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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 879

Last change on this file since 879 was 879, checked in by oabramkina, 8 years ago
Corrected submit for UGRID.
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: 100.1 KB

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1	#include "nc4_data_output.hpp"
2
3	#include <boost/lexical_cast.hpp>
4	#include "attribute_template.hpp"
5	#include "group_template.hpp"
6
7	#include "file.hpp"
8	#include "calendar.hpp"
9	#include "context.hpp"
10	#include "context_server.hpp"
11	#include "netCdfException.hpp"
12	#include "exception.hpp"
13
14	namespace xios
15	{
16	/// ////////////////////// Dfinitions ////////////////////// ///
17	CNc4DataOutput::CNc4DataOutput
18	(const StdString & filename, bool exist)
19	: SuperClass()
20	, SuperClassWriter(filename, exist)
21	, filename(filename)
22	{
23	SuperClass::type = MULTI_FILE;
24	}
25
26	CNc4DataOutput::CNc4DataOutput
27	(const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
28	MPI_Comm comm_file,bool multifile, bool isCollective, const StdString& timeCounterName)
29	: SuperClass()
30	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
31	, comm_file(comm_file)
32	, filename(filename)
33	, isCollective(isCollective)
34	{
35	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
36	}
37
38	CNc4DataOutput::~CNc4DataOutput(void)
39	{ /* Ne rien faire de plus */ }
40
41	///--------------------------------------------------------------
42
43	const StdString & CNc4DataOutput::getFileName(void) const
44	{
45	return (this->filename);
46	}
47
48	//---------------------------------------------------------------
49
50	void CNc4DataOutput::writeDomain_(CDomain* domain)
51	{
52	if (domain->type == CDomain::type_attr::unstructured)
53	{
54	if (SuperClassWriter::useCFConvention)
55	writeUnstructuredDomain(domain) ;
56	else
57	writeUnstructuredDomainUgrid(domain) ;
58	return ;
59	}
60
61	CContext* context = CContext::getCurrent() ;
62	CContextServer* server=context->server ;
63
64	if (domain->IsWritten(this->filename)) return;
65	domain->checkAttributes();
66
67	if (domain->isEmpty())
68	if (SuperClass::type==MULTI_FILE) return ;
69
70	std::vector<StdString> dim0, dim1;
71	StdString domid = domain->getDomainOutputName();
72	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
73	if (isWrittenDomain(domid)) return ;
74	else setWrittenDomain(domid);
75
76
77	StdString dimXid, dimYid ;
78
79	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
80	switch (domain->type)
81	{
82	case CDomain::type_attr::curvilinear :
83	dimXid = StdString("x").append(appendDomid);
84	dimYid = StdString("y").append(appendDomid);
85	break ;
86	case CDomain::type_attr::rectilinear :
87	dimXid = StdString("lon").append(appendDomid);
88	dimYid = StdString("lat").append(appendDomid);
89	break;
90	}
91
92	StdString dimVertId = StdString("nvertex").append(appendDomid);
93
94	string lonid,latid,bounds_lonid,bounds_latid ;
95	string areaId = "area" + appendDomid;
96	/*
97	StdString lonid_loc = (server->intraCommSize > 1)
98	? StdString("lon").append(appendDomid).append("_local")
99	: lonid;
100	StdString latid_loc = (server->intraCommSize > 1)
101	? StdString("lat").append(appendDomid).append("_local")
102	: latid;
103	*/
104
105	try
106	{
107	switch (SuperClass::type)
108	{
109	case (MULTI_FILE) :
110	{
111	// if (domain->isEmpty()) return;
112
113	if (server->intraCommSize > 1)
114	{
115	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
116	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
117	}
118
119	switch (domain->type)
120	{
121	case CDomain::type_attr::curvilinear :
122	dim0.push_back(dimYid); dim0.push_back(dimXid);
123	lonid = StdString("nav_lon").append(appendDomid);
124	latid = StdString("nav_lat").append(appendDomid);
125	break ;
126	case CDomain::type_attr::rectilinear :
127	lonid = StdString("lon").append(appendDomid);
128	latid = StdString("lat").append(appendDomid);
129	dim0.push_back(dimYid);
130	dim1.push_back(dimXid);
131	break;
132	}
133
134	bounds_lonid = StdString("bounds_lon").append(appendDomid);
135	bounds_latid = StdString("bounds_lat").append(appendDomid);
136
137	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
138	SuperClassWriter::addDimension(dimYid, domain->zoom_nj_srv);
139
140	if (domain->hasBounds)
141	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
142
143	if (server->intraCommSize > 1)
144	{
145	this->writeLocalAttributes(domain->zoom_ibegin_srv,
146	domain->zoom_ni_srv,
147	domain->zoom_jbegin_srv,
148	domain->zoom_nj_srv,
149	appendDomid);
150
151	if (singleDomain)
152	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
153	domain->zoom_ibegin_srv,
154	domain->zoom_ni_srv,
155	domain->zoom_jbegin_srv,
156	domain->zoom_nj_srv,
157	domain->ni_glo,domain->nj_glo,
158	server->intraCommRank,server->intraCommSize);
159	}
160
161	if (domain->hasLonLat)
162	{
163	switch (domain->type)
164	{
165	case CDomain::type_attr::curvilinear :
166	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
167	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
168	break ;
169	case CDomain::type_attr::rectilinear :
170	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
171	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
172	break ;
173	}
174
175	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
176	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
177
178	if (domain->hasBounds)
179	{
180	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
181	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
182
183	dim0.clear();
184	dim0.push_back(dimYid);
185	dim0.push_back(dimXid);
186	dim0.push_back(dimVertId);
187	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
188	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
189	}
190	}
191
192	dim0.clear();
193	dim0.push_back(dimYid);
194	dim0.push_back(dimXid);
195
196
197	// supress mask if (server->intraCommSize > 1)
198	// supress mask {
199	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
200	// supress mask
201	// supress mask this->writeMaskAttributes(maskid,
202	// supress mask domain->data_dim.getValue()/*,
203	// supress mask domain->data_ni.getValue(),
204	// supress mask domain->data_nj.getValue(),
205	// supress mask domain->data_ibegin.getValue(),
206	// supress mask domain->data_jbegin.getValue()*/);
207	// supress mask }
208
209	//SuperClassWriter::setDefaultValue(maskid, &dvm);
210
211	if (domain->hasArea)
212	{
213	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
214	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
215	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
216	}
217
218	SuperClassWriter::definition_end();
219
220	if (domain->hasLonLat)
221	{
222	switch (domain->type)
223	{
224	case CDomain::type_attr::curvilinear :
225	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
226	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
227	break;
228	case CDomain::type_attr::rectilinear :
229	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
230	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
231	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
232	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
233	break;
234	}
235
236	if (domain->hasBounds)
237	{
238	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
239	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
240	}
241	}
242
243	if (domain->hasArea)
244	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
245
246	SuperClassWriter::definition_start();
247
248	break;
249	}
250	case (ONE_FILE) :
251	{
252	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
253	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
254
255	if (domain->hasBounds)
256	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
257
258	if (domain->hasLonLat)
259	{
260	switch (domain->type)
261	{
262	case CDomain::type_attr::curvilinear :
263	dim0.push_back(dimYid); dim0.push_back(dimXid);
264	lonid = StdString("nav_lon").append(appendDomid);
265	latid = StdString("nav_lat").append(appendDomid);
266	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
267	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
268	break;
269
270	case CDomain::type_attr::rectilinear :
271	dim0.push_back(dimYid);
272	dim1.push_back(dimXid);
273	lonid = StdString("lon").append(appendDomid);
274	latid = StdString("lat").append(appendDomid);
275	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
276	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
277	break;
278	}
279
280	bounds_lonid = StdString("bounds_lon").append(appendDomid);
281	bounds_latid = StdString("bounds_lat").append(appendDomid);
282
283	this->writeAxisAttributes
284	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
285	this->writeAxisAttributes
286	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
287
288	if (domain->hasBounds)
289	{
290	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
291	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
292
293	dim0.clear();
294	dim0.push_back(dimYid);
295	dim0.push_back(dimXid);
296	dim0.push_back(dimVertId);
297	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
298	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
299	}
300	}
301
302	if (domain->hasArea)
303	{
304	dim0.clear();
305	dim0.push_back(dimYid); dim0.push_back(dimXid);
306	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
307	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
308	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
309	dim0.clear();
310	}
311
312	SuperClassWriter::definition_end();
313
314	switch (domain->type)
315	{
316	case CDomain::type_attr::curvilinear :
317	{
318	std::vector<StdSize> start(2) ;
319	std::vector<StdSize> count(2) ;
320	if (domain->isEmpty())
321	{
322	start[0]=0 ; start[1]=0 ;
323	count[0]=0 ; count[1]=0 ;
324	}
325	else
326	{
327	start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
328	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
329	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
330	}
331
332	if (domain->hasLonLat)
333	{
334	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
335	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
336	}
337	break;
338	}
339	case CDomain::type_attr::rectilinear :
340	{
341	if (domain->hasLonLat)
342	{
343	std::vector<StdSize> start(1) ;
344	std::vector<StdSize> count(1) ;
345	if (domain->isEmpty())
346	{
347	start[0]=0 ;
348	count[0]=0 ;
349	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
350	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
351
352	}
353	else
354	{
355	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
356	count[0]=domain->zoom_nj_srv ;
357	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
358	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
359
360	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
361	count[0]=domain->zoom_ni_srv ;
362	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
363	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
364	}
365	}
366	break;
367	}
368	}
369
370	if (domain->hasBounds)
371	{
372	std::vector<StdSize> start(3);
373	std::vector<StdSize> count(3);
374	if (domain->isEmpty())
375	{
376	start[2] = start[1] = start[0] = 0;
377	count[2] = count[1] = count[0] = 0;
378	}
379	else
380	{
381	start[2] = 0;
382	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
383	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
384	count[2] = domain->nvertex;
385	count[1] = domain->zoom_ni_srv;
386	count[0] = domain->zoom_nj_srv;
387	}
388
389	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0, &start, &count);
390	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0, &start, &count);
391	}
392
393	if (domain->hasArea)
394	{
395	std::vector<StdSize> start(2);
396	std::vector<StdSize> count(2);
397
398	if (domain->isEmpty())
399	{
400	start[0] = 0; start[1] = 0;
401	count[0] = 0; count[1] = 0;
402	}
403	else
404	{
405	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
406	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
407	count[1] = domain->zoom_ni_srv;
408	count[0] = domain->zoom_nj_srv;
409	}
410
411	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
412	}
413
414	SuperClassWriter::definition_start();
415	break;
416	}
417	default :
418	ERROR("CNc4DataOutput::writeDomain(domain)",
419	<< "[ type = " << SuperClass::type << "]"
420	<< " not implemented yet !");
421	}
422	}
423	catch (CNetCdfException& e)
424	{
425	StdString msg("On writing the domain : ");
426	msg.append(domid); msg.append("\n");
427	msg.append("In the context : ");
428	msg.append(context->getId()); msg.append("\n");
429	msg.append(e.what());
430	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
431	}
432
433	domain->addRelFile(this->filename);
434	}
435
436	//--------------------------------------------------------------
437
438	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
439	{
440	CContext* context = CContext::getCurrent() ;
441	CContextServer* server=context->server ;
442
443	if (domain->IsWritten(this->filename)) return;
444	domain->checkAttributes();
445	if (domain->isEmpty())
446	if (SuperClass::type==MULTI_FILE) return ;
447
448	std::vector<StdString> dim0;
449	StdString domid = domain->getDomainOutputName();
450	StdString domainName = domain->name;
451
452	if (domain->mesh->isWritten(domainName)) domain->mesh = CMesh::getMesh;
453
454	//domain->mesh->createMesh(domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
455	domain->mesh->createMeshEpsilon(domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
456
457	StdString node_x = domainName + "_node_x";
458	StdString node_y = domainName + "_node_y";
459
460	StdString edge_x = domainName + "_edge_x";
461	StdString edge_y = domainName + "_edge_y";
462	StdString edge_nodes = domainName + "_edge_nodes";
463
464	StdString face_x = domainName + "_face_x";
465	StdString face_y = domainName + "_face_y";
466	StdString face_nodes = domainName + "_face_nodes";
467
468	StdString dimNode = "n" + domainName + "_node";
469	StdString dimEdge = "n" + domainName + "_edge";
470	StdString dimFace = "n" + domainName + "_face";
471	StdString dimVertex = "n" + domainName + "_vertex";
472	StdString dimTwo = "Two";
473
474	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
475	if (!isWrittenDomain(domid))
476	{
477	dim0.clear();
478	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
479	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
480	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
481	}
482
483	try
484	{
485	switch (SuperClass::type)
486	{
487	case (ONE_FILE) :
488	{
489	// Adding nodes
490	if (domain->nvertex == 1)
491	{
492	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
493	{
494	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodes);
495	dim0.clear();
496	dim0.push_back(dimNode);
497	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
498	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
499	SuperClassWriter::addAttribute("longname_name", StdString("Longitude of mesh nodes."), &node_x);
500	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
501	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
502	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
503	SuperClassWriter::addAttribute("longname_name", StdString("Latitude of mesh nodes."), &node_y);
504	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
505	}
506	} // domain->nvertex == 1
507
508	// Adding edges and nodes, if nodes have not been defined previously
509	if (domain->nvertex == 2)
510	{
511	// Nodes
512	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
513	{
514	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodes);
515	dim0.clear();
516	dim0.push_back(dimNode);
517	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
518	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
519	SuperClassWriter::addAttribute("longname_name", StdString("Longitude of mesh nodes."), &node_x);
520	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
521	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
522	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
523	SuperClassWriter::addAttribute("longname_name", StdString("Latitude of mesh nodes."), &node_y);
524	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
525	}
526	// Edges
527	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
528	{
529	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
530	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
531	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdges);
532	dim0.clear();
533	dim0.push_back(dimEdge);
534	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
535	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
536	SuperClassWriter::addAttribute("longname_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
537	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
538	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
539	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
540	SuperClassWriter::addAttribute("longname_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
541	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
542	dim0.clear();
543	dim0.push_back(dimEdge);
544	dim0.push_back(dimTwo);
545	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
546	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
547	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
548	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
549	}
550	} // domain->nvertex == 2
551
552	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
553	if (domain->nvertex > 2)
554	{
555	// Nodes
556	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
557	{
558	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodes);
559	dim0.clear();
560	dim0.push_back(dimNode);
561	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
562	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
563	SuperClassWriter::addAttribute("longname_name", StdString("Longitude of mesh nodes."), &node_x);
564	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
565	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
566	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
567	SuperClassWriter::addAttribute("longname_name", StdString("Latitude of mesh nodes."), &node_y);
568	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
569	}
570	// Edges
571	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
572	{
573	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
574	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
575	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdges);
576	dim0.clear();
577	dim0.push_back(dimEdge);
578	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
579	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
580	SuperClassWriter::addAttribute("longname_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
581	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
582	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
583	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
584	SuperClassWriter::addAttribute("longname_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
585	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
586	dim0.clear();
587	dim0.push_back(dimEdge);
588	dim0.push_back(dimTwo);
589	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
590	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
591	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
592	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
593	}
594	// Faces
595	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
596	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
597	SuperClassWriter::addDimension(dimFace, domain->mesh->nbFaces);
598	SuperClassWriter::addDimension(dimVertex, domain->mesh->nvertex);
599	dim0.clear();
600	dim0.push_back(dimFace);
601	SuperClassWriter::addVariable(face_x, NC_FLOAT, dim0);
602	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
603	SuperClassWriter::addAttribute("longname_name", StdString("Characteristic longitude of mesh faces."), &face_x);
604	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
605	SuperClassWriter::addVariable(face_y, NC_FLOAT, dim0);
606	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
607	SuperClassWriter::addAttribute("longname_name", StdString("Characteristic latitude of mesh faces."), &face_y);
608	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
609	dim0.clear();
610	dim0.push_back(dimFace);
611	dim0.push_back(dimVertex);
612	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
613	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
614	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
615	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
616	} // domain->nvertex > 2
617
618	SuperClassWriter::definition_end();
619
620	if (!isWrittenDomain(domid))
621	{
622	if (domain->nvertex == 1)
623	{
624	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0);
625	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0);
626	}
627	else if (domain->nvertex == 2)
628	{
629	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0);
630	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0);
631	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0);
632	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0);
633	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes);
634	}
635	else
636	{
637	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0);
638	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0);
639	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0);
640	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0);
641	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes);
642	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0);
643	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0);
644	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes);
645	}
646	setWrittenDomain(domid);
647	} // !isWrittenDomain
648	else
649	{
650	if (domain->nvertex == 1)
651	{
652	if ( (!domain->mesh->edgesAreWritten) && (!domain->mesh->facesAreWritten) )
653	{
654	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0);
655	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0);
656	}
657	}
658	if (domain->nvertex == 2)
659	{
660	if (!domain->mesh->facesAreWritten)
661	{
662	if (!domain->mesh->nodesAreWritten)
663	{
664	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0);
665	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0);
666	}
667	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0);
668	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0);
669	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes);
670	}
671	}
672	if (domain->nvertex > 2)
673	{
674	if (!domain->mesh->edgesAreWritten)
675	{
676	if (!domain->mesh->nodesAreWritten)
677	{
678	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0);
679	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0);
680	}
681	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0);
682	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0);
683	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes);
684	}
685	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0);
686	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0);
687	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes);
688	}
689	}// isWrittenDomain
690
691	SuperClassWriter::definition_start();
692
693	break;
694	} // ONE_FILE
695
696	case (MULTI_FILE) :
697	{
698	break;
699	}
700
701	default :
702	ERROR("CNc4DataOutput::writeDomain(domain)",
703	<< "[ type = " << SuperClass::type << "]"
704	<< " not implemented yet !");
705	} // switch
706	} // try
707
708	catch (CNetCdfException& e)
709	{
710	StdString msg("On writing the domain : ");
711	msg.append(domid); msg.append("\n");
712	msg.append("In the context : ");
713	msg.append(context->getId()); msg.append("\n");
714	msg.append(e.what());
715	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
716	}
717
718	domain->addRelFile(this->filename);
719	}
720
721	//--------------------------------------------------------------
722
723	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
724	{
725	CContext* context = CContext::getCurrent() ;
726	CContextServer* server=context->server ;
727
728	if (domain->IsWritten(this->filename)) return;
729	domain->checkAttributes();
730
731	if (domain->isEmpty())
732	if (SuperClass::type==MULTI_FILE) return ;
733
734	std::vector<StdString> dim0, dim1;
735	StdString domid = domain->getDomainOutputName();
736	if (isWrittenDomain(domid)) return ;
737	else setWrittenDomain(domid);
738
739	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
740
741
742	StdString dimXid = StdString("cell").append(appendDomid);
743	StdString dimVertId = StdString("nvertex").append(appendDomid);
744
745	string lonid,latid,bounds_lonid,bounds_latid ;
746	string areaId = "area" + appendDomid;
747
748	try
749	{
750	switch (SuperClass::type)
751	{
752	case (MULTI_FILE) :
753	{
754	dim0.push_back(dimXid);
755	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
756
757	lonid = StdString("lon").append(appendDomid);
758	latid = StdString("lat").append(appendDomid);
759	bounds_lonid = StdString("bounds_lon").append(appendDomid);
760	bounds_latid = StdString("bounds_lat").append(appendDomid);
761	if (domain->hasLonLat)
762	{
763	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
764	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
765	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
766	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
767	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
768	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
769	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
770	}
771	dim0.clear();
772	if (domain->hasBounds)
773	{
774	dim0.push_back(dimXid);
775	dim0.push_back(dimVertId);
776	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
777	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
778	}
779
780	dim0.clear();
781	dim0.push_back(dimXid);
782	if (domain->hasArea)
783	{
784	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
785	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
786	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
787	}
788
789	SuperClassWriter::definition_end();
790
791	if (domain->hasLonLat)
792	{
793	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
794	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
795	if (domain->hasBounds)
796	{
797	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
798	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
799	}
800	}
801
802	if (domain->hasArea)
803	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
804
805	SuperClassWriter::definition_start();
806	break ;
807	}
808
809	case (ONE_FILE) :
810	{
811	lonid = StdString("lon").append(appendDomid);
812	latid = StdString("lat").append(appendDomid);
813	bounds_lonid = StdString("bounds_lon").append(appendDomid);
814	bounds_latid = StdString("bounds_lat").append(appendDomid);
815	dim0.push_back(dimXid);
816	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
817	if (domain->hasLonLat)
818	{
819	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
820	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
821
822	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
823	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
824	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
825	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
826	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
827	}
828	dim0.clear();
829
830	if (domain->hasBounds)
831	{
832	dim0.push_back(dimXid);
833	dim0.push_back(dimVertId);
834	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
835	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
836	}
837
838	if (domain->hasArea)
839	{
840	dim0.clear();
841	dim0.push_back(dimXid);
842	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
843	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
844	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
845	}
846
847	SuperClassWriter::definition_end();
848
849	std::vector<StdSize> start(1), startBounds(2) ;
850	std::vector<StdSize> count(1), countBounds(2) ;
851	if (domain->isEmpty())
852	{
853	start[0]=0 ;
854	count[0]=0 ;
855	startBounds[1]=0 ;
856	countBounds[1]=domain->nvertex ;
857	startBounds[0]=0 ;
858	countBounds[0]=0 ;
859	}
860	else
861	{
862	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
863	count[0]=domain->zoom_ni_srv ;
864	startBounds[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
865	startBounds[1]=0 ;
866	countBounds[0]=domain->zoom_ni_srv ;
867	countBounds[1]=domain->nvertex ;
868	}
869
870	if (domain->hasLonLat)
871	{
872	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
873	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
874	if (domain->hasBounds)
875	{
876	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
877	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0,&startBounds,&countBounds);
878	}
879	}
880
881	if (domain->hasArea)
882	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
883
884	SuperClassWriter::definition_start();
885
886	break;
887	}
888	default :
889	ERROR("CNc4DataOutput::writeDomain(domain)",
890	<< "[ type = " << SuperClass::type << "]"
891	<< " not implemented yet !");
892	}
893	}
894	catch (CNetCdfException& e)
895	{
896	StdString msg("On writing the domain : ");
897	msg.append(domid); msg.append("\n");
898	msg.append("In the context : ");
899	msg.append(context->getId()); msg.append("\n");
900	msg.append(e.what());
901	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
902	}
903	domain->addRelFile(this->filename);
904	}
905	//--------------------------------------------------------------
906
907	void CNc4DataOutput::writeAxis_(CAxis* axis)
908	{
909	if (axis->IsWritten(this->filename)) return;
910	axis->checkAttributes();
911	int zoom_size_srv = axis->zoom_size_srv;
912	int zoom_begin_srv = axis->zoom_begin_srv;
913	int zoom_size = (MULTI_FILE == SuperClass::type) ? zoom_size_srv
914	: axis->global_zoom_n;
915	int zoom_begin = (MULTI_FILE == SuperClass::type) ? zoom_begin_srv
916	: axis->global_zoom_begin;
917
918	if ((0 == zoom_size_srv) && (MULTI_FILE == SuperClass::type)) return;
919
920	std::vector<StdString> dims;
921	StdString axisid = axis->getAxisOutputName();
922	if (isWrittenAxis(axisid)) return ;
923	else setWrittenAxis(axisid);
924
925	try
926	{
927	SuperClassWriter::addDimension(axisid, zoom_size);
928	if (axis->hasValue)
929	{
930	dims.push_back(axisid);
931	SuperClassWriter::addVariable(axisid, NC_FLOAT, dims);
932
933	if (!axis->name.isEmpty())
934	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
935
936	if (!axis->standard_name.isEmpty())
937	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
938
939	if (!axis->long_name.isEmpty())
940	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
941
942	if (!axis->unit.isEmpty())
943	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
944
945	if (!axis->positive.isEmpty())
946	{
947	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
948	SuperClassWriter::addAttribute("positive",
949	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
950	&axisid);
951	}
952
953	StdString axisBoundsId = axisid + "_bounds";
954	if (!axis->bounds.isEmpty())
955	{
956	dims.push_back("axis_nbounds");
957	SuperClassWriter::addVariable(axisBoundsId, NC_FLOAT, dims);
958	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
959	}
960
961	SuperClassWriter::definition_end();
962
963	switch (SuperClass::type)
964	{
965	case MULTI_FILE:
966	{
967	CArray<double,1> axis_value(zoom_size_srv);
968	for (int i = 0; i < zoom_size_srv; i++) axis_value(i) = axis->value_srv(i);
969	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
970
971	if (!axis->bounds.isEmpty())
972	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0);
973
974	SuperClassWriter::definition_start();
975
976	break;
977	}
978	case ONE_FILE:
979	{
980	CArray<double,1> axis_value(zoom_size_srv);
981	axis_value = axis->value_srv;
982
983	std::vector<StdSize> start(1), startBounds(2) ;
984	std::vector<StdSize> count(1), countBounds(2) ;
985	start[0] = startBounds[0] = zoom_begin_srv-axis->global_zoom_begin;
986	count[0] = countBounds[0] = zoom_size_srv;
987	startBounds[1] = 0;
988	countBounds[1] = 2;
989	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
990
991	if (!axis->bounds.isEmpty())
992	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
993
994	SuperClassWriter::definition_start();
995
996	break;
997	}
998	default :
999	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1000	<< "[ type = " << SuperClass::type << "]"
1001	<< " not implemented yet !");
1002	}
1003	}
1004	}
1005	catch (CNetCdfException& e)
1006	{
1007	StdString msg("On writing the axis : ");
1008	msg.append(axisid); msg.append("\n");
1009	msg.append("In the context : ");
1010	CContext* context = CContext::getCurrent() ;
1011	msg.append(context->getId()); msg.append("\n");
1012	msg.append(e.what());
1013	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1014	}
1015	axis->addRelFile(this->filename);
1016	}
1017
1018	//--------------------------------------------------------------
1019
1020	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1021	{
1022	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1023
1024	try
1025	{
1026	CArray<bool,1> axisDomainOrder = grid->axis_domain_order;
1027	std::vector<StdString> domainList = grid->getDomainList();
1028	std::vector<StdString> axisList = grid->getAxisList();
1029	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0;
1030
1031	std::vector<StdString> dims;
1032
1033	if (grid->isCompressible())
1034	{
1035	StdString varId = grid->getId() + "_points";
1036
1037	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1038	SuperClassWriter::addDimension(varId, nbIndexes);
1039
1040	dims.push_back(varId);
1041	SuperClassWriter::addVariable(varId, NC_INT, dims);
1042
1043	StdOStringStream compress;
1044	for (int i = numElement - 1; i >= 0; --i)
1045	{
1046	if (axisDomainOrder(i))
1047	{
1048	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1049	StdString domId = domain->getDomainOutputName();
1050	StdString appendDomId = singleDomain ? "" : "_" + domId;
1051
1052	switch (domain->type)
1053	{
1054	case CDomain::type_attr::curvilinear:
1055	compress << "y" << appendDomId << " x" << appendDomId;
1056	break;
1057	case CDomain::type_attr::rectilinear:
1058	compress << "lat" << appendDomId << " lon" << appendDomId;
1059	break;
1060	case CDomain::type_attr::unstructured:
1061	compress << "cell" << appendDomId;
1062	break;
1063	}
1064	++idxDomain;
1065	}
1066	else
1067	{
1068	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1069	compress << axis->getAxisOutputName();
1070	++idxAxis;
1071	}
1072
1073	if (i != 0) compress << ' ';
1074	}
1075	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1076
1077	grid->computeCompressedIndex();
1078
1079	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1080	std::map<int, CArray<size_t, 1> >::const_iterator it;
1081	for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
1082	{
1083	const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
1084	for (int i = 0; i < it->second.numElements(); i++)
1085	indexes(compressedIndexes(i)) = it->second(i);
1086	}
1087
1088	switch (SuperClass::type)
1089	{
1090	case (MULTI_FILE):
1091	{
1092	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1093	break;
1094	}
1095	case (ONE_FILE):
1096	{
1097	if (grid->doGridHaveDataDistributed())
1098	grid->getDistributionServer()->computeGlobalIndex(indexes);
1099
1100	std::vector<StdSize> start, count;
1101	start.push_back(grid->getOffsetWrittenIndexes());
1102	count.push_back(grid->getNumberWrittenIndexes());
1103
1104	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1105	break;
1106	}
1107	}
1108	}
1109	else
1110	{
1111	for (int i = 0; i < numElement; ++i)
1112	{
1113	StdString varId, compress;
1114	CArray<int, 1> indexes;
1115	bool isDistributed;
1116	StdSize nbIndexes, totalNbIndexes, offset;
1117	int firstGlobalIndex;
1118
1119	if (axisDomainOrder(i))
1120	{
1121	CDomain* domain = CDomain::get(domainList[idxDomain]);
1122	StdString domId = domain->getDomainOutputName();
1123
1124	if (!domain->isCompressible()
1125	\|\| domain->type == CDomain::type_attr::unstructured
1126	\|\| domain->isWrittenCompressed(this->filename)
1127	\|\| isWrittenCompressedDomain(domId))
1128	continue;
1129
1130	StdString appendDomId = singleDomain ? "" : "_" + domId;
1131
1132	varId = domId + "_points";
1133	switch (domain->type)
1134	{
1135	case CDomain::type_attr::curvilinear:
1136	compress = "y" + appendDomId + " x" + appendDomId;
1137	break;
1138	case CDomain::type_attr::rectilinear:
1139	compress = "lat" + appendDomId + " lon" + appendDomId;
1140	break;
1141	}
1142
1143	const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
1144	indexes.resize(indexesToWrite.size());
1145	for (int n = 0; n < indexes.numElements(); ++n)
1146	indexes(n) = indexesToWrite[n];
1147
1148	isDistributed = domain->isDistributed();
1149	nbIndexes = domain->getNumberWrittenIndexes();
1150	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1151	offset = domain->getOffsetWrittenIndexes();
1152	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1153
1154	domain->addRelFileCompressed(this->filename);
1155	setWrittenCompressedDomain(domId);
1156	++idxDomain;
1157	}
1158	else
1159	{
1160	CAxis* axis = CAxis::get(axisList[idxAxis]);
1161	StdString axisId = axis->getAxisOutputName();
1162
1163	if (!axis->isCompressible()
1164	\|\| axis->isWrittenCompressed(this->filename)
1165	\|\| isWrittenCompressedAxis(axisId))
1166	continue;
1167
1168	varId = axisId + "_points";
1169	compress = axisId;
1170
1171	const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
1172	indexes.resize(indexesToWrite.size());
1173	for (int n = 0; n < indexes.numElements(); ++n)
1174	indexes(n) = indexesToWrite[n];
1175
1176	isDistributed = axis->isDistributed();
1177	nbIndexes = axis->getNumberWrittenIndexes();
1178	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1179	offset = axis->getOffsetWrittenIndexes();
1180	firstGlobalIndex = axis->begin;
1181
1182	axis->addRelFileCompressed(this->filename);
1183	setWrittenCompressedAxis(axisId);
1184	++idxAxis;
1185	}
1186
1187	if (!varId.empty())
1188	{
1189	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1190
1191	dims.clear();
1192	dims.push_back(varId);
1193	SuperClassWriter::addVariable(varId, NC_INT, dims);
1194
1195	SuperClassWriter::addAttribute("compress", compress, &varId);
1196
1197	switch (SuperClass::type)
1198	{
1199	case (MULTI_FILE):
1200	{
1201	indexes -= firstGlobalIndex;
1202	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1203	break;
1204	}
1205	case (ONE_FILE):
1206	{
1207	std::vector<StdSize> start, count;
1208	start.push_back(offset);
1209	count.push_back(nbIndexes);
1210
1211	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1212	break;
1213	}
1214	}
1215	}
1216	}
1217
1218	if (!dims.empty())
1219	grid->computeCompressedIndex();
1220	}
1221
1222	grid->addRelFileCompressed(this->filename);
1223	}
1224	catch (CNetCdfException& e)
1225	{
1226	StdString msg("On writing compressed grid : ");
1227	msg.append(grid->getId()); msg.append("\n");
1228	msg.append("In the context : ");
1229	CContext* context = CContext::getCurrent();
1230	msg.append(context->getId()); msg.append("\n");
1231	msg.append(e.what());
1232	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1233	}
1234	}
1235
1236	//--------------------------------------------------------------
1237
1238	void CNc4DataOutput::writeTimeDimension_(void)
1239	{
1240	try
1241	{
1242	SuperClassWriter::addDimension(getTimeCounterName());
1243	}
1244	catch (CNetCdfException& e)
1245	{
1246	StdString msg("On writing time dimension : time_couter\n");
1247	msg.append("In the context : ");
1248	CContext* context = CContext::getCurrent() ;
1249	msg.append(context->getId()); msg.append("\n");
1250	msg.append(e.what());
1251	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1252	}
1253	}
1254
1255	//--------------------------------------------------------------
1256
1257	void CNc4DataOutput::writeField_(CField* field)
1258	{
1259	CContext* context = CContext::getCurrent() ;
1260	CContextServer* server=context->server ;
1261
1262	std::vector<StdString> dims, coodinates;
1263	CGrid* grid = field->grid;
1264	if (!grid->doGridHaveDataToWrite())
1265	if (SuperClass::type==MULTI_FILE) return ;
1266
1267	CArray<bool,1> axisDomainOrder = grid->axis_domain_order;
1268	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0;
1269	std::vector<StdString> domainList = grid->getDomainList();
1270	std::vector<StdString> axisList = grid->getAxisList();
1271
1272	StdString timeid = getTimeCounterName();
1273	StdString dimXid,dimYid;
1274	std::deque<StdString> dimIdList, dimCoordList;
1275	bool hasArea = false;
1276	StdString cellMeasures = "area:";
1277	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1278
1279	for (int i = 0; i < numElement; ++i)
1280	{
1281	if (axisDomainOrder(i))
1282	{
1283	CDomain* domain = CDomain::get(domainList[idxDomain]);
1284	StdString domId = domain->getDomainOutputName();
1285	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1286
1287	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1288	{
1289	dimIdList.push_back(domId + "_points");
1290	field->setUseCompressedOutput();
1291	}
1292
1293	switch (domain->type)
1294	{
1295	case CDomain::type_attr::curvilinear:
1296	if (!compressedOutput \|\| !domain->isCompressible())
1297	{
1298	dimXid = StdString("x").append(appendDomId);
1299	dimIdList.push_back(dimXid);
1300	dimYid = StdString("y").append(appendDomId);
1301	dimIdList.push_back(dimYid);
1302	}
1303	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1304	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1305	break ;
1306	case CDomain::type_attr::rectilinear:
1307	if (!compressedOutput \|\| !domain->isCompressible())
1308	{
1309	dimXid = StdString("lon").append(appendDomId);
1310	dimIdList.push_back(dimXid);
1311	dimYid = StdString("lat").append(appendDomId);
1312	dimIdList.push_back(dimYid);
1313	}
1314	break ;
1315	case CDomain::type_attr::unstructured:
1316	{
1317	if (SuperClassWriter::useCFConvention)
1318	{
1319	dimXid = StdString("cell").append(appendDomId);
1320	dimIdList.push_back(dimXid);
1321	dimCoordList.push_back(StdString("lon").append(appendDomId));
1322	dimCoordList.push_back(StdString("lat").append(appendDomId));
1323	}
1324	else
1325	{
1326	StdString domainName = domain->name;
1327	if (domain->nvertex == 1)
1328	{
1329	dimXid = "n" + domainName + "_node";
1330	dimIdList.push_back(dimXid);
1331	dimCoordList.push_back(StdString(domainName + "_node_x"));
1332	dimCoordList.push_back(StdString(domainName + "_node_y"));
1333	}
1334	else if (domain->nvertex == 2)
1335	{
1336	dimXid = "n" + domainName + "_edge";
1337	dimIdList.push_back(dimXid);
1338	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1339	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1340	}
1341	else
1342	{
1343	dimXid = "n" + domainName + "_face";
1344	dimIdList.push_back(dimXid);
1345	dimCoordList.push_back(StdString(domainName + "_face_x"));
1346	dimCoordList.push_back(StdString(domainName + "_face_y"));
1347	}
1348	} // ugrid convention
1349	} // case unstructured domain
1350	}
1351
1352	if (domain->hasArea)
1353	{
1354	hasArea = true;
1355	cellMeasures += " area" + appendDomId;
1356	}
1357	++idxDomain;
1358	}
1359	else
1360	{
1361	CAxis* axis = CAxis::get(axisList[idxAxis]);
1362	StdString axisId = axis->getAxisOutputName();
1363
1364	if (compressedOutput && axis->isCompressible())
1365	{
1366	dimIdList.push_back(axisId + "_points");
1367	field->setUseCompressedOutput();
1368	}
1369	else
1370	dimIdList.push_back(axisId);
1371
1372	dimCoordList.push_back(axisId);
1373	++idxAxis;
1374	}
1375	}
1376
1377	/*
1378	StdString lonid_loc = (server->intraCommSize > 1)
1379	? StdString("lon").append(appendDomid).append("_local")
1380	: lonid;
1381	StdString latid_loc = (server->intraCommSize > 1)
1382	? StdString("lat").append(appendDomid).append("_local")
1383	: latid;
1384	*/
1385	StdString fieldid = field->getFieldOutputName();
1386
1387	// unsigned int ssize = domain->zoom_ni_loc.getValue() * domain->zoom_nj_loc.getValue();
1388	// bool isCurvilinear = (domain->lonvalue.getValue()->size() == ssize);
1389	// bool isCurvilinear = domain->isCurvilinear ;
1390
1391	nc_type type ;
1392	if (field->prec.isEmpty()) type = NC_FLOAT ;
1393	else
1394	{
1395	if (field->prec==2) type = NC_SHORT ;
1396	else if (field->prec==4) type = NC_FLOAT ;
1397	else if (field->prec==8) type = NC_DOUBLE ;
1398	}
1399
1400	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1401
1402	if (wtime)
1403	{
1404
1405	//StdOStringStream oss;
1406	// oss << "time_" << field->operation.getValue()
1407	// << "_" << field->getRelFile()->output_freq.getValue();
1408	//oss
1409	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
1410	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
1411	dims.push_back(timeid);
1412	}
1413
1414	if (compressedOutput && grid->isCompressible())
1415	{
1416	dims.push_back(grid->getId() + "_points");
1417	field->setUseCompressedOutput();
1418	}
1419	else
1420	{
1421	while (!dimIdList.empty())
1422	{
1423	dims.push_back(dimIdList.back());
1424	dimIdList.pop_back();
1425	}
1426	}
1427
1428	while (!dimCoordList.empty())
1429	{
1430	coodinates.push_back(dimCoordList.back());
1431	dimCoordList.pop_back();
1432	}
1433
1434	try
1435	{
1436	SuperClassWriter::addVariable(fieldid, type, dims);
1437
1438	if (!field->standard_name.isEmpty())
1439	SuperClassWriter::addAttribute
1440	("standard_name", field->standard_name.getValue(), &fieldid);
1441
1442	if (!field->long_name.isEmpty())
1443	SuperClassWriter::addAttribute
1444	("long_name", field->long_name.getValue(), &fieldid);
1445
1446	if (!field->unit.isEmpty())
1447	SuperClassWriter::addAttribute
1448	("units", field->unit.getValue(), &fieldid);
1449
1450	if (!field->valid_min.isEmpty())
1451	SuperClassWriter::addAttribute
1452	("valid_min", field->valid_min.getValue(), &fieldid);
1453
1454	if (!field->valid_max.isEmpty())
1455	SuperClassWriter::addAttribute
1456	("valid_max", field->valid_max.getValue(), &fieldid);
1457
1458	if (!field->scale_factor.isEmpty())
1459	SuperClassWriter::addAttribute
1460	("scale_factor", field->scale_factor.getValue(), &fieldid);
1461
1462	if (!field->add_offset.isEmpty())
1463	SuperClassWriter::addAttribute
1464	("add_offset", field->add_offset.getValue(), &fieldid);
1465
1466	SuperClassWriter::addAttribute
1467	("online_operation", field->operation.getValue(), &fieldid);
1468
1469	// write child variables as attributes
1470
1471
1472	vector<CVariable*> listVars = field->getAllVariables() ;
1473	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1474
1475
1476	if (wtime)
1477	{
1478	CDuration freqOp = field->freq_op.getValue();
1479	freqOp.solveTimeStep(*context->calendar);
1480	StdString freqOpStr = freqOp.toStringUDUnits();
1481	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1482
1483	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1484	freqOut.solveTimeStep(*context->calendar);
1485	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1486
1487	StdString cellMethods = "time: ";
1488	if (field->operation.getValue() == "instant") cellMethods += "point";
1489	else if (field->operation.getValue() == "average") cellMethods += "mean";
1490	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1491	else cellMethods += field->operation;
1492	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1493	cellMethods += " (interval: " + freqOpStr + ")";
1494	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1495	}
1496
1497	if (hasArea)
1498	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1499
1500	if (!field->default_value.isEmpty())
1501	{
1502	double default_value = field->default_value.getValue();
1503	float fdefault_value = (float)default_value;
1504	if (type == NC_DOUBLE)
1505	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1506	else
1507	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1508	}
1509	else
1510	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1511
1512	if (field->compression_level.isEmpty())
1513	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1514	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1515
1516	{ // Ecriture des coordonnes
1517
1518	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1519	std::vector<StdString>::iterator
1520	itc = coodinates.begin(), endc = coodinates.end();
1521
1522	for (; itc!= endc; itc++)
1523	{
1524	StdString & coord = *itc;
1525	if (itc+1 != endc)
1526	coordstr.append(coord).append(" ");
1527	else coordstr.append(coord);
1528	}
1529
1530	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1531
1532	}
1533	}
1534	catch (CNetCdfException& e)
1535	{
1536	StdString msg("On writing field : ");
1537	msg.append(fieldid); msg.append("\n");
1538	msg.append("In the context : ");
1539	msg.append(context->getId()); msg.append("\n");
1540	msg.append(e.what());
1541	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1542	}
1543	} // writeField_()
1544
1545	//--------------------------------------------------------------
1546
1547	void CNc4DataOutput::writeFile_ (CFile* file)
1548	{
1549	StdString filename = file->getFileOutputName();
1550	StdString description = (!file->description.isEmpty())
1551	? file->description.getValue()
1552	: StdString("Created by xios");
1553
1554	singleDomain = (file->nbDomains == 1);
1555
1556	try
1557	{
1558	if (SuperClassWriter::useCFConvention)
1559	this->writeFileAttributes(filename, description,
1560	StdString("CF-1.5"),
1561	StdString("An IPSL model"),
1562	this->getTimeStamp());
1563	else
1564	this->writeFileAttributes(filename, description,
1565	StdString("UGRID"),
1566	StdString("An IPSL model"),
1567	this->getTimeStamp());
1568
1569
1570	if (!appendMode)
1571	SuperClassWriter::addDimension("axis_nbounds", 2);
1572	}
1573	catch (CNetCdfException& e)
1574	{
1575	StdString msg("On writing file : ");
1576	msg.append(filename); msg.append("\n");
1577	msg.append("In the context : ");
1578	CContext* context = CContext::getCurrent() ;
1579	msg.append(context->getId()); msg.append("\n");
1580	msg.append(e.what());
1581	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1582	}
1583	}
1584
1585	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1586	{
1587	StdString name = var->getVariableOutputName();
1588
1589	try
1590	{
1591	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1592	addAttribute(name, var->getData<int>(), &fieldId);
1593	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1594	addAttribute(name, var->getData<short int>(), &fieldId);
1595	else if (var->type.getValue() == CVariable::type_attr::t_float)
1596	addAttribute(name, var->getData<float>(), &fieldId);
1597	else if (var->type.getValue() == CVariable::type_attr::t_double)
1598	addAttribute(name, var->getData<double>(), &fieldId);
1599	else if (var->type.getValue() == CVariable::type_attr::t_string)
1600	addAttribute(name, var->getData<string>(), &fieldId);
1601	else
1602	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1603	<< "Unsupported variable of type " << var->type.getStringValue());
1604	}
1605	catch (CNetCdfException& e)
1606	{
1607	StdString msg("On writing attributes of variable with name : ");
1608	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1609	msg.append("In the context : ");
1610	CContext* context = CContext::getCurrent() ;
1611	msg.append(context->getId()); msg.append("\n");
1612	msg.append(e.what());
1613	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1614	}
1615	}
1616
1617	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1618	{
1619	StdString name = var->getVariableOutputName();
1620
1621	try
1622	{
1623	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1624	addAttribute(name, var->getData<int>());
1625	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1626	addAttribute(name, var->getData<short int>());
1627	else if (var->type.getValue() == CVariable::type_attr::t_float)
1628	addAttribute(name, var->getData<float>());
1629	else if (var->type.getValue() == CVariable::type_attr::t_double)
1630	addAttribute(name, var->getData<double>());
1631	else if (var->type.getValue() == CVariable::type_attr::t_string)
1632	addAttribute(name, var->getData<string>());
1633	else
1634	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1635	<< "Unsupported variable of type " << var->type.getStringValue());
1636	}
1637	catch (CNetCdfException& e)
1638	{
1639	StdString msg("On writing attributes of variable with name : ");
1640	msg.append(name); msg.append("\n");
1641	msg.append("In the context : ");
1642	CContext* context = CContext::getCurrent() ;
1643	msg.append(context->getId()); msg.append("\n");
1644	msg.append(e.what());
1645	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1646	}
1647	}
1648
1649	void CNc4DataOutput::syncFile_ (void)
1650	{
1651	try
1652	{
1653	SuperClassWriter::sync() ;
1654	}
1655	catch (CNetCdfException& e)
1656	{
1657	StdString msg("On synchronizing the write among processes");
1658	msg.append("In the context : ");
1659	CContext* context = CContext::getCurrent() ;
1660	msg.append(context->getId()); msg.append("\n");
1661	msg.append(e.what());
1662	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1663	}
1664	}
1665
1666	void CNc4DataOutput::closeFile_ (void)
1667	{
1668	try
1669	{
1670	SuperClassWriter::close() ;
1671	}
1672	catch (CNetCdfException& e)
1673	{
1674	StdString msg("On closing file");
1675	msg.append("In the context : ");
1676	CContext* context = CContext::getCurrent() ;
1677	msg.append(context->getId()); msg.append("\n");
1678	msg.append(e.what());
1679	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1680	}
1681
1682	}
1683
1684	//---------------------------------------------------------------
1685
1686	StdString CNc4DataOutput::getTimeStamp(void) const
1687	{
1688	const int buffer_size = 100;
1689	time_t rawtime;
1690	struct tm * timeinfo = NULL;
1691	char buffer [buffer_size];
1692
1693	time ( &rawtime );
1694	timeinfo = localtime ( &rawtime );
1695	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
1696
1697	return (StdString(buffer));
1698	}
1699
1700	//---------------------------------------------------------------
1701
1702	void CNc4DataOutput::writeFieldData_ (CField* field)
1703	{
1704	CContext* context = CContext::getCurrent();
1705	CContextServer* server = context->server;
1706	CGrid* grid = field->grid;
1707
1708	if (!grid->doGridHaveDataToWrite())
1709	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
1710
1711	StdString fieldid = field->getFieldOutputName();
1712
1713	StdOStringStream oss;
1714	string timeAxisId;
1715	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
1716	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
1717
1718	StdString timeBoundId = getTimeCounterName() + "_bounds";
1719
1720	StdString timeAxisBoundId;
1721	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
1722	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
1723
1724	if (!field->wasWritten())
1725	{
1726	if (appendMode && field->file->record_offset.isEmpty())
1727	{
1728	field->resetNStep(getRecordFromTime(field->last_Write_srv) + 1);
1729	}
1730
1731	field->setWritten();
1732	}
1733
1734
1735	CArray<double,1> time_data(1);
1736	CArray<double,1> time_data_bound(2);
1737	CArray<double,1> time_counter(1);
1738	CArray<double,1> time_counter_bound(2);
1739
1740	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
1741
1742	if (wtime)
1743	{
1744	Time lastWrite = field->last_Write_srv;
1745	Time lastLastWrite = field->lastlast_Write_srv;
1746
1747	if (field->getOperationTimeType() == func::CFunctor::instant)
1748	time_data(0) = lastWrite;
1749	else if (field->getOperationTimeType() == func::CFunctor::centered)
1750	time_data(0) = (lastWrite + lastLastWrite) / 2;
1751
1752	if (field->getOperationTimeType() == func::CFunctor::instant)
1753	time_data_bound(0) = time_data_bound(1) = lastWrite;
1754	else if (field->getOperationTimeType() == func::CFunctor::centered)
1755	{
1756	time_data_bound(0) = lastLastWrite;
1757	time_data_bound(1) = lastWrite;
1758	}
1759
1760	if (field->file->time_counter == CFile::time_counter_attr::instant)
1761	time_counter(0) = lastWrite;
1762	else if (field->file->time_counter == CFile::time_counter_attr::centered)
1763	time_counter(0) = (lastWrite + lastLastWrite) / 2;
1764	else if (field->file->time_counter == CFile::time_counter_attr::record)
1765	time_counter(0) = field->getNStep() - 1;
1766
1767
1768	if (field->file->time_counter == CFile::time_counter_attr::instant)
1769	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
1770	else if (field->file->time_counter == CFile::time_counter_attr::centered)
1771	{
1772	time_counter_bound(0) = lastLastWrite;
1773	time_counter_bound(1) = lastWrite;
1774	}
1775	else if (field->file->time_counter == CFile::time_counter_attr::record)
1776	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
1777	}
1778
1779	bool isRoot = (server->intraCommRank == 0);
1780
1781	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
1782	{
1783	double scaleFactor = 1.0;
1784	double addOffset = 0.0;
1785	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
1786	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
1787	field->scaleFactorAddOffset(scaleFactor, addOffset);
1788	}
1789
1790	try
1791	{
1792	size_t writtenSize;
1793	if (field->getUseCompressedOutput())
1794	writtenSize = grid->getNumberWrittenIndexes();
1795	else
1796	writtenSize = grid->getWrittenDataSize();
1797
1798	CArray<double,1> fieldData(writtenSize);
1799	if (!field->default_value.isEmpty()) fieldData = field->default_value;
1800
1801	if (field->getUseCompressedOutput())
1802	field->outputCompressedField(fieldData);
1803	else
1804	field->outputField(fieldData);
1805
1806	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
1807
1808	switch (SuperClass::type)
1809	{
1810	case (MULTI_FILE) :
1811	{
1812	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
1813	if (wtime)
1814	{
1815	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
1816	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
1817	if (field->file->time_counter != CFile::time_counter_attr::none)
1818	{
1819	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
1820	if (field->file->time_counter != CFile::time_counter_attr::record)
1821	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
1822	}
1823	}
1824	break;
1825	}
1826	case (ONE_FILE) :
1827	{
1828	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
1829	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
1830	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
1831
1832	std::vector<StdSize> start, count;
1833
1834	if (field->getUseCompressedOutput())
1835	{
1836	if (grid->isCompressible())
1837	{
1838	start.push_back(grid->getOffsetWrittenIndexes());
1839	count.push_back(grid->getNumberWrittenIndexes());
1840	}
1841	else
1842	{
1843	CArray<bool,1> axisDomainOrder = grid->axis_domain_order;
1844	std::vector<StdString> domainList = grid->getDomainList();
1845	std::vector<StdString> axisList = grid->getAxisList();
1846	int numElement = axisDomainOrder.numElements();
1847	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
1848	int idx = nZoomBeginGlobal.size() - 1;
1849
1850	start.reserve(nZoomBeginGlobal.size());
1851	count.reserve(nZoomBeginGlobal.size());
1852
1853
1854	for (int i = numElement - 1; i >= 0; --i)
1855	{
1856	if (axisDomainOrder(i))
1857	{
1858	CDomain* domain = CDomain::get(domainList[idxDomain]);
1859
1860	if (domain->isCompressible())
1861	{
1862	start.push_back(domain->getOffsetWrittenIndexes());
1863	count.push_back(domain->getNumberWrittenIndexes());
1864	idx -= 2;
1865	}
1866	else
1867	{
1868	if ((domain->type) != CDomain::type_attr::unstructured)
1869	{
1870	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
1871	count.push_back(nZoomSizeServer[idx]);
1872	}
1873	--idx;
1874	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
1875	count.push_back(nZoomSizeServer[idx]);
1876	--idx;
1877	}
1878	--idxDomain;
1879	}
1880	else
1881	{
1882	CAxis* axis = CAxis::get(axisList[idxAxis]);
1883
1884	if (axis->isCompressible())
1885	{
1886	start.push_back(axis->getOffsetWrittenIndexes());
1887	count.push_back(axis->getNumberWrittenIndexes());
1888	}
1889	else
1890	{
1891	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
1892	count.push_back(nZoomSizeServer[idx]);
1893	}
1894
1895	--idxAxis;
1896	--idx;
1897	}
1898	}
1899	}
1900	}
1901	else
1902	{
1903
1904	CArray<bool,1> axisDomainOrder = grid->axis_domain_order;
1905	std::vector<StdString> domainList = grid->getDomainList();
1906	std::vector<StdString> axisList = grid->getAxisList();
1907	int numElement = axisDomainOrder.numElements();
1908	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
1909	int idx = nZoomBeginGlobal.size() - 1;
1910
1911	start.reserve(nZoomBeginGlobal.size());
1912	count.reserve(nZoomBeginGlobal.size());
1913
1914	for (int i = numElement - 1; i >= 0; --i)
1915	{
1916	if (axisDomainOrder(i))
1917	{
1918	CDomain* domain = CDomain::get(domainList[idxDomain]);
1919	if ((domain->type) != CDomain::type_attr::unstructured)
1920	{
1921	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
1922	count.push_back(nZoomSizeServer[idx]);
1923	}
1924	--idx ;
1925	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
1926	count.push_back(nZoomSizeServer[idx]);
1927	--idx ;
1928	--idxDomain;
1929	}
1930	else
1931	{
1932	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
1933	count.push_back(nZoomSizeServer[idx]);
1934	--idx;
1935	}
1936	}
1937	}
1938
1939	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
1940	if (wtime)
1941	{
1942	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
1943	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
1944	if (field->file->time_counter != CFile::time_counter_attr::none)
1945	{
1946	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
1947	if (field->file->time_counter != CFile::time_counter_attr::record)
1948	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
1949	}
1950	}
1951
1952	break;
1953	}
1954	}
1955	}
1956	catch (CNetCdfException& e)
1957	{
1958	StdString msg("On writing field data: ");
1959	msg.append(fieldid); msg.append("\n");
1960	msg.append("In the context : ");
1961	msg.append(context->getId()); msg.append("\n");
1962	msg.append(e.what());
1963	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
1964	}
1965	}
1966
1967	//---------------------------------------------------------------
1968
1969	void CNc4DataOutput::writeTimeAxis_
1970	(CField* field,
1971	const boost::shared_ptr<CCalendar> cal)
1972	{
1973	StdOStringStream oss;
1974
1975	if (field->getOperationTimeType() == func::CFunctor::once) return ;
1976
1977	// oss << "time_" << field->operation.getValue()
1978	// << "_" << field->getRelFile()->output_freq.getValue();
1979
1980	// StdString axisid = oss.str();
1981	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
1982	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
1983
1984	StdString axisid("time_centered") ;
1985	StdString axisBoundId("time_centered_bounds");
1986	StdString timeid(getTimeCounterName());
1987	StdString timeBoundId("axis_nbounds");
1988
1989	if (field->getOperationTimeType() == func::CFunctor::instant)
1990	{
1991	axisid = "time_instant";
1992	axisBoundId = "time_instant_bounds";
1993	}
1994
1995	try
1996	{
1997	// Adding time_instant or time_centered
1998	std::vector<StdString> dims;
1999	dims.push_back(timeid);
2000	if (!SuperClassWriter::varExist(axisid))
2001	{
2002	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2003
2004	CDate timeOrigin=cal->getTimeOrigin() ;
2005	StdOStringStream oss2;
2006	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
2007	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
2008	StdString strInitdate=oss2.str() ;
2009	StdString strTimeOrigin=timeOrigin.toString() ;
2010	this->writeTimeAxisAttributes
2011	(axisid, cal->getType(),
2012	StdString("seconds since ").append(strTimeOrigin),
2013	strTimeOrigin, axisBoundId);
2014	}
2015
2016	// Adding time_instant_bounds or time_centered_bounds variables
2017	if (!SuperClassWriter::varExist(axisBoundId))
2018	{
2019	dims.clear() ;
2020	dims.push_back(timeid);
2021	dims.push_back(timeBoundId);
2022	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2023	}
2024
2025	if (field->file->time_counter != CFile::time_counter_attr::none)
2026	{
2027	// Adding time_counter
2028	axisid = getTimeCounterName();
2029	axisBoundId = getTimeCounterName() + "_bounds";
2030	dims.clear();
2031	dims.push_back(timeid);
2032	if (!SuperClassWriter::varExist(axisid))
2033	{
2034	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2035	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
2036
2037	if (field->file->time_counter != CFile::time_counter_attr::record)
2038	{
2039	CDate timeOrigin = cal->getTimeOrigin();
2040	StdString strTimeOrigin = timeOrigin.toString();
2041
2042	this->writeTimeAxisAttributes(axisid, cal->getType(),
2043	StdString("seconds since ").append(strTimeOrigin),
2044	strTimeOrigin, axisBoundId);
2045	}
2046	}
2047
2048	// Adding time_counter_bound dimension
2049	if (field->file->time_counter != CFile::time_counter_attr::record)
2050	{
2051	if (!SuperClassWriter::varExist(axisBoundId))
2052	{
2053	dims.clear();
2054	dims.push_back(timeid);
2055	dims.push_back(timeBoundId);
2056	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2057	}
2058	}
2059	}
2060	}
2061	catch (CNetCdfException& e)
2062	{
2063	StdString msg("On writing time axis data: ");
2064	msg.append("In the context : ");
2065	CContext* context = CContext::getCurrent() ;
2066	msg.append(context->getId()); msg.append("\n");
2067	msg.append(e.what());
2068	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2069	const boost::shared_ptr<CCalendar> cal)", << msg);
2070	}
2071	}
2072
2073	//---------------------------------------------------------------
2074
2075	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2076	const StdString & calendar,
2077	const StdString & units,
2078	const StdString & time_origin,
2079	const StdString & time_bounds,
2080	const StdString & standard_name,
2081	const StdString & long_name)
2082	{
2083	try
2084	{
2085	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2086	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2087	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2088	SuperClassWriter::addAttribute("units", units , &axis_name);
2089	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2090	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2091	}
2092	catch (CNetCdfException& e)
2093	{
2094	StdString msg("On writing time axis Attribute: ");
2095	msg.append("In the context : ");
2096	CContext* context = CContext::getCurrent() ;
2097	msg.append(context->getId()); msg.append("\n");
2098	msg.append(e.what());
2099	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2100	const StdString & calendar,\
2101	const StdString & units, \
2102	const StdString & time_origin, \
2103	const StdString & time_bounds, \
2104	const StdString & standard_name, \
2105	const StdString & long_name)", << msg);
2106	}
2107	}
2108
2109	//---------------------------------------------------------------
2110
2111	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2112	const StdString & axis,
2113	const StdString & standard_name,
2114	const StdString & long_name,
2115	const StdString & units,
2116	const StdString & nav_model)
2117	{
2118	try
2119	{
2120	if (!axis.empty())
2121	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2122
2123	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2124	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2125	SuperClassWriter::addAttribute("units" , units , &axis_name);
2126	SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2127	}
2128	catch (CNetCdfException& e)
2129	{
2130	StdString msg("On writing Axis Attribute: ");
2131	msg.append("In the context : ");
2132	CContext* context = CContext::getCurrent() ;
2133	msg.append(context->getId()); msg.append("\n");
2134	msg.append(e.what());
2135	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2136	const StdString & axis, \
2137	const StdString & standard_name, \
2138	const StdString & long_name, \
2139	const StdString & units, \
2140	const StdString & nav_model)", << msg);
2141	}
2142	}
2143
2144	//---------------------------------------------------------------
2145
2146	void CNc4DataOutput::writeLocalAttributes
2147	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2148	{
2149	try
2150	{
2151	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2152	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2153	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2154	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2155	}
2156	catch (CNetCdfException& e)
2157	{
2158	StdString msg("On writing Local Attributes: ");
2159	msg.append("In the context : ");
2160	CContext* context = CContext::getCurrent() ;
2161	msg.append(context->getId()); msg.append("\n");
2162	msg.append(e.what());
2163	ERROR("CNc4DataOutput::writeLocalAttributes \
2164	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2165	}
2166
2167	}
2168
2169	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2170	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2171	{
2172	CArray<int,1> array(2) ;
2173
2174	try
2175	{
2176	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2177	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2178	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2179	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2180	array=ni_glo,nj_glo ;
2181	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2182	array=ni,nj ;
2183	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2184	array=ibegin+1,jbegin+1 ;
2185	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2186	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2187	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2188	array=0,0 ;
2189	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2190	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2191	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2192	/*
2193	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2194	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2195	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2196	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2197	*/
2198	}
2199	catch (CNetCdfException& e)
2200	{
2201	StdString msg("On writing Local Attributes IOIPSL \n");
2202	msg.append("In the context : ");
2203	CContext* context = CContext::getCurrent() ;
2204	msg.append(context->getId()); msg.append("\n");
2205	msg.append(e.what());
2206	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2207	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2208	}
2209	}
2210	//---------------------------------------------------------------
2211
2212	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2213	const StdString & description,
2214	const StdString & conventions,
2215	const StdString & production,
2216	const StdString & timeStamp)
2217	{
2218	try
2219	{
2220	SuperClassWriter::addAttribute("name" , name);
2221	SuperClassWriter::addAttribute("description", description);
2222	SuperClassWriter::addAttribute("title" , description);
2223	SuperClassWriter::addAttribute("Conventions", conventions);
2224	SuperClassWriter::addAttribute("production" , production);
2225	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
2226	}
2227	catch (CNetCdfException& e)
2228	{
2229	StdString msg("On writing File Attributes \n ");
2230	msg.append("In the context : ");
2231	CContext* context = CContext::getCurrent() ;
2232	msg.append(context->getId()); msg.append("\n");
2233	msg.append(e.what());
2234	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2235	const StdString & description, \
2236	const StdString & conventions, \
2237	const StdString & production, \
2238	const StdString & timeStamp)", << msg);
2239	}
2240	}
2241
2242	//---------------------------------------------------------------
2243
2244	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2245	int data_dim,
2246	int data_ni,
2247	int data_nj,
2248	int data_ibegin,
2249	int data_jbegin)
2250	{
2251	try
2252	{
2253	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2254	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2255	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2256	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2257	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2258	}
2259	catch (CNetCdfException& e)
2260	{
2261	StdString msg("On writing Mask Attributes \n ");
2262	msg.append("In the context : ");
2263	CContext* context = CContext::getCurrent() ;
2264	msg.append(context->getId()); msg.append("\n");
2265	msg.append(e.what());
2266	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2267	int data_dim, \
2268	int data_ni, \
2269	int data_nj, \
2270	int data_ibegin, \
2271	int data_jbegin)", << msg);
2272	}
2273	}
2274
2275	///--------------------------------------------------------------
2276
2277	StdSize CNc4DataOutput::getRecordFromTime(Time time)
2278	{
2279	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2280	if (it == timeToRecordCache.end())
2281	{
2282	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2283	if (!SuperClassWriter::varExist(timeAxisBoundsId))
2284	timeAxisBoundsId = "time_instant_bounds";
2285
2286	CArray<double,2> timeAxisBounds;
2287	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
2288
2289	StdSize record = 0;
2290	double dtime(time);
2291	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
2292	{
2293	if (timeAxisBounds(1, n) < dtime)
2294	{
2295	record = n + 1;
2296	break;
2297	}
2298	}
2299	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2300	}
2301	return it->second;
2302	}
2303
2304	///--------------------------------------------------------------
2305
2306	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2307	{
2308	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2309	}
2310
2311	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2312	{
2313	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2314	}
2315
2316	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2317	{
2318	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2319	}
2320
2321	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2322	{
2323	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2324	}
2325
2326	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2327	{
2328	this->writtenDomains.insert(domainName);
2329	}
2330
2331	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2332	{
2333	this->writtenCompressedDomains.insert(domainName);
2334	}
2335
2336	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2337	{
2338	this->writtenAxis.insert(axisName);
2339	}
2340
2341	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2342	{
2343	this->writtenCompressedAxis.insert(axisName);
2344	}
2345	} // namespace xios

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