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source: XIOS/dev/branch_yushan_merged/src/io/nc4_data_output.cpp @ 1205

Last change on this file since 1205 was 1205, checked in by yushan, 7 years ago
branch merged with trunk @1200
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: 121.2 KB

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

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