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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 1108

Last change on this file since 1108 was 1108, checked in by ymipsl, 7 years ago

Bug fix in append mode : when replay same period with only one temporal record in a file, netcdf crash due to large index dimension.

YM

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

File size: 119.6 KB

Line
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 "uuid.hpp"
14
15	namespace xios
16	{
17	/// ////////////////////// Dfinitions ////////////////////// ///
18	CNc4DataOutput::CNc4DataOutput
19	(CFile* file, const StdString & filename, bool exist)
20	: SuperClass()
21	, SuperClassWriter(filename, exist)
22	, filename(filename)
23	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
24	{
25	SuperClass::type = MULTI_FILE;
26	}
27
28	CNc4DataOutput::CNc4DataOutput
29	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
30	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
31	: SuperClass()
32	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
33	, comm_file(comm_file)
34	, filename(filename)
35	, isCollective(isCollective)
36	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
37	{
38	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
39	}
40
41	CNc4DataOutput::~CNc4DataOutput(void)
42	{ /* Ne rien faire de plus */ }
43
44	///--------------------------------------------------------------
45
46	const StdString & CNc4DataOutput::getFileName(void) const
47	{
48	return (this->filename);
49	}
50
51	//---------------------------------------------------------------
52
53	void CNc4DataOutput::writeDomain_(CDomain* domain)
54	{
55	if (domain->type == CDomain::type_attr::unstructured)
56	{
57	if (SuperClassWriter::useCFConvention)
58	writeUnstructuredDomain(domain) ;
59	else
60	writeUnstructuredDomainUgrid(domain) ;
61	return ;
62	}
63
64	CContext* context = CContext::getCurrent() ;
65	CContextServer* server=context->server ;
66
67	if (domain->IsWritten(this->filename)) return;
68	domain->checkAttributes();
69
70	if (domain->isEmpty())
71	if (SuperClass::type==MULTI_FILE) return;
72
73	std::vector<StdString> dim0, dim1;
74	StdString domid = domain->getDomainOutputName();
75	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
76	if (isWrittenDomain(domid)) return ;
77	else setWrittenDomain(domid);
78
79
80	StdString dimXid, dimYid ;
81
82	nc_type typePrec ;
83	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
84	else if (domain->prec==4) typePrec = NC_FLOAT ;
85	else if (domain->prec==8) typePrec = NC_DOUBLE ;
86
87	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
88	switch (domain->type)
89	{
90	case CDomain::type_attr::curvilinear :
91	dimXid = StdString("x").append(appendDomid);
92	dimYid = StdString("y").append(appendDomid);
93	break ;
94	case CDomain::type_attr::rectilinear :
95	dimXid = StdString("lon").append(appendDomid);
96	dimYid = StdString("lat").append(appendDomid);
97	break;
98	}
99
100	StdString dimVertId = StdString("nvertex").append(appendDomid);
101
102	string lonid,latid,bounds_lonid,bounds_latid ;
103	string areaId = "area" + appendDomid;
104	/*
105	StdString lonid_loc = (server->intraCommSize > 1)
106	? StdString("lon").append(appendDomid).append("_local")
107	: lonid;
108	StdString latid_loc = (server->intraCommSize > 1)
109	? StdString("lat").append(appendDomid).append("_local")
110	: latid;
111	*/
112
113	try
114	{
115	switch (SuperClass::type)
116	{
117	case (MULTI_FILE) :
118	{
119	// if (domain->isEmpty()) return;
120
121	if (server->intraCommSize > 1)
122	{
123	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
124	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
125	}
126
127	switch (domain->type)
128	{
129	case CDomain::type_attr::curvilinear :
130	dim0.push_back(dimYid); dim0.push_back(dimXid);
131	lonid = StdString("nav_lon").append(appendDomid);
132	latid = StdString("nav_lat").append(appendDomid);
133	break ;
134	case CDomain::type_attr::rectilinear :
135	lonid = StdString("lon").append(appendDomid);
136	latid = StdString("lat").append(appendDomid);
137	dim0.push_back(dimYid);
138	dim1.push_back(dimXid);
139	break;
140	}
141
142	bounds_lonid = StdString("bounds_lon").append(appendDomid);
143	bounds_latid = StdString("bounds_lat").append(appendDomid);
144
145	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
146	SuperClassWriter::addDimension(dimYid, domain->zoom_nj_srv);
147
148	if (domain->hasBounds)
149	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
150
151	if (server->intraCommSize > 1)
152	{
153	this->writeLocalAttributes(domain->zoom_ibegin_srv,
154	domain->zoom_ni_srv,
155	domain->zoom_jbegin_srv,
156	domain->zoom_nj_srv,
157	appendDomid);
158
159	if (singleDomain)
160	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
161	domain->zoom_ibegin_srv,
162	domain->zoom_ni_srv,
163	domain->zoom_jbegin_srv,
164	domain->zoom_nj_srv,
165	domain->ni_glo,domain->nj_glo,
166	server->intraCommRank,server->intraCommSize);
167	}
168
169	if (domain->hasLonLat)
170	{
171	switch (domain->type)
172	{
173	case CDomain::type_attr::curvilinear :
174	SuperClassWriter::addVariable(latid, typePrec, dim0);
175	SuperClassWriter::addVariable(lonid, typePrec, dim0);
176	break ;
177	case CDomain::type_attr::rectilinear :
178	SuperClassWriter::addVariable(latid, typePrec, dim0);
179	SuperClassWriter::addVariable(lonid, typePrec, dim1);
180	break ;
181	}
182
183	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
184	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
185
186	if (domain->hasBounds)
187	{
188	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
189	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
190
191	dim0.clear();
192	dim0.push_back(dimYid);
193	dim0.push_back(dimXid);
194	dim0.push_back(dimVertId);
195	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
196	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
197	}
198	}
199
200	dim0.clear();
201	dim0.push_back(dimYid);
202	dim0.push_back(dimXid);
203
204
205	// supress mask if (server->intraCommSize > 1)
206	// supress mask {
207	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
208	// supress mask
209	// supress mask this->writeMaskAttributes(maskid,
210	// supress mask domain->data_dim.getValue()/*,
211	// supress mask domain->data_ni.getValue(),
212	// supress mask domain->data_nj.getValue(),
213	// supress mask domain->data_ibegin.getValue(),
214	// supress mask domain->data_jbegin.getValue()*/);
215	// supress mask }
216
217	//SuperClassWriter::setDefaultValue(maskid, &dvm);
218
219	if (domain->hasArea)
220	{
221	SuperClassWriter::addVariable(areaId, typePrec, dim0);
222	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
223	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
224	}
225
226	SuperClassWriter::definition_end();
227
228	if (domain->hasLonLat)
229	{
230	switch (domain->type)
231	{
232	case CDomain::type_attr::curvilinear :
233	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
234	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
235	break;
236	case CDomain::type_attr::rectilinear :
237	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
238	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
239	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
240	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
241	break;
242	}
243
244	if (domain->hasBounds)
245	{
246	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
247	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
248	}
249	}
250
251	if (domain->hasArea)
252	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
253
254	SuperClassWriter::definition_start();
255
256	break;
257	}
258	case (ONE_FILE) :
259	{
260	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
261	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
262
263	if (domain->hasBounds)
264	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
265
266	if (domain->hasLonLat)
267	{
268	switch (domain->type)
269	{
270	case CDomain::type_attr::curvilinear :
271	dim0.push_back(dimYid); dim0.push_back(dimXid);
272	lonid = StdString("nav_lon").append(appendDomid);
273	latid = StdString("nav_lat").append(appendDomid);
274	SuperClassWriter::addVariable(latid, typePrec, dim0);
275	SuperClassWriter::addVariable(lonid, typePrec, dim0);
276	break;
277
278	case CDomain::type_attr::rectilinear :
279	dim0.push_back(dimYid);
280	dim1.push_back(dimXid);
281	lonid = StdString("lon").append(appendDomid);
282	latid = StdString("lat").append(appendDomid);
283	SuperClassWriter::addVariable(latid, typePrec, dim0);
284	SuperClassWriter::addVariable(lonid, typePrec, dim1);
285	break;
286	}
287
288	bounds_lonid = StdString("bounds_lon").append(appendDomid);
289	bounds_latid = StdString("bounds_lat").append(appendDomid);
290
291	this->writeAxisAttributes
292	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
293	this->writeAxisAttributes
294	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
295
296	if (domain->hasBounds)
297	{
298	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
299	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
300
301	dim0.clear();
302	dim0.push_back(dimYid);
303	dim0.push_back(dimXid);
304	dim0.push_back(dimVertId);
305	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
306	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
307	}
308	}
309
310	if (domain->hasArea)
311	{
312	dim0.clear();
313	dim0.push_back(dimYid); dim0.push_back(dimXid);
314	SuperClassWriter::addVariable(areaId, typePrec, dim0);
315	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
316	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
317	dim0.clear();
318	}
319
320	SuperClassWriter::definition_end();
321
322	switch (domain->type)
323	{
324	case CDomain::type_attr::curvilinear :
325	{
326	std::vector<StdSize> start(2) ;
327	std::vector<StdSize> count(2) ;
328	if (domain->isEmpty())
329	{
330	start[0]=0 ; start[1]=0 ;
331	count[0]=0 ; count[1]=0 ;
332	}
333	else
334	{
335	start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
336	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
337	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
338	}
339
340	if (domain->hasLonLat)
341	{
342	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
343	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
344	}
345	break;
346	}
347	case CDomain::type_attr::rectilinear :
348	{
349	if (domain->hasLonLat)
350	{
351	std::vector<StdSize> start(1) ;
352	std::vector<StdSize> count(1) ;
353	if (domain->isEmpty())
354	{
355	start[0]=0 ;
356	count[0]=0 ;
357	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
358	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
359
360	}
361	else
362	{
363	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
364	count[0]=domain->zoom_nj_srv ;
365	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
366	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
367
368	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
369	count[0]=domain->zoom_ni_srv ;
370	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
371	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
372	}
373	}
374	break;
375	}
376	}
377
378	if (domain->hasBounds)
379	{
380	std::vector<StdSize> start(3);
381	std::vector<StdSize> count(3);
382	if (domain->isEmpty())
383	{
384	start[2] = start[1] = start[0] = 0;
385	count[2] = count[1] = count[0] = 0;
386	}
387	else
388	{
389	start[2] = 0;
390	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
391	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
392	count[2] = domain->nvertex;
393	count[1] = domain->zoom_ni_srv;
394	count[0] = domain->zoom_nj_srv;
395	}
396
397	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0, &start, &count);
398	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0, &start, &count);
399	}
400
401	if (domain->hasArea)
402	{
403	std::vector<StdSize> start(2);
404	std::vector<StdSize> count(2);
405
406	if (domain->isEmpty())
407	{
408	start[0] = 0; start[1] = 0;
409	count[0] = 0; count[1] = 0;
410	}
411	else
412	{
413	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
414	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
415	count[1] = domain->zoom_ni_srv;
416	count[0] = domain->zoom_nj_srv;
417	}
418
419	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
420	}
421
422	SuperClassWriter::definition_start();
423	break;
424	}
425	default :
426	ERROR("CNc4DataOutput::writeDomain(domain)",
427	<< "[ type = " << SuperClass::type << "]"
428	<< " not implemented yet !");
429	}
430	}
431	catch (CNetCdfException& e)
432	{
433	StdString msg("On writing the domain : ");
434	msg.append(domid); msg.append("\n");
435	msg.append("In the context : ");
436	msg.append(context->getId()); msg.append("\n");
437	msg.append(e.what());
438	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
439	}
440
441	domain->addRelFile(this->filename);
442	}
443
444	//--------------------------------------------------------------
445
446	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
447	{
448	CContext* context = CContext::getCurrent() ;
449	CContextServer* server=context->server ;
450
451	if (domain->IsWritten(this->filename)) return;
452	domain->checkAttributes();
453	if (domain->isEmpty())
454	if (SuperClass::type==MULTI_FILE) return ;
455
456	nc_type typePrec ;
457	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
458	else if (domain->prec==4) typePrec = NC_FLOAT ;
459	else if (domain->prec==8) typePrec = NC_DOUBLE ;
460
461	std::vector<StdString> dim0;
462	StdString domid = domain->getDomainOutputName();
463	StdString domainName = domain->name;
464	domain->assignMesh(domainName, domain->nvertex);
465	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
466
467	StdString node_x = domainName + "_node_x";
468	StdString node_y = domainName + "_node_y";
469
470	StdString edge_x = domainName + "_edge_x";
471	StdString edge_y = domainName + "_edge_y";
472	StdString edge_nodes = domainName + "_edge_nodes";
473
474	StdString face_x = domainName + "_face_x";
475	StdString face_y = domainName + "_face_y";
476	StdString face_nodes = domainName + "_face_nodes";
477	StdString face_edges = domainName + "_face_edges";
478	StdString edge_faces = domainName + "_edge_face_links";
479	StdString face_faces = domainName + "_face_links";
480
481	StdString dimNode = "n" + domainName + "_node";
482	StdString dimEdge = "n" + domainName + "_edge";
483	StdString dimFace = "n" + domainName + "_face";
484	StdString dimVertex = "n" + domainName + "_vertex";
485	StdString dimTwo = "Two";
486
487	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
488	if (!isWrittenDomain(domid))
489	{
490	dim0.clear();
491	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
492	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
493	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
494	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
495	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
496	}
497
498	try
499	{
500	switch (SuperClass::type)
501	{
502	case (ONE_FILE) :
503	{
504	// Adding nodes
505	if (domain->nvertex == 1)
506	{
507	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
508	{
509	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
510	dim0.clear();
511	dim0.push_back(dimNode);
512	SuperClassWriter::addVariable(node_x, typePrec, dim0);
513	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
514	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
515	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
516	SuperClassWriter::addVariable(node_y, typePrec, dim0);
517	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
518	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
519	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
520	}
521	} // domain->nvertex == 1
522
523	// Adding edges and nodes, if nodes have not been defined previously
524	if (domain->nvertex == 2)
525	{
526	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
527	{
528	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
529	dim0.clear();
530	dim0.push_back(dimNode);
531	SuperClassWriter::addVariable(node_x, typePrec, dim0);
532	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
533	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
534	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
535	SuperClassWriter::addVariable(node_y, typePrec, dim0);
536	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
537	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
538	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
539	}
540	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
541	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
542	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
543	dim0.clear();
544	dim0.push_back(dimEdge);
545	SuperClassWriter::addVariable(edge_x, typePrec, dim0);
546	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
547	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
548	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
549	SuperClassWriter::addVariable(edge_y, typePrec, dim0);
550	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
551	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
552	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
553	dim0.clear();
554	dim0.push_back(dimEdge);
555	dim0.push_back(dimTwo);
556	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
557	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
558	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
559	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
560	} // domain->nvertex == 2
561
562	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
563	if (domain->nvertex > 2)
564	{
565	// Nodes
566	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
567	{
568	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
569	dim0.clear();
570	dim0.push_back(dimNode);
571	SuperClassWriter::addVariable(node_x, typePrec, dim0);
572	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
573	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
574	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
575	SuperClassWriter::addVariable(node_y, typePrec, dim0);
576	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
577	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
578	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
579	}
580	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
581	{
582	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
583	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
584	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
585	dim0.clear();
586	dim0.push_back(dimEdge);
587	SuperClassWriter::addVariable(edge_x, typePrec, dim0);
588	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
589	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
590	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
591	SuperClassWriter::addVariable(edge_y, typePrec, dim0);
592	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
593	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
594	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
595	dim0.clear();
596	dim0.push_back(dimEdge);
597	dim0.push_back(dimTwo);
598	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
599	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
600	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
601	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
602	}
603	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
604	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
605	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
606	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
607	dim0.clear();
608	dim0.push_back(dimFace);
609	SuperClassWriter::addVariable(face_x, typePrec, dim0);
610	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
611	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
612	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
613	SuperClassWriter::addVariable(face_y, typePrec, dim0);
614	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
615	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
616	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
617	dim0.clear();
618	dim0.push_back(dimFace);
619	dim0.push_back(dimVertex);
620	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
621	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
622	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
623	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
624	dim0.clear();
625	dim0.push_back(dimFace);
626	dim0.push_back(dimVertex);
627	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
628	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
629	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
630	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
631	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
632	dim0.clear();
633	dim0.push_back(dimEdge);
634	dim0.push_back(dimTwo);
635	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
636	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
637	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
638	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
639	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
640	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
641	dim0.clear();
642	dim0.push_back(dimFace);
643	dim0.push_back(dimVertex);
644	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
645	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
646	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
647	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
648	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
649	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
650	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
651	} // domain->nvertex > 2
652
653	SuperClassWriter::definition_end();
654
655	std::vector<StdSize> startEdges(1) ;
656	std::vector<StdSize> countEdges(1) ;
657	std::vector<StdSize> startNodes(1) ;
658	std::vector<StdSize> countNodes(1) ;
659	std::vector<StdSize> startFaces(1) ;
660	std::vector<StdSize> countFaces(1) ;
661	std::vector<StdSize> startEdgeNodes(2) ;
662	std::vector<StdSize> countEdgeNodes(2) ;
663	std::vector<StdSize> startEdgeFaces(2) ;
664	std::vector<StdSize> countEdgeFaces(2) ;
665	std::vector<StdSize> startFaceConctv(2) ;
666	std::vector<StdSize> countFaceConctv(2) ;
667
668	if (!isWrittenDomain(domid))
669	{
670	if (domain->nvertex == 1)
671	{
672	if (domain->isEmpty())
673	{
674	startNodes[0]=0 ;
675	countNodes[0]=0 ;
676	}
677	else
678	{
679	startNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
680	countNodes[0] = domain->zoom_ni_srv ;
681	}
682
683	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
684	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
685	}
686	else if (domain->nvertex == 2)
687	{
688	if (domain->isEmpty())
689	{
690	startEdges[0]=0 ;
691	countEdges[0]=0 ;
692	startNodes[0]=0 ;
693	countNodes[0]=0 ;
694	startEdgeNodes[0]=0;
695	startEdgeNodes[1]=0;
696	countEdgeNodes[0]=0;
697	countEdgeNodes[1]=0;
698
699	}
700	else
701	{
702	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
703	countEdges[0] = domain->zoom_ni_srv ;
704	startNodes[0] = domain->mesh->node_start;
705	countNodes[0] = domain->mesh->node_count;
706	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
707	startEdgeNodes[1] = 0;
708	countEdgeNodes[0] = domain->zoom_ni_srv;
709	countEdgeNodes[1]= 2;
710	}
711	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
712	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
713	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
714	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
715	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
716	}
717	else
718	{
719	if (domain->isEmpty())
720	{
721	startFaces[0] = 0 ;
722	countFaces[0] = 0 ;
723	startNodes[0] = 0;
724	countNodes[0] = 0;
725	startEdges[0] = 0;
726	countEdges[0] = 0;
727	startEdgeFaces[0] = 0;
728	startEdgeFaces[1] = 0;
729	countEdgeFaces[0] = 0;
730	countEdgeFaces[1] = 0;
731	startFaceConctv[0] = 0;
732	startFaceConctv[1] = 0;
733	countFaceConctv[0] = 0;
734	countFaceConctv[1] = 0;
735	}
736	else
737	{
738	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
739	countFaces[0] = domain->zoom_ni_srv ;
740	startNodes[0] = domain->mesh->node_start;
741	countNodes[0] = domain->mesh->node_count;
742	startEdges[0] = domain->mesh->edge_start;
743	countEdges[0] = domain->mesh->edge_count;
744	startEdgeNodes[0] = domain->mesh->edge_start;
745	startEdgeNodes[1] = 0;
746	countEdgeNodes[0] = domain->mesh->edge_count;
747	countEdgeNodes[1]= 2;
748	startEdgeFaces[0] = domain->mesh->edge_start;
749	startEdgeFaces[1]= 0;
750	countEdgeFaces[0] = domain->mesh->edge_count;
751	countEdgeFaces[1]= 2;
752	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
753	startFaceConctv[1] = 0;
754	countFaceConctv[0] = domain->zoom_ni_srv;
755	countFaceConctv[1] = domain->nvertex;
756	}
757	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
758	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
759	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
760	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
761	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
762	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
763	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
764	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
765	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
766	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
767	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
768	}
769	setWrittenDomain(domid);
770	} // !isWrittenDomain
771	else
772	{
773	if (domain->nvertex == 2)
774	{
775	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
776	countEdges[0] = domain->zoom_ni_srv ;
777	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
778	startEdgeNodes[1] = 0;
779	countEdgeNodes[0] = domain->zoom_ni_srv;
780	countEdgeNodes[1]= 2;
781	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
782	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
783	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
784	}
785	if (domain->nvertex > 2)
786	{
787
788	if (!domain->mesh->edgesAreWritten)
789	{
790	startEdges[0] = domain->mesh->edge_start;
791	countEdges[0] = domain->mesh->edge_count;
792	startEdgeNodes[0] = domain->mesh->edge_start;
793	startEdgeNodes[1] = 0;
794	countEdgeNodes[0] = domain->mesh->edge_count;
795	countEdgeNodes[1]= 2;
796	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
797	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
798	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
799	}
800	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
801	countFaces[0] = domain->zoom_ni_srv;
802	startEdgeFaces[0] = domain->mesh->edge_start;
803	startEdgeFaces[1]= 0;
804	countEdgeFaces[0] = domain->mesh->edge_count;
805	countEdgeFaces[1]= 2;
806	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
807	startFaceConctv[1] = 0;
808	countFaceConctv[0] = domain->zoom_ni_srv;
809	countFaceConctv[1]= domain->nvertex;
810	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
811	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
812	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
813	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
814	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
815	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
816	}
817	}// isWrittenDomain
818
819	SuperClassWriter::definition_start();
820
821	break;
822	} // ONE_FILE
823
824	case (MULTI_FILE) :
825	{
826	break;
827	}
828
829	default :
830	ERROR("CNc4DataOutput::writeDomain(domain)",
831	<< "[ type = " << SuperClass::type << "]"
832	<< " not implemented yet !");
833	} // switch
834	} // try
835
836	catch (CNetCdfException& e)
837	{
838	StdString msg("On writing the domain : ");
839	msg.append(domid); msg.append("\n");
840	msg.append("In the context : ");
841	msg.append(context->getId()); msg.append("\n");
842	msg.append(e.what());
843	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
844	}
845
846	domain->addRelFile(this->filename);
847	}
848
849	//--------------------------------------------------------------
850
851	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
852	{
853	CContext* context = CContext::getCurrent() ;
854	CContextServer* server=context->server ;
855
856	if (domain->IsWritten(this->filename)) return;
857	domain->checkAttributes();
858
859	if (domain->isEmpty())
860	if (SuperClass::type==MULTI_FILE) return ;
861
862	std::vector<StdString> dim0, dim1;
863	StdString domid = domain->getDomainOutputName();
864	if (isWrittenDomain(domid)) return ;
865	else setWrittenDomain(domid);
866
867	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
868
869	StdString dimXid = StdString("cell").append(appendDomid);
870	StdString dimVertId = StdString("nvertex").append(appendDomid);
871
872	string lonid,latid,bounds_lonid,bounds_latid ;
873	string areaId = "area" + appendDomid;
874
875	nc_type typePrec ;
876	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
877	else if (domain->prec==4) typePrec = NC_FLOAT ;
878	else if (domain->prec==8) typePrec = NC_DOUBLE ;
879
880	try
881	{
882	switch (SuperClass::type)
883	{
884	case (MULTI_FILE) :
885	{
886	dim0.push_back(dimXid);
887	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
888
889	lonid = StdString("lon").append(appendDomid);
890	latid = StdString("lat").append(appendDomid);
891	bounds_lonid = StdString("bounds_lon").append(appendDomid);
892	bounds_latid = StdString("bounds_lat").append(appendDomid);
893	if (domain->hasLonLat)
894	{
895	SuperClassWriter::addVariable(latid, typePrec, dim0);
896	SuperClassWriter::addVariable(lonid, typePrec, dim0);
897	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
898	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
899	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
900	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
901	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
902	}
903	dim0.clear();
904	if (domain->hasBounds)
905	{
906	dim0.push_back(dimXid);
907	dim0.push_back(dimVertId);
908	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
909	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
910	}
911
912	dim0.clear();
913	dim0.push_back(dimXid);
914	if (domain->hasArea)
915	{
916	SuperClassWriter::addVariable(areaId, typePrec, dim0);
917	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
918	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
919	}
920
921	SuperClassWriter::definition_end();
922
923	if (domain->hasLonLat)
924	{
925	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
926	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
927	if (domain->hasBounds)
928	{
929	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
930	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
931	}
932	}
933
934	if (domain->hasArea)
935	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
936
937	SuperClassWriter::definition_start();
938	break ;
939	}
940
941	case (ONE_FILE) :
942	{
943	lonid = StdString("lon").append(appendDomid);
944	latid = StdString("lat").append(appendDomid);
945	bounds_lonid = StdString("bounds_lon").append(appendDomid);
946	bounds_latid = StdString("bounds_lat").append(appendDomid);
947	dim0.push_back(dimXid);
948	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
949	if (domain->hasLonLat)
950	{
951	SuperClassWriter::addVariable(latid, typePrec, dim0);
952	SuperClassWriter::addVariable(lonid, typePrec, dim0);
953
954	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
955	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
956	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
957	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
958	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
959	}
960	dim0.clear();
961
962	if (domain->hasBounds)
963	{
964	dim0.push_back(dimXid);
965	dim0.push_back(dimVertId);
966	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
967	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
968	}
969
970	if (domain->hasArea)
971	{
972	dim0.clear();
973	dim0.push_back(dimXid);
974	SuperClassWriter::addVariable(areaId, typePrec, dim0);
975	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
976	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
977	}
978
979	SuperClassWriter::definition_end();
980
981	std::vector<StdSize> start(1), startBounds(2) ;
982	std::vector<StdSize> count(1), countBounds(2) ;
983	if (domain->isEmpty())
984	{
985	start[0]=0 ;
986	count[0]=0 ;
987	startBounds[1]=0 ;
988	countBounds[1]=domain->nvertex ;
989	startBounds[0]=0 ;
990	countBounds[0]=0 ;
991	}
992	else
993	{
994	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
995	count[0]=domain->zoom_ni_srv ;
996	startBounds[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
997	startBounds[1]=0 ;
998	countBounds[0]=domain->zoom_ni_srv ;
999	countBounds[1]=domain->nvertex ;
1000	}
1001
1002	if (domain->hasLonLat)
1003	{
1004	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
1005	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
1006	if (domain->hasBounds)
1007	{
1008	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1009	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1010	}
1011	}
1012
1013	if (domain->hasArea)
1014	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
1015
1016	SuperClassWriter::definition_start();
1017
1018	break;
1019	}
1020	default :
1021	ERROR("CNc4DataOutput::writeDomain(domain)",
1022	<< "[ type = " << SuperClass::type << "]"
1023	<< " not implemented yet !");
1024	}
1025	}
1026	catch (CNetCdfException& e)
1027	{
1028	StdString msg("On writing the domain : ");
1029	msg.append(domid); msg.append("\n");
1030	msg.append("In the context : ");
1031	msg.append(context->getId()); msg.append("\n");
1032	msg.append(e.what());
1033	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1034	}
1035	domain->addRelFile(this->filename);
1036	}
1037	//--------------------------------------------------------------
1038
1039	void CNc4DataOutput::writeAxis_(CAxis* axis)
1040	{
1041	if (axis->IsWritten(this->filename)) return;
1042	axis->checkAttributes();
1043	int zoom_size_srv = axis->zoom_size_srv;
1044	int zoom_begin_srv = axis->zoom_begin_srv;
1045	int zoom_size = (MULTI_FILE == SuperClass::type) ? zoom_size_srv
1046	: axis->global_zoom_n;
1047	int zoom_begin = (MULTI_FILE == SuperClass::type) ? zoom_begin_srv
1048	: axis->global_zoom_begin;
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;
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	try
1835	{
1836	if (SuperClassWriter::useCFConvention)
1837	this->writeFileAttributes(filename, description,
1838	StdString("CF-1.6"),
1839	StdString("An IPSL model"),
1840	this->getTimeStamp());
1841	else
1842	this->writeFileAttributes(filename, description,
1843	StdString("UGRID"),
1844	StdString("An IPSL model"),
1845	this->getTimeStamp());
1846
1847
1848	if (!appendMode)
1849	SuperClassWriter::addDimension("axis_nbounds", 2);
1850	}
1851	catch (CNetCdfException& e)
1852	{
1853	StdString msg("On writing file : ");
1854	msg.append(filename); msg.append("\n");
1855	msg.append("In the context : ");
1856	CContext* context = CContext::getCurrent() ;
1857	msg.append(context->getId()); msg.append("\n");
1858	msg.append(e.what());
1859	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1860	}
1861	}
1862
1863	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1864	{
1865	StdString name = var->getVariableOutputName();
1866
1867	try
1868	{
1869	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1870	addAttribute(name, var->getData<int>(), &fieldId);
1871	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1872	addAttribute(name, var->getData<short int>(), &fieldId);
1873	else if (var->type.getValue() == CVariable::type_attr::t_float)
1874	addAttribute(name, var->getData<float>(), &fieldId);
1875	else if (var->type.getValue() == CVariable::type_attr::t_double)
1876	addAttribute(name, var->getData<double>(), &fieldId);
1877	else if (var->type.getValue() == CVariable::type_attr::t_string)
1878	addAttribute(name, var->getData<string>(), &fieldId);
1879	else
1880	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1881	<< "Unsupported variable of type " << var->type.getStringValue());
1882	}
1883	catch (CNetCdfException& e)
1884	{
1885	StdString msg("On writing attributes of variable with name : ");
1886	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1887	msg.append("In the context : ");
1888	CContext* context = CContext::getCurrent() ;
1889	msg.append(context->getId()); msg.append("\n");
1890	msg.append(e.what());
1891	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1892	}
1893	}
1894
1895	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1896	{
1897	StdString name = var->getVariableOutputName();
1898
1899	try
1900	{
1901	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1902	addAttribute(name, var->getData<int>());
1903	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1904	addAttribute(name, var->getData<short int>());
1905	else if (var->type.getValue() == CVariable::type_attr::t_float)
1906	addAttribute(name, var->getData<float>());
1907	else if (var->type.getValue() == CVariable::type_attr::t_double)
1908	addAttribute(name, var->getData<double>());
1909	else if (var->type.getValue() == CVariable::type_attr::t_string)
1910	addAttribute(name, var->getData<string>());
1911	else
1912	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1913	<< "Unsupported variable of type " << var->type.getStringValue());
1914	}
1915	catch (CNetCdfException& e)
1916	{
1917	StdString msg("On writing attributes of variable with name : ");
1918	msg.append(name); msg.append("\n");
1919	msg.append("In the context : ");
1920	CContext* context = CContext::getCurrent() ;
1921	msg.append(context->getId()); msg.append("\n");
1922	msg.append(e.what());
1923	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1924	}
1925	}
1926
1927	void CNc4DataOutput::syncFile_ (void)
1928	{
1929	try
1930	{
1931	SuperClassWriter::sync() ;
1932	}
1933	catch (CNetCdfException& e)
1934	{
1935	StdString msg("On synchronizing the write among processes");
1936	msg.append("In the context : ");
1937	CContext* context = CContext::getCurrent() ;
1938	msg.append(context->getId()); msg.append("\n");
1939	msg.append(e.what());
1940	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1941	}
1942	}
1943
1944	void CNc4DataOutput::closeFile_ (void)
1945	{
1946	try
1947	{
1948	SuperClassWriter::close() ;
1949	}
1950	catch (CNetCdfException& e)
1951	{
1952	StdString msg("On closing file");
1953	msg.append("In the context : ");
1954	CContext* context = CContext::getCurrent() ;
1955	msg.append(context->getId()); msg.append("\n");
1956	msg.append(e.what());
1957	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1958	}
1959
1960	}
1961
1962	//---------------------------------------------------------------
1963
1964	StdString CNc4DataOutput::getTimeStamp(void) const
1965	{
1966	const int buffer_size = 100;
1967	time_t rawtime;
1968	struct tm * timeinfo = NULL;
1969	char buffer [buffer_size];
1970	StdString formatStr;
1971	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
1972	else formatStr=file->time_stamp_format;
1973
1974	// time ( &rawtime );
1975	// timeinfo = localtime ( &rawtime );
1976	time ( &rawtime );
1977	timeinfo = gmtime ( &rawtime );
1978	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
1979
1980	return (StdString(buffer));
1981	}
1982
1983	//---------------------------------------------------------------
1984
1985	void CNc4DataOutput::writeFieldData_ (CField* field)
1986	{
1987	CContext* context = CContext::getCurrent();
1988	CContextServer* server = context->server;
1989	CGrid* grid = field->grid;
1990
1991	if (field->getNStep()<1) return ;
1992
1993	if (!grid->doGridHaveDataToWrite())
1994	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
1995
1996	StdString fieldid = field->getFieldOutputName();
1997
1998	StdOStringStream oss;
1999	string timeAxisId;
2000	if (field->hasTimeInstant) timeAxisId = "time_instant";
2001	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2002
2003	StdString timeBoundId = getTimeCounterName() + "_bounds";
2004
2005	StdString timeAxisBoundId;
2006	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2007	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2008
2009	if (!field->wasWritten())
2010	{
2011	if (appendMode && field->file->record_offset.isEmpty() &&
2012	field->getOperationTimeType() != func::CFunctor::once)
2013	{
2014	double factorUnit;
2015	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2016	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2017	else factorUnit=1 ;
2018	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2019	}
2020
2021	field->setWritten();
2022	}
2023
2024
2025	CArray<double,1> time_data(1);
2026	CArray<double,1> time_data_bound(2);
2027	CArray<double,1> time_counter(1);
2028	CArray<double,1> time_counter_bound(2);
2029
2030	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2031	bool wtimeCounter =false ;
2032	bool wtimeData =false ;
2033
2034
2035	if (wtime)
2036	{
2037
2038	Time lastWrite = field->last_Write_srv;
2039	Time lastLastWrite = field->lastlast_Write_srv;
2040
2041
2042	if (field->hasTimeInstant)
2043	{
2044	time_data(0) = time_data_bound(1) = lastWrite;
2045	time_data_bound(0) = time_data_bound(1) = lastWrite;
2046	if (timeCounterType==instant)
2047	{
2048	time_counter(0) = time_data(0);
2049	time_counter_bound(0) = time_data_bound(0);
2050	time_counter_bound(1) = time_data_bound(1);
2051	wtimeCounter=true ;
2052	}
2053	if (hasTimeInstant) wtimeData=true ;
2054	}
2055	else if (field->hasTimeCentered)
2056	{
2057	time_data(0) = (lastWrite + lastLastWrite) / 2;
2058	time_data_bound(0) = lastLastWrite;
2059	time_data_bound(1) = lastWrite;
2060	if (timeCounterType==centered)
2061	{
2062	time_counter(0) = time_data(0) ;
2063	time_counter_bound(0) = time_data_bound(0) ;
2064	time_counter_bound(1) = time_data_bound(1) ;
2065	wtimeCounter=true ;
2066	}
2067	if (hasTimeCentered) wtimeData=true ;
2068	}
2069
2070	if (timeCounterType==record)
2071	{
2072	time_counter(0) = field->getNStep() - 1;
2073	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2074	wtimeCounter=true ;
2075	}
2076
2077	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2078	{
2079	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2080	time_data/=secByDay;
2081	time_data_bound/=secByDay;
2082	time_counter/=secByDay;
2083	time_counter_bound/=secByDay;
2084	}
2085	}
2086
2087	bool isRoot = (server->intraCommRank == 0);
2088
2089	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2090	{
2091	double scaleFactor = 1.0;
2092	double addOffset = 0.0;
2093	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2094	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2095	field->scaleFactorAddOffset(scaleFactor, addOffset);
2096	}
2097
2098	try
2099	{
2100	size_t writtenSize;
2101	if (field->getUseCompressedOutput())
2102	writtenSize = grid->getNumberWrittenIndexes();
2103	else
2104	writtenSize = grid->getWrittenDataSize();
2105
2106	CArray<double,1> fieldData(writtenSize);
2107	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2108
2109	if (field->getUseCompressedOutput())
2110	field->outputCompressedField(fieldData);
2111	else
2112	field->outputField(fieldData);
2113
2114	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2115
2116	switch (SuperClass::type)
2117	{
2118	case (MULTI_FILE) :
2119	{
2120	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2121	if (wtime)
2122	{
2123	if ( wtimeData)
2124	{
2125	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2126	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2127	}
2128	if (wtimeCounter)
2129	{
2130	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2131	if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2132	}
2133	}
2134	break;
2135	}
2136	case (ONE_FILE) :
2137	{
2138	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2139	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2140	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2141
2142	std::vector<StdSize> start, count;
2143
2144	if (field->getUseCompressedOutput())
2145	{
2146	if (grid->isCompressible())
2147	{
2148	start.push_back(grid->getOffsetWrittenIndexes());
2149	count.push_back(grid->getNumberWrittenIndexes());
2150	}
2151	else
2152	{
2153	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2154	std::vector<StdString> domainList = grid->getDomainList();
2155	std::vector<StdString> axisList = grid->getAxisList();
2156	int numElement = axisDomainOrder.numElements();
2157	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2158	int idx = nZoomBeginGlobal.size() - 1;
2159
2160	start.reserve(nZoomBeginGlobal.size());
2161	count.reserve(nZoomBeginGlobal.size());
2162
2163
2164	for (int i = numElement - 1; i >= 0; --i)
2165	{
2166	if (2 == axisDomainOrder(i))
2167	{
2168	CDomain* domain = CDomain::get(domainList[idxDomain]);
2169
2170	if (domain->isCompressible())
2171	{
2172	start.push_back(domain->getOffsetWrittenIndexes());
2173	count.push_back(domain->getNumberWrittenIndexes());
2174	idx -= 2;
2175	}
2176	else
2177	{
2178	if ((domain->type) != CDomain::type_attr::unstructured)
2179	{
2180	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2181	count.push_back(nZoomSizeServer[idx]);
2182	}
2183	--idx;
2184	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2185	count.push_back(nZoomSizeServer[idx]);
2186	--idx;
2187	}
2188	--idxDomain;
2189	}
2190	else if (1 == axisDomainOrder(i))
2191	{
2192	CAxis* axis = CAxis::get(axisList[idxAxis]);
2193
2194	if (axis->isCompressible())
2195	{
2196	start.push_back(axis->getOffsetWrittenIndexes());
2197	count.push_back(axis->getNumberWrittenIndexes());
2198	}
2199	else
2200	{
2201	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2202	count.push_back(nZoomSizeServer[idx]);
2203	}
2204
2205	--idxAxis;
2206	--idx;
2207	}
2208	}
2209	}
2210	}
2211	else
2212	{
2213
2214	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2215	std::vector<StdString> domainList = grid->getDomainList();
2216	std::vector<StdString> axisList = grid->getAxisList();
2217	int numElement = axisDomainOrder.numElements();
2218	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2219	int idx = nZoomBeginGlobal.size() - 1;
2220
2221	start.reserve(nZoomBeginGlobal.size());
2222	count.reserve(nZoomBeginGlobal.size());
2223
2224	for (int i = numElement - 1; i >= 0; --i)
2225	{
2226	if (2 == axisDomainOrder(i))
2227	{
2228	CDomain* domain = CDomain::get(domainList[idxDomain]);
2229	if ((domain->type) != CDomain::type_attr::unstructured)
2230	{
2231	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2232	count.push_back(nZoomSizeServer[idx]);
2233	}
2234	--idx ;
2235	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2236	count.push_back(nZoomSizeServer[idx]);
2237	--idx ;
2238	--idxDomain;
2239	}
2240	else if (1 == axisDomainOrder(i))
2241	{
2242	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2243	count.push_back(nZoomSizeServer[idx]);
2244	--idx;
2245	}
2246	else
2247	{
2248	if (1 == axisDomainOrder.numElements())
2249	{
2250	start.push_back(0);
2251	count.push_back(1);
2252	}
2253	--idx;
2254	}
2255	}
2256	}
2257
2258	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2259	if (wtime)
2260	{
2261	if ( wtimeData)
2262	{
2263	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2264	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2265	}
2266	if (wtimeCounter)
2267	{
2268	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2269	if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2270	}
2271	}
2272
2273	break;
2274	}
2275	}
2276	}
2277	catch (CNetCdfException& e)
2278	{
2279	StdString msg("On writing field data: ");
2280	msg.append(fieldid); msg.append("\n");
2281	msg.append("In the context : ");
2282	msg.append(context->getId()); msg.append("\n");
2283	msg.append(e.what());
2284	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2285	}
2286	}
2287
2288	//---------------------------------------------------------------
2289
2290	void CNc4DataOutput::writeTimeAxis_
2291	(CField* field,
2292	const boost::shared_ptr<CCalendar> cal)
2293	{
2294	StdOStringStream oss;
2295	bool createInstantAxis=false ;
2296	bool createCenteredAxis=false ;
2297	bool createTimeCounterAxis=false ;
2298
2299	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2300
2301
2302	StdString axisId ;
2303	StdString axisBoundId;
2304	StdString timeid(getTimeCounterName());
2305	StdString timeBoundId("axis_nbounds");
2306
2307	StdString strTimeUnits ;
2308	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2309	else strTimeUnits="seconds since " ;
2310
2311	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2312	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2313
2314
2315	if (field->file->time_counter.isEmpty())
2316	{
2317	if (timeCounterType==none) createTimeCounterAxis=true ;
2318	if (field->hasTimeCentered)
2319	{
2320	timeCounterType=centered ;
2321	if (!hasTimeCentered) createCenteredAxis=true ;
2322	}
2323	if (field->hasTimeInstant)
2324	{
2325	if (timeCounterType==none) timeCounterType=instant ;
2326	if (!hasTimeInstant) createInstantAxis=true ;
2327	}
2328	}
2329	else if (field->file->time_counter==CFile::time_counter_attr::instant)
2330	{
2331	if (field->hasTimeCentered)
2332	{
2333	if (!hasTimeCentered) createCenteredAxis=true ;
2334	}
2335	if (field->hasTimeInstant)
2336	{
2337	if (timeCounterType==none) createTimeCounterAxis=true ;
2338	timeCounterType=instant ;
2339	if (!hasTimeInstant) createInstantAxis=true ;
2340	}
2341	}
2342	else if (field->file->time_counter==CFile::time_counter_attr::centered)
2343	{
2344	if (field->hasTimeCentered)
2345	{
2346	if (timeCounterType==none) createTimeCounterAxis=true ;
2347	timeCounterType=centered ;
2348	if (!hasTimeCentered) createCenteredAxis=true ;
2349	}
2350	if (field->hasTimeInstant)
2351	{
2352	if (!hasTimeInstant) createInstantAxis=true ;
2353	}
2354	}
2355	else if (field->file->time_counter==CFile::time_counter_attr::instant_exclusive)
2356	{
2357	if (field->hasTimeCentered)
2358	{
2359	if (!hasTimeCentered) createCenteredAxis=true ;
2360	}
2361	if (field->hasTimeInstant)
2362	{
2363	if (timeCounterType==none) createTimeCounterAxis=true ;
2364	timeCounterType=instant ;
2365	}
2366	}
2367	else if (field->file->time_counter==CFile::time_counter_attr::centered_exclusive)
2368	{
2369	if (field->hasTimeCentered)
2370	{
2371	if (timeCounterType==none) createTimeCounterAxis=true ;
2372	timeCounterType=centered ;
2373	}
2374	if (field->hasTimeInstant)
2375	{
2376	if (!hasTimeInstant) createInstantAxis=true ;
2377	}
2378	}
2379	else if (field->file->time_counter==CFile::time_counter_attr::exclusive)
2380	{
2381	if (field->hasTimeCentered)
2382	{
2383	if (timeCounterType==none) createTimeCounterAxis=true ;
2384	if (timeCounterType==instant) createInstantAxis=true ;
2385	timeCounterType=centered ;
2386	}
2387	if (field->hasTimeInstant)
2388	{
2389	if (timeCounterType==none)
2390	{
2391	createTimeCounterAxis=true ;
2392	timeCounterType=instant ;
2393	}
2394	if (timeCounterType==centered)
2395	{
2396	if (!hasTimeInstant) createInstantAxis=true ;
2397	}
2398	}
2399	}
2400	else if (field->file->time_counter==CFile::time_counter_attr::none)
2401	{
2402	if (field->hasTimeCentered)
2403	{
2404	if (!hasTimeCentered) createCenteredAxis=true ;
2405	}
2406	if (field->hasTimeInstant)
2407	{
2408	if (!hasTimeInstant) createInstantAxis=true ;
2409	}
2410	}
2411	else if (field->file->time_counter==CFile::time_counter_attr::record)
2412	{
2413	if (timeCounterType==none) createTimeCounterAxis=true ;
2414	timeCounterType=record ;
2415	if (field->hasTimeCentered)
2416	{
2417	if (!hasTimeCentered) createCenteredAxis=true ;
2418	}
2419	if (field->hasTimeInstant)
2420	{
2421	if (!hasTimeInstant) createInstantAxis=true ;
2422	}
2423	}
2424
2425	if (createInstantAxis)
2426	{
2427	axisId="time_instant" ;
2428	axisBoundId="time_instant_bounds";
2429	hasTimeInstant=true ;
2430	}
2431
2432	if (createCenteredAxis)
2433	{
2434	axisId="time_centered" ;
2435	axisBoundId="time_centered_bounds";
2436	hasTimeCentered=true ;
2437	}
2438
2439
2440	try
2441	{
2442	std::vector<StdString> dims;
2443
2444	if (createInstantAxis \|\| createCenteredAxis)
2445	{
2446	// Adding time_instant or time_centered
2447	dims.push_back(timeid);
2448	if (!SuperClassWriter::varExist(axisId))
2449	{
2450	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2451
2452	CDate timeOrigin=cal->getTimeOrigin() ;
2453	StdOStringStream oss2;
2454	StdString strInitdate=oss2.str() ;
2455	StdString strTimeOrigin=timeOrigin.toString() ;
2456	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2457	strTimeOrigin, axisBoundId);
2458	}
2459
2460	// Adding time_instant_bounds or time_centered_bounds variables
2461	if (!SuperClassWriter::varExist(axisBoundId))
2462	{
2463	dims.clear() ;
2464	dims.push_back(timeid);
2465	dims.push_back(timeBoundId);
2466	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2467	}
2468	}
2469
2470	if (createTimeCounterAxis)
2471	{
2472	// Adding time_counter
2473	axisId = getTimeCounterName();
2474	axisBoundId = getTimeCounterName() + "_bounds";
2475	dims.clear();
2476	dims.push_back(timeid);
2477	if (!SuperClassWriter::varExist(axisId))
2478	{
2479	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2480	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2481
2482	if (field->file->time_counter.isEmpty() \|\|
2483	(field->file->time_counter != CFile::time_counter_attr::record))
2484	{
2485	CDate timeOrigin = cal->getTimeOrigin();
2486	StdString strTimeOrigin = timeOrigin.toString();
2487
2488	this->writeTimeAxisAttributes(axisId, cal->getType(),
2489	strTimeUnits+strTimeOrigin,
2490	strTimeOrigin, axisBoundId);
2491	}
2492	}
2493
2494	// Adding time_counter_bound dimension
2495	if (field->file->time_counter.isEmpty() \|\| (field->file->time_counter != CFile::time_counter_attr::record))
2496	{
2497	if (!SuperClassWriter::varExist(axisBoundId))
2498	{
2499	dims.clear();
2500	dims.push_back(timeid);
2501	dims.push_back(timeBoundId);
2502	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2503	}
2504	}
2505	}
2506	}
2507	catch (CNetCdfException& e)
2508	{
2509	StdString msg("On writing time axis data: ");
2510	msg.append("In the context : ");
2511	CContext* context = CContext::getCurrent() ;
2512	msg.append(context->getId()); msg.append("\n");
2513	msg.append(e.what());
2514	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2515	const boost::shared_ptr<CCalendar> cal)", << msg);
2516	}
2517	}
2518
2519	//---------------------------------------------------------------
2520
2521	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2522	const StdString & calendar,
2523	const StdString & units,
2524	const StdString & time_origin,
2525	const StdString & time_bounds,
2526	const StdString & standard_name,
2527	const StdString & long_name)
2528	{
2529	try
2530	{
2531	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2532	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2533	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2534	SuperClassWriter::addAttribute("units", units , &axis_name);
2535	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2536	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2537	}
2538	catch (CNetCdfException& e)
2539	{
2540	StdString msg("On writing time axis Attribute: ");
2541	msg.append("In the context : ");
2542	CContext* context = CContext::getCurrent() ;
2543	msg.append(context->getId()); msg.append("\n");
2544	msg.append(e.what());
2545	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2546	const StdString & calendar,\
2547	const StdString & units, \
2548	const StdString & time_origin, \
2549	const StdString & time_bounds, \
2550	const StdString & standard_name, \
2551	const StdString & long_name)", << msg);
2552	}
2553	}
2554
2555	//---------------------------------------------------------------
2556
2557	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2558	const StdString & axis,
2559	const StdString & standard_name,
2560	const StdString & long_name,
2561	const StdString & units,
2562	const StdString & nav_model)
2563	{
2564	try
2565	{
2566	if (!axis.empty())
2567	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2568
2569	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2570	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2571	SuperClassWriter::addAttribute("units" , units , &axis_name);
2572	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2573	}
2574	catch (CNetCdfException& e)
2575	{
2576	StdString msg("On writing Axis Attribute: ");
2577	msg.append("In the context : ");
2578	CContext* context = CContext::getCurrent() ;
2579	msg.append(context->getId()); msg.append("\n");
2580	msg.append(e.what());
2581	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2582	const StdString & axis, \
2583	const StdString & standard_name, \
2584	const StdString & long_name, \
2585	const StdString & units, \
2586	const StdString & nav_model)", << msg);
2587	}
2588	}
2589
2590	//---------------------------------------------------------------
2591
2592	void CNc4DataOutput::writeLocalAttributes
2593	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2594	{
2595	try
2596	{
2597	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2598	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2599	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2600	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2601	}
2602	catch (CNetCdfException& e)
2603	{
2604	StdString msg("On writing Local Attributes: ");
2605	msg.append("In the context : ");
2606	CContext* context = CContext::getCurrent() ;
2607	msg.append(context->getId()); msg.append("\n");
2608	msg.append(e.what());
2609	ERROR("CNc4DataOutput::writeLocalAttributes \
2610	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2611	}
2612
2613	}
2614
2615	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2616	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2617	{
2618	CArray<int,1> array(2) ;
2619
2620	try
2621	{
2622	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2623	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2624	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2625	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2626	array=ni_glo,nj_glo ;
2627	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2628	array=ni,nj ;
2629	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2630	array=ibegin+1,jbegin+1 ;
2631	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2632	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2633	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2634	array=0,0 ;
2635	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2636	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2637	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2638	/*
2639	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2640	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2641	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2642	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2643	*/
2644	}
2645	catch (CNetCdfException& e)
2646	{
2647	StdString msg("On writing Local Attributes IOIPSL \n");
2648	msg.append("In the context : ");
2649	CContext* context = CContext::getCurrent() ;
2650	msg.append(context->getId()); msg.append("\n");
2651	msg.append(e.what());
2652	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2653	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2654	}
2655	}
2656	//---------------------------------------------------------------
2657
2658	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2659	const StdString & description,
2660	const StdString & conventions,
2661	const StdString & production,
2662	const StdString & timeStamp)
2663	{
2664	try
2665	{
2666	SuperClassWriter::addAttribute("name" , name);
2667	SuperClassWriter::addAttribute("description", description);
2668	SuperClassWriter::addAttribute("title" , description);
2669	SuperClassWriter::addAttribute("Conventions", conventions);
2670	// SuperClassWriter::addAttribute("production" , production);
2671
2672	StdString timeStampStr ;
2673	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
2674	else timeStampStr=file->time_stamp_name ;
2675	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
2676
2677	StdString uuidName ;
2678	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
2679	else uuidName=file->uuid_name ;
2680
2681	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
2682	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
2683
2684	}
2685	catch (CNetCdfException& e)
2686	{
2687	StdString msg("On writing File Attributes \n ");
2688	msg.append("In the context : ");
2689	CContext* context = CContext::getCurrent() ;
2690	msg.append(context->getId()); msg.append("\n");
2691	msg.append(e.what());
2692	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2693	const StdString & description, \
2694	const StdString & conventions, \
2695	const StdString & production, \
2696	const StdString & timeStamp)", << msg);
2697	}
2698	}
2699
2700	//---------------------------------------------------------------
2701
2702	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2703	int data_dim,
2704	int data_ni,
2705	int data_nj,
2706	int data_ibegin,
2707	int data_jbegin)
2708	{
2709	try
2710	{
2711	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2712	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2713	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2714	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2715	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2716	}
2717	catch (CNetCdfException& e)
2718	{
2719	StdString msg("On writing Mask Attributes \n ");
2720	msg.append("In the context : ");
2721	CContext* context = CContext::getCurrent() ;
2722	msg.append(context->getId()); msg.append("\n");
2723	msg.append(e.what());
2724	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2725	int data_dim, \
2726	int data_ni, \
2727	int data_nj, \
2728	int data_ibegin, \
2729	int data_jbegin)", << msg);
2730	}
2731	}
2732
2733	///--------------------------------------------------------------
2734
2735	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
2736	{
2737	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2738	if (it == timeToRecordCache.end())
2739	{
2740	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2741	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
2742	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
2743
2744	CArray<double,2> timeAxisBounds;
2745	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
2746
2747	StdSize record = 0;
2748	double dtime(time);
2749	for (int n = dimSize[0] - 1; n >= 0; n--)
2750	{
2751	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
2752	timeAxisBounds*=factorUnit ;
2753	if (timeAxisBounds(1, 0) < dtime)
2754	{
2755	record = n + 1;
2756	break;
2757	}
2758	}
2759	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2760	}
2761	return it->second;
2762	}
2763
2764	///--------------------------------------------------------------
2765
2766	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2767	{
2768	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2769	}
2770
2771	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2772	{
2773	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2774	}
2775
2776	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2777	{
2778	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2779	}
2780
2781	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2782	{
2783	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2784	}
2785
2786	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2787	{
2788	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2789	}
2790
2791	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2792	{
2793	this->writtenDomains.insert(domainName);
2794	}
2795
2796	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2797	{
2798	this->writtenCompressedDomains.insert(domainName);
2799	}
2800
2801	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2802	{
2803	this->writtenAxis.insert(axisName);
2804	}
2805
2806	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2807	{
2808	this->writtenCompressedAxis.insert(axisName);
2809	}
2810
2811	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2812	{
2813	this->writtenScalar.insert(scalarName);
2814	}
2815	} // namespace xios

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