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source: XIOS/dev/dev_olga/src/io/nc4_data_output.cpp @ 1054

Last change on this file since 1054 was 1054, checked in by oabramkina, 7 years ago
dev: intermediate commit.
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: 119.2 KB

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1	#include "nc4_data_output.hpp"
2
3	#include <boost/lexical_cast.hpp>
4	#include "attribute_template.hpp"
5	#include "group_template.hpp"
6
7	#include "file.hpp"
8	#include "calendar.hpp"
9	#include "context.hpp"
10	#include "context_server.hpp"
11	#include "netCdfException.hpp"
12	#include "exception.hpp"
13
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	const std::vector<int>& local_size_write = domain->getLocalWriteSize();
77	const std::vector<int>& global_size_write = domain->getGlobalWriteSize();
78	const std::vector<int>& start_write = domain->getStartWriteIndex();
79	const std::vector<int>& count_write = domain->getCountWriteIndex();
80	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
81
82	StdString dimXid, dimYid ;
83
84	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
85	switch (domain->type)
86	{
87	case CDomain::type_attr::curvilinear :
88	dimXid = StdString("x").append(appendDomid);
89	dimYid = StdString("y").append(appendDomid);
90	break ;
91	case CDomain::type_attr::rectilinear :
92	dimXid = StdString("lon").append(appendDomid);
93	dimYid = StdString("lat").append(appendDomid);
94	break;
95	}
96
97	StdString dimVertId = StdString("nvertex").append(appendDomid);
98
99	string lonid,latid,bounds_lonid,bounds_latid ;
100	string areaId = "area" + appendDomid;
101	/*
102	StdString lonid_loc = (server->intraCommSize > 1)
103	? StdString("lon").append(appendDomid).append("_local")
104	: lonid;
105	StdString latid_loc = (server->intraCommSize > 1)
106	? StdString("lat").append(appendDomid).append("_local")
107	: latid;
108	*/
109
110	try
111	{
112	switch (SuperClass::type)
113	{
114	case (MULTI_FILE) :
115	{
116	// if (domain->isEmpty()) return;
117
118	if (server->intraCommSize > 1)
119	{
120	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
121	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
122	}
123
124	switch (domain->type)
125	{
126	case CDomain::type_attr::curvilinear :
127	dim0.push_back(dimYid); dim0.push_back(dimXid);
128	lonid = StdString("nav_lon").append(appendDomid);
129	latid = StdString("nav_lat").append(appendDomid);
130	break ;
131	case CDomain::type_attr::rectilinear :
132	lonid = StdString("lon").append(appendDomid);
133	latid = StdString("lat").append(appendDomid);
134	dim0.push_back(dimYid);
135	dim1.push_back(dimXid);
136	break;
137	}
138
139	bounds_lonid = StdString("bounds_lon").append(appendDomid);
140	bounds_latid = StdString("bounds_lat").append(appendDomid);
141
142	SuperClassWriter::addDimension(dimXid, local_size_write[0]);
143	SuperClassWriter::addDimension(dimYid, local_size_write[1]);
144
145	if (domain->hasBounds)
146	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
147
148	if (server->intraCommSize > 1)
149	{
150	this->writeLocalAttributes(0, count_write[0],
151	0, count_write[1],
152	appendDomid);
153
154	if (singleDomain)
155	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
156	0, count_write[0],
157	0, count_write[1],
158	domain->ni_glo,domain->nj_glo,
159	server->intraCommRank,server->intraCommSize);
160	}
161
162	if (domain->hasLonLat)
163	{
164	switch (domain->type)
165	{
166	case CDomain::type_attr::curvilinear :
167	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
168	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
169	break ;
170	case CDomain::type_attr::rectilinear :
171	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
172	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
173	break ;
174	}
175
176	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
177	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
178
179	if (domain->hasBounds)
180	{
181	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
182	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
183
184	dim0.clear();
185	dim0.push_back(dimYid);
186	dim0.push_back(dimXid);
187	dim0.push_back(dimVertId);
188	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
189	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
190	}
191	}
192
193	dim0.clear();
194	dim0.push_back(dimYid);
195	dim0.push_back(dimXid);
196
197
198	// supress mask if (server->intraCommSize > 1)
199	// supress mask {
200	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
201	// supress mask
202	// supress mask this->writeMaskAttributes(maskid,
203	// supress mask domain->data_dim.getValue()/*,
204	// supress mask domain->data_ni.getValue(),
205	// supress mask domain->data_nj.getValue(),
206	// supress mask domain->data_ibegin.getValue(),
207	// supress mask domain->data_jbegin.getValue()*/);
208	// supress mask }
209
210	//SuperClassWriter::setDefaultValue(maskid, &dvm);
211
212	if (domain->hasArea)
213	{
214	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
215	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
216	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
217	}
218
219	SuperClassWriter::definition_end();
220
221	if (domain->hasLonLat)
222	{
223	switch (domain->type)
224	{
225	case CDomain::type_attr::curvilinear :
226	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
227	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
228	break;
229	case CDomain::type_attr::rectilinear :
230	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,local_size_write[0])) ;
231	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
232	CArray<double,1> lon = domain->lonvalue(Range(0,local_size_write[1])) ;
233	// CArray<double,1> lon = domain->lonvalue(Range(0,local_size_write[1]-1)) ;
234	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
235	break;
236	}
237
238	if (domain->hasBounds)
239	{
240	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
241	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
242	}
243	}
244
245	if (domain->hasArea)
246	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
247
248	SuperClassWriter::definition_start();
249
250	break;
251	}
252	case (ONE_FILE) :
253	{
254	SuperClassWriter::addDimension(dimXid, global_size_write[0]);
255	SuperClassWriter::addDimension(dimYid, global_size_write[1]);
256
257	if (domain->hasBounds)
258	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
259
260	if (domain->hasLonLat)
261	{
262	switch (domain->type)
263	{
264	case CDomain::type_attr::curvilinear :
265	dim0.push_back(dimYid); dim0.push_back(dimXid);
266	lonid = StdString("nav_lon").append(appendDomid);
267	latid = StdString("nav_lat").append(appendDomid);
268	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
269	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
270	break;
271
272	case CDomain::type_attr::rectilinear :
273	dim0.push_back(dimYid);
274	dim1.push_back(dimXid);
275	lonid = StdString("lon").append(appendDomid);
276	latid = StdString("lat").append(appendDomid);
277	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
278	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
279	break;
280	}
281
282	bounds_lonid = StdString("bounds_lon").append(appendDomid);
283	bounds_latid = StdString("bounds_lat").append(appendDomid);
284
285	this->writeAxisAttributes
286	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
287	this->writeAxisAttributes
288	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
289
290	if (domain->hasBounds)
291	{
292	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
293	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
294
295	dim0.clear();
296	dim0.push_back(dimYid);
297	dim0.push_back(dimXid);
298	dim0.push_back(dimVertId);
299	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
300	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
301	}
302	}
303
304	if (domain->hasArea)
305	{
306	dim0.clear();
307	dim0.push_back(dimYid); dim0.push_back(dimXid);
308	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
309	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
310	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
311	dim0.clear();
312	}
313
314	SuperClassWriter::definition_end();
315
316	switch (domain->type)
317	{
318	case CDomain::type_attr::curvilinear :
319	{
320	std::vector<StdSize> start(2) ;
321	std::vector<StdSize> count(2) ;
322	if (domain->isEmpty())
323	{
324	start[0]=0 ; start[1]=0 ;
325	count[0]=0 ; count[1]=0 ;
326	}
327	else
328	{
329	// start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
330	// start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
331	// count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
332	start[1]= start_write[0];
333	start[0]= start_write[1];
334	count[1]= count_write[0];
335	count[0]= count_write[1];
336	}
337
338	if (domain->hasLonLat)
339	{
340	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
341	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
342	}
343	break;
344	}
345	case CDomain::type_attr::rectilinear :
346	{
347	if (domain->hasLonLat)
348	{
349	std::vector<StdSize> start(1) ;
350	std::vector<StdSize> count(1) ;
351	if (domain->isEmpty())
352	{
353	start[0]=0 ;
354	count[0]=0 ;
355	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
356	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
357
358	}
359	else
360	{
361	start[0]= start_write[1];
362	count[0]= count_write[1];
363	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,count_write[0])) ;
364	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
365
366	start[0]= start_write[0];
367	count[0]= count_write[0];
368	CArray<double,1> lon=domain->lonvalue(Range(0,count_write[1])) ;
369	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
370	}
371	}
372	break;
373	}
374	}
375
376	if (domain->hasBounds)
377	{
378	std::vector<StdSize> start(3);
379	std::vector<StdSize> count(3);
380	if (domain->isEmpty())
381	{
382	start[2] = start[1] = start[0] = 0;
383	count[2] = count[1] = count[0] = 0;
384	}
385	else
386	{
387	start[2] = 0;
388	start[1] = start_write[0];
389	start[0] = start_write[1];
390	count[2] = nvertex;
391	count[1] = count_write[0];
392	count[0] = count_write[1];
393	}
394
395	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count);
396	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
397	}
398
399	if (domain->hasArea)
400	{
401	std::vector<StdSize> start(2);
402	std::vector<StdSize> count(2);
403
404	if (domain->isEmpty())
405	{
406	start[0] = 0; start[1] = 0;
407	count[0] = 0; count[1] = 0;
408	}
409	else
410	{
411	// start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
412	// start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
413	// count[1] = domain->zoom_ni_srv;
414	// count[0] = domain->zoom_nj_srv;
415
416	start[1]= start_write[0];
417	start[0]= start_write[1];
418	count[1]= count_write[0];
419	count[0]= count_write[1];
420	}
421
422	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
423	}
424
425	SuperClassWriter::definition_start();
426	break;
427	}
428	default :
429	ERROR("CNc4DataOutput::writeDomain(domain)",
430	<< "[ type = " << SuperClass::type << "]"
431	<< " not implemented yet !");
432	}
433	}
434	catch (CNetCdfException& e)
435	{
436	StdString msg("On writing the domain : ");
437	msg.append(domid); msg.append("\n");
438	msg.append("In the context : ");
439	msg.append(context->getId()); msg.append("\n");
440	msg.append(e.what());
441	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
442	}
443
444	domain->addRelFile(this->filename);
445	}
446
447	//--------------------------------------------------------------
448
449	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
450	{
451	CContext* context = CContext::getCurrent() ;
452	CContextServer* server=context->server ;
453
454	if (domain->IsWritten(this->filename)) return;
455	domain->checkAttributes();
456	if (domain->isEmpty())
457	if (SuperClass::type==MULTI_FILE) return ;
458
459	std::vector<StdString> dim0;
460	StdString domid = domain->getDomainOutputName();
461	StdString domainName = domain->name;
462	domain->assignMesh(domainName, domain->nvertex);
463	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
464
465	StdString node_x = domainName + "_node_x";
466	StdString node_y = domainName + "_node_y";
467
468	StdString edge_x = domainName + "_edge_x";
469	StdString edge_y = domainName + "_edge_y";
470	StdString edge_nodes = domainName + "_edge_nodes";
471
472	StdString face_x = domainName + "_face_x";
473	StdString face_y = domainName + "_face_y";
474	StdString face_nodes = domainName + "_face_nodes";
475	StdString face_edges = domainName + "_face_edges";
476	StdString edge_faces = domainName + "_edge_face_links";
477	StdString face_faces = domainName + "_face_links";
478
479	StdString dimNode = "n" + domainName + "_node";
480	StdString dimEdge = "n" + domainName + "_edge";
481	StdString dimFace = "n" + domainName + "_face";
482	StdString dimVertex = "n" + domainName + "_vertex";
483	StdString dimTwo = "Two";
484
485	const std::vector<int>& local_size_write = domain->getLocalWriteSize();
486	const std::vector<int>& global_size_write = domain->getGlobalWriteSize();
487	const std::vector<int>& start_write = domain->getStartWriteIndex();
488	const std::vector<int>& count_write = domain->getCountWriteIndex();
489
490	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
491	if (!isWrittenDomain(domid))
492	{
493	dim0.clear();
494	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
495	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
496	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
497	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
498	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
499	}
500
501	try
502	{
503	switch (SuperClass::type)
504	{
505	case (ONE_FILE) :
506	{
507	// Adding nodes
508	if (domain->nvertex == 1)
509	{
510	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
511	{
512	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
513	dim0.clear();
514	dim0.push_back(dimNode);
515	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
516	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
517	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
518	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
519	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
520	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
521	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
522	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
523	}
524	} // domain->nvertex == 1
525
526	// Adding edges and nodes, if nodes have not been defined previously
527	if (domain->nvertex == 2)
528	{
529	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
530	{
531	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
532	dim0.clear();
533	dim0.push_back(dimNode);
534	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
535	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
536	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
537	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
538	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
539	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
540	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
541	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
542	}
543	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
544	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
545	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
546	dim0.clear();
547	dim0.push_back(dimEdge);
548	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
549	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
550	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
551	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
552	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
553	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
554	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
555	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
556	dim0.clear();
557	dim0.push_back(dimEdge);
558	dim0.push_back(dimTwo);
559	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
560	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
561	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
562	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
563	} // domain->nvertex == 2
564
565	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
566	if (domain->nvertex > 2)
567	{
568	// Nodes
569	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
570	{
571	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
572	dim0.clear();
573	dim0.push_back(dimNode);
574	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
575	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
576	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
577	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
578	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
579	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
580	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
581	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
582	}
583	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
584	{
585	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
586	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
587	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
588	dim0.clear();
589	dim0.push_back(dimEdge);
590	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
591	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
592	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
593	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
594	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
595	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
596	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
597	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
598	dim0.clear();
599	dim0.push_back(dimEdge);
600	dim0.push_back(dimTwo);
601	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
602	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
603	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
604	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
605	}
606	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
607	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
608	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
609	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
610	dim0.clear();
611	dim0.push_back(dimFace);
612	SuperClassWriter::addVariable(face_x, NC_FLOAT, dim0);
613	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
614	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
615	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
616	SuperClassWriter::addVariable(face_y, NC_FLOAT, dim0);
617	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
618	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
619	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
620	dim0.clear();
621	dim0.push_back(dimFace);
622	dim0.push_back(dimVertex);
623	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
624	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
625	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
626	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
627	dim0.clear();
628	dim0.push_back(dimFace);
629	dim0.push_back(dimVertex);
630	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
631	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
632	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
633	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
634	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
635	dim0.clear();
636	dim0.push_back(dimEdge);
637	dim0.push_back(dimTwo);
638	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
639	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
640	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
641	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
642	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
643	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
644	dim0.clear();
645	dim0.push_back(dimFace);
646	dim0.push_back(dimVertex);
647	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
648	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
649	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
650	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
651	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
652	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
653	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
654	} // domain->nvertex > 2
655
656	SuperClassWriter::definition_end();
657
658	std::vector<StdSize> startEdges(1) ;
659	std::vector<StdSize> countEdges(1) ;
660	std::vector<StdSize> startNodes(1) ;
661	std::vector<StdSize> countNodes(1) ;
662	std::vector<StdSize> startFaces(1) ;
663	std::vector<StdSize> countFaces(1) ;
664	std::vector<StdSize> startEdgeNodes(2) ;
665	std::vector<StdSize> countEdgeNodes(2) ;
666	std::vector<StdSize> startEdgeFaces(2) ;
667	std::vector<StdSize> countEdgeFaces(2) ;
668	std::vector<StdSize> startFaceConctv(2) ;
669	std::vector<StdSize> countFaceConctv(2) ;
670
671	if (!isWrittenDomain(domid))
672	{
673	if (domain->nvertex == 1)
674	{
675	if (domain->isEmpty())
676	{
677	startNodes[0]=0 ;
678	countNodes[0]=0 ;
679	}
680	else
681	{
682	startNodes[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
683	countNodes[0] = count_write[0]; //domain->zoom_ni_srv ;
684	}
685
686	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
687	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
688	}
689	else if (domain->nvertex == 2)
690	{
691	if (domain->isEmpty())
692	{
693	startEdges[0]=0 ;
694	countEdges[0]=0 ;
695	startNodes[0]=0 ;
696	countNodes[0]=0 ;
697	startEdgeNodes[0]=0;
698	startEdgeNodes[1]=0;
699	countEdgeNodes[0]=0;
700	countEdgeNodes[1]=0;
701
702	}
703	else
704	{
705	startEdges[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
706	countEdges[0] = count_write[0];
707	startNodes[0] = domain->mesh->node_start;
708	countNodes[0] = domain->mesh->node_count;
709	startEdgeNodes[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
710	startEdgeNodes[1] = 0;
711	countEdgeNodes[0] = count_write[0]; //domain->zoom_ni_srv;
712	countEdgeNodes[1]= 2;
713	}
714	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
715	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
716	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
717	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
718	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
719	}
720	else
721	{
722	if (domain->isEmpty())
723	{
724	startFaces[0] = 0 ;
725	countFaces[0] = 0 ;
726	startNodes[0] = 0;
727	countNodes[0] = 0;
728	startEdges[0] = 0;
729	countEdges[0] = 0;
730	startEdgeFaces[0] = 0;
731	startEdgeFaces[1] = 0;
732	countEdgeFaces[0] = 0;
733	countEdgeFaces[1] = 0;
734	startFaceConctv[0] = 0;
735	startFaceConctv[1] = 0;
736	countFaceConctv[0] = 0;
737	countFaceConctv[1] = 0;
738	}
739	else
740	{
741	startFaces[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
742	countFaces[0] = count_write[0]; //domain->zoom_ni_srv ;
743	startNodes[0] = domain->mesh->node_start;
744	countNodes[0] = domain->mesh->node_count;
745	startEdges[0] = domain->mesh->edge_start;
746	countEdges[0] = domain->mesh->edge_count;
747	startEdgeNodes[0] = domain->mesh->edge_start;
748	startEdgeNodes[1] = 0;
749	countEdgeNodes[0] = domain->mesh->edge_count;
750	countEdgeNodes[1]= 2;
751	startEdgeFaces[0] = domain->mesh->edge_start;
752	startEdgeFaces[1]= 0;
753	countEdgeFaces[0] = domain->mesh->edge_count;
754	countEdgeFaces[1]= 2;
755	startFaceConctv[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
756	startFaceConctv[1] = 0; //0;
757	countFaceConctv[0] = count_write[0]; //domain->zoom_ni_srv;
758	countFaceConctv[1] = domain->nvertex;
759	}
760	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
761	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
762	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
763	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
764	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
765	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
766	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
767	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
768	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
769	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
770	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
771	}
772	setWrittenDomain(domid);
773	} // !isWrittenDomain
774	else
775	{
776	if (domain->nvertex == 2)
777	{
778	startEdges[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
779	countEdges[0] = count_write[0]; //domain->zoom_ni_srv ;
780	startEdgeNodes[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
781	startEdgeNodes[1] = 0; //0;
782	countEdgeNodes[0] = count_write[0]; //domain->zoom_ni_srv;
783	countEdgeNodes[1]= 2;
784	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
785	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
786	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
787	}
788	if (domain->nvertex > 2)
789	{
790
791	if (!domain->mesh->edgesAreWritten)
792	{
793	startEdges[0] = domain->mesh->edge_start;
794	countEdges[0] = domain->mesh->edge_count;
795	startEdgeNodes[0] = domain->mesh->edge_start;
796	startEdgeNodes[1] = 0;
797	countEdgeNodes[0] = domain->mesh->edge_count;
798	countEdgeNodes[1]= 2;
799	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
800	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
801	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
802	}
803	startFaces[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
804	countFaces[0] = count_write[0]; //domain->zoom_ni_srv;
805	startEdgeFaces[0] = domain->mesh->edge_start;
806	startEdgeFaces[1]= 0;
807	countEdgeFaces[0] = domain->mesh->edge_count;
808	countEdgeFaces[1]= 2;
809	startFaceConctv[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
810	startFaceConctv[1] = 0; //0;
811	countFaceConctv[0] = count_write[0]; //domain->zoom_ni_srv;
812	countFaceConctv[1]= domain->nvertex;
813	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
814	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
815	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
816	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
817	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
818	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
819	}
820	}// isWrittenDomain
821
822	SuperClassWriter::definition_start();
823
824	break;
825	} // ONE_FILE
826
827	case (MULTI_FILE) :
828	{
829	break;
830	}
831
832	default :
833	ERROR("CNc4DataOutput::writeDomain(domain)",
834	<< "[ type = " << SuperClass::type << "]"
835	<< " not implemented yet !");
836	} // switch
837	} // try
838
839	catch (CNetCdfException& e)
840	{
841	StdString msg("On writing the domain : ");
842	msg.append(domid); msg.append("\n");
843	msg.append("In the context : ");
844	msg.append(context->getId()); msg.append("\n");
845	msg.append(e.what());
846	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
847	}
848
849	domain->addRelFile(this->filename);
850	}
851
852	//--------------------------------------------------------------
853
854	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
855	{
856	CContext* context = CContext::getCurrent() ;
857	CContextServer* server=context->server ;
858
859	if (domain->IsWritten(this->filename)) return;
860	domain->checkAttributes();
861
862	if (domain->isEmpty())
863	if (SuperClass::type==MULTI_FILE) return ;
864
865	std::vector<StdString> dim0, dim1;
866	StdString domid = domain->getDomainOutputName();
867	if (isWrittenDomain(domid)) return ;
868	else setWrittenDomain(domid);
869
870	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
871
872	StdString dimXid = StdString("cell").append(appendDomid);
873	StdString dimVertId = StdString("nvertex").append(appendDomid);
874
875	string lonid,latid,bounds_lonid,bounds_latid ;
876	string areaId = "area" + appendDomid;
877
878	const std::vector<int>& local_size_write = domain->getLocalWriteSize();
879	const std::vector<int>& global_size_write = domain->getGlobalWriteSize();
880	const std::vector<int>& start_write = domain->getStartWriteIndex();
881	const std::vector<int>& count_write = domain->getCountWriteIndex();
882	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
883
884	try
885	{
886	switch (SuperClass::type)
887	{
888	case (MULTI_FILE) :
889	{
890	dim0.push_back(dimXid);
891	SuperClassWriter::addDimension(dimXid, local_size_write[0]);
892
893	lonid = StdString("lon").append(appendDomid);
894	latid = StdString("lat").append(appendDomid);
895	bounds_lonid = StdString("bounds_lon").append(appendDomid);
896	bounds_latid = StdString("bounds_lat").append(appendDomid);
897	if (domain->hasLonLat)
898	{
899	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
900	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
901	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
902	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
903	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
904	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
905	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
906	}
907	dim0.clear();
908	if (domain->hasBounds)
909	{
910	dim0.push_back(dimXid);
911	dim0.push_back(dimVertId);
912	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
913	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
914	}
915
916	dim0.clear();
917	dim0.push_back(dimXid);
918	if (domain->hasArea)
919	{
920	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
921	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
922	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
923	}
924
925	SuperClassWriter::definition_end();
926
927	if (domain->hasLonLat)
928	{
929	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
930	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
931	if (domain->hasBounds)
932	{
933	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
934	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
935	}
936	}
937
938	if (domain->hasArea)
939	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
940
941	SuperClassWriter::definition_start();
942	break ;
943	}
944
945	case (ONE_FILE) :
946	{
947	lonid = StdString("lon").append(appendDomid);
948	latid = StdString("lat").append(appendDomid);
949	bounds_lonid = StdString("bounds_lon").append(appendDomid);
950	bounds_latid = StdString("bounds_lat").append(appendDomid);
951	dim0.push_back(dimXid);
952	SuperClassWriter::addDimension(dimXid, global_size_write[0]);
953	if (domain->hasLonLat)
954	{
955	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
956	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
957
958	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
959	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
960	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
961	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
962	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
963	}
964	dim0.clear();
965
966	if (domain->hasBounds)
967	{
968	dim0.push_back(dimXid);
969	dim0.push_back(dimVertId);
970	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
971	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
972	}
973
974	if (domain->hasArea)
975	{
976	dim0.clear();
977	dim0.push_back(dimXid);
978	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
979	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
980	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
981	}
982
983	SuperClassWriter::definition_end();
984
985	std::vector<StdSize> start(1), startBounds(2) ;
986	std::vector<StdSize> count(1), countBounds(2) ;
987	if (domain->isEmpty())
988	{
989	start[0]=0 ;
990	count[0]=0 ;
991	startBounds[1]=0 ;
992	countBounds[1]=nvertex ;
993	startBounds[0]=0 ;
994	countBounds[0]=0 ;
995	}
996	else
997	{
998	start[0]=start_write[0];
999	count[0]=count_write[0];
1000	startBounds[0]=start_write[0];
1001	startBounds[1]=0 ;
1002	countBounds[0]=count_write[0];
1003	countBounds[1]=nvertex ;
1004	}
1005
1006	if (domain->hasLonLat)
1007	{
1008	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
1009	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
1010	if (domain->hasBounds)
1011	{
1012	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1013	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1014	}
1015	}
1016
1017	if (domain->hasArea)
1018	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
1019
1020	SuperClassWriter::definition_start();
1021
1022	break;
1023	}
1024	default :
1025	ERROR("CNc4DataOutput::writeDomain(domain)",
1026	<< "[ type = " << SuperClass::type << "]"
1027	<< " not implemented yet !");
1028	}
1029	}
1030	catch (CNetCdfException& e)
1031	{
1032	StdString msg("On writing the domain : ");
1033	msg.append(domid); msg.append("\n");
1034	msg.append("In the context : ");
1035	msg.append(context->getId()); msg.append("\n");
1036	msg.append(e.what());
1037	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1038	}
1039	domain->addRelFile(this->filename);
1040	}
1041	//--------------------------------------------------------------
1042
1043	void CNc4DataOutput::writeAxis_(CAxis* axis)
1044	{
1045	CContext* context = CContext::getCurrent();
1046
1047	if (axis->IsWritten(this->filename)) return;
1048	axis->checkAttributes();
1049
1050	int local_size_write = axis->getLocalWriteSize();
1051	int global_size_write = axis->getGlobalWriteSize();
1052	int start_write = axis->getStartWriteIndex();
1053	int count_write = axis->getCountWriteIndex();
1054
1055	if ((0 == local_size_write) && (MULTI_FILE == SuperClass::type)) return;
1056
1057	std::vector<StdString> dims;
1058	StdString axisid = axis->getAxisOutputName();
1059	if (isWrittenAxis(axisid)) return ;
1060	else setWrittenAxis(axisid);
1061
1062	try
1063	{
1064	SuperClassWriter::addDimension(axisid, global_size_write);
1065	if (axis->hasValue)
1066	{
1067	dims.push_back(axisid);
1068	SuperClassWriter::addVariable(axisid, NC_FLOAT, dims);
1069
1070	if (!axis->name.isEmpty())
1071	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1072
1073	if (!axis->standard_name.isEmpty())
1074	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1075
1076	if (!axis->long_name.isEmpty())
1077	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1078
1079	if (!axis->unit.isEmpty())
1080	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1081
1082	if (!axis->positive.isEmpty())
1083	{
1084	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1085	SuperClassWriter::addAttribute("positive",
1086	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1087	&axisid);
1088	}
1089
1090	StdString axisBoundsId = axisid + "_bounds";
1091	if (!axis->bounds.isEmpty())
1092	{
1093	dims.push_back("axis_nbounds");
1094	SuperClassWriter::addVariable(axisBoundsId, NC_FLOAT, dims);
1095	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1096	}
1097
1098	SuperClassWriter::definition_end();
1099
1100	switch (SuperClass::type)
1101	{
1102	case MULTI_FILE:
1103	{
1104	CArray<double,1> axis_value(local_size_write);
1105	for (int i = 0; i < local_size_write; i++) axis_value(i) = axis->value(i);
1106	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1107
1108	if (!axis->bounds.isEmpty())
1109	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
1110
1111	SuperClassWriter::definition_start();
1112
1113	break;
1114	}
1115	case ONE_FILE:
1116	{
1117	CArray<double,1> axis_value(count_write);
1118	axis_value = axis->value;
1119
1120	std::vector<StdSize> start(1), startBounds(2) ;
1121	std::vector<StdSize> count(1), countBounds(2) ;
1122	start[0] = startBounds[0] = start_write;
1123	count[0] = countBounds[0] = count_write;
1124	startBounds[1] = 0;
1125	countBounds[1] = 2;
1126	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1127
1128	if (!axis->bounds.isEmpty())
1129	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1130
1131	SuperClassWriter::definition_start();
1132
1133	break;
1134	}
1135	default :
1136	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1137	<< "[ type = " << SuperClass::type << "]"
1138	<< " not implemented yet !");
1139	}
1140	}
1141	}
1142	catch (CNetCdfException& e)
1143	{
1144	StdString msg("On writing the axis : ");
1145	msg.append(axisid); msg.append("\n");
1146	msg.append("In the context : ");
1147	CContext* context = CContext::getCurrent() ;
1148	msg.append(context->getId()); msg.append("\n");
1149	msg.append(e.what());
1150	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1151	}
1152
1153	axis->addRelFile(this->filename);
1154	}
1155
1156	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1157	{
1158	if (scalar->IsWritten(this->filename)) return;
1159	scalar->checkAttributes();
1160	int scalarSize = 1;
1161
1162	StdString scalaId = scalar->getScalarOutputName();
1163	if (isWrittenAxis(scalaId)) return ;
1164	else setWrittenAxis(scalaId);
1165
1166	try
1167	{
1168	if (!scalar->value.isEmpty())
1169	{
1170	// dims.push_back(scalaId);
1171	std::vector<StdString> dims;
1172	SuperClassWriter::addVariable(scalaId, NC_FLOAT, dims);
1173
1174	if (!scalar->name.isEmpty())
1175	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1176
1177	if (!scalar->standard_name.isEmpty())
1178	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1179
1180	if (!scalar->long_name.isEmpty())
1181	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1182
1183	if (!scalar->unit.isEmpty())
1184	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1185
1186	SuperClassWriter::definition_end();
1187
1188	switch (SuperClass::type)
1189	{
1190	case MULTI_FILE:
1191	{
1192	CArray<double,1> scalarValue(scalarSize);
1193	scalarValue(0) = scalar->value;
1194	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1195	SuperClassWriter::definition_start();
1196
1197	break;
1198	}
1199	case ONE_FILE:
1200	{
1201	CArray<double,1> scalarValue(scalarSize);
1202	scalarValue(0) = scalar->value;
1203
1204	std::vector<StdSize> start(1);
1205	std::vector<StdSize> count(1);
1206	start[0] = 0;
1207	count[0] = 1;
1208	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1209	SuperClassWriter::definition_start();
1210
1211	break;
1212	}
1213	default :
1214	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1215	<< "[ type = " << SuperClass::type << "]"
1216	<< " not implemented yet !");
1217	}
1218	}
1219	}
1220	catch (CNetCdfException& e)
1221	{
1222	StdString msg("On writing the scalar : ");
1223	msg.append(scalaId); msg.append("\n");
1224	msg.append("In the context : ");
1225	CContext* context = CContext::getCurrent() ;
1226	msg.append(context->getId()); msg.append("\n");
1227	msg.append(e.what());
1228	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1229	}
1230	scalar->addRelFile(this->filename);
1231	}
1232
1233	//--------------------------------------------------------------
1234
1235	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1236	{
1237	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1238
1239	try
1240	{
1241	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1242	std::vector<StdString> domainList = grid->getDomainList();
1243	std::vector<StdString> axisList = grid->getAxisList();
1244	std::vector<StdString> scalarList = grid->getScalarList();
1245	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1246
1247	std::vector<StdString> dims;
1248
1249	if (grid->isCompressible())
1250	{
1251	StdString varId = grid->getId() + "_points";
1252
1253	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1254	SuperClassWriter::addDimension(varId, nbIndexes);
1255
1256	dims.push_back(varId);
1257	SuperClassWriter::addVariable(varId, NC_INT, dims);
1258
1259	StdOStringStream compress;
1260	for (int i = numElement - 1; i >= 0; --i)
1261	{
1262	if (2 == axisDomainOrder(i))
1263	{
1264	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1265	StdString domId = domain->getDomainOutputName();
1266	StdString appendDomId = singleDomain ? "" : "_" + domId;
1267
1268	switch (domain->type)
1269	{
1270	case CDomain::type_attr::curvilinear:
1271	compress << "y" << appendDomId << " x" << appendDomId;
1272	break;
1273	case CDomain::type_attr::rectilinear:
1274	compress << "lat" << appendDomId << " lon" << appendDomId;
1275	break;
1276	case CDomain::type_attr::unstructured:
1277	compress << "cell" << appendDomId;
1278	break;
1279	}
1280	++idxDomain;
1281	}
1282	else if (1 == axisDomainOrder(i))
1283	{
1284	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1285	compress << axis->getAxisOutputName();
1286	++idxAxis;
1287	}
1288	else
1289	{
1290	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1291	compress << scalar->getScalarOutputName();
1292	++idxScalar;
1293	}
1294
1295	if (i != 0) compress << ' ';
1296	}
1297	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1298
1299	grid->computeCompressedIndex();
1300
1301	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1302	std::map<int, CArray<size_t, 1> >::const_iterator it;
1303	for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
1304	{
1305	const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
1306	for (int i = 0; i < it->second.numElements(); i++)
1307	indexes(compressedIndexes(i)) = it->second(i);
1308	}
1309
1310	switch (SuperClass::type)
1311	{
1312	case (MULTI_FILE):
1313	{
1314	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1315	break;
1316	}
1317	case (ONE_FILE):
1318	{
1319	if (grid->doGridHaveDataDistributed())
1320	grid->getDistributionServer()->computeGlobalIndex(indexes);
1321
1322	std::vector<StdSize> start, count;
1323	start.push_back(grid->getOffsetWrittenIndexes());
1324	count.push_back(grid->getNumberWrittenIndexes());
1325
1326	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1327	break;
1328	}
1329	}
1330	}
1331	else
1332	{
1333	for (int i = 0; i < numElement; ++i)
1334	{
1335	StdString varId, compress;
1336	CArray<int, 1> indexes;
1337	bool isDistributed;
1338	StdSize nbIndexes, totalNbIndexes, offset;
1339	int firstGlobalIndex;
1340
1341	if (2 == axisDomainOrder(i))
1342	{
1343	CDomain* domain = CDomain::get(domainList[idxDomain]);
1344	StdString domId = domain->getDomainOutputName();
1345
1346	if (!domain->isCompressible()
1347	\|\| domain->type == CDomain::type_attr::unstructured
1348	\|\| domain->isWrittenCompressed(this->filename)
1349	\|\| isWrittenCompressedDomain(domId))
1350	continue;
1351
1352	StdString appendDomId = singleDomain ? "" : "_" + domId;
1353
1354	varId = domId + "_points";
1355	switch (domain->type)
1356	{
1357	case CDomain::type_attr::curvilinear:
1358	compress = "y" + appendDomId + " x" + appendDomId;
1359	break;
1360	case CDomain::type_attr::rectilinear:
1361	compress = "lat" + appendDomId + " lon" + appendDomId;
1362	break;
1363	}
1364
1365	const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
1366	indexes.resize(indexesToWrite.size());
1367	for (int n = 0; n < indexes.numElements(); ++n)
1368	indexes(n) = indexesToWrite[n];
1369
1370	isDistributed = domain->isDistributed();
1371	nbIndexes = domain->getNumberWrittenIndexes();
1372	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1373	offset = domain->getOffsetWrittenIndexes();
1374	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1375
1376	domain->addRelFileCompressed(this->filename);
1377	setWrittenCompressedDomain(domId);
1378	++idxDomain;
1379	}
1380	else if (1 == axisDomainOrder(i))
1381	{
1382	CAxis* axis = CAxis::get(axisList[idxAxis]);
1383	StdString axisId = axis->getAxisOutputName();
1384
1385	if (!axis->isCompressible()
1386	\|\| axis->isWrittenCompressed(this->filename)
1387	\|\| isWrittenCompressedAxis(axisId))
1388	continue;
1389
1390	varId = axisId + "_points";
1391	compress = axisId;
1392
1393	const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
1394	indexes.resize(indexesToWrite.size());
1395	for (int n = 0; n < indexes.numElements(); ++n)
1396	indexes(n) = indexesToWrite[n];
1397
1398	isDistributed = axis->isDistributed();
1399	nbIndexes = axis->getNumberWrittenIndexes();
1400	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1401	offset = axis->getOffsetWrittenIndexes();
1402	firstGlobalIndex = axis->begin;
1403
1404	axis->addRelFileCompressed(this->filename);
1405	setWrittenCompressedAxis(axisId);
1406	++idxAxis;
1407	}
1408	else
1409	{
1410	}
1411
1412	if (!varId.empty())
1413	{
1414	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1415
1416	dims.clear();
1417	dims.push_back(varId);
1418	SuperClassWriter::addVariable(varId, NC_INT, dims);
1419
1420	SuperClassWriter::addAttribute("compress", compress, &varId);
1421
1422	switch (SuperClass::type)
1423	{
1424	case (MULTI_FILE):
1425	{
1426	indexes -= firstGlobalIndex;
1427	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1428	break;
1429	}
1430	case (ONE_FILE):
1431	{
1432	std::vector<StdSize> start, count;
1433	start.push_back(offset);
1434	count.push_back(nbIndexes);
1435
1436	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1437	break;
1438	}
1439	}
1440	}
1441	}
1442
1443	if (!dims.empty())
1444	grid->computeCompressedIndex();
1445	}
1446
1447	grid->addRelFileCompressed(this->filename);
1448	}
1449	catch (CNetCdfException& e)
1450	{
1451	StdString msg("On writing compressed grid : ");
1452	msg.append(grid->getId()); msg.append("\n");
1453	msg.append("In the context : ");
1454	CContext* context = CContext::getCurrent();
1455	msg.append(context->getId()); msg.append("\n");
1456	msg.append(e.what());
1457	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1458	}
1459	}
1460
1461	//--------------------------------------------------------------
1462
1463	void CNc4DataOutput::writeTimeDimension_(void)
1464	{
1465	try
1466	{
1467	SuperClassWriter::addDimension(getTimeCounterName());
1468	}
1469	catch (CNetCdfException& e)
1470	{
1471	StdString msg("On writing time dimension : time_couter\n");
1472	msg.append("In the context : ");
1473	CContext* context = CContext::getCurrent() ;
1474	msg.append(context->getId()); msg.append("\n");
1475	msg.append(e.what());
1476	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1477	}
1478	}
1479
1480	//--------------------------------------------------------------
1481
1482	void CNc4DataOutput::writeField_(CField* field)
1483	{
1484	CContext* context = CContext::getCurrent() ;
1485	CContextServer* server=context->server ;
1486
1487	std::vector<StdString> dims, coodinates;
1488	CGrid* grid = field->grid;
1489	if (!grid->doGridHaveDataToWrite())
1490	if (SuperClass::type==MULTI_FILE) return ;
1491
1492	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1493	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1494	std::vector<StdString> domainList = grid->getDomainList();
1495	std::vector<StdString> axisList = grid->getAxisList();
1496	std::vector<StdString> scalarList = grid->getScalarList();
1497
1498	StdString timeid = getTimeCounterName();
1499	StdString dimXid,dimYid;
1500	std::deque<StdString> dimIdList, dimCoordList;
1501	bool hasArea = false;
1502	StdString cellMeasures = "area:";
1503	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1504
1505	for (int i = 0; i < numElement; ++i)
1506	{
1507	if (2 == axisDomainOrder(i))
1508	{
1509	CDomain* domain = CDomain::get(domainList[idxDomain]);
1510	StdString domId = domain->getDomainOutputName();
1511	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1512
1513	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1514	{
1515	dimIdList.push_back(domId + "_points");
1516	field->setUseCompressedOutput();
1517	}
1518
1519	switch (domain->type)
1520	{
1521	case CDomain::type_attr::curvilinear:
1522	if (!compressedOutput \|\| !domain->isCompressible())
1523	{
1524	dimXid = StdString("x").append(appendDomId);
1525	dimIdList.push_back(dimXid);
1526	dimYid = StdString("y").append(appendDomId);
1527	dimIdList.push_back(dimYid);
1528	}
1529	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1530	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1531	break ;
1532	case CDomain::type_attr::rectilinear:
1533	if (!compressedOutput \|\| !domain->isCompressible())
1534	{
1535	dimXid = StdString("lon").append(appendDomId);
1536	dimIdList.push_back(dimXid);
1537	dimYid = StdString("lat").append(appendDomId);
1538	dimIdList.push_back(dimYid);
1539	}
1540	break ;
1541	case CDomain::type_attr::unstructured:
1542	{
1543	if (SuperClassWriter::useCFConvention)
1544	{
1545	dimXid = StdString("cell").append(appendDomId);
1546	dimIdList.push_back(dimXid);
1547	dimCoordList.push_back(StdString("lon").append(appendDomId));
1548	dimCoordList.push_back(StdString("lat").append(appendDomId));
1549	}
1550	else
1551	{
1552	StdString domainName = domain->name;
1553	if (domain->nvertex == 1)
1554	{
1555	dimXid = "n" + domainName + "_node";
1556	dimIdList.push_back(dimXid);
1557	dimCoordList.push_back(StdString(domainName + "_node_x"));
1558	dimCoordList.push_back(StdString(domainName + "_node_y"));
1559	}
1560	else if (domain->nvertex == 2)
1561	{
1562	dimXid = "n" + domainName + "_edge";
1563	dimIdList.push_back(dimXid);
1564	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1565	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1566	}
1567	else
1568	{
1569	dimXid = "n" + domainName + "_face";
1570	dimIdList.push_back(dimXid);
1571	dimCoordList.push_back(StdString(domainName + "_face_x"));
1572	dimCoordList.push_back(StdString(domainName + "_face_y"));
1573	}
1574	} // ugrid convention
1575	} // case unstructured domain
1576	}
1577
1578	if (domain->hasArea)
1579	{
1580	hasArea = true;
1581	cellMeasures += " area" + appendDomId;
1582	}
1583	++idxDomain;
1584	}
1585	else if (1 == axisDomainOrder(i))
1586	{
1587	CAxis* axis = CAxis::get(axisList[idxAxis]);
1588	StdString axisId = axis->getAxisOutputName();
1589
1590	if (compressedOutput && axis->isCompressible())
1591	{
1592	dimIdList.push_back(axisId + "_points");
1593	field->setUseCompressedOutput();
1594	}
1595	else
1596	dimIdList.push_back(axisId);
1597
1598	dimCoordList.push_back(axisId);
1599	++idxAxis;
1600	}
1601	else // scalar
1602	{
1603	/* Do nothing here */
1604	}
1605	}
1606
1607	/*
1608	StdString lonid_loc = (server->intraCommSize > 1)
1609	? StdString("lon").append(appendDomid).append("_local")
1610	: lonid;
1611	StdString latid_loc = (server->intraCommSize > 1)
1612	? StdString("lat").append(appendDomid).append("_local")
1613	: latid;
1614	*/
1615	StdString fieldid = field->getFieldOutputName();
1616
1617	nc_type type ;
1618	if (field->prec.isEmpty()) type = NC_FLOAT ;
1619	else
1620	{
1621	if (field->prec==2) type = NC_SHORT ;
1622	else if (field->prec==4) type = NC_FLOAT ;
1623	else if (field->prec==8) type = NC_DOUBLE ;
1624	}
1625
1626	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1627
1628	if (wtime)
1629	{
1630
1631	//StdOStringStream oss;
1632	// oss << "time_" << field->operation.getValue()
1633	// << "_" << field->getRelFile()->output_freq.getValue();
1634	//oss
1635	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
1636	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
1637	dims.push_back(timeid);
1638	}
1639
1640	if (compressedOutput && grid->isCompressible())
1641	{
1642	dims.push_back(grid->getId() + "_points");
1643	field->setUseCompressedOutput();
1644	}
1645	else
1646	{
1647	while (!dimIdList.empty())
1648	{
1649	dims.push_back(dimIdList.back());
1650	dimIdList.pop_back();
1651	}
1652	}
1653
1654	while (!dimCoordList.empty())
1655	{
1656	coodinates.push_back(dimCoordList.back());
1657	dimCoordList.pop_back();
1658	}
1659
1660	try
1661	{
1662	SuperClassWriter::addVariable(fieldid, type, dims);
1663
1664	if (!field->standard_name.isEmpty())
1665	SuperClassWriter::addAttribute
1666	("standard_name", field->standard_name.getValue(), &fieldid);
1667
1668	if (!field->long_name.isEmpty())
1669	SuperClassWriter::addAttribute
1670	("long_name", field->long_name.getValue(), &fieldid);
1671
1672	if (!field->unit.isEmpty())
1673	SuperClassWriter::addAttribute
1674	("units", field->unit.getValue(), &fieldid);
1675
1676	if (!field->valid_min.isEmpty())
1677	SuperClassWriter::addAttribute
1678	("valid_min", field->valid_min.getValue(), &fieldid);
1679
1680	if (!field->valid_max.isEmpty())
1681	SuperClassWriter::addAttribute
1682	("valid_max", field->valid_max.getValue(), &fieldid);
1683
1684	if (!field->scale_factor.isEmpty())
1685	SuperClassWriter::addAttribute
1686	("scale_factor", field->scale_factor.getValue(), &fieldid);
1687
1688	if (!field->add_offset.isEmpty())
1689	SuperClassWriter::addAttribute
1690	("add_offset", field->add_offset.getValue(), &fieldid);
1691
1692	SuperClassWriter::addAttribute
1693	("online_operation", field->operation.getValue(), &fieldid);
1694
1695	// write child variables as attributes
1696
1697
1698	vector<CVariable*> listVars = field->getAllVariables() ;
1699	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1700
1701	bool alreadyAddCellMethod = false;
1702	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1703	if (!field->cell_methods.isEmpty())
1704	{
1705	StdString cellMethodString = field->cell_methods;
1706	if (field->cell_methods_mode.isEmpty() \|\|
1707	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1708	{
1709	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1710	alreadyAddCellMethod = true;
1711	}
1712	else
1713	{
1714	switch (field->cell_methods_mode)
1715	{
1716	case (CField::cell_methods_mode_attr::prefix):
1717	cellMethodsPrefix = cellMethodString;
1718	cellMethodsPrefix += " ";
1719	break;
1720	case (CField::cell_methods_mode_attr::suffix):
1721	cellMethodsSuffix = " ";
1722	cellMethodsSuffix += cellMethodString;
1723	break;
1724	case (CField::cell_methods_mode_attr::none):
1725	break;
1726	default:
1727	break;
1728	}
1729	}
1730	}
1731
1732
1733	if (wtime)
1734	{
1735	CDuration freqOp = field->freq_op.getValue();
1736	freqOp.solveTimeStep(*context->calendar);
1737	StdString freqOpStr = freqOp.toStringUDUnits();
1738	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1739
1740	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1741	freqOut.solveTimeStep(*context->calendar);
1742	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1743
1744	StdString cellMethods(cellMethodsPrefix + "time: ");
1745	if (field->operation.getValue() == "instant") cellMethods += "point";
1746	else if (field->operation.getValue() == "average") cellMethods += "mean";
1747	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1748	else cellMethods += field->operation;
1749	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1750	cellMethods += " (interval: " + freqOpStr + ")";
1751	cellMethods += cellMethodsSuffix;
1752	if (!alreadyAddCellMethod)
1753	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1754	}
1755
1756	if (hasArea)
1757	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1758
1759	if (!field->default_value.isEmpty())
1760	{
1761	double default_value = field->default_value.getValue();
1762	float fdefault_value = (float)default_value;
1763	if (type == NC_DOUBLE)
1764	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1765	else
1766	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1767	}
1768	else
1769	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1770
1771	if (field->compression_level.isEmpty())
1772	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1773	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1774
1775	{ // Ecriture des coordonnes
1776
1777	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1778	std::vector<StdString>::iterator
1779	itc = coodinates.begin(), endc = coodinates.end();
1780
1781	for (; itc!= endc; itc++)
1782	{
1783	StdString & coord = *itc;
1784	if (itc+1 != endc)
1785	coordstr.append(coord).append(" ");
1786	else coordstr.append(coord);
1787	}
1788
1789	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1790
1791	}
1792	}
1793	catch (CNetCdfException& e)
1794	{
1795	StdString msg("On writing field : ");
1796	msg.append(fieldid); msg.append("\n");
1797	msg.append("In the context : ");
1798	msg.append(context->getId()); msg.append("\n");
1799	msg.append(e.what());
1800	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1801	}
1802	} // writeField_()
1803
1804	//--------------------------------------------------------------
1805
1806	void CNc4DataOutput::writeFile_ (CFile* file)
1807	{
1808	StdString filename = file->getFileOutputName();
1809	StdString description = (!file->description.isEmpty())
1810	? file->description.getValue()
1811	: StdString("Created by xios");
1812
1813	singleDomain = (file->nbDomains == 1);
1814
1815	try
1816	{
1817	if (SuperClassWriter::useCFConvention)
1818	this->writeFileAttributes(filename, description,
1819	StdString("CF-1.5"),
1820	StdString("An IPSL model"),
1821	this->getTimeStamp());
1822	else
1823	this->writeFileAttributes(filename, description,
1824	StdString("UGRID"),
1825	StdString("An IPSL model"),
1826	this->getTimeStamp());
1827
1828
1829	if (!appendMode)
1830	SuperClassWriter::addDimension("axis_nbounds", 2);
1831	}
1832	catch (CNetCdfException& e)
1833	{
1834	StdString msg("On writing file : ");
1835	msg.append(filename); msg.append("\n");
1836	msg.append("In the context : ");
1837	CContext* context = CContext::getCurrent() ;
1838	msg.append(context->getId()); msg.append("\n");
1839	msg.append(e.what());
1840	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1841	}
1842	}
1843
1844	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1845	{
1846	StdString name = var->getVariableOutputName();
1847
1848	try
1849	{
1850	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1851	addAttribute(name, var->getData<int>(), &fieldId);
1852	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1853	addAttribute(name, var->getData<short int>(), &fieldId);
1854	else if (var->type.getValue() == CVariable::type_attr::t_float)
1855	addAttribute(name, var->getData<float>(), &fieldId);
1856	else if (var->type.getValue() == CVariable::type_attr::t_double)
1857	addAttribute(name, var->getData<double>(), &fieldId);
1858	else if (var->type.getValue() == CVariable::type_attr::t_string)
1859	addAttribute(name, var->getData<string>(), &fieldId);
1860	else
1861	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1862	<< "Unsupported variable of type " << var->type.getStringValue());
1863	}
1864	catch (CNetCdfException& e)
1865	{
1866	StdString msg("On writing attributes of variable with name : ");
1867	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1868	msg.append("In the context : ");
1869	CContext* context = CContext::getCurrent() ;
1870	msg.append(context->getId()); msg.append("\n");
1871	msg.append(e.what());
1872	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1873	}
1874	}
1875
1876	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1877	{
1878	StdString name = var->getVariableOutputName();
1879
1880	try
1881	{
1882	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1883	addAttribute(name, var->getData<int>());
1884	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1885	addAttribute(name, var->getData<short int>());
1886	else if (var->type.getValue() == CVariable::type_attr::t_float)
1887	addAttribute(name, var->getData<float>());
1888	else if (var->type.getValue() == CVariable::type_attr::t_double)
1889	addAttribute(name, var->getData<double>());
1890	else if (var->type.getValue() == CVariable::type_attr::t_string)
1891	addAttribute(name, var->getData<string>());
1892	else
1893	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1894	<< "Unsupported variable of type " << var->type.getStringValue());
1895	}
1896	catch (CNetCdfException& e)
1897	{
1898	StdString msg("On writing attributes of variable with name : ");
1899	msg.append(name); msg.append("\n");
1900	msg.append("In the context : ");
1901	CContext* context = CContext::getCurrent() ;
1902	msg.append(context->getId()); msg.append("\n");
1903	msg.append(e.what());
1904	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1905	}
1906	}
1907
1908	void CNc4DataOutput::syncFile_ (void)
1909	{
1910	try
1911	{
1912	SuperClassWriter::sync() ;
1913	}
1914	catch (CNetCdfException& e)
1915	{
1916	StdString msg("On synchronizing the write among processes");
1917	msg.append("In the context : ");
1918	CContext* context = CContext::getCurrent() ;
1919	msg.append(context->getId()); msg.append("\n");
1920	msg.append(e.what());
1921	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1922	}
1923	}
1924
1925	void CNc4DataOutput::closeFile_ (void)
1926	{
1927	try
1928	{
1929	SuperClassWriter::close() ;
1930	}
1931	catch (CNetCdfException& e)
1932	{
1933	StdString msg("On closing file");
1934	msg.append("In the context : ");
1935	CContext* context = CContext::getCurrent() ;
1936	msg.append(context->getId()); msg.append("\n");
1937	msg.append(e.what());
1938	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1939	}
1940
1941	}
1942
1943	//---------------------------------------------------------------
1944
1945	StdString CNc4DataOutput::getTimeStamp(void) const
1946	{
1947	const int buffer_size = 100;
1948	time_t rawtime;
1949	struct tm * timeinfo = NULL;
1950	char buffer [buffer_size];
1951
1952	time ( &rawtime );
1953	timeinfo = localtime ( &rawtime );
1954	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
1955
1956	return (StdString(buffer));
1957	}
1958
1959	//---------------------------------------------------------------
1960
1961	void CNc4DataOutput::writeFieldData_ (CField* field)
1962	{
1963	CContext* context = CContext::getCurrent();
1964	CContextServer* server = context->server;
1965	CGrid* grid = field->grid;
1966
1967	if (field->getNStep()<1) return ;
1968
1969	if (!grid->doGridHaveDataToWrite())
1970	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
1971
1972	StdString fieldid = field->getFieldOutputName();
1973
1974	StdOStringStream oss;
1975	string timeAxisId;
1976	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
1977	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
1978
1979	StdString timeBoundId = getTimeCounterName() + "_bounds";
1980
1981	StdString timeAxisBoundId;
1982	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
1983	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
1984
1985	if (!field->wasWritten())
1986	{
1987	if (appendMode && field->file->record_offset.isEmpty() &&
1988	field->getOperationTimeType() != func::CFunctor::once)
1989	{
1990	field->resetNStep(getRecordFromTime(field->last_Write_srv) + 1);
1991	}
1992
1993	field->setWritten();
1994	}
1995
1996
1997	CArray<double,1> time_data(1);
1998	CArray<double,1> time_data_bound(2);
1999	CArray<double,1> time_counter(1);
2000	CArray<double,1> time_counter_bound(2);
2001
2002	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2003
2004	if (wtime)
2005	{
2006	Time lastWrite = field->last_Write_srv;
2007	Time lastLastWrite = field->lastlast_Write_srv;
2008
2009	if (field->getOperationTimeType() == func::CFunctor::instant)
2010	time_data(0) = lastWrite;
2011	else if (field->getOperationTimeType() == func::CFunctor::centered)
2012	time_data(0) = (lastWrite + lastLastWrite) / 2;
2013
2014	if (field->getOperationTimeType() == func::CFunctor::instant)
2015	time_data_bound(0) = time_data_bound(1) = lastWrite;
2016	else if (field->getOperationTimeType() == func::CFunctor::centered)
2017	{
2018	time_data_bound(0) = lastLastWrite;
2019	time_data_bound(1) = lastWrite;
2020	}
2021
2022	if (field->file->time_counter == CFile::time_counter_attr::instant)
2023	time_counter(0) = lastWrite;
2024	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2025	time_counter(0) = (lastWrite + lastLastWrite) / 2;
2026	else if (field->file->time_counter == CFile::time_counter_attr::record)
2027	time_counter(0) = field->getNStep() - 1;
2028
2029
2030	if (field->file->time_counter == CFile::time_counter_attr::instant)
2031	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
2032	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2033	{
2034	time_counter_bound(0) = lastLastWrite;
2035	time_counter_bound(1) = lastWrite;
2036	}
2037	else if (field->file->time_counter == CFile::time_counter_attr::record)
2038	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2039	}
2040
2041	bool isRoot = (server->intraCommRank == 0);
2042
2043	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2044	{
2045	double scaleFactor = 1.0;
2046	double addOffset = 0.0;
2047	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2048	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2049	field->scaleFactorAddOffset(scaleFactor, addOffset);
2050	}
2051
2052	try
2053	{
2054	size_t writtenSize;
2055	if (field->getUseCompressedOutput())
2056	writtenSize = grid->getNumberWrittenIndexes();
2057	else
2058	writtenSize = grid->getWrittenDataSize();
2059
2060	CArray<double,1> fieldData(writtenSize);
2061	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2062
2063	if (field->getUseCompressedOutput())
2064	field->outputCompressedField(fieldData);
2065	else
2066	field->outputField(fieldData);
2067
2068	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2069
2070	switch (SuperClass::type)
2071	{
2072	case (MULTI_FILE) :
2073	{
2074	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2075	if (wtime)
2076	{
2077	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2078	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2079	if (field->file->time_counter != CFile::time_counter_attr::none)
2080	{
2081	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2082	if (field->file->time_counter != CFile::time_counter_attr::record)
2083	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2084	}
2085	}
2086	break;
2087	}
2088	case (ONE_FILE) :
2089	{
2090	// const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2091	// const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2092	// const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2093
2094	// std::vector<StdSize> start, count;
2095
2096	// if (field->getUseCompressedOutput())
2097	// {
2098	// if (grid->isCompressible())
2099	// {
2100	// start.push_back(grid->getOffsetWrittenIndexes());
2101	// count.push_back(grid->getNumberWrittenIndexes());
2102	// }
2103	// else
2104	// {
2105	// CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2106	// std::vector<StdString> domainList = grid->getDomainList();
2107	// std::vector<StdString> axisList = grid->getAxisList();
2108	// int numElement = axisDomainOrder.numElements();
2109	// int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2110	// int idx = nZoomBeginGlobal.size() - 1;
2111
2112	// start.reserve(nZoomBeginGlobal.size());
2113	// count.reserve(nZoomBeginGlobal.size());
2114
2115
2116	// for (int i = numElement - 1; i >= 0; --i)
2117	// {
2118	// if (2 == axisDomainOrder(i))
2119	// {
2120	// CDomain* domain = CDomain::get(domainList[idxDomain]);
2121
2122	// if (domain->isCompressible())
2123	// {
2124	// start.push_back(domain->getOffsetWrittenIndexes());
2125	// count.push_back(domain->getNumberWrittenIndexes());
2126	// idx -= 2;
2127	// }
2128	// else
2129	// {
2130	// if ((domain->type) != CDomain::type_attr::unstructured)
2131	// {
2132	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2133	// count.push_back(nZoomSizeServer[idx]);
2134	// }
2135	// --idx;
2136	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2137	// count.push_back(nZoomSizeServer[idx]);
2138	// --idx;
2139	// }
2140	// --idxDomain;
2141	// }
2142	// else if (1 == axisDomainOrder(i))
2143	// {
2144	// CAxis* axis = CAxis::get(axisList[idxAxis]);
2145
2146	// if (axis->isCompressible())
2147	// {
2148	// start.push_back(axis->getOffsetWrittenIndexes());
2149	// count.push_back(axis->getNumberWrittenIndexes());
2150	// }
2151	// else
2152	// {
2153	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2154	// count.push_back(nZoomSizeServer[idx]);
2155	// }
2156
2157	// --idxAxis;
2158	// --idx;
2159	// }
2160	// }
2161	// }
2162	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2163	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2164	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2165
2166	std::vector<StdSize> start, count;
2167
2168	if (field->getUseCompressedOutput())
2169	{
2170	if (grid->isCompressible())
2171	{
2172	start.push_back(grid->getOffsetWrittenIndexes());
2173	count.push_back(grid->getNumberWrittenIndexes());
2174	}
2175	else
2176	{
2177	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2178	std::vector<StdString> domainList = grid->getDomainList();
2179	std::vector<StdString> axisList = grid->getAxisList();
2180	int numElement = axisDomainOrder.numElements();
2181	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2182	int idx = nZoomBeginGlobal.size() - 1;
2183
2184	start.reserve(nZoomBeginGlobal.size());
2185	count.reserve(nZoomBeginGlobal.size());
2186
2187
2188	for (int i = numElement - 1; i >= 0; --i)
2189	{
2190	if (2 == axisDomainOrder(i))
2191	{
2192	CDomain* domain = CDomain::get(domainList[idxDomain]);
2193
2194	if (domain->isCompressible())
2195	{
2196	start.push_back(domain->getOffsetWrittenIndexes());
2197	count.push_back(domain->getNumberWrittenIndexes());
2198	idx -= 2;
2199	}
2200	else
2201	{
2202	if ((domain->type) != CDomain::type_attr::unstructured)
2203	{
2204	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2205	count.push_back(nZoomSizeServer[idx]);
2206	}
2207	--idx;
2208	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2209	count.push_back(nZoomSizeServer[idx]);
2210	--idx;
2211	}
2212	--idxDomain;
2213	}
2214	else if (1 == axisDomainOrder(i))
2215	{
2216	CAxis* axis = CAxis::get(axisList[idxAxis]);
2217
2218	if (axis->isCompressible())
2219	{
2220	start.push_back(axis->getOffsetWrittenIndexes());
2221	count.push_back(axis->getNumberWrittenIndexes());
2222	}
2223	else
2224	{
2225	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2226	count.push_back(nZoomSizeServer[idx]);
2227	}
2228
2229	--idxAxis;
2230	--idx;
2231	}
2232	}
2233	}
2234	}
2235	else
2236	{
2237	// CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2238	// std::vector<StdString> domainList = grid->getDomainList();
2239	// std::vector<StdString> axisList = grid->getAxisList();
2240	// int numElement = axisDomainOrder.numElements();
2241	// int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2242	// int idx = nZoomBeginGlobal.size() - 1;
2243
2244	// start.reserve(nZoomBeginGlobal.size());
2245	// count.reserve(nZoomBeginGlobal.size());
2246
2247	// for (int i = numElement - 1; i >= 0; --i)
2248	// {
2249	// if (2 == axisDomainOrder(i))
2250	// {
2251	// CDomain* domain = CDomain::get(domainList[idxDomain]);
2252	// if ((domain->type) != CDomain::type_attr::unstructured)
2253	// {
2254	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2255	// count.push_back(nZoomSizeServer[idx]);
2256	// }
2257	// --idx ;
2258	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2259	// count.push_back(nZoomSizeServer[idx]);
2260	// --idx ;
2261	// --idxDomain;
2262	// }
2263	// else if (1 == axisDomainOrder(i))
2264	// {
2265	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2266	// count.push_back(nZoomSizeServer[idx]);
2267	// --idx;
2268	// }
2269	// else
2270	// {
2271	// if (1 == axisDomainOrder.numElements())
2272	// {
2273	// start.push_back(0);
2274	// count.push_back(1);
2275	// }
2276	// --idx;
2277	// }
2278	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2279	std::vector<StdString> domainList = grid->getDomainList();
2280	std::vector<StdString> axisList = grid->getAxisList();
2281	int numElement = axisDomainOrder.numElements();
2282	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2283	int idx = domainList.size() * 2 + axisList.size() - 1;// nZoomBeginGlobal.size() - 1;
2284
2285	start.reserve(nZoomBeginGlobal.size());
2286	count.reserve(nZoomBeginGlobal.size());
2287
2288	for (int i = numElement - 1; i >= 0; --i)
2289	{
2290	if (2 == axisDomainOrder(i))
2291	{
2292	CDomain* domain = CDomain::get(domainList[idxDomain]);
2293	if ((domain->type) != CDomain::type_attr::unstructured)
2294	{
2295	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2296	// count.push_back(nZoomSizeServer[idx]);
2297	start.push_back((domain->getStartWriteIndex())[idx]);
2298	count.push_back((domain->getCountWriteIndex())[idx]);
2299	}
2300	--idx ;
2301	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2302	// count.push_back(nZoomSizeServer[idx]);
2303	start.push_back((domain->getStartWriteIndex())[idx]);
2304	count.push_back((domain->getCountWriteIndex())[idx]);
2305	--idx ;
2306	--idxDomain;
2307	}
2308	else if (1 == axisDomainOrder(i))
2309	{
2310	CAxis* axis = CAxis::get(axisList[idxAxis]);
2311	start.push_back(axis->getStartWriteIndex());
2312	count.push_back(axis->getCountWriteIndex());
2313	--idx;
2314	--idxAxis;
2315	}
2316	else
2317	{
2318	if (1 == axisDomainOrder.numElements())
2319	{
2320	start.push_back(0);
2321	count.push_back(1);
2322	}
2323	--idx;
2324	}
2325	}
2326	}
2327
2328	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2329	if (wtime)
2330	{
2331	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2332	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2333	if (field->file->time_counter != CFile::time_counter_attr::none)
2334	{
2335	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
2336	if (field->file->time_counter != CFile::time_counter_attr::record)
2337	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2338	}
2339	}
2340
2341	break;
2342	}
2343	}
2344	}
2345	catch (CNetCdfException& e)
2346	{
2347	StdString msg("On writing field data: ");
2348	msg.append(fieldid); msg.append("\n");
2349	msg.append("In the context : ");
2350	msg.append(context->getId()); msg.append("\n");
2351	msg.append(e.what());
2352	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2353	}
2354	}
2355
2356	//---------------------------------------------------------------
2357
2358	void CNc4DataOutput::writeTimeAxis_
2359	(CField* field,
2360	const boost::shared_ptr<CCalendar> cal)
2361	{
2362	StdOStringStream oss;
2363
2364	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2365
2366	// oss << "time_" << field->operation.getValue()
2367	// << "_" << field->getRelFile()->output_freq.getValue();
2368
2369	// StdString axisid = oss.str();
2370	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
2371	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
2372
2373	StdString axisid("time_centered") ;
2374	StdString axisBoundId("time_centered_bounds");
2375	StdString timeid(getTimeCounterName());
2376	StdString timeBoundId("axis_nbounds");
2377
2378	if (field->getOperationTimeType() == func::CFunctor::instant)
2379	{
2380	axisid = "time_instant";
2381	axisBoundId = "time_instant_bounds";
2382	}
2383
2384	try
2385	{
2386	// Adding time_instant or time_centered
2387	std::vector<StdString> dims;
2388	dims.push_back(timeid);
2389	if (!SuperClassWriter::varExist(axisid))
2390	{
2391	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2392
2393	CDate timeOrigin=cal->getTimeOrigin() ;
2394	StdOStringStream oss2;
2395	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
2396	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
2397	StdString strInitdate=oss2.str() ;
2398	StdString strTimeOrigin=timeOrigin.toString() ;
2399	this->writeTimeAxisAttributes
2400	(axisid, cal->getType(),
2401	StdString("seconds since ").append(strTimeOrigin),
2402	strTimeOrigin, axisBoundId);
2403	}
2404
2405	// Adding time_instant_bounds or time_centered_bounds variables
2406	if (!SuperClassWriter::varExist(axisBoundId))
2407	{
2408	dims.clear() ;
2409	dims.push_back(timeid);
2410	dims.push_back(timeBoundId);
2411	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2412	}
2413
2414	if (field->file->time_counter != CFile::time_counter_attr::none)
2415	{
2416	// Adding time_counter
2417	axisid = getTimeCounterName();
2418	axisBoundId = getTimeCounterName() + "_bounds";
2419	dims.clear();
2420	dims.push_back(timeid);
2421	if (!SuperClassWriter::varExist(axisid))
2422	{
2423	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2424	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
2425
2426	if (field->file->time_counter != CFile::time_counter_attr::record)
2427	{
2428	CDate timeOrigin = cal->getTimeOrigin();
2429	StdString strTimeOrigin = timeOrigin.toString();
2430
2431	this->writeTimeAxisAttributes(axisid, cal->getType(),
2432	StdString("seconds since ").append(strTimeOrigin),
2433	strTimeOrigin, axisBoundId);
2434	}
2435	}
2436
2437	// Adding time_counter_bound dimension
2438	if (field->file->time_counter != CFile::time_counter_attr::record)
2439	{
2440	if (!SuperClassWriter::varExist(axisBoundId))
2441	{
2442	dims.clear();
2443	dims.push_back(timeid);
2444	dims.push_back(timeBoundId);
2445	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2446	}
2447	}
2448	}
2449	}
2450	catch (CNetCdfException& e)
2451	{
2452	StdString msg("On writing time axis data: ");
2453	msg.append("In the context : ");
2454	CContext* context = CContext::getCurrent() ;
2455	msg.append(context->getId()); msg.append("\n");
2456	msg.append(e.what());
2457	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2458	const boost::shared_ptr<CCalendar> cal)", << msg);
2459	}
2460	}
2461
2462	//---------------------------------------------------------------
2463
2464	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2465	const StdString & calendar,
2466	const StdString & units,
2467	const StdString & time_origin,
2468	const StdString & time_bounds,
2469	const StdString & standard_name,
2470	const StdString & long_name)
2471	{
2472	try
2473	{
2474	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2475	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2476	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2477	SuperClassWriter::addAttribute("units", units , &axis_name);
2478	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2479	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2480	}
2481	catch (CNetCdfException& e)
2482	{
2483	StdString msg("On writing time axis Attribute: ");
2484	msg.append("In the context : ");
2485	CContext* context = CContext::getCurrent() ;
2486	msg.append(context->getId()); msg.append("\n");
2487	msg.append(e.what());
2488	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2489	const StdString & calendar,\
2490	const StdString & units, \
2491	const StdString & time_origin, \
2492	const StdString & time_bounds, \
2493	const StdString & standard_name, \
2494	const StdString & long_name)", << msg);
2495	}
2496	}
2497
2498	//---------------------------------------------------------------
2499
2500	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2501	const StdString & axis,
2502	const StdString & standard_name,
2503	const StdString & long_name,
2504	const StdString & units,
2505	const StdString & nav_model)
2506	{
2507	try
2508	{
2509	if (!axis.empty())
2510	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2511
2512	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2513	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2514	SuperClassWriter::addAttribute("units" , units , &axis_name);
2515	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2516	}
2517	catch (CNetCdfException& e)
2518	{
2519	StdString msg("On writing Axis Attribute: ");
2520	msg.append("In the context : ");
2521	CContext* context = CContext::getCurrent() ;
2522	msg.append(context->getId()); msg.append("\n");
2523	msg.append(e.what());
2524	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2525	const StdString & axis, \
2526	const StdString & standard_name, \
2527	const StdString & long_name, \
2528	const StdString & units, \
2529	const StdString & nav_model)", << msg);
2530	}
2531	}
2532
2533	//---------------------------------------------------------------
2534
2535	void CNc4DataOutput::writeLocalAttributes
2536	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2537	{
2538	try
2539	{
2540	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2541	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2542	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2543	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2544	}
2545	catch (CNetCdfException& e)
2546	{
2547	StdString msg("On writing Local Attributes: ");
2548	msg.append("In the context : ");
2549	CContext* context = CContext::getCurrent() ;
2550	msg.append(context->getId()); msg.append("\n");
2551	msg.append(e.what());
2552	ERROR("CNc4DataOutput::writeLocalAttributes \
2553	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2554	}
2555
2556	}
2557
2558	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2559	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2560	{
2561	CArray<int,1> array(2) ;
2562
2563	try
2564	{
2565	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2566	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2567	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2568	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2569	array=ni_glo,nj_glo ;
2570	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2571	array=ni,nj ;
2572	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2573	array=ibegin+1,jbegin+1 ;
2574	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2575	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2576	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2577	array=0,0 ;
2578	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2579	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2580	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2581	/*
2582	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2583	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2584	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2585	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2586	*/
2587	}
2588	catch (CNetCdfException& e)
2589	{
2590	StdString msg("On writing Local Attributes IOIPSL \n");
2591	msg.append("In the context : ");
2592	CContext* context = CContext::getCurrent() ;
2593	msg.append(context->getId()); msg.append("\n");
2594	msg.append(e.what());
2595	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2596	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2597	}
2598	}
2599	//---------------------------------------------------------------
2600
2601	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2602	const StdString & description,
2603	const StdString & conventions,
2604	const StdString & production,
2605	const StdString & timeStamp)
2606	{
2607	try
2608	{
2609	SuperClassWriter::addAttribute("name" , name);
2610	SuperClassWriter::addAttribute("description", description);
2611	SuperClassWriter::addAttribute("title" , description);
2612	SuperClassWriter::addAttribute("Conventions", conventions);
2613	SuperClassWriter::addAttribute("production" , production);
2614	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
2615	}
2616	catch (CNetCdfException& e)
2617	{
2618	StdString msg("On writing File Attributes \n ");
2619	msg.append("In the context : ");
2620	CContext* context = CContext::getCurrent() ;
2621	msg.append(context->getId()); msg.append("\n");
2622	msg.append(e.what());
2623	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2624	const StdString & description, \
2625	const StdString & conventions, \
2626	const StdString & production, \
2627	const StdString & timeStamp)", << msg);
2628	}
2629	}
2630
2631	//---------------------------------------------------------------
2632
2633	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2634	int data_dim,
2635	int data_ni,
2636	int data_nj,
2637	int data_ibegin,
2638	int data_jbegin)
2639	{
2640	try
2641	{
2642	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2643	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2644	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2645	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2646	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2647	}
2648	catch (CNetCdfException& e)
2649	{
2650	StdString msg("On writing Mask Attributes \n ");
2651	msg.append("In the context : ");
2652	CContext* context = CContext::getCurrent() ;
2653	msg.append(context->getId()); msg.append("\n");
2654	msg.append(e.what());
2655	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2656	int data_dim, \
2657	int data_ni, \
2658	int data_nj, \
2659	int data_ibegin, \
2660	int data_jbegin)", << msg);
2661	}
2662	}
2663
2664	///--------------------------------------------------------------
2665
2666	StdSize CNc4DataOutput::getRecordFromTime(Time time)
2667	{
2668	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2669	if (it == timeToRecordCache.end())
2670	{
2671	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2672	if (!SuperClassWriter::varExist(timeAxisBoundsId))
2673	timeAxisBoundsId = "time_instant_bounds";
2674
2675	CArray<double,2> timeAxisBounds;
2676	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
2677
2678	StdSize record = 0;
2679	double dtime(time);
2680	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
2681	{
2682	if (timeAxisBounds(1, n) < dtime)
2683	{
2684	record = n + 1;
2685	break;
2686	}
2687	}
2688	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2689	}
2690	return it->second;
2691	}
2692
2693	///--------------------------------------------------------------
2694
2695	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2696	{
2697	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2698	}
2699
2700	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2701	{
2702	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2703	}
2704
2705	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2706	{
2707	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2708	}
2709
2710	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2711	{
2712	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2713	}
2714
2715	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2716	{
2717	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2718	}
2719
2720	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2721	{
2722	this->writtenDomains.insert(domainName);
2723	}
2724
2725	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2726	{
2727	this->writtenCompressedDomains.insert(domainName);
2728	}
2729
2730	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2731	{
2732	this->writtenAxis.insert(axisName);
2733	}
2734
2735	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2736	{
2737	this->writtenCompressedAxis.insert(axisName);
2738	}
2739
2740	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2741	{
2742	this->writtenScalar.insert(scalarName);
2743	}
2744	} // namespace xios

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