789	{
2790	if (field->hasTimeCentered)
2791	{
2792	if (!hasTimeCentered) createCenteredAxis=true ;
2793	}
2794	if (field->hasTimeInstant)
2795	{
2796	if (!hasTimeInstant) createInstantAxis=true ;
2797	}
2798	}
2799	else if (field->file->time_counter==CFile::time_counter_attr::record)
2800	{
2801	if (timeCounterType==none) createTimeCounterAxis=true ;
2802	timeCounterType=record ;
2803	if (field->hasTimeCentered)
2804	{
2805	if (!hasTimeCentered) createCenteredAxis=true ;
2806	}
2807	if (field->hasTimeInstant)
2808	{
2809	if (!hasTimeInstant) createInstantAxis=true ;
2810	}
2811	}
2812
2813	if (createInstantAxis)
2814	{
2815	axisId="time_instant" ;
2816	axisBoundId="time_instant_bounds";
2817	hasTimeInstant=true ;
2818	}
2819
2820	if (createCenteredAxis)
2821	{
2822	axisId="time_centered" ;
2823	axisBoundId="time_centered_bounds";
2824	hasTimeCentered=true ;
2825	}
2826
2827
2828	try
2829	{
2830	std::vector<StdString> dims;
2831
2832	if (createInstantAxis \|\| createCenteredAxis)
2833	{
2834	// Adding time_instant or time_centered
2835	dims.push_back(timeid);
2836	if (!SuperClassWriter::varExist(axisId))
2837	{
2838	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2839
2840	CDate timeOrigin=cal->getTimeOrigin() ;
2841	StdOStringStream oss2;
2842	StdString strInitdate=oss2.str() ;
2843	StdString strTimeOrigin=timeOrigin.toString() ;
2844	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2845	strTimeOrigin, axisBoundId);
2846	}
2847
2848	// Adding time_instant_bounds or time_centered_bounds variables
2849	if (!SuperClassWriter::varExist(axisBoundId))
2850	{
2851	dims.clear() ;
2852	dims.push_back(timeid);
2853	dims.push_back(timeBoundId);
2854	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2855	}
2856	}
2857
2858	if (createTimeCounterAxis)
2859	{
2860	// Adding time_counter
2861	axisId = getTimeCounterName();
2862	axisBoundId = getTimeCounterName() + "_bounds";
2863	dims.clear();
2864	dims.push_back(timeid);
2865	if (!SuperClassWriter::varExist(axisId))
2866	{
2867	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2868	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2869
2870	if (field->file->time_counter.isEmpty() \|\|
2871	(field->file->time_counter != CFile::time_counter_attr::record))
2872	{
2873	CDate timeOrigin = cal->getTimeOrigin();
2874	StdString strTimeOrigin = timeOrigin.toString();
2875
2876	this->writeTimeAxisAttributes(axisId, cal->getType(),
2877	strTimeUnits+strTimeOrigin,
2878	strTimeOrigin, axisBoundId);
2879	}
2880	}
2881
2882	// Adding time_counter_bound dimension
2883	if (field->file->time_counter.isEmpty() \|\| (field->file->time_counter != CFile::time_counter_attr::record))
2884	{
2885	if (!SuperClassWriter::varExist(axisBoundId))
2886	{
2887	dims.clear();
2888	dims.push_back(timeid);
2889	dims.push_back(timeBoundId);
2890	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2891	}
2892	}
2893	}
2894	}
2895	catch (CNetCdfException& e)
2896	{
2897	StdString msg("On writing time axis data: ");
2898	msg.append("In the context : ");
2899	CContext* context = CContext::getCurrent() ;
2900	msg.append(context->getId()); msg.append("\n");
2901	msg.append(e.what());
2902	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2903	const std::shared_ptr<CCalendar> cal)", << msg);
2904	}
2905	}
2906
2907	//---------------------------------------------------------------
2908
2909	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2910	const StdString & calendar,
2911	const StdString & units,
2912	const StdString & time_origin,
2913	const StdString & time_bounds,
2914	const StdString & standard_name,
2915	const StdString & long_name)
2916	{
2917	try
2918	{
2919	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2920	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2921	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2922	SuperClassWriter::addAttribute("units", units , &axis_name);
2923	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2924	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2925	}
2926	catch (CNetCdfException& e)
2927	{
2928	StdString msg("On writing time axis Attribute: ");
2929	msg.append("In the context : ");
2930	CContext* context = CContext::getCurrent() ;
2931	msg.append(context->getId()); msg.append("\n");
2932	msg.append(e.what());
2933	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2934	const StdString & calendar,\
2935	const StdString & units, \
2936	const StdString & time_origin, \
2937	const StdString & time_bounds, \
2938	const StdString & standard_name, \
2939	const StdString & long_name)", << msg);
2940	}
2941	}
2942
2943	//---------------------------------------------------------------
2944
2945	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2946	const StdString & axis,
2947	const StdString & standard_name,
2948	const StdString & long_name,
2949	const StdString & units,
2950	const StdString & nav_model)
2951	{
2952	try
2953	{
2954	if (!axis.empty())
2955	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2956
2957	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2958	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2959	SuperClassWriter::addAttribute("units" , units , &axis_name);
2960	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2961	}
2962	catch (CNetCdfException& e)
2963	{
2964	StdString msg("On writing Axis Attribute: ");
2965	msg.append("In the context : ");
2966	CContext* context = CContext::getCurrent() ;
2967	msg.append(context->getId()); msg.append("\n");
2968	msg.append(e.what());
2969	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2970	const StdString & axis, \
2971	const StdString & standard_name, \
2972	const StdString & long_name, \
2973	const StdString & units, \
2974	const StdString & nav_model)", << msg);
2975	}
2976	}
2977
2978	//---------------------------------------------------------------
2979
2980	void CNc4DataOutput::writeLocalAttributes
2981	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2982	{
2983	try
2984	{
2985	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2986	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2987	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2988	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2989	}
2990	catch (CNetCdfException& e)
2991	{
2992	StdString msg("On writing Local Attributes: ");
2993	msg.append("In the context : ");
2994	CContext* context = CContext::getCurrent() ;
2995	msg.append(context->getId()); msg.append("\n");
2996	msg.append(e.what());
2997	ERROR("CNc4DataOutput::writeLocalAttributes \
2998	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2999	}
3000
3001	}
3002
3003	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
3004	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
3005	{
3006	CArray<int,1> array(2) ;
3007
3008	try
3009	{
3010	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
3011	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
3012	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
3013	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
3014	array=ni_glo,nj_glo ;
3015	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
3016	array=ni,nj ;
3017	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
3018	array=ibegin+1,jbegin+1 ;
3019	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
3020	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
3021	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
3022	array=0,0 ;
3023	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
3024	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
3025	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
3026	/*
3027	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
3028	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
3029	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
3030	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
3031	*/
3032	}
3033	catch (CNetCdfException& e)
3034	{
3035	StdString msg("On writing Local Attributes IOIPSL \n");
3036	msg.append("In the context : ");
3037	CContext* context = CContext::getCurrent() ;
3038	msg.append(context->getId()); msg.append("\n");
3039	msg.append(e.what());
3040	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
3041	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
3042	}
3043	}
3044	//---------------------------------------------------------------
3045
3046	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
3047	const StdString & description,
3048	const StdString & conventions,
3049	const StdString & production,
3050	const StdString & timeStamp)
3051	{
3052	try
3053	{
3054	SuperClassWriter::addAttribute("name" , name);
3055	SuperClassWriter::addAttribute("description", description);
3056	SuperClassWriter::addAttribute("title" , description);
3057	SuperClassWriter::addAttribute("Conventions", conventions);
3058	// SuperClassWriter::addAttribute("production" , production);
3059
3060	StdString timeStampStr ;
3061	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
3062	else timeStampStr=file->time_stamp_name ;
3063	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
3064
3065	StdString uuidName ;
3066	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
3067	else uuidName=file->uuid_name ;
3068
3069	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
3070	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
3071
3072	}
3073	catch (CNetCdfException& e)
3074	{
3075	StdString msg("On writing File Attributes \n ");
3076	msg.append("In the context : ");
3077	CContext* context = CContext::getCurrent() ;
3078	msg.append(context->getId()); msg.append("\n");
3079	msg.append(e.what());
3080	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
3081	const StdString & description, \
3082	const StdString & conventions, \
3083	const StdString & production, \
3084	const StdString & timeStamp)", << msg);
3085	}
3086	}
3087
3088	//---------------------------------------------------------------
3089
3090	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
3091	int data_dim,
3092	int data_ni,
3093	int data_nj,
3094	int data_ibegin,
3095	int data_jbegin)
3096	{
3097	try
3098	{
3099	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
3100	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
3101	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
3102	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
3103	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
3104	}
3105	catch (CNetCdfException& e)
3106	{
3107	StdString msg("On writing Mask Attributes \n ");
3108	msg.append("In the context : ");
3109	CContext* context = CContext::getCurrent() ;
3110	msg.append(context->getId()); msg.append("\n");
3111	msg.append(e.what());
3112	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
3113	int data_dim, \
3114	int data_ni, \
3115	int data_nj, \
3116	int data_ibegin, \
3117	int data_jbegin)", << msg);
3118	}
3119	}
3120
3121	///--------------------------------------------------------------
3122
3123	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
3124	{
3125	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
3126	if (it == timeToRecordCache.end())
3127	{
3128	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
3129	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
3130	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
3131
3132	CArray<double,2> timeAxisBounds;
3133	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
3134
3135	StdSize record = 0;
3136	double dtime(time);
3137	for (int n = dimSize[0] - 1; n >= 0; n--)
3138	{
3139	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3140	timeAxisBounds*=factorUnit ;
3141	if (timeAxisBounds(1, 0) < dtime)
3142	{
3143	record = n + 1;
3144	break;
3145	}
3146	}
3147	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3148	}
3149	return it->second;
3150	}
3151
3152	///--------------------------------------------------------------
3153
3154	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3155	{
3156	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3157	}
3158
3159	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3160	{
3161	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3162	}
3163
3164	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3165	{
3166	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3167	}
3168
3169	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3170	{
3171	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3172	}
3173
3174	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3175	{
3176	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3177	}
3178
3179	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3180	{
3181	this->writtenDomains.insert(domainName);
3182	}
3183
3184	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3185	{
3186	this->writtenCompressedDomains.insert(domainName);
3187	}
3188
3189	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3190	{
3191	this->writtenAxis.insert(axisName);
3192	}
3193
3194	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3195	{
3196	this->writtenCompressedAxis.insert(axisName);
3197	}
3198
3199	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3200	{
3201	this->writtenScalar.insert(scalarName);
3202	}
3203	} // namespace xios

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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 2181

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