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source: XIOS/dev/XIOS_DEV_CMIP6/src/io/nc4_data_output.cpp @ 1456

Last change on this file since 1456 was 1456, checked in by ymipsl, 6 years ago

Add compression for lon, lat and axis.
Activated only if file attribute compression_level>0.

YM

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: 137.8 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	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
40	}
41
42	CNc4DataOutput::~CNc4DataOutput(void)
43	{ /* Ne rien faire de plus */ }
44
45	///--------------------------------------------------------------
46
47	const StdString & CNc4DataOutput::getFileName(void) const
48	{
49	return (this->filename);
50	}
51
52	//---------------------------------------------------------------
53
54	void CNc4DataOutput::writeDomain_(CDomain* domain)
55	{
56	StdString lonName,latName ;
57
58	domain->computeWrittenIndex();
59	domain->computeWrittenCompressedIndex(comm_file);
60
61	if (domain->type == CDomain::type_attr::unstructured)
62	{
63	if (SuperClassWriter::useCFConvention)
64	writeUnstructuredDomain(domain) ;
65	else
66	writeUnstructuredDomainUgrid(domain) ;
67	return ;
68	}
69
70	CContext* context = CContext::getCurrent() ;
71	CContextServer* server=context->server ;
72
73	if (domain->IsWritten(this->filename)) return;
74	domain->checkAttributes();
75
76	if (domain->isEmpty())
77	if (SuperClass::type==MULTI_FILE) return;
78
79	std::vector<StdString> dim0, dim1;
80	StdString domid = domain->getDomainOutputName();
81	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
82	if (isWrittenDomain(domid)) return ;
83	else setWrittenDomain(domid);
84
85	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
86
87
88	StdString dimXid, dimYid ;
89
90	nc_type typePrec ;
91	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
92	else if (domain->prec==4) typePrec = NC_FLOAT ;
93	else if (domain->prec==8) typePrec = NC_DOUBLE ;
94
95	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
96	switch (domain->type)
97	{
98	case CDomain::type_attr::curvilinear :
99
100	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
101	else lonName = domain->lon_name;
102
103	if (domain->lat_name.isEmpty()) latName = "nav_lat";
104	else latName = domain->lat_name;
105
106	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
107	else dimXid=domain->dim_i_name.getValue() + appendDomid;
108
109	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
110	else dimYid=domain->dim_j_name.getValue() + appendDomid;
111
112	break ;
113
114	case CDomain::type_attr::rectilinear :
115
116	if (domain->lon_name.isEmpty())
117	{
118	if (domain->dim_i_name.isEmpty())
119	lonName = "lon";
120	else
121	lonName = domain->dim_i_name.getValue();
122	}
123	else lonName = domain->lon_name;
124
125	if (domain->lat_name.isEmpty())
126	{
127	if (domain->dim_j_name.isEmpty())
128	latName = "lat";
129	else
130	latName = domain->dim_j_name.getValue();
131	}
132	else latName = domain->lat_name;
133
134	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
135	else dimXid = domain->dim_i_name.getValue()+appendDomid;
136
137	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
138	else dimYid = domain->dim_j_name.getValue()+appendDomid;
139	break;
140	}
141
142	StdString dimVertId = StdString("nvertex").append(appendDomid);
143
144	string lonid,latid,bounds_lonid,bounds_latid ;
145	string areaId = "area" + appendDomid;
146	/*
147	StdString lonid_loc = (server->intraCommSize > 1)
148	? StdString("lon").append(appendDomid).append("_local")
149	: lonid;
150	StdString latid_loc = (server->intraCommSize > 1)
151	? StdString("lat").append(appendDomid).append("_local")
152	: latid;
153	*/
154
155	CArray<size_t, 1>& indexToWrite = domain->localIndexToWriteOnServer;
156	int nbWritten = indexToWrite.numElements();
157	CArray<double,1> writtenLat, writtenLon;
158	CArray<double,2> writtenBndsLat, writtenBndsLon;
159	CArray<double,1> writtenArea;
160
161	if (domain->hasLonLat)
162	{
163	writtenLat.resize(nbWritten);
164	writtenLon.resize(nbWritten);
165	for (int idx = 0; idx < nbWritten; ++idx)
166	{
167	if (idx < domain->latvalue.numElements())
168	{
169	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
170	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
171	}
172	else
173	{
174	writtenLat(idx) = 0.;
175	writtenLon(idx) = 0.;
176	}
177	}
178
179
180	if (domain->hasBounds)
181	{
182	int nvertex = domain->nvertex, idx;
183	writtenBndsLat.resize(nvertex, nbWritten);
184	writtenBndsLon.resize(nvertex, nbWritten);
185	CArray<double,2>& boundslat = domain->bounds_latvalue;
186	CArray<double,2>& boundslon = domain->bounds_lonvalue;
187	for (idx = 0; idx < nbWritten; ++idx)
188	for (int nv = 0; nv < nvertex; ++nv)
189	{
190	if (idx < boundslat.columns())
191	{
192	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
193	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
194	}
195	else
196	{
197	writtenBndsLat(nv, idx) = 0.;
198	writtenBndsLon(nv, idx) = 0.;
199	}
200	}
201	}
202	}
203
204	if (domain->hasArea)
205	{
206	writtenArea.resize(nbWritten);
207	for (int idx = 0; idx < nbWritten; ++idx)
208	{
209	if (idx < domain->areavalue.numElements())
210	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
211	else
212	writtenArea(idx) = 0.;
213	}
214	}
215
216	try
217	{
218	switch (SuperClass::type)
219	{
220	case (MULTI_FILE) :
221	{
222	// if (domain->isEmpty()) return;
223
224	if (server->intraCommSize > 1)
225	{
226	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
227	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
228	}
229
230	switch (domain->type)
231	{
232	case CDomain::type_attr::curvilinear :
233	dim0.push_back(dimYid); dim0.push_back(dimXid);
234	lonid = lonName+appendDomid;
235	latid = latName+appendDomid;
236	break ;
237	case CDomain::type_attr::rectilinear :
238	lonid = lonName+appendDomid;
239	latid = latName+appendDomid;
240	dim0.push_back(dimYid);
241	dim1.push_back(dimXid);
242	break;
243	}
244	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
245	else bounds_lonid = "bounds_"+lonName+appendDomid;
246	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
247	else bounds_latid = "bounds_"+latName+appendDomid;
248
249	SuperClassWriter::addDimension(dimXid, domain->zoom_ni);
250	SuperClassWriter::addDimension(dimYid, domain->zoom_nj);
251
252	if (domain->hasBounds)
253	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
254
255	if (server->intraCommSize > 1)
256	{
257	this->writeLocalAttributes(domain->zoom_ibegin,
258	domain->zoom_ni,
259	domain->zoom_jbegin,
260	domain->zoom_nj,
261	appendDomid);
262
263	if (singleDomain)
264	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
265	domain->zoom_ibegin,
266	domain->zoom_ni,
267	domain->zoom_jbegin,
268	domain->zoom_nj,
269	domain->ni_glo,domain->nj_glo,
270	server->intraCommRank,server->intraCommSize);
271	}
272
273	if (domain->hasLonLat)
274	{
275	switch (domain->type)
276	{
277	case CDomain::type_attr::curvilinear :
278	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
279	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
280	break ;
281	case CDomain::type_attr::rectilinear :
282	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
283	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
284	break ;
285	}
286
287	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
288	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
289
290	if (domain->hasBounds)
291	{
292	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
293	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
294
295	dim0.clear();
296	dim0.push_back(dimYid);
297	dim0.push_back(dimXid);
298	dim0.push_back(dimVertId);
299	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
300	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
301	}
302	}
303
304	dim0.clear();
305	dim0.push_back(dimYid);
306	dim0.push_back(dimXid);
307
308
309	// supress mask if (server->intraCommSize > 1)
310	// supress mask {
311	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
312	// supress mask
313	// supress mask this->writeMaskAttributes(maskid,
314	// supress mask domain->data_dim.getValue()/*,
315	// supress mask domain->data_ni.getValue(),
316	// supress mask domain->data_nj.getValue(),
317	// supress mask domain->data_ibegin.getValue(),
318	// supress mask domain->data_jbegin.getValue()*/);
319	// supress mask }
320
321	//SuperClassWriter::setDefaultValue(maskid, &dvm);
322
323	if (domain->hasArea)
324	{
325	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
326	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
327	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
328	}
329
330	SuperClassWriter::definition_end();
331
332	if (domain->hasLonLat)
333	{
334	switch (domain->type)
335	{
336	case CDomain::type_attr::curvilinear :
337	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
338	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
339	break;
340	case CDomain::type_attr::rectilinear :
341	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni)) ;
342	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
343	CArray<double,1> lon = writtenLon(Range(0,domain->zoom_ni-1)) ;
344	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
345	break;
346	}
347
348	if (domain->hasBounds)
349	{
350	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
351	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
352	}
353	}
354
355	if (domain->hasArea)
356	{
357	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
358	}
359
360	SuperClassWriter::definition_start();
361
362	break;
363	}
364	case (ONE_FILE) :
365	{
366	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
367	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
368
369	if (domain->hasBounds)
370	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
371
372	if (domain->hasLonLat)
373	{
374	switch (domain->type)
375	{
376	case CDomain::type_attr::curvilinear :
377	dim0.push_back(dimYid); dim0.push_back(dimXid);
378	lonid = lonName+appendDomid;
379	latid = latName+appendDomid;
380	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
381	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
382	break;
383
384	case CDomain::type_attr::rectilinear :
385	dim0.push_back(dimYid);
386	dim1.push_back(dimXid);
387	lonid = lonName+appendDomid;
388	latid = latName+appendDomid;
389	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
390	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
391	break;
392	}
393	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
394	else bounds_lonid = "bounds_"+lonName+appendDomid;
395	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
396	else bounds_latid = "bounds_"+latName+appendDomid;
397
398	this->writeAxisAttributes
399	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
400	this->writeAxisAttributes
401	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
402
403	if (domain->hasBounds)
404	{
405	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
406	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
407
408	dim0.clear();
409	dim0.push_back(dimYid);
410	dim0.push_back(dimXid);
411	dim0.push_back(dimVertId);
412	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
413	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
414	}
415	}
416
417	if (domain->hasArea)
418	{
419	dim0.clear();
420	dim0.push_back(dimYid); dim0.push_back(dimXid);
421	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
422	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
423	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
424	dim0.clear();
425	}
426
427	SuperClassWriter::definition_end();
428
429	switch (domain->type)
430	{
431	case CDomain::type_attr::curvilinear :
432	{
433	std::vector<StdSize> start(2) ;
434	std::vector<StdSize> count(2) ;
435	if (domain->isEmpty())
436	{
437	start[0]=0 ; start[1]=0 ;
438	count[0]=0 ; count[1]=0 ;
439	}
440	else
441	{
442	start[1]=domain->zoom_ibegin-domain->global_zoom_ibegin;
443	start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
444	count[1]=domain->zoom_ni ; count[0]=domain->zoom_nj ;
445	}
446
447	if (domain->hasLonLat)
448	{
449	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
450	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
451	}
452	break;
453	}
454	case CDomain::type_attr::rectilinear :
455	{
456	if (domain->hasLonLat)
457	{
458	std::vector<StdSize> start(1) ;
459	std::vector<StdSize> count(1) ;
460	if (domain->isEmpty())
461	{
462	start[0]=0 ;
463	count[0]=0 ;
464	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
465	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
466	}
467	else
468	{
469	start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
470	count[0]=domain->zoom_nj;
471	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni));
472	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
473
474	start[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
475	count[0]=domain->zoom_ni;
476	CArray<double,1> lon = writtenLon(Range(0,domain->zoom_ni-1));
477	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
478	}
479	}
480	break;
481	}
482	}
483
484	if (domain->hasBounds)
485	{
486	std::vector<StdSize> start(3);
487	std::vector<StdSize> count(3);
488	if (domain->isEmpty())
489	{
490	start[2] = start[1] = start[0] = 0;
491	count[2] = count[1] = count[0] = 0;
492	}
493	else
494	{
495	start[2] = 0;
496	start[1] = domain->zoom_ibegin - domain->global_zoom_ibegin;
497	start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
498	count[2] = domain->nvertex;
499	count[1] = domain->zoom_ni;
500	count[0] = domain->zoom_nj;
501	}
502
503	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0, &start, &count);
504	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0, &start, &count);
505	}
506
507	if (domain->hasArea)
508	{
509	std::vector<StdSize> start(2);
510	std::vector<StdSize> count(2);
511
512	if (domain->isEmpty())
513	{
514	start[0] = 0; start[1] = 0;
515	count[0] = 0; count[1] = 0;
516	}
517	else
518	{
519	start[1] = domain->zoom_ibegin - domain->global_zoom_ibegin;
520	start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
521	count[1] = domain->zoom_ni;
522	count[0] = domain->zoom_nj;
523	}
524
525	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
526	}
527
528	SuperClassWriter::definition_start();
529	break;
530	}
531	default :
532	ERROR("CNc4DataOutput::writeDomain(domain)",
533	<< "[ type = " << SuperClass::type << "]"
534	<< " not implemented yet !");
535	}
536	}
537	catch (CNetCdfException& e)
538	{
539	StdString msg("On writing the domain : ");
540	msg.append(domid); msg.append("\n");
541	msg.append("In the context : ");
542	msg.append(context->getId()); msg.append("\n");
543	msg.append(e.what());
544	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
545	}
546
547	domain->addRelFile(this->filename);
548	}
549
550	//--------------------------------------------------------------
551
552	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
553	{
554	CContext* context = CContext::getCurrent() ;
555	CContextServer* server=context->server ;
556
557	if (domain->IsWritten(this->filename)) return;
558	domain->checkAttributes();
559	if (domain->isEmpty())
560	if (SuperClass::type==MULTI_FILE) return ;
561
562	nc_type typePrec ;
563	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
564	else if (domain->prec==4) typePrec = NC_FLOAT ;
565	else if (domain->prec==8) typePrec = NC_DOUBLE ;
566
567	std::vector<StdString> dim0;
568	StdString domid = domain->getDomainOutputName();
569	StdString domainName = domain->name;
570	domain->assignMesh(domainName, domain->nvertex);
571	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
572
573	StdString node_x = domainName + "_node_x";
574	StdString node_y = domainName + "_node_y";
575
576	StdString edge_x = domainName + "_edge_x";
577	StdString edge_y = domainName + "_edge_y";
578	StdString edge_nodes = domainName + "_edge_nodes";
579
580	StdString face_x = domainName + "_face_x";
581	StdString face_y = domainName + "_face_y";
582	StdString face_nodes = domainName + "_face_nodes";
583	StdString face_edges = domainName + "_face_edges";
584	StdString edge_faces = domainName + "_edge_face_links";
585	StdString face_faces = domainName + "_face_links";
586
587	StdString dimNode = "n" + domainName + "_node";
588	StdString dimEdge = "n" + domainName + "_edge";
589	StdString dimFace = "n" + domainName + "_face";
590	StdString dimVertex = "n" + domainName + "_vertex";
591	StdString dimTwo = "Two";
592
593	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
594	if (!isWrittenDomain(domid))
595	{
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
604	try
605	{
606	switch (SuperClass::type)
607	{
608	case (ONE_FILE) :
609	{
610	// Adding nodes
611	if (domain->nvertex == 1)
612	{
613	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
614	{
615	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
616	dim0.clear();
617	dim0.push_back(dimNode);
618	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
619	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
620	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
621	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
622	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
623	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
624	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
625	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
626	}
627	} // domain->nvertex == 1
628
629	// Adding edges and nodes, if nodes have not been defined previously
630	if (domain->nvertex == 2)
631	{
632	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
633	{
634	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
635	dim0.clear();
636	dim0.push_back(dimNode);
637	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
638	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
639	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
640	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
641	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
642	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
643	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
644	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
645	}
646	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
647	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
648	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
649	dim0.clear();
650	dim0.push_back(dimEdge);
651	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
652	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
653	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
654	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
655	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
656	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
657	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
658	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
659	dim0.clear();
660	dim0.push_back(dimEdge);
661	dim0.push_back(dimTwo);
662	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
663	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
664	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
665	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
666	} // domain->nvertex == 2
667
668	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
669	if (domain->nvertex > 2)
670	{
671	// Nodes
672	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
673	{
674	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
675	dim0.clear();
676	dim0.push_back(dimNode);
677	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
678	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
679	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
680	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
681	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
682	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
683	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
684	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
685	}
686	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
687	{
688	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
689	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
690	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
691	dim0.clear();
692	dim0.push_back(dimEdge);
693	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
694	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
695	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
696	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
697	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
698	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
699	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
700	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
701	dim0.clear();
702	dim0.push_back(dimEdge);
703	dim0.push_back(dimTwo);
704	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
705	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
706	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
707	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
708	}
709	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
710	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
711	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
712	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
713	dim0.clear();
714	dim0.push_back(dimFace);
715	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
716	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
717	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
718	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
719	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
720	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
721	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
722	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
723	dim0.clear();
724	dim0.push_back(dimFace);
725	dim0.push_back(dimVertex);
726	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
727	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
728	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
729	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
730	dim0.clear();
731	dim0.push_back(dimFace);
732	dim0.push_back(dimVertex);
733	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
734	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
735	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
736	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
737	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
738	dim0.clear();
739	dim0.push_back(dimEdge);
740	dim0.push_back(dimTwo);
741	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
742	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
743	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
744	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
745	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
746	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
747	dim0.clear();
748	dim0.push_back(dimFace);
749	dim0.push_back(dimVertex);
750	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
751	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
752	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
753	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
754	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
755	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
756	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
757	} // domain->nvertex > 2
758
759	SuperClassWriter::definition_end();
760
761	std::vector<StdSize> startEdges(1) ;
762	std::vector<StdSize> countEdges(1) ;
763	std::vector<StdSize> startNodes(1) ;
764	std::vector<StdSize> countNodes(1) ;
765	std::vector<StdSize> startFaces(1) ;
766	std::vector<StdSize> countFaces(1) ;
767	std::vector<StdSize> startEdgeNodes(2) ;
768	std::vector<StdSize> countEdgeNodes(2) ;
769	std::vector<StdSize> startEdgeFaces(2) ;
770	std::vector<StdSize> countEdgeFaces(2) ;
771	std::vector<StdSize> startFaceConctv(2) ;
772	std::vector<StdSize> countFaceConctv(2) ;
773
774	if (!isWrittenDomain(domid))
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->zoom_ibegin-domain->global_zoom_ibegin;
786	countNodes[0] = domain->zoom_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->zoom_ibegin-domain->global_zoom_ibegin;
809	countEdges[0] = domain->zoom_ni;
810	startNodes[0] = domain->mesh->node_start;
811	countNodes[0] = domain->mesh->node_count;
812	startEdgeNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
813	startEdgeNodes[1] = 0;
814	countEdgeNodes[0] = domain->zoom_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->zoom_ibegin-domain->global_zoom_ibegin;
845	countFaces[0] = domain->zoom_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->zoom_ibegin-domain->global_zoom_ibegin;
859	startFaceConctv[1] = 0;
860	countFaceConctv[0] = domain->zoom_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	setWrittenDomain(domid);
876	} // !isWrittenDomain
877	else
878	{
879	if (domain->nvertex == 2)
880	{
881	startEdges[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
882	countEdges[0] = domain->zoom_ni;
883	startEdgeNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
884	startEdgeNodes[1] = 0;
885	countEdgeNodes[0] = domain->zoom_ni;
886	countEdgeNodes[1]= 2;
887	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
888	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
889	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
890	}
891	if (domain->nvertex > 2)
892	{
893
894	if (!domain->mesh->edgesAreWritten)
895	{
896	startEdges[0] = domain->mesh->edge_start;
897	countEdges[0] = domain->mesh->edge_count;
898	startEdgeNodes[0] = domain->mesh->edge_start;
899	startEdgeNodes[1] = 0;
900	countEdgeNodes[0] = domain->mesh->edge_count;
901	countEdgeNodes[1]= 2;
902	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
903	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
904	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
905	}
906	startFaces[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
907	countFaces[0] = domain->zoom_ni;
908	startEdgeFaces[0] = domain->mesh->edge_start;
909	startEdgeFaces[1]= 0;
910	countEdgeFaces[0] = domain->mesh->edge_count;
911	countEdgeFaces[1]= 2;
912	startFaceConctv[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
913	startFaceConctv[1] = 0;
914	countFaceConctv[0] = domain->zoom_ni;
915	countFaceConctv[1] = domain->nvertex;
916	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
917	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
918	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
919	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
920	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
921	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
922	}
923	}// isWrittenDomain
924
925	SuperClassWriter::definition_start();
926
927	break;
928	} // ONE_FILE
929
930	case (MULTI_FILE) :
931	{
932	break;
933	}
934
935	default :
936	ERROR("CNc4DataOutput::writeDomain(domain)",
937	<< "[ type = " << SuperClass::type << "]"
938	<< " not implemented yet !");
939	} // switch
940	} // try
941
942	catch (CNetCdfException& e)
943	{
944	StdString msg("On writing the domain : ");
945	msg.append(domid); msg.append("\n");
946	msg.append("In the context : ");
947	msg.append(context->getId()); msg.append("\n");
948	msg.append(e.what());
949	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
950	}
951
952	domain->addRelFile(this->filename);
953	}
954
955	//--------------------------------------------------------------
956
957	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
958	{
959	CContext* context = CContext::getCurrent() ;
960	CContextServer* server=context->server ;
961
962	if (domain->IsWritten(this->filename)) return;
963	domain->checkAttributes();
964
965	if (domain->isEmpty())
966	if (SuperClass::type==MULTI_FILE) return ;
967
968	std::vector<StdString> dim0, dim1;
969	StdString domid = domain->getDomainOutputName();
970	if (isWrittenDomain(domid)) return ;
971	else setWrittenDomain(domid);
972
973	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
974
975	StdString lonName,latName, cellName ;
976	if (domain->lon_name.isEmpty()) lonName = "lon";
977	else lonName = domain->lon_name;
978
979	if (domain->lat_name.isEmpty()) latName = "lat";
980	else latName = domain->lat_name;
981
982	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
983	else cellName="cell";
984	StdString dimXid = cellName+appendDomid;
985	StdString dimVertId = StdString("nvertex").append(appendDomid);
986
987	string lonid,latid,bounds_lonid,bounds_latid ;
988	string areaId = "area" + appendDomid;
989
990	nc_type typePrec ;
991	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
992	else if (domain->prec==4) typePrec = NC_FLOAT ;
993	else if (domain->prec==8) typePrec = NC_DOUBLE ;
994
995	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
996
997	CArray<size_t, 1>& indexToWrite = domain->localIndexToWriteOnServer;
998	int nbWritten = indexToWrite.numElements();
999	CArray<double,1> writtenLat, writtenLon;
1000	CArray<double,2> writtenBndsLat, writtenBndsLon;
1001	CArray<double,1> writtenArea;
1002
1003	if (domain->hasLonLat)
1004	{
1005	writtenLat.resize(nbWritten);
1006	writtenLon.resize(nbWritten);
1007	for (int idx = 0; idx < nbWritten; ++idx)
1008	{
1009	if (idx < domain->latvalue.numElements())
1010	{
1011	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
1012	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
1013	}
1014	else
1015	{
1016	writtenLat(idx) = 0.;
1017	writtenLon(idx) = 0.;
1018	}
1019	}
1020	}
1021
1022	if (domain->hasBounds)
1023	{
1024	int nvertex = domain->nvertex, idx;
1025	writtenBndsLat.resize(nvertex, nbWritten);
1026	writtenBndsLon.resize(nvertex, nbWritten);
1027	CArray<double,2>& boundslat = domain->bounds_latvalue;
1028	CArray<double,2>& boundslon = domain->bounds_lonvalue;
1029	for (idx = 0; idx < nbWritten; ++idx)
1030	{
1031	for (int nv = 0; nv < nvertex; ++nv)
1032	{
1033	if (idx < boundslat.columns())
1034	{
1035	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
1036	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
1037	}
1038	else
1039	{
1040	writtenBndsLat(nv, idx) = 0.;
1041	writtenBndsLon(nv, idx) = 0.;
1042	}
1043	}
1044	}
1045	}
1046
1047	if (domain->hasArea)
1048	{
1049	writtenArea.resize(nbWritten);
1050	for (int idx = 0; idx < nbWritten; ++idx)
1051	{
1052	if (idx < domain->areavalue.numElements())
1053	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
1054	else
1055	writtenArea(idx) = 0.;
1056	}
1057	}
1058
1059	try
1060	{
1061	switch (SuperClass::type)
1062	{
1063	case (MULTI_FILE) :
1064	{
1065	dim0.push_back(dimXid);
1066	SuperClassWriter::addDimension(dimXid, domain->zoom_ni);
1067
1068	lonid = lonName+appendDomid;
1069	latid = latName+appendDomid;
1070	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1071	else bounds_lonid = "bounds_"+lonName+appendDomid;
1072	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1073	else bounds_latid = "bounds_"+latName+appendDomid;
1074
1075	if (domain->hasLonLat)
1076	{
1077	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1078	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1079	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1080	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1081	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1082	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1083	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
1084	}
1085	dim0.clear();
1086	if (domain->hasBounds)
1087	{
1088	dim0.push_back(dimXid);
1089	dim0.push_back(dimVertId);
1090	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1091	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1092	}
1093
1094	dim0.clear();
1095	dim0.push_back(dimXid);
1096	if (domain->hasArea)
1097	{
1098	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1099	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1100	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1101	}
1102
1103	SuperClassWriter::definition_end();
1104
1105	if (domain->hasLonLat)
1106	{
1107	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
1108	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
1109	if (domain->hasBounds)
1110	{
1111	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
1112	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
1113	}
1114	}
1115
1116	if (domain->hasArea)
1117	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
1118
1119	SuperClassWriter::definition_start();
1120	break ;
1121	}
1122
1123	case (ONE_FILE) :
1124	{
1125	lonid = lonName+appendDomid;
1126	latid = latName+appendDomid;
1127	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
1128	else bounds_lonid = "bounds_"+lonName+appendDomid;
1129	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
1130	else bounds_latid = "bounds_"+latName+appendDomid;
1131
1132	dim0.push_back(dimXid);
1133	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
1134	if (domain->hasLonLat)
1135	{
1136	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
1137	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
1138
1139	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1140	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1141	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1142	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1143	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
1144	}
1145	dim0.clear();
1146
1147	if (domain->hasBounds)
1148	{
1149	dim0.push_back(dimXid);
1150	dim0.push_back(dimVertId);
1151	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
1152	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
1153	}
1154
1155	if (domain->hasArea)
1156	{
1157	dim0.clear();
1158	dim0.push_back(dimXid);
1159	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
1160	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1161	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1162	}
1163
1164	SuperClassWriter::definition_end();
1165
1166	std::vector<StdSize> start(1), startBounds(2) ;
1167	std::vector<StdSize> count(1), countBounds(2) ;
1168	if (domain->isEmpty())
1169	{
1170	start[0]=0 ;
1171	count[0]=0 ;
1172	startBounds[1]=0 ;
1173	countBounds[1]=nvertex ;
1174	startBounds[0]=0 ;
1175	countBounds[0]=0 ;
1176	}
1177	else
1178	{
1179	start[0]=domain->zoom_ibegin - domain->global_zoom_ibegin;
1180	count[0]=domain->zoom_ni;
1181	startBounds[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
1182	startBounds[1]=0 ;
1183	countBounds[0]=domain->zoom_ni;
1184	countBounds[1]=nvertex ;
1185	}
1186
1187	if (domain->hasLonLat)
1188	{
1189	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
1190	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
1191	if (domain->hasBounds)
1192	{
1193	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1194	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1195	}
1196	}
1197
1198	if (domain->hasArea)
1199	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
1200
1201	SuperClassWriter::definition_start();
1202
1203	break;
1204	}
1205	default :
1206	ERROR("CNc4DataOutput::writeDomain(domain)",
1207	<< "[ type = " << SuperClass::type << "]"
1208	<< " not implemented yet !");
1209	}
1210	}
1211	catch (CNetCdfException& e)
1212	{
1213	StdString msg("On writing the domain : ");
1214	msg.append(domid); msg.append("\n");
1215	msg.append("In the context : ");
1216	msg.append(context->getId()); msg.append("\n");
1217	msg.append(e.what());
1218	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1219	}
1220	domain->addRelFile(this->filename);
1221	}
1222	//--------------------------------------------------------------
1223
1224	void CNc4DataOutput::writeAxis_(CAxis* axis)
1225	{
1226	if (axis->IsWritten(this->filename)) return;
1227	axis->checkAttributes();
1228
1229	axis->computeWrittenIndex();
1230	axis->computeWrittenCompressedIndex(comm_file);
1231
1232	int zoom_size = (MULTI_FILE == SuperClass::type) ? axis->zoom_n
1233	: axis->global_zoom_n;
1234
1235	int zoom_count = axis->zoom_n;
1236	int zoom_begin = axis->zoom_begin;
1237	// int zoom_begin = (MULTI_FILE == SuperClass::type) ? axis->global_zoom_begin
1238	// : axis->zoom_begin;
1239
1240	if ((0 == axis->zoom_n) && (MULTI_FILE == SuperClass::type)) return;
1241
1242	std::vector<StdString> dims;
1243	StdString axisid = axis->getAxisOutputName();
1244	StdString axisDim, axisBoundsId;
1245	if (isWrittenAxis(axisid)) return ;
1246	else setWrittenAxis(axisid);
1247
1248	nc_type typePrec ;
1249	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1250	else if (axis->prec==4) typePrec = NC_FLOAT ;
1251	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1252
1253	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1254	string strId="str_len" ;
1255	try
1256	{
1257	if (axis->dim_name.isEmpty()) axisDim = axisid;
1258	else axisDim=axis->dim_name.getValue();
1259	SuperClassWriter::addDimension(axisDim, zoom_size);
1260	dims.push_back(axisDim);
1261
1262	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1263
1264	if (axis->hasValue \|\| !axis->label.isEmpty())
1265	{
1266	if (!axis->label.isEmpty()) dims.push_back(strId);
1267
1268	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
1269
1270	if (!axis->name.isEmpty())
1271	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1272
1273	if (!axis->standard_name.isEmpty())
1274	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1275
1276	if (!axis->long_name.isEmpty())
1277	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1278
1279	if (!axis->unit.isEmpty())
1280	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1281
1282	if (!axis->axis_type.isEmpty())
1283	{
1284	switch(axis->axis_type)
1285	{
1286	case CAxis::axis_type_attr::X :
1287	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
1288	break;
1289	case CAxis::axis_type_attr::Y :
1290	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
1291	break;
1292	case CAxis::axis_type_attr::Z :
1293	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1294	break;
1295	case CAxis::axis_type_attr::T :
1296	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
1297	break;
1298	}
1299	}
1300
1301	if (!axis->positive.isEmpty())
1302	{
1303	SuperClassWriter::addAttribute("positive",
1304	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1305	&axisid);
1306	}
1307
1308	if (!axis->formula.isEmpty())
1309	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
1310
1311	if (!axis->formula_term.isEmpty())
1312	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
1313
1314	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
1315	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1316	{
1317	dims.push_back("axis_nbounds");
1318	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
1319	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1320
1321	if (!axis->standard_name.isEmpty())
1322	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
1323
1324	if (!axis->unit.isEmpty())
1325	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
1326
1327	if (!axis->formula_bounds.isEmpty())
1328	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
1329
1330	if (!axis->formula_term_bounds.isEmpty())
1331	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
1332	}
1333	}
1334
1335	SuperClassWriter::definition_end();
1336
1337	CArray<size_t, 1>& indexToWrite = axis->localIndexToWriteOnServer;
1338	int nbWritten = indexToWrite.numElements();
1339	CArray<double,1> axis_value(indexToWrite.numElements());
1340	if (!axis->value.isEmpty())
1341	{
1342	for (int i = 0; i < nbWritten; i++)
1343	{
1344	if (i < axis->value.numElements())
1345	axis_value(i) = axis->value(indexToWrite(i));
1346	else
1347	axis_value(i) = 0.;
1348	}
1349	}
1350	CArray<double,2> axis_bounds;
1351	CArray<string,1> axis_label;
1352	if (!axis->label.isEmpty())
1353	{
1354	axis_label.resize(indexToWrite.numElements());
1355	for (int i = 0; i < nbWritten; i++)
1356	{
1357	if (i < axis->label.numElements())
1358	axis_label(i) = axis->label(indexToWrite(i));
1359	else
1360	axis_label(i) = boost::lexical_cast<string>(0); // Write 0 as a label
1361	}
1362	}
1363
1364	switch (SuperClass::type)
1365	{
1366	case MULTI_FILE:
1367	{
1368	if (axis->label.isEmpty())
1369	{
1370	if (!axis->value.isEmpty())
1371	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1372
1373	if (!axis->bounds.isEmpty())
1374	{
1375	axis_bounds.resize(2, indexToWrite.numElements());
1376	for (int i = 0; i < nbWritten; ++i)
1377	{
1378	if (i < axis->bounds.columns())
1379	{
1380	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1381	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1382	}
1383	else
1384	{
1385	axis_bounds(0, i) = 0.;
1386	axis_bounds(1, i) = 0.;
1387
1388	}
1389	}
1390	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0);
1391	}
1392	}
1393	else
1394	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0);
1395
1396	SuperClassWriter::definition_start();
1397	break;
1398	}
1399	case ONE_FILE:
1400	{
1401	std::vector<StdSize> start(1), startBounds(2) ;
1402	std::vector<StdSize> count(1), countBounds(2) ;
1403	start[0] = startBounds[0] = zoom_begin - axis->global_zoom_begin;
1404	count[0] = countBounds[0] = zoom_count; // zoom_size
1405	startBounds[1] = 0;
1406	countBounds[1] = 2;
1407
1408	if (axis->label.isEmpty())
1409	{
1410	if (!axis->value.isEmpty())
1411	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1412
1413	if (!axis->bounds.isEmpty())
1414	{
1415	axis_bounds.resize(2, indexToWrite.numElements());
1416	for (int i = 0; i < nbWritten; ++i)
1417	{
1418	if (i < axis->bounds.columns())
1419	{
1420	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1421	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1422	}
1423	else
1424	{
1425	axis_bounds(0, i) = 0.;
1426	axis_bounds(1, i) = 0.;
1427	}
1428	}
1429	SuperClassWriter::writeData(axis_bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1430	}
1431	}
1432	else
1433	{
1434	std::vector<StdSize> startLabel(2), countLabel(2);
1435	startLabel[0] = start[0]; startLabel[1] = 0;
1436	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
1437	SuperClassWriter::writeData(axis_label, axisid, isCollective, 0, &startLabel, &countLabel);
1438	}
1439
1440	SuperClassWriter::definition_start();
1441
1442	break;
1443	}
1444	default :
1445	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1446	<< "[ type = " << SuperClass::type << "]"
1447	<< " not implemented yet !");
1448	}
1449	}
1450	catch (CNetCdfException& e)
1451	{
1452	StdString msg("On writing the axis : ");
1453	msg.append(axisid); msg.append("\n");
1454	msg.append("In the context : ");
1455	CContext* context = CContext::getCurrent() ;
1456	msg.append(context->getId()); msg.append("\n");
1457	msg.append(e.what());
1458	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1459	}
1460	axis->addRelFile(this->filename);
1461	}
1462
1463	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1464	{
1465	if (scalar->IsWritten(this->filename)) return;
1466	scalar->checkAttributes();
1467	int scalarSize = 1;
1468
1469	StdString scalaId = scalar->getScalarOutputName();
1470	StdString boundsId;
1471	if (isWrittenAxis(scalaId)) return ;
1472	else setWrittenAxis(scalaId);
1473
1474	nc_type typePrec ;
1475	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1476	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1477	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1478
1479	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
1480	string strId="str_len" ;
1481
1482	try
1483	{
1484	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
1485
1486	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
1487	{
1488	std::vector<StdString> dims;
1489	StdString scalarDim = scalaId;
1490
1491	if (!scalar->label.isEmpty()) dims.push_back(strId);
1492
1493	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1494
1495	if (!scalar->name.isEmpty())
1496	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1497
1498	if (!scalar->standard_name.isEmpty())
1499	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1500
1501	if (!scalar->long_name.isEmpty())
1502	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1503
1504	if (!scalar->unit.isEmpty())
1505	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1506
1507	if (!scalar->axis_type.isEmpty())
1508	{
1509	switch(scalar->axis_type)
1510	{
1511	case CScalar::axis_type_attr::X :
1512	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
1513	break;
1514	case CScalar::axis_type_attr::Y :
1515	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
1516	break;
1517	case CScalar::axis_type_attr::Z :
1518	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
1519	break;
1520	case CScalar::axis_type_attr::T :
1521	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
1522	break;
1523	}
1524	}
1525
1526	if (!scalar->positive.isEmpty())
1527	{
1528	SuperClassWriter::addAttribute("positive",
1529	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
1530	&scalaId);
1531	}
1532
1533	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1534	{
1535	dims.clear();
1536	dims.push_back("axis_nbounds");
1537	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
1538	SuperClassWriter::addVariable(boundsId, typePrec, dims);
1539	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
1540	}
1541
1542	SuperClassWriter::definition_end();
1543
1544	switch (SuperClass::type)
1545	{
1546	case MULTI_FILE:
1547	{
1548	CArray<double,1> scalarValue(scalarSize);
1549	CArray<string,1> scalarLabel(scalarSize);
1550	CArray<double,1> scalarBounds(scalarSize*2);
1551
1552	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1553	{
1554	scalarValue(0) = scalar->value;
1555	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1556	}
1557
1558	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1559	{
1560	scalarBounds(0) = scalar->bounds(0);
1561	scalarBounds(1) = scalar->bounds(1);
1562	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
1563	}
1564
1565	if (!scalar->label.isEmpty())
1566	{
1567	scalarLabel(0) = scalar->label;
1568	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
1569	}
1570
1571	SuperClassWriter::definition_start();
1572
1573	break;
1574	}
1575	case ONE_FILE:
1576	{
1577	CArray<double,1> scalarValue(scalarSize);
1578	CArray<string,1> scalarLabel(scalarSize);
1579	CArray<double,1> scalarBounds(scalarSize*2);
1580
1581	std::vector<StdSize> start(1);
1582	std::vector<StdSize> count(1);
1583	start[0] = 0;
1584	count[0] = 1;
1585	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
1586	{
1587	scalarValue(0) = scalar->value;
1588	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1589	}
1590	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
1591	{
1592	scalarBounds(0) = scalar->bounds(0);
1593	scalarBounds(1) = scalar->bounds(1);
1594	count[0] = 2;
1595	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
1596	}
1597	if (!scalar->label.isEmpty())
1598	{
1599	scalarLabel(0) = scalar->label;
1600	count[0] = stringArrayLen;
1601	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
1602	}
1603
1604	SuperClassWriter::definition_start();
1605
1606	break;
1607	}
1608	default :
1609	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1610	<< "[ type = " << SuperClass::type << "]"
1611	<< " not implemented yet !");
1612	}
1613	}
1614	}
1615	catch (CNetCdfException& e)
1616	{
1617	StdString msg("On writing the scalar : ");
1618	msg.append(scalaId); msg.append("\n");
1619	msg.append("In the context : ");
1620	CContext* context = CContext::getCurrent() ;
1621	msg.append(context->getId()); msg.append("\n");
1622	msg.append(e.what());
1623	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1624	}
1625	scalar->addRelFile(this->filename);
1626	}
1627
1628	//--------------------------------------------------------------
1629
1630	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1631	{
1632	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1633
1634	try
1635	{
1636	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1637	std::vector<StdString> domainList = grid->getDomainList();
1638	std::vector<StdString> axisList = grid->getAxisList();
1639	std::vector<StdString> scalarList = grid->getScalarList();
1640	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1641
1642	std::vector<StdString> dims;
1643
1644	if (grid->isCompressible())
1645	{
1646	StdString varId = grid->getId() + "_points";
1647
1648	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1649	SuperClassWriter::addDimension(varId, nbIndexes);
1650
1651	dims.push_back(varId);
1652	SuperClassWriter::addVariable(varId, NC_INT, dims);
1653
1654	StdOStringStream compress;
1655	for (int i = numElement - 1; i >= 0; --i)
1656	{
1657	if (2 == axisDomainOrder(i))
1658	{
1659	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1660	StdString domId = domain->getDomainOutputName();
1661	StdString appendDomId = singleDomain ? "" : "_" + domId;
1662
1663	switch (domain->type)
1664	{
1665	case CDomain::type_attr::curvilinear:
1666	compress << "y" << appendDomId << " x" << appendDomId;
1667	break;
1668	case CDomain::type_attr::rectilinear:
1669	compress << "lat" << appendDomId << " lon" << appendDomId;
1670	break;
1671	case CDomain::type_attr::unstructured:
1672	StdString cellName = (!domain->dim_i_name.isEmpty()) ? cellName=domain->dim_i_name : "cell";
1673	compress << cellName << appendDomId;
1674	// compress << "cell" << appendDomId;
1675	break;
1676	}
1677	++idxDomain;
1678	}
1679	else if (1 == axisDomainOrder(i))
1680	{
1681	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1682	compress << axis->getAxisOutputName();
1683	++idxAxis;
1684	}
1685	else
1686	{
1687	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1688	compress << scalar->getScalarOutputName();
1689	++idxScalar;
1690	}
1691
1692	if (i != 0) compress << ' ';
1693	}
1694	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1695
1696	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1697	indexes = grid->localIndexToWriteOnServer;
1698
1699	switch (SuperClass::type)
1700	{
1701	case (MULTI_FILE):
1702	{
1703	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1704	break;
1705	}
1706	case (ONE_FILE):
1707	{
1708	if (grid->doGridHaveDataDistributed())
1709	grid->getDistributionServer()->computeGlobalIndex(indexes);
1710
1711	std::vector<StdSize> start, count;
1712	start.push_back(grid->getOffsetWrittenIndexes());
1713	count.push_back(grid->getNumberWrittenIndexes());
1714
1715	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1716	break;
1717	}
1718	}
1719	}
1720	else
1721	{
1722	for (int i = 0; i < numElement; ++i)
1723	{
1724	StdString varId, compress;
1725	CArray<int, 1> indexes;
1726	bool isDistributed;
1727	StdSize nbIndexes, totalNbIndexes, offset;
1728	int firstGlobalIndex;
1729
1730	if (2 == axisDomainOrder(i))
1731	{
1732	CDomain* domain = CDomain::get(domainList[idxDomain]);
1733	StdString domId = domain->getDomainOutputName();
1734
1735	if (!domain->isCompressible()
1736	\|\| domain->type == CDomain::type_attr::unstructured
1737	\|\| domain->isWrittenCompressed(this->filename)
1738	\|\| isWrittenCompressedDomain(domId))
1739	continue;
1740
1741	StdString appendDomId = singleDomain ? "" : "_" + domId;
1742
1743	varId = domId + "_points";
1744	switch (domain->type)
1745	{
1746	case CDomain::type_attr::curvilinear:
1747	compress = "y" + appendDomId + " x" + appendDomId;
1748	break;
1749	case CDomain::type_attr::rectilinear:
1750	compress = "lat" + appendDomId + " lon" + appendDomId;
1751	break;
1752	}
1753
1754	// indexes.resize(domain->compressedIndexToWriteOnServer[comm_file].numElements());
1755	// indexes = domain->compressedIndexToWriteOnServer[com_file];
1756	indexes.resize(domain->getCompressedIndexToWriteOnServer(comm_file).numElements());
1757	indexes = domain->getCompressedIndexToWriteOnServer(comm_file);
1758
1759	isDistributed = domain->isDistributed();
1760	nbIndexes = domain->getNumberWrittenIndexes(comm_file);
1761	totalNbIndexes = domain->getTotalNumberWrittenIndexes(comm_file);
1762	offset = domain->getOffsetWrittenIndexes(comm_file);
1763	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1764
1765	domain->addRelFileCompressed(this->filename);
1766	setWrittenCompressedDomain(domId);
1767	++idxDomain;
1768	}
1769	else if (1 == axisDomainOrder(i))
1770	{
1771	CAxis* axis = CAxis::get(axisList[idxAxis]);
1772	StdString axisId = axis->getAxisOutputName();
1773
1774	if (!axis->isCompressible()
1775	\|\| axis->isWrittenCompressed(this->filename)
1776	\|\| isWrittenCompressedAxis(axisId))
1777	continue;
1778
1779	varId = axisId + "_points";
1780	compress = axisId;
1781
1782	// indexes.resize(axis->compressedIndexToWriteOnServer.numElements());
1783	// indexes = axis->compressedIndexToWriteOnServer;
1784
1785	indexes.resize(axis->getCompressedIndexToWriteOnServer(comm_file).numElements());
1786	indexes = axis->getCompressedIndexToWriteOnServer(comm_file);
1787
1788	isDistributed = axis->isDistributed();
1789	nbIndexes = axis->getNumberWrittenIndexes(comm_file);
1790	totalNbIndexes = axis->getTotalNumberWrittenIndexes(comm_file);
1791	offset = axis->getOffsetWrittenIndexes(comm_file);
1792	firstGlobalIndex = axis->begin;
1793
1794	axis->addRelFileCompressed(this->filename);
1795	setWrittenCompressedAxis(axisId);
1796	++idxAxis;
1797	}
1798	else
1799	{
1800	}
1801
1802	if (!varId.empty())
1803	{
1804	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1805
1806	dims.clear();
1807	dims.push_back(varId);
1808	SuperClassWriter::addVariable(varId, NC_INT, dims);
1809
1810	SuperClassWriter::addAttribute("compress", compress, &varId);
1811
1812	switch (SuperClass::type)
1813	{
1814	case (MULTI_FILE):
1815	{
1816	indexes -= firstGlobalIndex;
1817	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1818	break;
1819	}
1820	case (ONE_FILE):
1821	{
1822	std::vector<StdSize> start, count;
1823	start.push_back(offset);
1824	count.push_back(nbIndexes);
1825
1826	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1827	break;
1828	}
1829	}
1830	}
1831	}
1832	}
1833
1834	grid->addRelFileCompressed(this->filename);
1835	}
1836	catch (CNetCdfException& e)
1837	{
1838	StdString msg("On writing compressed grid : ");
1839	msg.append(grid->getId()); msg.append("\n");
1840	msg.append("In the context : ");
1841	CContext* context = CContext::getCurrent();
1842	msg.append(context->getId()); msg.append("\n");
1843	msg.append(e.what());
1844	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1845	}
1846	}
1847
1848	//--------------------------------------------------------------
1849
1850	void CNc4DataOutput::writeTimeDimension_(void)
1851	{
1852	try
1853	{
1854	SuperClassWriter::addDimension(getTimeCounterName());
1855	}
1856	catch (CNetCdfException& e)
1857	{
1858	StdString msg("On writing time dimension : time_couter\n");
1859	msg.append("In the context : ");
1860	CContext* context = CContext::getCurrent() ;
1861	msg.append(context->getId()); msg.append("\n");
1862	msg.append(e.what());
1863	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1864	}
1865	}
1866
1867	//--------------------------------------------------------------
1868
1869	void CNc4DataOutput::writeField_(CField* field)
1870	{
1871	CContext* context = CContext::getCurrent() ;
1872	CContextServer* server=context->server ;
1873
1874	std::vector<StdString> dims, coodinates;
1875	CGrid* grid = field->grid;
1876	if (!grid->doGridHaveDataToWrite())
1877	if (SuperClass::type==MULTI_FILE) return ;
1878
1879	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1880	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1881	std::vector<StdString> domainList = grid->getDomainList();
1882	std::vector<StdString> axisList = grid->getAxisList();
1883	std::vector<StdString> scalarList = grid->getScalarList();
1884
1885	StdString timeid = getTimeCounterName();
1886	StdString dimXid,dimYid;
1887	std::deque<StdString> dimIdList, dimCoordList;
1888	bool hasArea = false;
1889	StdString cellMeasures = "area:";
1890	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1891
1892	for (int i = 0; i < numElement; ++i)
1893	{
1894	if (2 == axisDomainOrder(i))
1895	{
1896	CDomain* domain = CDomain::get(domainList[idxDomain]);
1897	StdString domId = domain->getDomainOutputName();
1898	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1899	StdString lonName,latName ;
1900	StdString dimIname,dimJname ;
1901
1902	if (domain->lon_name.isEmpty())
1903	{
1904	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
1905	else lonName = "lon";
1906	}
1907	else lonName = domain->lon_name;
1908
1909	if (domain->lat_name.isEmpty())
1910	{
1911	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
1912	else latName = "lat";
1913	}
1914	else latName = domain->lat_name;
1915
1916	if (domain->dim_i_name.isEmpty())
1917	{
1918	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
1919	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
1920	else dimIname = lonName;
1921	}
1922	else dimIname = domain->dim_i_name;
1923
1924	if (domain->dim_j_name.isEmpty())
1925	{
1926	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
1927	else dimJname = latName;
1928	}
1929	else dimJname = domain->dim_j_name;
1930
1931	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1932	{
1933	dimIdList.push_back(domId + "_points");
1934	field->setUseCompressedOutput();
1935	}
1936
1937	switch (domain->type)
1938	{
1939	case CDomain::type_attr::curvilinear:
1940	if (!compressedOutput \|\| !domain->isCompressible())
1941	{
1942	dimXid=dimIname+appendDomId;
1943	dimYid=dimJname+appendDomId;
1944	dimIdList.push_back(dimXid);
1945	dimIdList.push_back(dimYid);
1946	}
1947	dimCoordList.push_back(lonName+appendDomId);
1948	dimCoordList.push_back(latName+appendDomId);
1949	break ;
1950	case CDomain::type_attr::rectilinear:
1951	if (!compressedOutput \|\| !domain->isCompressible())
1952	{
1953	dimXid = dimIname+appendDomId;
1954	dimYid = dimJname+appendDomId;
1955	dimIdList.push_back(dimXid);
1956	dimIdList.push_back(dimYid);
1957	}
1958	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
1959	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
1960
1961	break ;
1962	case CDomain::type_attr::unstructured:
1963	{
1964	if (SuperClassWriter::useCFConvention)
1965	{
1966	dimXid = dimIname + appendDomId;
1967	dimIdList.push_back(dimXid);
1968	dimCoordList.push_back(lonName+appendDomId);
1969	dimCoordList.push_back(latName+appendDomId);
1970	}
1971	else
1972	{
1973	StdString domainName = domain->name;
1974	if (domain->nvertex == 1)
1975	{
1976	dimXid = "n" + domainName + "_node";
1977	dimIdList.push_back(dimXid);
1978	dimCoordList.push_back(StdString(domainName + "_node_x"));
1979	dimCoordList.push_back(StdString(domainName + "_node_y"));
1980	}
1981	else if (domain->nvertex == 2)
1982	{
1983	dimXid = "n" + domainName + "_edge";
1984	dimIdList.push_back(dimXid);
1985	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1986	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1987	}
1988	else
1989	{
1990	dimXid = "n" + domainName + "_face";
1991	dimIdList.push_back(dimXid);
1992	dimCoordList.push_back(StdString(domainName + "_face_x"));
1993	dimCoordList.push_back(StdString(domainName + "_face_y"));
1994	}
1995	} // ugrid convention
1996	} // case unstructured domain
1997	}
1998
1999	if (domain->hasArea)
2000	{
2001	hasArea = true;
2002	cellMeasures += " area" + appendDomId;
2003	}
2004	++idxDomain;
2005	}
2006	else if (1 == axisDomainOrder(i))
2007	{
2008	CAxis* axis = CAxis::get(axisList[idxAxis]);
2009	StdString axisId = axis->getAxisOutputName();
2010	StdString axisDim;
2011
2012	if (axis->dim_name.isEmpty()) axisDim = axisId;
2013	else axisDim=axis->dim_name.getValue();
2014
2015	if (compressedOutput && axis->isCompressible())
2016	{
2017	dimIdList.push_back(axisDim + "_points");
2018	field->setUseCompressedOutput();
2019	}
2020	else
2021	dimIdList.push_back(axisDim);
2022
2023	if (axisDim != axisId) dimCoordList.push_back(axisId);
2024	++idxAxis;
2025	}
2026	else
2027	{
2028	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
2029	StdString scalarId = scalar->getScalarOutputName();
2030	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
2031	dimCoordList.push_back(scalarId);
2032	++idxScalar;
2033	}
2034	}
2035
2036	StdString fieldid = field->getFieldOutputName();
2037
2038	nc_type type ;
2039	if (field->prec.isEmpty()) type = NC_FLOAT ;
2040	else
2041	{
2042	if (field->prec==2) type = NC_SHORT ;
2043	else if (field->prec==4) type = NC_FLOAT ;
2044	else if (field->prec==8) type = NC_DOUBLE ;
2045	}
2046
2047	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
2048
2049	if (wtime)
2050	{
2051	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
2052	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
2053	dims.push_back(timeid);
2054	}
2055
2056	if (compressedOutput && grid->isCompressible())
2057	{
2058	dims.push_back(grid->getId() + "_points");
2059	field->setUseCompressedOutput();
2060	}
2061	else
2062	{
2063	while (!dimIdList.empty())
2064	{
2065	dims.push_back(dimIdList.back());
2066	dimIdList.pop_back();
2067	}
2068	}
2069
2070	while (!dimCoordList.empty())
2071	{
2072	coodinates.push_back(dimCoordList.back());
2073	dimCoordList.pop_back();
2074	}
2075
2076	try
2077	{
2078	SuperClassWriter::addVariable(fieldid, type, dims);
2079
2080	if (!field->standard_name.isEmpty())
2081	SuperClassWriter::addAttribute
2082	("standard_name", field->standard_name.getValue(), &fieldid);
2083
2084	if (!field->long_name.isEmpty())
2085	SuperClassWriter::addAttribute
2086	("long_name", field->long_name.getValue(), &fieldid);
2087
2088	if (!field->unit.isEmpty())
2089	SuperClassWriter::addAttribute
2090	("units", field->unit.getValue(), &fieldid);
2091
2092	// Ugrid field attributes "mesh" and "location"
2093	if (!SuperClassWriter::useCFConvention)
2094	{
2095	if (!domainList.empty())
2096	{
2097	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
2098	StdString mesh = domain->name;
2099	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
2100	StdString location;
2101	if (domain->nvertex == 1)
2102	location = "node";
2103	else if (domain->nvertex == 2)
2104	location = "edge";
2105	else if (domain->nvertex > 2)
2106	location = "face";
2107	SuperClassWriter::addAttribute("location", location, &fieldid);
2108	}
2109
2110	}
2111
2112	if (!field->valid_min.isEmpty())
2113	SuperClassWriter::addAttribute
2114	("valid_min", field->valid_min.getValue(), &fieldid);
2115
2116	if (!field->valid_max.isEmpty())
2117	SuperClassWriter::addAttribute
2118	("valid_max", field->valid_max.getValue(), &fieldid);
2119
2120	if (!field->scale_factor.isEmpty())
2121	SuperClassWriter::addAttribute
2122	("scale_factor", field->scale_factor.getValue(), &fieldid);
2123
2124	if (!field->add_offset.isEmpty())
2125	SuperClassWriter::addAttribute
2126	("add_offset", field->add_offset.getValue(), &fieldid);
2127
2128	SuperClassWriter::addAttribute
2129	("online_operation", field->operation.getValue(), &fieldid);
2130
2131	// write child variables as attributes
2132
2133
2134	bool alreadyAddCellMethod = false;
2135	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
2136	if (!field->cell_methods.isEmpty())
2137	{
2138	StdString cellMethodString = field->cell_methods;
2139	if (field->cell_methods_mode.isEmpty() \|\|
2140	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
2141	{
2142	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
2143	alreadyAddCellMethod = true;
2144	}
2145	else
2146	{
2147	switch (field->cell_methods_mode)
2148	{
2149	case (CField::cell_methods_mode_attr::prefix):
2150	cellMethodsPrefix = cellMethodString;
2151	cellMethodsPrefix += " ";
2152	break;
2153	case (CField::cell_methods_mode_attr::suffix):
2154	cellMethodsSuffix = " ";
2155	cellMethodsSuffix += cellMethodString;
2156	break;
2157	case (CField::cell_methods_mode_attr::none):
2158	break;
2159	default:
2160	break;
2161	}
2162	}
2163	}
2164
2165
2166	if (wtime)
2167	{
2168	CDuration freqOp = field->freq_op.getValue();
2169	freqOp.solveTimeStep(*context->calendar);
2170	StdString freqOpStr = freqOp.toStringUDUnits();
2171	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
2172
2173	CDuration freqOut = field->getRelFile()->output_freq.getValue();
2174	freqOut.solveTimeStep(*context->calendar);
2175	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
2176
2177	StdString cellMethods(cellMethodsPrefix + "time: ");
2178	if (field->operation.getValue() == "instant") cellMethods += "point";
2179	else if (field->operation.getValue() == "average") cellMethods += "mean";
2180	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
2181	else cellMethods += field->operation;
2182	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
2183	cellMethods += " (interval: " + freqOpStr + ")";
2184	cellMethods += cellMethodsSuffix;
2185	if (!alreadyAddCellMethod)
2186	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
2187	}
2188
2189	if (hasArea)
2190	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
2191
2192	if (!field->default_value.isEmpty())
2193	{
2194	double default_value = field->default_value.getValue();
2195	if (type == NC_DOUBLE)
2196	{
2197	SuperClassWriter::setDefaultValue(fieldid, &default_value);
2198	}
2199	else if (type == NC_SHORT)
2200	{
2201	short sdefault_value = (short)default_value;
2202	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
2203	}
2204	else
2205	{
2206	float fdefault_value = (float)default_value;
2207	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
2208	}
2209	}
2210	else
2211	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
2212
2213	if (field->compression_level.isEmpty())
2214	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
2215	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
2216
2217	{ // Ecriture des coordonnes
2218
2219	StdString coordstr; //boost::algorithm::join(coodinates, " ")
2220	std::vector<StdString>::iterator
2221	itc = coodinates.begin(), endc = coodinates.end();
2222
2223	for (; itc!= endc; itc++)
2224	{
2225	StdString & coord = *itc;
2226	if (itc+1 != endc)
2227	coordstr.append(coord).append(" ");
2228	else coordstr.append(coord);
2229	}
2230
2231	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
2232
2233	}
2234
2235	vector<CVariable*> listVars = field->getAllVariables() ;
2236	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
2237
2238	}
2239	catch (CNetCdfException& e)
2240	{
2241	StdString msg("On writing field : ");
2242	msg.append(fieldid); msg.append("\n");
2243	msg.append("In the context : ");
2244	msg.append(context->getId()); msg.append("\n");
2245	msg.append(e.what());
2246	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
2247	}
2248	} // writeField_()
2249
2250	//--------------------------------------------------------------
2251
2252	void CNc4DataOutput::writeFile_ (CFile* file)
2253	{
2254	StdString filename = file->getFileOutputName();
2255	StdString description = (!file->description.isEmpty())
2256	? file->description.getValue()
2257	: StdString("Created by xios");
2258
2259	singleDomain = (file->nbDomains == 1);
2260
2261	StdString conv_str ;
2262	if (file->convention_str.isEmpty())
2263	{
2264	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
2265	else conv_str="UGRID" ;
2266	}
2267	else conv_str=file->convention_str ;
2268
2269	try
2270	{
2271	if (!appendMode) this->writeFileAttributes(filename, description,
2272	conv_str,
2273	StdString("An IPSL model"),
2274	this->getTimeStamp());
2275
2276	if (!appendMode)
2277	SuperClassWriter::addDimension("axis_nbounds", 2);
2278	}
2279	catch (CNetCdfException& e)
2280	{
2281	StdString msg("On writing file : ");
2282	msg.append(filename); msg.append("\n");
2283	msg.append("In the context : ");
2284	CContext* context = CContext::getCurrent() ;
2285	msg.append(context->getId()); msg.append("\n");
2286	msg.append(e.what());
2287	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
2288	}
2289	}
2290
2291	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
2292	{
2293	StdString name = var->getVariableOutputName();
2294
2295	try
2296	{
2297	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2298	addAttribute(name, var->getData<int>(), &fieldId);
2299	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2300	addAttribute(name, var->getData<short int>(), &fieldId);
2301	else if (var->type.getValue() == CVariable::type_attr::t_float)
2302	addAttribute(name, var->getData<float>(), &fieldId);
2303	else if (var->type.getValue() == CVariable::type_attr::t_double)
2304	addAttribute(name, var->getData<double>(), &fieldId);
2305	else if (var->type.getValue() == CVariable::type_attr::t_string)
2306	addAttribute(name, var->getData<string>(), &fieldId);
2307	else
2308	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
2309	<< "Unsupported variable of type " << var->type.getStringValue());
2310	}
2311	catch (CNetCdfException& e)
2312	{
2313	StdString msg("On writing attributes of variable with name : ");
2314	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
2315	msg.append("In the context : ");
2316	CContext* context = CContext::getCurrent() ;
2317	msg.append(context->getId()); msg.append("\n");
2318	msg.append(e.what());
2319	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
2320	}
2321	}
2322
2323	void CNc4DataOutput::writeAttribute_ (CVariable* var)
2324	{
2325	StdString name = var->getVariableOutputName();
2326
2327	try
2328	{
2329	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
2330	addAttribute(name, var->getData<int>());
2331	else if (var->type.getValue() == CVariable::type_attr::t_int16)
2332	addAttribute(name, var->getData<short int>());
2333	else if (var->type.getValue() == CVariable::type_attr::t_float)
2334	addAttribute(name, var->getData<float>());
2335	else if (var->type.getValue() == CVariable::type_attr::t_double)
2336	addAttribute(name, var->getData<double>());
2337	else if (var->type.getValue() == CVariable::type_attr::t_string)
2338	addAttribute(name, var->getData<string>());
2339	else
2340	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
2341	<< "Unsupported variable of type " << var->type.getStringValue());
2342	}
2343	catch (CNetCdfException& e)
2344	{
2345	StdString msg("On writing attributes of variable with name : ");
2346	msg.append(name); msg.append("\n");
2347	msg.append("In the context : ");
2348	CContext* context = CContext::getCurrent() ;
2349	msg.append(context->getId()); msg.append("\n");
2350	msg.append(e.what());
2351	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
2352	}
2353	}
2354
2355	void CNc4DataOutput::syncFile_ (void)
2356	{
2357	try
2358	{
2359	SuperClassWriter::sync() ;
2360	}
2361	catch (CNetCdfException& e)
2362	{
2363	StdString msg("On synchronizing the write among processes");
2364	msg.append("In the context : ");
2365	CContext* context = CContext::getCurrent() ;
2366	msg.append(context->getId()); msg.append("\n");
2367	msg.append(e.what());
2368	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2369	}
2370	}
2371
2372	void CNc4DataOutput::closeFile_ (void)
2373	{
2374	try
2375	{
2376	SuperClassWriter::close() ;
2377	}
2378	catch (CNetCdfException& e)
2379	{
2380	StdString msg("On closing file");
2381	msg.append("In the context : ");
2382	CContext* context = CContext::getCurrent() ;
2383	msg.append(context->getId()); msg.append("\n");
2384	msg.append(e.what());
2385	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2386	}
2387
2388	}
2389
2390	//---------------------------------------------------------------
2391
2392	StdString CNc4DataOutput::getTimeStamp(void) const
2393	{
2394	const int buffer_size = 100;
2395	time_t rawtime;
2396	struct tm * timeinfo = NULL;
2397	char buffer [buffer_size];
2398	StdString formatStr;
2399	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
2400	else formatStr=file->time_stamp_format;
2401
2402	// time ( &rawtime );
2403	// timeinfo = localtime ( &rawtime );
2404	time ( &rawtime );
2405	timeinfo = gmtime ( &rawtime );
2406	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
2407
2408	return (StdString(buffer));
2409	}
2410
2411	//---------------------------------------------------------------
2412
2413	void CNc4DataOutput::writeFieldData_ (CField* field)
2414	{
2415	CContext* context = CContext::getCurrent();
2416	CContextServer* server = context->server;
2417	CGrid* grid = field->grid;
2418
2419	if (field->getNStep()<1)
2420	{
2421	return;
2422	}
2423
2424	if (!grid->doGridHaveDataToWrite())
2425	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
2426	{
2427	return;
2428	}
2429
2430	StdString fieldid = field->getFieldOutputName();
2431
2432	StdOStringStream oss;
2433	string timeAxisId;
2434	if (field->hasTimeInstant) timeAxisId = "time_instant";
2435	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2436
2437	StdString timeBoundId = getTimeCounterName() + "_bounds";
2438
2439	StdString timeAxisBoundId;
2440	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2441	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2442
2443	if (!field->wasWritten())
2444	{
2445	if (appendMode && field->file->record_offset.isEmpty() &&
2446	field->getOperationTimeType() != func::CFunctor::once)
2447	{
2448	double factorUnit;
2449	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2450	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2451	else factorUnit=1 ;
2452	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2453	}
2454
2455	field->setWritten();
2456	}
2457
2458
2459	CArray<double,1> time_data(1);
2460	CArray<double,1> time_data_bound(2);
2461	CArray<double,1> time_counter(1);
2462	CArray<double,1> time_counter_bound(2);
2463
2464	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2465	bool wtimeCounter =false ;
2466	bool wtimeData =false ;
2467
2468
2469	if (wtime)
2470	{
2471	Time lastWrite = field->last_Write_srv;
2472	Time lastLastWrite = field->lastlast_Write_srv;
2473
2474
2475	if (field->hasTimeInstant)
2476	{
2477	time_data(0) = time_data_bound(1) = lastWrite;
2478	time_data_bound(0) = time_data_bound(1) = lastWrite;
2479	if (timeCounterType==instant)
2480	{
2481	time_counter(0) = time_data(0);
2482	time_counter_bound(0) = time_data_bound(0);
2483	time_counter_bound(1) = time_data_bound(1);
2484	wtimeCounter=true ;
2485	}
2486	if (hasTimeInstant) wtimeData=true ;
2487	}
2488	else if (field->hasTimeCentered)
2489	{
2490	time_data(0) = (lastWrite + lastLastWrite) / 2;
2491	time_data_bound(0) = lastLastWrite;
2492	time_data_bound(1) = lastWrite;
2493	if (timeCounterType==centered)
2494	{
2495	time_counter(0) = time_data(0) ;
2496	time_counter_bound(0) = time_data_bound(0) ;
2497	time_counter_bound(1) = time_data_bound(1) ;
2498	wtimeCounter=true ;
2499	}
2500	if (hasTimeCentered) wtimeData=true ;
2501	}
2502
2503	if (timeCounterType==record)
2504	{
2505	time_counter(0) = field->getNStep() - 1;
2506	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2507	wtimeCounter=true ;
2508	}
2509
2510	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2511	{
2512	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2513	time_data/=secByDay;
2514	time_data_bound/=secByDay;
2515	time_counter/=secByDay;
2516	time_counter_bound/=secByDay;
2517	}
2518	}
2519
2520	bool isRoot = (server->intraCommRank == 0);
2521
2522	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2523	{
2524	double scaleFactor = 1.0;
2525	double addOffset = 0.0;
2526	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2527	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2528	field->scaleFactorAddOffset(scaleFactor, addOffset);
2529	}
2530
2531	try
2532	{
2533	size_t writtenSize;
2534	if (field->getUseCompressedOutput())
2535	writtenSize = grid->getNumberWrittenIndexes();
2536	else
2537	writtenSize = grid->getWrittenDataSize();
2538
2539	CArray<double,1> fieldData(writtenSize);
2540	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2541
2542	if (field->getUseCompressedOutput())
2543	field->outputCompressedField(fieldData);
2544	else
2545	field->outputField(fieldData);
2546
2547	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2548
2549	switch (SuperClass::type)
2550	{
2551	case (MULTI_FILE) :
2552	{
2553	CTimer::get("Files : writing data").resume();
2554	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2555	CTimer::get("Files : writing data").suspend();
2556	if (wtime)
2557	{
2558	CTimer::get("Files : writing time axis").resume();
2559	if ( wtimeData)
2560	{
2561	// SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2562	// SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2563	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2564	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2565	}
2566	if (wtimeCounter)
2567	{
2568	// SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2569	// if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2570	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2571	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2572	}
2573	CTimer::get("Files : writing time axis").suspend();
2574	}
2575	break;
2576	}
2577	case (ONE_FILE) :
2578	{
2579	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2580	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2581	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2582
2583	std::vector<StdSize> start, count;
2584
2585	if (field->getUseCompressedOutput())
2586	{
2587	if (grid->isCompressible())
2588	{
2589	start.push_back(grid->getOffsetWrittenIndexes());
2590	count.push_back(grid->getNumberWrittenIndexes());
2591	}
2592	else
2593	{
2594	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2595	std::vector<StdString> domainList = grid->getDomainList();
2596	std::vector<StdString> axisList = grid->getAxisList();
2597	int numElement = axisDomainOrder.numElements();
2598	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2599	int idx = nZoomBeginGlobal.size() - 1;
2600
2601	start.reserve(nZoomBeginGlobal.size());
2602	count.reserve(nZoomBeginGlobal.size());
2603
2604
2605	for (int i = numElement - 1; i >= 0; --i)
2606	{
2607	if (2 == axisDomainOrder(i))
2608	{
2609	CDomain* domain = CDomain::get(domainList[idxDomain]);
2610
2611	if (domain->isCompressible())
2612	{
2613	start.push_back(domain->getOffsetWrittenIndexes(comm_file));
2614	count.push_back(domain->getNumberWrittenIndexes(comm_file));
2615	idx -= 2;
2616	}
2617	else
2618	{
2619	if ((domain->type) != CDomain::type_attr::unstructured)
2620	{
2621	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2622	count.push_back(nZoomSizeServer[idx]);
2623	}
2624	--idx;
2625	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2626	count.push_back(nZoomSizeServer[idx]);
2627	--idx;
2628	}
2629	--idxDomain;
2630	}
2631	else if (1 == axisDomainOrder(i))
2632	{
2633	CAxis* axis = CAxis::get(axisList[idxAxis]);
2634
2635	if (axis->isCompressible())
2636	{
2637	start.push_back(axis->getOffsetWrittenIndexes(comm_file));
2638	count.push_back(axis->getNumberWrittenIndexes(comm_file));
2639	}
2640	else
2641	{
2642	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2643	count.push_back(nZoomSizeServer[idx]);
2644	}
2645
2646	--idxAxis;
2647	--idx;
2648	}
2649	}
2650	}
2651	}
2652	else
2653	{
2654	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2655	std::vector<StdString> domainList = grid->getDomainList();
2656	std::vector<StdString> axisList = grid->getAxisList();
2657	int numElement = axisDomainOrder.numElements();
2658	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2659	int idx = domainList.size() * 2 + axisList.size() - 1;// nZoomBeginGlobal.size() - 1;
2660
2661	start.reserve(nZoomBeginGlobal.size());
2662	count.reserve(nZoomBeginGlobal.size());
2663
2664	for (int i = numElement - 1; i >= 0; --i)
2665	{
2666	if (2 == axisDomainOrder(i))
2667	{
2668	CDomain* domain = CDomain::get(domainList[idxDomain]);
2669	if ((domain->type) != CDomain::type_attr::unstructured)
2670	{
2671	start.push_back(domain->zoom_jbegin - domain->global_zoom_jbegin);
2672	count.push_back(domain->zoom_nj);
2673	}
2674	--idx ;
2675
2676	start.push_back(domain->zoom_ibegin - domain->global_zoom_ibegin);
2677	count.push_back(domain->zoom_ni);
2678	--idx ;
2679	--idxDomain;
2680	}
2681	else if (1 == axisDomainOrder(i))
2682	{
2683	CAxis* axis = CAxis::get(axisList[idxAxis]);
2684	start.push_back(axis->zoom_begin - axis->global_zoom_begin);
2685	count.push_back(axis->zoom_n);
2686	--idx;
2687	--idxAxis;
2688	}
2689	else
2690	{
2691	if (1 == axisDomainOrder.numElements())
2692	{
2693	start.push_back(0);
2694	count.push_back(1);
2695	}
2696	--idx;
2697	}
2698	}
2699	}
2700
2701
2702	CTimer::get("Files : writing data").resume();
2703	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2704	CTimer::get("Files : writing data").suspend();
2705
2706	if (wtime)
2707	{
2708	CTimer::get("Files : writing time axis").resume();
2709	if ( wtimeData)
2710	{
2711	// SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2712	// SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2713	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2714	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2715	}
2716	if (wtimeCounter)
2717	{
2718	// SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2719	// if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2720	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2721	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2722
2723	}
2724	CTimer::get("Files : writing time axis").suspend();
2725	}
2726
2727	break;
2728	}
2729	}
2730	}
2731	catch (CNetCdfException& e)
2732	{
2733	StdString msg("On writing field data: ");
2734	msg.append(fieldid); msg.append("\n");
2735	msg.append("In the context : ");
2736	msg.append(context->getId()); msg.append("\n");
2737	msg.append(e.what());
2738	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2739	}
2740	}
2741
2742	//---------------------------------------------------------------
2743
2744	void CNc4DataOutput::writeTimeAxis_
2745	(CField* field,
2746	const boost::shared_ptr<CCalendar> cal)
2747	{
2748	StdOStringStream oss;
2749	bool createInstantAxis=false ;
2750	bool createCenteredAxis=false ;
2751	bool createTimeCounterAxis=false ;
2752
2753	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2754
2755
2756	StdString axisId ;
2757	StdString axisBoundId;
2758	StdString timeid(getTimeCounterName());
2759	StdString timeBoundId("axis_nbounds");
2760
2761	StdString strTimeUnits ;
2762	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2763	else strTimeUnits="seconds since " ;
2764
2765	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2766	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2767
2768
2769	if (field->file->time_counter.isEmpty())
2770	{
2771	if (timeCounterType==none) createTimeCounterAxis=true ;
2772	if (field->hasTimeCentered)
2773	{
2774	timeCounterType=centered ;
2775	if (!hasTimeCentered) createCenteredAxis=true ;
2776	}
2777	if (field->hasTimeInstant)
2778	{
2779	if (timeCounterType==none) timeCounterType=instant ;
2780	if (!hasTimeInstant) createInstantAxis=true ;
2781	}
2782	}
2783	else if (field->file->time_counter==CFile::time_counter_attr::instant)
2784	{
2785	if (field->hasTimeCentered)
2786	{
2787	if (!hasTimeCentered) createCenteredAxis=true ;
2788	}
2789	if (field->hasTimeInstant)
2790	{
2791	if (timeCounterType==none) createTimeCounterAxis=true ;
2792	timeCounterType=instant ;
2793	if (!hasTimeInstant) createInstantAxis=true ;
2794	}
2795	}
2796	else if (field->file->time_counter==CFile::time_counter_attr::centered)
2797	{
2798	if (field->hasTimeCentered)
2799	{
2800	if (timeCounterType==none) createTimeCounterAxis=true ;
2801	timeCounterType=centered ;
2802	if (!hasTimeCentered) createCenteredAxis=true ;
2803	}
2804	if (field->hasTimeInstant)
2805	{
2806	if (!hasTimeInstant) createInstantAxis=true ;
2807	}
2808	}
2809	else if (field->file->time_counter==CFile::time_counter_attr::instant_exclusive)
2810	{
2811	if (field->hasTimeCentered)
2812	{
2813	if (!hasTimeCentered) createCenteredAxis=true ;
2814	}
2815	if (field->hasTimeInstant)
2816	{
2817	if (timeCounterType==none) createTimeCounterAxis=true ;
2818	timeCounterType=instant ;
2819	}
2820	}
2821	else if (field->file->time_counter==CFile::time_counter_attr::centered_exclusive)
2822	{
2823	if (field->hasTimeCentered)
2824	{
2825	if (timeCounterType==none) createTimeCounterAxis=true ;
2826	timeCounterType=centered ;
2827	}
2828	if (field->hasTimeInstant)
2829	{
2830	if (!hasTimeInstant) createInstantAxis=true ;
2831	}
2832	}
2833	else if (field->file->time_counter==CFile::time_counter_attr::exclusive)
2834	{
2835	if (field->hasTimeCentered)
2836	{
2837	if (timeCounterType==none) createTimeCounterAxis=true ;
2838	if (timeCounterType==instant) createInstantAxis=true ;
2839	timeCounterType=centered ;
2840	}
2841	if (field->hasTimeInstant)
2842	{
2843	if (timeCounterType==none)
2844	{
2845	createTimeCounterAxis=true ;
2846	timeCounterType=instant ;
2847	}
2848	if (timeCounterType==centered)
2849	{
2850	if (!hasTimeInstant) createInstantAxis=true ;
2851	}
2852	}
2853	}
2854	else if (field->file->time_counter==CFile::time_counter_attr::none)
2855	{
2856	if (field->hasTimeCentered)
2857	{
2858	if (!hasTimeCentered) createCenteredAxis=true ;
2859	}
2860	if (field->hasTimeInstant)
2861	{
2862	if (!hasTimeInstant) createInstantAxis=true ;
2863	}
2864	}
2865	else if (field->file->time_counter==CFile::time_counter_attr::record)
2866	{
2867	if (timeCounterType==none) createTimeCounterAxis=true ;
2868	timeCounterType=record ;
2869	if (field->hasTimeCentered)
2870	{
2871	if (!hasTimeCentered) createCenteredAxis=true ;
2872	}
2873	if (field->hasTimeInstant)
2874	{
2875	if (!hasTimeInstant) createInstantAxis=true ;
2876	}
2877	}
2878
2879	if (createInstantAxis)
2880	{
2881	axisId="time_instant" ;
2882	axisBoundId="time_instant_bounds";
2883	hasTimeInstant=true ;
2884	}
2885
2886	if (createCenteredAxis)
2887	{
2888	axisId="time_centered" ;
2889	axisBoundId="time_centered_bounds";
2890	hasTimeCentered=true ;
2891	}
2892
2893
2894	try
2895	{
2896	std::vector<StdString> dims;
2897
2898	if (createInstantAxis \|\| createCenteredAxis)
2899	{
2900	// Adding time_instant or time_centered
2901	dims.push_back(timeid);
2902	if (!SuperClassWriter::varExist(axisId))
2903	{
2904	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2905
2906	CDate timeOrigin=cal->getTimeOrigin() ;
2907	StdOStringStream oss2;
2908	StdString strInitdate=oss2.str() ;
2909	StdString strTimeOrigin=timeOrigin.toString() ;
2910	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2911	strTimeOrigin, axisBoundId);
2912	}
2913
2914	// Adding time_instant_bounds or time_centered_bounds variables
2915	if (!SuperClassWriter::varExist(axisBoundId))
2916	{
2917	dims.clear() ;
2918	dims.push_back(timeid);
2919	dims.push_back(timeBoundId);
2920	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2921	}
2922	}
2923
2924	if (createTimeCounterAxis)
2925	{
2926	// Adding time_counter
2927	axisId = getTimeCounterName();
2928	axisBoundId = getTimeCounterName() + "_bounds";
2929	dims.clear();
2930	dims.push_back(timeid);
2931	if (!SuperClassWriter::varExist(axisId))
2932	{
2933	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2934	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2935
2936	if (field->file->time_counter.isEmpty() \|\|
2937	(field->file->time_counter != CFile::time_counter_attr::record))
2938	{
2939	CDate timeOrigin = cal->getTimeOrigin();
2940	StdString strTimeOrigin = timeOrigin.toString();
2941
2942	this->writeTimeAxisAttributes(axisId, cal->getType(),
2943	strTimeUnits+strTimeOrigin,
2944	strTimeOrigin, axisBoundId);
2945	}
2946	}
2947
2948	// Adding time_counter_bound dimension
2949	if (field->file->time_counter.isEmpty() \|\| (field->file->time_counter != CFile::time_counter_attr::record))
2950	{
2951	if (!SuperClassWriter::varExist(axisBoundId))
2952	{
2953	dims.clear();
2954	dims.push_back(timeid);
2955	dims.push_back(timeBoundId);
2956	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2957	}
2958	}
2959	}
2960	}
2961	catch (CNetCdfException& e)
2962	{
2963	StdString msg("On writing time axis data: ");
2964	msg.append("In the context : ");
2965	CContext* context = CContext::getCurrent() ;
2966	msg.append(context->getId()); msg.append("\n");
2967	msg.append(e.what());
2968	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2969	const boost::shared_ptr<CCalendar> cal)", << msg);
2970	}
2971	}
2972
2973	//---------------------------------------------------------------
2974
2975	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2976	const StdString & calendar,
2977	const StdString & units,
2978	const StdString & time_origin,
2979	const StdString & time_bounds,
2980	const StdString & standard_name,
2981	const StdString & long_name)
2982	{
2983	try
2984	{
2985	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2986	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2987	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2988	SuperClassWriter::addAttribute("units", units , &axis_name);
2989	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2990	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2991	}
2992	catch (CNetCdfException& e)
2993	{
2994	StdString msg("On writing time axis Attribute: ");
2995	msg.append("In the context : ");
2996	CContext* context = CContext::getCurrent() ;
2997	msg.append(context->getId()); msg.append("\n");
2998	msg.append(e.what());
2999	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
3000	const StdString & calendar,\
3001	const StdString & units, \
3002	const StdString & time_origin, \
3003	const StdString & time_bounds, \
3004	const StdString & standard_name, \
3005	const StdString & long_name)", << msg);
3006	}
3007	}
3008
3009	//---------------------------------------------------------------
3010
3011	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
3012	const StdString & axis,
3013	const StdString & standard_name,
3014	const StdString & long_name,
3015	const StdString & units,
3016	const StdString & nav_model)
3017	{
3018	try
3019	{
3020	if (!axis.empty())
3021	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
3022
3023	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
3024	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
3025	SuperClassWriter::addAttribute("units" , units , &axis_name);
3026	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
3027	}
3028	catch (CNetCdfException& e)
3029	{
3030	StdString msg("On writing Axis Attribute: ");
3031	msg.append("In the context : ");
3032	CContext* context = CContext::getCurrent() ;
3033	msg.append(context->getId()); msg.append("\n");
3034	msg.append(e.what());
3035	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
3036	const StdString & axis, \
3037	const StdString & standard_name, \
3038	const StdString & long_name, \
3039	const StdString & units, \
3040	const StdString & nav_model)", << msg);
3041	}
3042	}
3043
3044	//---------------------------------------------------------------
3045
3046	void CNc4DataOutput::writeLocalAttributes
3047	(int ibegin, int ni, int jbegin, int nj, StdString domid)
3048	{
3049	try
3050	{
3051	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
3052	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
3053	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
3054	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
3055	}
3056	catch (CNetCdfException& e)
3057	{
3058	StdString msg("On writing Local Attributes: ");
3059	msg.append("In the context : ");
3060	CContext* context = CContext::getCurrent() ;
3061	msg.append(context->getId()); msg.append("\n");
3062	msg.append(e.what());
3063	ERROR("CNc4DataOutput::writeLocalAttributes \
3064	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
3065	}
3066
3067	}
3068
3069	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
3070	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
3071	{
3072	CArray<int,1> array(2) ;
3073
3074	try
3075	{
3076	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
3077	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
3078	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
3079	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
3080	array=ni_glo,nj_glo ;
3081	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
3082	array=ni,nj ;
3083	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
3084	array=ibegin+1,jbegin+1 ;
3085	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
3086	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
3087	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
3088	array=0,0 ;
3089	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
3090	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
3091	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
3092	/*
3093	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
3094	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
3095	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
3096	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
3097	*/
3098	}
3099	catch (CNetCdfException& e)
3100	{
3101	StdString msg("On writing Local Attributes IOIPSL \n");
3102	msg.append("In the context : ");
3103	CContext* context = CContext::getCurrent() ;
3104	msg.append(context->getId()); msg.append("\n");
3105	msg.append(e.what());
3106	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
3107	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
3108	}
3109	}
3110	//---------------------------------------------------------------
3111
3112	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
3113	const StdString & description,
3114	const StdString & conventions,
3115	const StdString & production,
3116	const StdString & timeStamp)
3117	{
3118	try
3119	{
3120	SuperClassWriter::addAttribute("name" , name);
3121	SuperClassWriter::addAttribute("description", description);
3122	SuperClassWriter::addAttribute("title" , description);
3123	SuperClassWriter::addAttribute("Conventions", conventions);
3124	// SuperClassWriter::addAttribute("production" , production);
3125
3126	StdString timeStampStr ;
3127	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
3128	else timeStampStr=file->time_stamp_name ;
3129	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
3130
3131	StdString uuidName ;
3132	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
3133	else uuidName=file->uuid_name ;
3134
3135	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
3136	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
3137
3138	}
3139	catch (CNetCdfException& e)
3140	{
3141	StdString msg("On writing File Attributes \n ");
3142	msg.append("In the context : ");
3143	CContext* context = CContext::getCurrent() ;
3144	msg.append(context->getId()); msg.append("\n");
3145	msg.append(e.what());
3146	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
3147	const StdString & description, \
3148	const StdString & conventions, \
3149	const StdString & production, \
3150	const StdString & timeStamp)", << msg);
3151	}
3152	}
3153
3154	//---------------------------------------------------------------
3155
3156	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
3157	int data_dim,
3158	int data_ni,
3159	int data_nj,
3160	int data_ibegin,
3161	int data_jbegin)
3162	{
3163	try
3164	{
3165	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
3166	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
3167	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
3168	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
3169	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
3170	}
3171	catch (CNetCdfException& e)
3172	{
3173	StdString msg("On writing Mask Attributes \n ");
3174	msg.append("In the context : ");
3175	CContext* context = CContext::getCurrent() ;
3176	msg.append(context->getId()); msg.append("\n");
3177	msg.append(e.what());
3178	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
3179	int data_dim, \
3180	int data_ni, \
3181	int data_nj, \
3182	int data_ibegin, \
3183	int data_jbegin)", << msg);
3184	}
3185	}
3186
3187	///--------------------------------------------------------------
3188
3189	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
3190	{
3191	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
3192	if (it == timeToRecordCache.end())
3193	{
3194	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
3195	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
3196	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
3197
3198	CArray<double,2> timeAxisBounds;
3199	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
3200
3201	StdSize record = 0;
3202	double dtime(time);
3203	for (int n = dimSize[0] - 1; n >= 0; n--)
3204	{
3205	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
3206	timeAxisBounds*=factorUnit ;
3207	if (timeAxisBounds(1, 0) < dtime)
3208	{
3209	record = n + 1;
3210	break;
3211	}
3212	}
3213	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
3214	}
3215	return it->second;
3216	}
3217
3218	///--------------------------------------------------------------
3219
3220	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
3221	{
3222	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
3223	}
3224
3225	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
3226	{
3227	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
3228	}
3229
3230	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
3231	{
3232	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
3233	}
3234
3235	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
3236	{
3237	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
3238	}
3239
3240	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
3241	{
3242	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
3243	}
3244
3245	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
3246	{
3247	this->writtenDomains.insert(domainName);
3248	}
3249
3250	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
3251	{
3252	this->writtenCompressedDomains.insert(domainName);
3253	}
3254
3255	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
3256	{
3257	this->writtenAxis.insert(axisName);
3258	}
3259
3260	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
3261	{
3262	this->writtenCompressedAxis.insert(axisName);
3263	}
3264
3265	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
3266	{
3267	this->writtenScalar.insert(scalarName);
3268	}
3269	} // namespace xios

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