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source: XIOS/dev/dev_olga/src/io/nc4_data_output.cpp @ 1144

Last change on this file since 1144 was 1144, checked in by mhnguyen, 7 years ago
Cleaning up some redundant codes
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: 115.5 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	domain->computeWrittenIndex();
53	if (domain->type == CDomain::type_attr::unstructured)
54	{
55	if (SuperClassWriter::useCFConvention)
56	writeUnstructuredDomain(domain) ;
57	else
58	writeUnstructuredDomainUgrid(domain) ;
59	return ;
60	}
61
62
63	CContext* context = CContext::getCurrent() ;
64	CContextServer* server=context->server ;
65
66	if (domain->IsWritten(this->filename)) return;
67	domain->checkAttributes();
68
69	if (domain->isEmpty())
70	if (SuperClass::type==MULTI_FILE) return;
71
72	std::vector<StdString> dim0, dim1;
73	StdString domid = domain->getDomainOutputName();
74	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
75	if (isWrittenDomain(domid)) return ;
76	else setWrittenDomain(domid);
77
78	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
79
80	StdString dimXid, dimYid ;
81
82	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
83	switch (domain->type)
84	{
85	case CDomain::type_attr::curvilinear :
86	dimXid = StdString("x").append(appendDomid);
87	dimYid = StdString("y").append(appendDomid);
88	break ;
89	case CDomain::type_attr::rectilinear :
90	dimXid = StdString("lon").append(appendDomid);
91	dimYid = StdString("lat").append(appendDomid);
92	break;
93	}
94
95	StdString dimVertId = StdString("nvertex").append(appendDomid);
96
97	string lonid,latid,bounds_lonid,bounds_latid ;
98	string areaId = "area" + appendDomid;
99	/*
100	StdString lonid_loc = (server->intraCommSize > 1)
101	? StdString("lon").append(appendDomid).append("_local")
102	: lonid;
103	StdString latid_loc = (server->intraCommSize > 1)
104	? StdString("lat").append(appendDomid).append("_local")
105	: latid;
106	*/
107
108	CArray<size_t, 1>& indexToWrite = domain->localIndexToWriteOnServer;
109	int nbWritten = indexToWrite.numElements();
110	CArray<double,1> writtenLat, writtenLon;
111	CArray<double,2> writtenBndsLat, writtenBndsLon;
112	CArray<double,1> writtenArea;
113
114	if (domain->hasLonLat)
115	{
116	writtenLat.resize(nbWritten);
117	writtenLon.resize(nbWritten);
118	for (int idx = 0; idx < nbWritten; ++idx)
119	{
120	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
121	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
122	}
123
124
125	if (domain->hasBounds)
126	{
127	int nvertex = domain->nvertex, idx;
128	writtenBndsLat.resize(nvertex, nbWritten);
129	writtenBndsLon.resize(nvertex, nbWritten);
130	CArray<double,2>& boundslat = domain->bounds_latvalue;
131	CArray<double,2>& boundslon = domain->bounds_lonvalue;
132	for (idx = 0; idx < nbWritten; ++idx)
133	for (int nv = 0; nv < nvertex; ++nv)
134	{
135	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
136	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
137	}
138	}
139	}
140
141	if (domain->hasArea)
142	{
143	writtenArea.resize(nbWritten);
144	for (int idx = 0; idx < nbWritten; ++idx)
145	{
146	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
147	}
148	}
149
150	try
151	{
152	switch (SuperClass::type)
153	{
154	case (MULTI_FILE) :
155	{
156	// if (domain->isEmpty()) return;
157
158	if (server->intraCommSize > 1)
159	{
160	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
161	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
162	}
163
164	switch (domain->type)
165	{
166	case CDomain::type_attr::curvilinear :
167	dim0.push_back(dimYid); dim0.push_back(dimXid);
168	lonid = StdString("nav_lon").append(appendDomid);
169	latid = StdString("nav_lat").append(appendDomid);
170	break ;
171	case CDomain::type_attr::rectilinear :
172	lonid = StdString("lon").append(appendDomid);
173	latid = StdString("lat").append(appendDomid);
174	dim0.push_back(dimYid);
175	dim1.push_back(dimXid);
176	break;
177	}
178
179	bounds_lonid = StdString("bounds_lon").append(appendDomid);
180	bounds_latid = StdString("bounds_lat").append(appendDomid);
181
182	SuperClassWriter::addDimension(dimXid, domain->zoom_ni);
183	SuperClassWriter::addDimension(dimYid, domain->zoom_nj);
184
185	if (domain->hasBounds)
186	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
187
188	if (server->intraCommSize > 1)
189	{
190	this->writeLocalAttributes(domain->zoom_ibegin,
191	domain->zoom_ni,
192	domain->zoom_jbegin,
193	domain->zoom_nj,
194	appendDomid);
195
196	if (singleDomain)
197	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
198	domain->zoom_ibegin,
199	domain->zoom_ni,
200	domain->zoom_jbegin,
201	domain->zoom_nj,
202	domain->ni_glo,domain->nj_glo,
203	server->intraCommRank,server->intraCommSize);
204	}
205
206	if (domain->hasLonLat)
207	{
208	switch (domain->type)
209	{
210	case CDomain::type_attr::curvilinear :
211	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
212	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
213	break ;
214	case CDomain::type_attr::rectilinear :
215	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
216	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
217	break ;
218	}
219
220	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
221	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
222
223	if (domain->hasBounds)
224	{
225	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
226	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
227
228	dim0.clear();
229	dim0.push_back(dimYid);
230	dim0.push_back(dimXid);
231	dim0.push_back(dimVertId);
232	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
233	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
234	}
235	}
236
237	dim0.clear();
238	dim0.push_back(dimYid);
239	dim0.push_back(dimXid);
240
241
242	// supress mask if (server->intraCommSize > 1)
243	// supress mask {
244	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
245	// supress mask
246	// supress mask this->writeMaskAttributes(maskid,
247	// supress mask domain->data_dim.getValue()/*,
248	// supress mask domain->data_ni.getValue(),
249	// supress mask domain->data_nj.getValue(),
250	// supress mask domain->data_ibegin.getValue(),
251	// supress mask domain->data_jbegin.getValue()*/);
252	// supress mask }
253
254	//SuperClassWriter::setDefaultValue(maskid, &dvm);
255
256	if (domain->hasArea)
257	{
258	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
259	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
260	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
261	}
262
263	SuperClassWriter::definition_end();
264
265	if (domain->hasLonLat)
266	{
267	switch (domain->type)
268	{
269	case CDomain::type_attr::curvilinear :
270	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
271	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
272	break;
273	case CDomain::type_attr::rectilinear :
274	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni)) ;
275	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
276	CArray<double,1> lon = writtenLon(Range(0,domain->zoom_ni-1)) ;
277	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
278	break;
279	}
280
281	if (domain->hasBounds)
282	{
283	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
284	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
285	}
286	}
287
288	if (domain->hasArea)
289	{
290	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
291	}
292
293	SuperClassWriter::definition_start();
294
295	break;
296	}
297	case (ONE_FILE) :
298	{
299	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
300	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
301
302	if (domain->hasBounds)
303	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
304
305	if (domain->hasLonLat)
306	{
307	switch (domain->type)
308	{
309	case CDomain::type_attr::curvilinear :
310	dim0.push_back(dimYid); dim0.push_back(dimXid);
311	lonid = StdString("nav_lon").append(appendDomid);
312	latid = StdString("nav_lat").append(appendDomid);
313	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
314	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
315	break;
316
317	case CDomain::type_attr::rectilinear :
318	dim0.push_back(dimYid);
319	dim1.push_back(dimXid);
320	lonid = StdString("lon").append(appendDomid);
321	latid = StdString("lat").append(appendDomid);
322	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
323	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
324	break;
325	}
326
327	bounds_lonid = StdString("bounds_lon").append(appendDomid);
328	bounds_latid = StdString("bounds_lat").append(appendDomid);
329
330	this->writeAxisAttributes
331	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
332	this->writeAxisAttributes
333	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
334
335	if (domain->hasBounds)
336	{
337	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
338	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
339
340	dim0.clear();
341	dim0.push_back(dimYid);
342	dim0.push_back(dimXid);
343	dim0.push_back(dimVertId);
344	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
345	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
346	}
347	}
348
349	if (domain->hasArea)
350	{
351	dim0.clear();
352	dim0.push_back(dimYid); dim0.push_back(dimXid);
353	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
354	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
355	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
356	dim0.clear();
357	}
358
359	SuperClassWriter::definition_end();
360
361	switch (domain->type)
362	{
363	case CDomain::type_attr::curvilinear :
364	{
365	std::vector<StdSize> start(2) ;
366	std::vector<StdSize> count(2) ;
367	if (domain->isEmpty())
368	{
369	start[0]=0 ; start[1]=0 ;
370	count[0]=0 ; count[1]=0 ;
371	}
372	else
373	{
374	start[1]=domain->zoom_ibegin-domain->global_zoom_ibegin;
375	start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
376	count[1]=domain->zoom_ni ; count[0]=domain->zoom_nj ;
377	}
378
379	if (domain->hasLonLat)
380	{
381	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
382	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
383	}
384	break;
385	}
386	case CDomain::type_attr::rectilinear :
387	{
388	if (domain->hasLonLat)
389	{
390	std::vector<StdSize> start(1) ;
391	std::vector<StdSize> count(1) ;
392	if (domain->isEmpty())
393	{
394	start[0]=0 ;
395	count[0]=0 ;
396	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
397	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
398	}
399	else
400	{
401	start[0]=domain->zoom_jbegin-domain->global_zoom_jbegin;
402	count[0]=domain->zoom_nj;
403	CArray<double,1> lat = writtenLat(Range(fromStart,toEnd,domain->zoom_ni));
404	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
405
406	start[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
407	count[0]=domain->zoom_ni;
408	CArray<double,1> lon = writtenLon(Range(0,domain->zoom_ni-1));
409	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
410	}
411	}
412	break;
413	}
414	}
415
416	if (domain->hasBounds)
417	{
418	std::vector<StdSize> start(3);
419	std::vector<StdSize> count(3);
420	if (domain->isEmpty())
421	{
422	start[2] = start[1] = start[0] = 0;
423	count[2] = count[1] = count[0] = 0;
424	}
425	else
426	{
427	start[2] = 0;
428	start[1] = domain->zoom_ibegin - domain->global_zoom_ibegin;
429	start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
430	count[2] = domain->nvertex;
431	count[1] = domain->zoom_ni;
432	count[0] = domain->zoom_nj;
433	}
434
435	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0, &start, &count);
436	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0, &start, &count);
437	}
438
439	if (domain->hasArea)
440	{
441	std::vector<StdSize> start(2);
442	std::vector<StdSize> count(2);
443
444	if (domain->isEmpty())
445	{
446	start[0] = 0; start[1] = 0;
447	count[0] = 0; count[1] = 0;
448	}
449	else
450	{
451	start[1] = domain->zoom_ibegin - domain->global_zoom_ibegin;
452	start[0] = domain->zoom_jbegin - domain->global_zoom_jbegin;
453	count[1] = domain->zoom_ni;
454	count[0] = domain->zoom_nj;
455	}
456
457	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
458	}
459
460	SuperClassWriter::definition_start();
461	break;
462	}
463	default :
464	ERROR("CNc4DataOutput::writeDomain(domain)",
465	<< "[ type = " << SuperClass::type << "]"
466	<< " not implemented yet !");
467	}
468	}
469	catch (CNetCdfException& e)
470	{
471	StdString msg("On writing the domain : ");
472	msg.append(domid); msg.append("\n");
473	msg.append("In the context : ");
474	msg.append(context->getId()); msg.append("\n");
475	msg.append(e.what());
476	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
477	}
478
479	domain->addRelFile(this->filename);
480	}
481
482	//--------------------------------------------------------------
483
484	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
485	{
486	CContext* context = CContext::getCurrent() ;
487	CContextServer* server=context->server ;
488
489	if (domain->IsWritten(this->filename)) return;
490	domain->checkAttributes();
491	if (domain->isEmpty())
492	if (SuperClass::type==MULTI_FILE) return ;
493
494	std::vector<StdString> dim0;
495	StdString domid = domain->getDomainOutputName();
496	StdString domainName = domain->name;
497	domain->assignMesh(domainName, domain->nvertex);
498	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
499
500	StdString node_x = domainName + "_node_x";
501	StdString node_y = domainName + "_node_y";
502
503	StdString edge_x = domainName + "_edge_x";
504	StdString edge_y = domainName + "_edge_y";
505	StdString edge_nodes = domainName + "_edge_nodes";
506
507	StdString face_x = domainName + "_face_x";
508	StdString face_y = domainName + "_face_y";
509	StdString face_nodes = domainName + "_face_nodes";
510	StdString face_edges = domainName + "_face_edges";
511	StdString edge_faces = domainName + "_edge_face_links";
512	StdString face_faces = domainName + "_face_links";
513
514	StdString dimNode = "n" + domainName + "_node";
515	StdString dimEdge = "n" + domainName + "_edge";
516	StdString dimFace = "n" + domainName + "_face";
517	StdString dimVertex = "n" + domainName + "_vertex";
518	StdString dimTwo = "Two";
519
520	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
521	if (!isWrittenDomain(domid))
522	{
523	dim0.clear();
524	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
525	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
526	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
527	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
528	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
529	}
530
531	try
532	{
533	switch (SuperClass::type)
534	{
535	case (ONE_FILE) :
536	{
537	// Adding nodes
538	if (domain->nvertex == 1)
539	{
540	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
541	{
542	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
543	dim0.clear();
544	dim0.push_back(dimNode);
545	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
546	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
547	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
548	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
549	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
550	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
551	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
552	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
553	}
554	} // domain->nvertex == 1
555
556	// Adding edges and nodes, if nodes have not been defined previously
557	if (domain->nvertex == 2)
558	{
559	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
560	{
561	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
562	dim0.clear();
563	dim0.push_back(dimNode);
564	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
565	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
566	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
567	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
568	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
569	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
570	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
571	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
572	}
573	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
574	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
575	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
576	dim0.clear();
577	dim0.push_back(dimEdge);
578	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
579	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
580	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
581	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
582	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
583	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
584	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
585	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
586	dim0.clear();
587	dim0.push_back(dimEdge);
588	dim0.push_back(dimTwo);
589	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
590	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
591	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
592	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
593	} // domain->nvertex == 2
594
595	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
596	if (domain->nvertex > 2)
597	{
598	// Nodes
599	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
600	{
601	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
602	dim0.clear();
603	dim0.push_back(dimNode);
604	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
605	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
606	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
607	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
608	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
609	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
610	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
611	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
612	}
613	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
614	{
615	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
616	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
617	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
618	dim0.clear();
619	dim0.push_back(dimEdge);
620	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
621	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
622	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
623	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
624	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
625	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
626	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
627	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
628	dim0.clear();
629	dim0.push_back(dimEdge);
630	dim0.push_back(dimTwo);
631	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
632	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
633	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
634	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
635	}
636	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
637	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
638	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
639	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
640	dim0.clear();
641	dim0.push_back(dimFace);
642	SuperClassWriter::addVariable(face_x, NC_FLOAT, dim0);
643	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
644	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
645	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
646	SuperClassWriter::addVariable(face_y, NC_FLOAT, dim0);
647	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
648	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
649	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
650	dim0.clear();
651	dim0.push_back(dimFace);
652	dim0.push_back(dimVertex);
653	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
654	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
655	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
656	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
657	dim0.clear();
658	dim0.push_back(dimFace);
659	dim0.push_back(dimVertex);
660	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
661	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
662	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
663	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
664	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
665	dim0.clear();
666	dim0.push_back(dimEdge);
667	dim0.push_back(dimTwo);
668	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
669	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
670	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
671	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
672	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
673	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
674	dim0.clear();
675	dim0.push_back(dimFace);
676	dim0.push_back(dimVertex);
677	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
678	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
679	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
680	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
681	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
682	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
683	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
684	} // domain->nvertex > 2
685
686	SuperClassWriter::definition_end();
687
688	std::vector<StdSize> startEdges(1) ;
689	std::vector<StdSize> countEdges(1) ;
690	std::vector<StdSize> startNodes(1) ;
691	std::vector<StdSize> countNodes(1) ;
692	std::vector<StdSize> startFaces(1) ;
693	std::vector<StdSize> countFaces(1) ;
694	std::vector<StdSize> startEdgeNodes(2) ;
695	std::vector<StdSize> countEdgeNodes(2) ;
696	std::vector<StdSize> startEdgeFaces(2) ;
697	std::vector<StdSize> countEdgeFaces(2) ;
698	std::vector<StdSize> startFaceConctv(2) ;
699	std::vector<StdSize> countFaceConctv(2) ;
700
701	if (!isWrittenDomain(domid))
702	{
703	if (domain->nvertex == 1)
704	{
705	if (domain->isEmpty())
706	{
707	startNodes[0]=0 ;
708	countNodes[0]=0 ;
709	}
710	else
711	{
712	startNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
713	countNodes[0] = domain->zoom_ni ;
714	}
715
716	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
717	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
718	}
719	else if (domain->nvertex == 2)
720	{
721	if (domain->isEmpty())
722	{
723	startEdges[0]=0 ;
724	countEdges[0]=0 ;
725	startNodes[0]=0 ;
726	countNodes[0]=0 ;
727	startEdgeNodes[0]=0;
728	startEdgeNodes[1]=0;
729	countEdgeNodes[0]=0;
730	countEdgeNodes[1]=0;
731
732	}
733	else
734	{
735	startEdges[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
736	countEdges[0] = domain->zoom_ni;
737	startNodes[0] = domain->mesh->node_start;
738	countNodes[0] = domain->mesh->node_count;
739	startEdgeNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
740	startEdgeNodes[1] = 0;
741	countEdgeNodes[0] = domain->zoom_ni;
742	countEdgeNodes[1] = 2;
743	}
744	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
745	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
746	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
747	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
748	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
749	}
750	else
751	{
752	if (domain->isEmpty())
753	{
754	startFaces[0] = 0 ;
755	countFaces[0] = 0 ;
756	startNodes[0] = 0;
757	countNodes[0] = 0;
758	startEdges[0] = 0;
759	countEdges[0] = 0;
760	startEdgeFaces[0] = 0;
761	startEdgeFaces[1] = 0;
762	countEdgeFaces[0] = 0;
763	countEdgeFaces[1] = 0;
764	startFaceConctv[0] = 0;
765	startFaceConctv[1] = 0;
766	countFaceConctv[0] = 0;
767	countFaceConctv[1] = 0;
768	}
769	else
770	{
771	startFaces[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
772	countFaces[0] = domain->zoom_ni ;
773	startNodes[0] = domain->mesh->node_start;
774	countNodes[0] = domain->mesh->node_count;
775	startEdges[0] = domain->mesh->edge_start;
776	countEdges[0] = domain->mesh->edge_count;
777	startEdgeNodes[0] = domain->mesh->edge_start;
778	startEdgeNodes[1] = 0;
779	countEdgeNodes[0] = domain->mesh->edge_count;
780	countEdgeNodes[1]= 2;
781	startEdgeFaces[0] = domain->mesh->edge_start;
782	startEdgeFaces[1]= 0;
783	countEdgeFaces[0] = domain->mesh->edge_count;
784	countEdgeFaces[1]= 2;
785	startFaceConctv[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
786	startFaceConctv[1] = 0;
787	countFaceConctv[0] = domain->zoom_ni;
788	countFaceConctv[1] = domain->nvertex;
789	}
790	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
791	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
792	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
793	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
794	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
795	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
796	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
797	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
798	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
799	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
800	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
801	}
802	setWrittenDomain(domid);
803	} // !isWrittenDomain
804	else
805	{
806	if (domain->nvertex == 2)
807	{
808	startEdges[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
809	countEdges[0] = domain->zoom_ni;
810	startEdgeNodes[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
811	startEdgeNodes[1] = 0;
812	countEdgeNodes[0] = domain->zoom_ni;
813	countEdgeNodes[1]= 2;
814	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
815	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
816	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
817	}
818	if (domain->nvertex > 2)
819	{
820
821	if (!domain->mesh->edgesAreWritten)
822	{
823	startEdges[0] = domain->mesh->edge_start;
824	countEdges[0] = domain->mesh->edge_count;
825	startEdgeNodes[0] = domain->mesh->edge_start;
826	startEdgeNodes[1] = 0;
827	countEdgeNodes[0] = domain->mesh->edge_count;
828	countEdgeNodes[1]= 2;
829	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
830	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
831	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
832	}
833	startFaces[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
834	countFaces[0] = domain->zoom_ni;
835	startEdgeFaces[0] = domain->mesh->edge_start;
836	startEdgeFaces[1]= 0;
837	countEdgeFaces[0] = domain->mesh->edge_count;
838	countEdgeFaces[1]= 2;
839	startFaceConctv[0] = domain->zoom_ibegin-domain->global_zoom_ibegin;
840	startFaceConctv[1] = 0;
841	countFaceConctv[0] = domain->zoom_ni;
842	countFaceConctv[1] = domain->nvertex;
843	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
844	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
845	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
846	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
847	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
848	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
849	}
850	}// isWrittenDomain
851
852	SuperClassWriter::definition_start();
853
854	break;
855	} // ONE_FILE
856
857	case (MULTI_FILE) :
858	{
859	break;
860	}
861
862	default :
863	ERROR("CNc4DataOutput::writeDomain(domain)",
864	<< "[ type = " << SuperClass::type << "]"
865	<< " not implemented yet !");
866	} // switch
867	} // try
868
869	catch (CNetCdfException& e)
870	{
871	StdString msg("On writing the domain : ");
872	msg.append(domid); msg.append("\n");
873	msg.append("In the context : ");
874	msg.append(context->getId()); msg.append("\n");
875	msg.append(e.what());
876	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
877	}
878
879	domain->addRelFile(this->filename);
880	}
881
882	//--------------------------------------------------------------
883
884	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
885	{
886	CContext* context = CContext::getCurrent() ;
887	CContextServer* server=context->server ;
888
889	if (domain->IsWritten(this->filename)) return;
890	domain->checkAttributes();
891
892	if (domain->isEmpty())
893	if (SuperClass::type==MULTI_FILE) return ;
894
895	std::vector<StdString> dim0, dim1;
896	StdString domid = domain->getDomainOutputName();
897	if (isWrittenDomain(domid)) return ;
898	else setWrittenDomain(domid);
899
900	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
901
902	StdString dimXid = StdString("cell").append(appendDomid);
903	StdString dimVertId = StdString("nvertex").append(appendDomid);
904
905	string lonid,latid,bounds_lonid,bounds_latid ;
906	string areaId = "area" + appendDomid;
907
908	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
909
910	CArray<size_t, 1>& indexToWrite = domain->localIndexToWriteOnServer;
911	int nbWritten = indexToWrite.numElements();
912	CArray<double,1> writtenLat, writtenLon;
913	CArray<double,2> writtenBndsLat, writtenBndsLon;
914	CArray<double,1> writtenArea;
915
916	if (domain->hasLonLat)
917	{
918	writtenLat.resize(nbWritten);
919	writtenLon.resize(nbWritten);
920	for (int idx = 0; idx < nbWritten; ++idx)
921	{
922	writtenLat(idx) = domain->latvalue(indexToWrite(idx));
923	writtenLon(idx) = domain->lonvalue(indexToWrite(idx));
924	}
925
926
927	if (domain->hasBounds)
928	{
929	int nvertex = domain->nvertex, idx;
930	writtenBndsLat.resize(nvertex, nbWritten);
931	writtenBndsLon.resize(nvertex, nbWritten);
932	CArray<double,2>& boundslat = domain->bounds_latvalue;
933	CArray<double,2>& boundslon = domain->bounds_lonvalue;
934	for (idx = 0; idx < nbWritten; ++idx)
935	for (int nv = 0; nv < nvertex; ++nv)
936	{
937	writtenBndsLat(nv, idx) = boundslat(nv, int(indexToWrite(idx)));
938	writtenBndsLon(nv, idx) = boundslon(nv, int(indexToWrite(idx)));
939	}
940	}
941	}
942
943	if (domain->hasArea)
944	{
945	writtenArea.resize(nbWritten);
946	for (int idx = 0; idx < nbWritten; ++idx)
947	{
948	writtenArea(idx) = domain->areavalue(indexToWrite(idx));
949	}
950	}
951
952	try
953	{
954	switch (SuperClass::type)
955	{
956	case (MULTI_FILE) :
957	{
958	dim0.push_back(dimXid);
959	SuperClassWriter::addDimension(dimXid, domain->zoom_ni);
960
961	lonid = StdString("lon").append(appendDomid);
962	latid = StdString("lat").append(appendDomid);
963	bounds_lonid = StdString("bounds_lon").append(appendDomid);
964	bounds_latid = StdString("bounds_lat").append(appendDomid);
965	if (domain->hasLonLat)
966	{
967	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
968	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
969	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
970	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
971	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
972	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
973	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
974	}
975	dim0.clear();
976	if (domain->hasBounds)
977	{
978	dim0.push_back(dimXid);
979	dim0.push_back(dimVertId);
980	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
981	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
982	}
983
984	dim0.clear();
985	dim0.push_back(dimXid);
986	if (domain->hasArea)
987	{
988	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
989	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
990	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
991	}
992
993	SuperClassWriter::definition_end();
994
995	if (domain->hasLonLat)
996	{
997	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0);
998	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0);
999	if (domain->hasBounds)
1000	{
1001	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0);
1002	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0);
1003	}
1004	}
1005
1006	if (domain->hasArea)
1007	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0);
1008
1009	SuperClassWriter::definition_start();
1010	break ;
1011	}
1012
1013	case (ONE_FILE) :
1014	{
1015	lonid = StdString("lon").append(appendDomid);
1016	latid = StdString("lat").append(appendDomid);
1017	bounds_lonid = StdString("bounds_lon").append(appendDomid);
1018	bounds_latid = StdString("bounds_lat").append(appendDomid);
1019	dim0.push_back(dimXid);
1020	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
1021	if (domain->hasLonLat)
1022	{
1023	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
1024	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
1025
1026	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
1027	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
1028	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
1029	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
1030	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
1031	}
1032	dim0.clear();
1033
1034	if (domain->hasBounds)
1035	{
1036	dim0.push_back(dimXid);
1037	dim0.push_back(dimVertId);
1038	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
1039	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
1040	}
1041
1042	if (domain->hasArea)
1043	{
1044	dim0.clear();
1045	dim0.push_back(dimXid);
1046	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
1047	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
1048	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
1049	}
1050
1051	SuperClassWriter::definition_end();
1052
1053	std::vector<StdSize> start(1), startBounds(2) ;
1054	std::vector<StdSize> count(1), countBounds(2) ;
1055	if (domain->isEmpty())
1056	{
1057	start[0]=0 ;
1058	count[0]=0 ;
1059	startBounds[1]=0 ;
1060	countBounds[1]=nvertex ;
1061	startBounds[0]=0 ;
1062	countBounds[0]=0 ;
1063	}
1064	else
1065	{
1066	start[0]=domain->zoom_ibegin - domain->global_zoom_ibegin;
1067	count[0]=domain->zoom_ni;
1068	startBounds[0]=domain->zoom_ibegin-domain->global_zoom_ibegin;
1069	startBounds[1]=0 ;
1070	countBounds[0]=domain->zoom_ni;
1071	countBounds[1]=nvertex ;
1072	}
1073
1074	if (domain->hasLonLat)
1075	{
1076	SuperClassWriter::writeData(writtenLat, latid, isCollective, 0,&start,&count);
1077	SuperClassWriter::writeData(writtenLon, lonid, isCollective, 0,&start,&count);
1078	if (domain->hasBounds)
1079	{
1080	SuperClassWriter::writeData(writtenBndsLon, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1081	SuperClassWriter::writeData(writtenBndsLat, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1082	}
1083	}
1084
1085	if (domain->hasArea)
1086	SuperClassWriter::writeData(writtenArea, areaId, isCollective, 0, &start, &count);
1087
1088	SuperClassWriter::definition_start();
1089
1090	break;
1091	}
1092	default :
1093	ERROR("CNc4DataOutput::writeDomain(domain)",
1094	<< "[ type = " << SuperClass::type << "]"
1095	<< " not implemented yet !");
1096	}
1097	}
1098	catch (CNetCdfException& e)
1099	{
1100	StdString msg("On writing the domain : ");
1101	msg.append(domid); msg.append("\n");
1102	msg.append("In the context : ");
1103	msg.append(context->getId()); msg.append("\n");
1104	msg.append(e.what());
1105	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1106	}
1107	domain->addRelFile(this->filename);
1108	}
1109	//--------------------------------------------------------------
1110
1111	void CNc4DataOutput::writeAxis_(CAxis* axis)
1112	{
1113	CContext* context = CContext::getCurrent();
1114
1115	if (axis->IsWritten(this->filename)) return;
1116	axis->checkAttributes();
1117
1118	axis->computeWrittenIndex();
1119
1120	int zoom_size = (MULTI_FILE == SuperClass::type) ? axis->zoom_n
1121	: axis->global_zoom_n;
1122	int zoom_begin = (MULTI_FILE == SuperClass::type) ? axis->zoom_begin
1123	: axis->global_zoom_begin;
1124
1125	if ((0 == axis->zoom_n) && (MULTI_FILE == SuperClass::type)) return;
1126
1127	std::vector<StdString> dims;
1128	StdString axisid = axis->getAxisOutputName();
1129	if (isWrittenAxis(axisid)) return ;
1130	else setWrittenAxis(axisid);
1131
1132	try
1133	{
1134	SuperClassWriter::addDimension(axisid, zoom_size);
1135	if (axis->hasValue)
1136	{
1137	dims.push_back(axisid);
1138	SuperClassWriter::addVariable(axisid, NC_FLOAT, dims);
1139
1140	if (!axis->name.isEmpty())
1141	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1142
1143	if (!axis->standard_name.isEmpty())
1144	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1145
1146	if (!axis->long_name.isEmpty())
1147	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1148
1149	if (!axis->unit.isEmpty())
1150	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1151
1152	if (!axis->positive.isEmpty())
1153	{
1154	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1155	SuperClassWriter::addAttribute("positive",
1156	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1157	&axisid);
1158	}
1159
1160	StdString axisBoundsId = axisid + "_bounds";
1161	if (!axis->bounds.isEmpty())
1162	{
1163	dims.push_back("axis_nbounds");
1164	SuperClassWriter::addVariable(axisBoundsId, NC_FLOAT, dims);
1165	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1166	}
1167
1168	SuperClassWriter::definition_end();
1169
1170	CArray<size_t, 1>& indexToWrite = axis->localIndexToWriteOnServer;
1171	int nbWritten = indexToWrite.numElements();
1172	CArray<double,1> axis_value(indexToWrite.numElements());
1173	for (int i = 0; i < nbWritten; i++) axis_value(i) = axis->value(indexToWrite(i));
1174	CArray<double,2> axis_bounds;
1175
1176	switch (SuperClass::type)
1177	{
1178	case MULTI_FILE:
1179	{
1180	// CArray<double,1> axis_value(axis->zoom_n);
1181	// for (int i = 0; i < axis->zoom_n; i++) axis_value(i) = axis->value(i);
1182	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1183
1184	if (!axis->bounds.isEmpty())
1185	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
1186
1187	SuperClassWriter::definition_start();
1188
1189	break;
1190	}
1191	case ONE_FILE:
1192	{
1193	// CArray<double,1> axis_value(axis->zoom_n);
1194	// axis_value = axis->value;
1195	std::vector<StdSize> start(1), startBounds(2) ;
1196	std::vector<StdSize> count(1), countBounds(2) ;
1197	start[0] = startBounds[0] = zoom_begin - axis->global_zoom_begin;
1198	count[0] = countBounds[0] = zoom_size;
1199	startBounds[1] = 0;
1200	countBounds[1] = 2;
1201	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1202
1203	if (!axis->bounds.isEmpty())
1204	{
1205	axis_bounds.resize(2, indexToWrite.numElements());
1206	for (int i = 0; i < nbWritten; ++i)
1207	{
1208	axis_bounds(0, i) = axis->bounds(0, int(indexToWrite(i)));
1209	axis_bounds(1, i) = axis->bounds(1, int(indexToWrite(i)));
1210	}
1211	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1212	}
1213
1214	SuperClassWriter::definition_start();
1215
1216	break;
1217	}
1218	default :
1219	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1220	<< "[ type = " << SuperClass::type << "]"
1221	<< " not implemented yet !");
1222	}
1223	}
1224	}
1225	catch (CNetCdfException& e)
1226	{
1227	StdString msg("On writing the axis : ");
1228	msg.append(axisid); msg.append("\n");
1229	msg.append("In the context : ");
1230	CContext* context = CContext::getCurrent() ;
1231	msg.append(context->getId()); msg.append("\n");
1232	msg.append(e.what());
1233	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1234	}
1235
1236	axis->addRelFile(this->filename);
1237	}
1238
1239	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1240	{
1241	if (scalar->IsWritten(this->filename)) return;
1242	scalar->checkAttributes();
1243	int scalarSize = 1;
1244
1245	StdString scalaId = scalar->getScalarOutputName();
1246	if (isWrittenAxis(scalaId)) return ;
1247	else setWrittenAxis(scalaId);
1248
1249	try
1250	{
1251	if (!scalar->value.isEmpty())
1252	{
1253	// dims.push_back(scalaId);
1254	std::vector<StdString> dims;
1255	SuperClassWriter::addVariable(scalaId, NC_FLOAT, dims);
1256
1257	if (!scalar->name.isEmpty())
1258	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1259
1260	if (!scalar->standard_name.isEmpty())
1261	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1262
1263	if (!scalar->long_name.isEmpty())
1264	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1265
1266	if (!scalar->unit.isEmpty())
1267	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1268
1269	SuperClassWriter::definition_end();
1270
1271	switch (SuperClass::type)
1272	{
1273	case MULTI_FILE:
1274	{
1275	CArray<double,1> scalarValue(scalarSize);
1276	scalarValue(0) = scalar->value;
1277	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1278	SuperClassWriter::definition_start();
1279
1280	break;
1281	}
1282	case ONE_FILE:
1283	{
1284	CArray<double,1> scalarValue(scalarSize);
1285	scalarValue(0) = scalar->value;
1286
1287	std::vector<StdSize> start(1);
1288	std::vector<StdSize> count(1);
1289	start[0] = 0;
1290	count[0] = 1;
1291	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1292	SuperClassWriter::definition_start();
1293
1294	break;
1295	}
1296	default :
1297	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1298	<< "[ type = " << SuperClass::type << "]"
1299	<< " not implemented yet !");
1300	}
1301	}
1302	}
1303	catch (CNetCdfException& e)
1304	{
1305	StdString msg("On writing the scalar : ");
1306	msg.append(scalaId); msg.append("\n");
1307	msg.append("In the context : ");
1308	CContext* context = CContext::getCurrent() ;
1309	msg.append(context->getId()); msg.append("\n");
1310	msg.append(e.what());
1311	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1312	}
1313	scalar->addRelFile(this->filename);
1314	}
1315
1316	//--------------------------------------------------------------
1317
1318	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1319	{
1320	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1321
1322	try
1323	{
1324	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1325	std::vector<StdString> domainList = grid->getDomainList();
1326	std::vector<StdString> axisList = grid->getAxisList();
1327	std::vector<StdString> scalarList = grid->getScalarList();
1328	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1329
1330	std::vector<StdString> dims;
1331
1332	if (grid->isCompressible())
1333	{
1334	StdString varId = grid->getId() + "_points";
1335
1336	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1337	SuperClassWriter::addDimension(varId, nbIndexes);
1338
1339	dims.push_back(varId);
1340	SuperClassWriter::addVariable(varId, NC_INT, dims);
1341
1342	StdOStringStream compress;
1343	for (int i = numElement - 1; i >= 0; --i)
1344	{
1345	if (2 == axisDomainOrder(i))
1346	{
1347	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1348	StdString domId = domain->getDomainOutputName();
1349	StdString appendDomId = singleDomain ? "" : "_" + domId;
1350
1351	switch (domain->type)
1352	{
1353	case CDomain::type_attr::curvilinear:
1354	compress << "y" << appendDomId << " x" << appendDomId;
1355	break;
1356	case CDomain::type_attr::rectilinear:
1357	compress << "lat" << appendDomId << " lon" << appendDomId;
1358	break;
1359	case CDomain::type_attr::unstructured:
1360	compress << "cell" << appendDomId;
1361	break;
1362	}
1363	++idxDomain;
1364	}
1365	else if (1 == axisDomainOrder(i))
1366	{
1367	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1368	compress << axis->getAxisOutputName();
1369	++idxAxis;
1370	}
1371	else
1372	{
1373	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1374	compress << scalar->getScalarOutputName();
1375	++idxScalar;
1376	}
1377
1378	if (i != 0) compress << ' ';
1379	}
1380	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1381
1382	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1383	indexes = grid->localIndexToWriteOnServer;
1384
1385	switch (SuperClass::type)
1386	{
1387	case (MULTI_FILE):
1388	{
1389	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1390	break;
1391	}
1392	case (ONE_FILE):
1393	{
1394	if (grid->doGridHaveDataDistributed())
1395	grid->getDistributionServer()->computeGlobalIndex(indexes);
1396
1397	std::vector<StdSize> start, count;
1398	start.push_back(grid->getOffsetWrittenIndexes());
1399	count.push_back(grid->getNumberWrittenIndexes());
1400
1401	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1402	break;
1403	}
1404	}
1405	}
1406	else
1407	{
1408	for (int i = 0; i < numElement; ++i)
1409	{
1410	StdString varId, compress;
1411	CArray<int, 1> indexes;
1412	bool isDistributed;
1413	StdSize nbIndexes, totalNbIndexes, offset;
1414	int firstGlobalIndex;
1415
1416	if (2 == axisDomainOrder(i))
1417	{
1418	CDomain* domain = CDomain::get(domainList[idxDomain]);
1419	StdString domId = domain->getDomainOutputName();
1420
1421	if (!domain->isCompressible()
1422	\|\| domain->type == CDomain::type_attr::unstructured
1423	\|\| domain->isWrittenCompressed(this->filename)
1424	\|\| isWrittenCompressedDomain(domId))
1425	continue;
1426
1427	StdString appendDomId = singleDomain ? "" : "_" + domId;
1428
1429	varId = domId + "_points";
1430	switch (domain->type)
1431	{
1432	case CDomain::type_attr::curvilinear:
1433	compress = "y" + appendDomId + " x" + appendDomId;
1434	break;
1435	case CDomain::type_attr::rectilinear:
1436	compress = "lat" + appendDomId + " lon" + appendDomId;
1437	break;
1438	}
1439
1440	indexes.resize(domain->compressedIndexToWriteOnServer.numElements());
1441	indexes = domain->compressedIndexToWriteOnServer;
1442
1443	isDistributed = domain->isDistributed();
1444	nbIndexes = domain->getNumberWrittenIndexes();
1445	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1446	offset = domain->getOffsetWrittenIndexes();
1447	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1448
1449	domain->addRelFileCompressed(this->filename);
1450	setWrittenCompressedDomain(domId);
1451	++idxDomain;
1452	}
1453	else if (1 == axisDomainOrder(i))
1454	{
1455	CAxis* axis = CAxis::get(axisList[idxAxis]);
1456	StdString axisId = axis->getAxisOutputName();
1457
1458	if (!axis->isCompressible()
1459	\|\| axis->isWrittenCompressed(this->filename)
1460	\|\| isWrittenCompressedAxis(axisId))
1461	continue;
1462
1463	varId = axisId + "_points";
1464	compress = axisId;
1465
1466	indexes.resize(axis->compressedIndexToWriteOnServer.numElements());
1467	indexes = axis->compressedIndexToWriteOnServer;
1468
1469	isDistributed = axis->isDistributed();
1470	nbIndexes = axis->getNumberWrittenIndexes();
1471	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1472	offset = axis->getOffsetWrittenIndexes();
1473	firstGlobalIndex = axis->begin;
1474
1475	axis->addRelFileCompressed(this->filename);
1476	setWrittenCompressedAxis(axisId);
1477	++idxAxis;
1478	}
1479	else
1480	{
1481	}
1482
1483	if (!varId.empty())
1484	{
1485	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1486
1487	dims.clear();
1488	dims.push_back(varId);
1489	SuperClassWriter::addVariable(varId, NC_INT, dims);
1490
1491	SuperClassWriter::addAttribute("compress", compress, &varId);
1492
1493	switch (SuperClass::type)
1494	{
1495	case (MULTI_FILE):
1496	{
1497	indexes -= firstGlobalIndex;
1498	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1499	break;
1500	}
1501	case (ONE_FILE):
1502	{
1503	std::vector<StdSize> start, count;
1504	start.push_back(offset);
1505	count.push_back(nbIndexes);
1506
1507	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1508	break;
1509	}
1510	}
1511	}
1512	}
1513	}
1514
1515	grid->addRelFileCompressed(this->filename);
1516	}
1517	catch (CNetCdfException& e)
1518	{
1519	StdString msg("On writing compressed grid : ");
1520	msg.append(grid->getId()); msg.append("\n");
1521	msg.append("In the context : ");
1522	CContext* context = CContext::getCurrent();
1523	msg.append(context->getId()); msg.append("\n");
1524	msg.append(e.what());
1525	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1526	}
1527	}
1528
1529	//--------------------------------------------------------------
1530
1531	void CNc4DataOutput::writeTimeDimension_(void)
1532	{
1533	try
1534	{
1535	SuperClassWriter::addDimension(getTimeCounterName());
1536	}
1537	catch (CNetCdfException& e)
1538	{
1539	StdString msg("On writing time dimension : time_couter\n");
1540	msg.append("In the context : ");
1541	CContext* context = CContext::getCurrent() ;
1542	msg.append(context->getId()); msg.append("\n");
1543	msg.append(e.what());
1544	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1545	}
1546	}
1547
1548	//--------------------------------------------------------------
1549
1550	void CNc4DataOutput::writeField_(CField* field)
1551	{
1552	CContext* context = CContext::getCurrent() ;
1553	CContextServer* server=context->server ;
1554
1555	std::vector<StdString> dims, coodinates;
1556	CGrid* grid = field->grid;
1557	if (!grid->doGridHaveDataToWrite())
1558	if (SuperClass::type==MULTI_FILE) return ;
1559
1560	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1561	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1562	std::vector<StdString> domainList = grid->getDomainList();
1563	std::vector<StdString> axisList = grid->getAxisList();
1564	std::vector<StdString> scalarList = grid->getScalarList();
1565
1566	StdString timeid = getTimeCounterName();
1567	StdString dimXid,dimYid;
1568	std::deque<StdString> dimIdList, dimCoordList;
1569	bool hasArea = false;
1570	StdString cellMeasures = "area:";
1571	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1572
1573	for (int i = 0; i < numElement; ++i)
1574	{
1575	if (2 == axisDomainOrder(i))
1576	{
1577	CDomain* domain = CDomain::get(domainList[idxDomain]);
1578	StdString domId = domain->getDomainOutputName();
1579	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1580
1581	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1582	{
1583	dimIdList.push_back(domId + "_points");
1584	field->setUseCompressedOutput();
1585	}
1586
1587	switch (domain->type)
1588	{
1589	case CDomain::type_attr::curvilinear:
1590	if (!compressedOutput \|\| !domain->isCompressible())
1591	{
1592	dimXid = StdString("x").append(appendDomId);
1593	dimIdList.push_back(dimXid);
1594	dimYid = StdString("y").append(appendDomId);
1595	dimIdList.push_back(dimYid);
1596	}
1597	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1598	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1599	break ;
1600	case CDomain::type_attr::rectilinear:
1601	if (!compressedOutput \|\| !domain->isCompressible())
1602	{
1603	dimXid = StdString("lon").append(appendDomId);
1604	dimIdList.push_back(dimXid);
1605	dimYid = StdString("lat").append(appendDomId);
1606	dimIdList.push_back(dimYid);
1607	}
1608	break ;
1609	case CDomain::type_attr::unstructured:
1610	{
1611	if (SuperClassWriter::useCFConvention)
1612	{
1613	dimXid = StdString("cell").append(appendDomId);
1614	dimIdList.push_back(dimXid);
1615	dimCoordList.push_back(StdString("lon").append(appendDomId));
1616	dimCoordList.push_back(StdString("lat").append(appendDomId));
1617	}
1618	else
1619	{
1620	StdString domainName = domain->name;
1621	if (domain->nvertex == 1)
1622	{
1623	dimXid = "n" + domainName + "_node";
1624	dimIdList.push_back(dimXid);
1625	dimCoordList.push_back(StdString(domainName + "_node_x"));
1626	dimCoordList.push_back(StdString(domainName + "_node_y"));
1627	}
1628	else if (domain->nvertex == 2)
1629	{
1630	dimXid = "n" + domainName + "_edge";
1631	dimIdList.push_back(dimXid);
1632	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1633	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1634	}
1635	else
1636	{
1637	dimXid = "n" + domainName + "_face";
1638	dimIdList.push_back(dimXid);
1639	dimCoordList.push_back(StdString(domainName + "_face_x"));
1640	dimCoordList.push_back(StdString(domainName + "_face_y"));
1641	}
1642	} // ugrid convention
1643	} // case unstructured domain
1644	}
1645
1646	if (domain->hasArea)
1647	{
1648	hasArea = true;
1649	cellMeasures += " area" + appendDomId;
1650	}
1651	++idxDomain;
1652	}
1653	else if (1 == axisDomainOrder(i))
1654	{
1655	CAxis* axis = CAxis::get(axisList[idxAxis]);
1656	StdString axisId = axis->getAxisOutputName();
1657
1658	if (compressedOutput && axis->isCompressible())
1659	{
1660	dimIdList.push_back(axisId + "_points");
1661	field->setUseCompressedOutput();
1662	}
1663	else
1664	dimIdList.push_back(axisId);
1665
1666	dimCoordList.push_back(axisId);
1667	++idxAxis;
1668	}
1669	else // scalar
1670	{
1671	/* Do nothing here */
1672	}
1673	}
1674
1675	/*
1676	StdString lonid_loc = (server->intraCommSize > 1)
1677	? StdString("lon").append(appendDomid).append("_local")
1678	: lonid;
1679	StdString latid_loc = (server->intraCommSize > 1)
1680	? StdString("lat").append(appendDomid).append("_local")
1681	: latid;
1682	*/
1683	StdString fieldid = field->getFieldOutputName();
1684
1685	nc_type type ;
1686	if (field->prec.isEmpty()) type = NC_FLOAT ;
1687	else
1688	{
1689	if (field->prec==2) type = NC_SHORT ;
1690	else if (field->prec==4) type = NC_FLOAT ;
1691	else if (field->prec==8) type = NC_DOUBLE ;
1692	}
1693
1694	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1695
1696	if (wtime)
1697	{
1698
1699	//StdOStringStream oss;
1700	// oss << "time_" << field->operation.getValue()
1701	// << "_" << field->getRelFile()->output_freq.getValue();
1702	//oss
1703	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
1704	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
1705	dims.push_back(timeid);
1706	}
1707
1708	if (compressedOutput && grid->isCompressible())
1709	{
1710	dims.push_back(grid->getId() + "_points");
1711	field->setUseCompressedOutput();
1712	}
1713	else
1714	{
1715	while (!dimIdList.empty())
1716	{
1717	dims.push_back(dimIdList.back());
1718	dimIdList.pop_back();
1719	}
1720	}
1721
1722	while (!dimCoordList.empty())
1723	{
1724	coodinates.push_back(dimCoordList.back());
1725	dimCoordList.pop_back();
1726	}
1727
1728	try
1729	{
1730	SuperClassWriter::addVariable(fieldid, type, dims);
1731
1732	if (!field->standard_name.isEmpty())
1733	SuperClassWriter::addAttribute
1734	("standard_name", field->standard_name.getValue(), &fieldid);
1735
1736	if (!field->long_name.isEmpty())
1737	SuperClassWriter::addAttribute
1738	("long_name", field->long_name.getValue(), &fieldid);
1739
1740	if (!field->unit.isEmpty())
1741	SuperClassWriter::addAttribute
1742	("units", field->unit.getValue(), &fieldid);
1743
1744	if (!field->valid_min.isEmpty())
1745	SuperClassWriter::addAttribute
1746	("valid_min", field->valid_min.getValue(), &fieldid);
1747
1748	if (!field->valid_max.isEmpty())
1749	SuperClassWriter::addAttribute
1750	("valid_max", field->valid_max.getValue(), &fieldid);
1751
1752	if (!field->scale_factor.isEmpty())
1753	SuperClassWriter::addAttribute
1754	("scale_factor", field->scale_factor.getValue(), &fieldid);
1755
1756	if (!field->add_offset.isEmpty())
1757	SuperClassWriter::addAttribute
1758	("add_offset", field->add_offset.getValue(), &fieldid);
1759
1760	SuperClassWriter::addAttribute
1761	("online_operation", field->operation.getValue(), &fieldid);
1762
1763	// write child variables as attributes
1764
1765
1766	vector<CVariable*> listVars = field->getAllVariables() ;
1767	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1768
1769	bool alreadyAddCellMethod = false;
1770	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1771	if (!field->cell_methods.isEmpty())
1772	{
1773	StdString cellMethodString = field->cell_methods;
1774	if (field->cell_methods_mode.isEmpty() \|\|
1775	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1776	{
1777	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1778	alreadyAddCellMethod = true;
1779	}
1780	else
1781	{
1782	switch (field->cell_methods_mode)
1783	{
1784	case (CField::cell_methods_mode_attr::prefix):
1785	cellMethodsPrefix = cellMethodString;
1786	cellMethodsPrefix += " ";
1787	break;
1788	case (CField::cell_methods_mode_attr::suffix):
1789	cellMethodsSuffix = " ";
1790	cellMethodsSuffix += cellMethodString;
1791	break;
1792	case (CField::cell_methods_mode_attr::none):
1793	break;
1794	default:
1795	break;
1796	}
1797	}
1798	}
1799
1800
1801	if (wtime)
1802	{
1803	CDuration freqOp = field->freq_op.getValue();
1804	freqOp.solveTimeStep(*context->calendar);
1805	StdString freqOpStr = freqOp.toStringUDUnits();
1806	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1807
1808	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1809	freqOut.solveTimeStep(*context->calendar);
1810	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1811
1812	StdString cellMethods(cellMethodsPrefix + "time: ");
1813	if (field->operation.getValue() == "instant") cellMethods += "point";
1814	else if (field->operation.getValue() == "average") cellMethods += "mean";
1815	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1816	else cellMethods += field->operation;
1817	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1818	cellMethods += " (interval: " + freqOpStr + ")";
1819	cellMethods += cellMethodsSuffix;
1820	if (!alreadyAddCellMethod)
1821	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1822	}
1823
1824	if (hasArea)
1825	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1826
1827	if (!field->default_value.isEmpty())
1828	{
1829	double default_value = field->default_value.getValue();
1830	float fdefault_value = (float)default_value;
1831	if (type == NC_DOUBLE)
1832	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1833	else
1834	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1835	}
1836	else
1837	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1838
1839	if (field->compression_level.isEmpty())
1840	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1841	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1842
1843	{ // Ecriture des coordonnes
1844
1845	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1846	std::vector<StdString>::iterator
1847	itc = coodinates.begin(), endc = coodinates.end();
1848
1849	for (; itc!= endc; itc++)
1850	{
1851	StdString & coord = *itc;
1852	if (itc+1 != endc)
1853	coordstr.append(coord).append(" ");
1854	else coordstr.append(coord);
1855	}
1856
1857	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1858
1859	}
1860	}
1861	catch (CNetCdfException& e)
1862	{
1863	StdString msg("On writing field : ");
1864	msg.append(fieldid); msg.append("\n");
1865	msg.append("In the context : ");
1866	msg.append(context->getId()); msg.append("\n");
1867	msg.append(e.what());
1868	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1869	}
1870	} // writeField_()
1871
1872	//--------------------------------------------------------------
1873
1874	void CNc4DataOutput::writeFile_ (CFile* file)
1875	{
1876	StdString filename = file->getFileOutputName();
1877	StdString description = (!file->description.isEmpty())
1878	? file->description.getValue()
1879	: StdString("Created by xios");
1880
1881	singleDomain = (file->nbDomains == 1);
1882
1883	try
1884	{
1885	if (SuperClassWriter::useCFConvention)
1886	this->writeFileAttributes(filename, description,
1887	StdString("CF-1.5"),
1888	StdString("An IPSL model"),
1889	this->getTimeStamp());
1890	else
1891	this->writeFileAttributes(filename, description,
1892	StdString("UGRID"),
1893	StdString("An IPSL model"),
1894	this->getTimeStamp());
1895
1896
1897	if (!appendMode)
1898	SuperClassWriter::addDimension("axis_nbounds", 2);
1899	}
1900	catch (CNetCdfException& e)
1901	{
1902	StdString msg("On writing file : ");
1903	msg.append(filename); msg.append("\n");
1904	msg.append("In the context : ");
1905	CContext* context = CContext::getCurrent() ;
1906	msg.append(context->getId()); msg.append("\n");
1907	msg.append(e.what());
1908	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1909	}
1910	}
1911
1912	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1913	{
1914	StdString name = var->getVariableOutputName();
1915
1916	try
1917	{
1918	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1919	addAttribute(name, var->getData<int>(), &fieldId);
1920	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1921	addAttribute(name, var->getData<short int>(), &fieldId);
1922	else if (var->type.getValue() == CVariable::type_attr::t_float)
1923	addAttribute(name, var->getData<float>(), &fieldId);
1924	else if (var->type.getValue() == CVariable::type_attr::t_double)
1925	addAttribute(name, var->getData<double>(), &fieldId);
1926	else if (var->type.getValue() == CVariable::type_attr::t_string)
1927	addAttribute(name, var->getData<string>(), &fieldId);
1928	else
1929	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1930	<< "Unsupported variable of type " << var->type.getStringValue());
1931	}
1932	catch (CNetCdfException& e)
1933	{
1934	StdString msg("On writing attributes of variable with name : ");
1935	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1936	msg.append("In the context : ");
1937	CContext* context = CContext::getCurrent() ;
1938	msg.append(context->getId()); msg.append("\n");
1939	msg.append(e.what());
1940	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1941	}
1942	}
1943
1944	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1945	{
1946	StdString name = var->getVariableOutputName();
1947
1948	try
1949	{
1950	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1951	addAttribute(name, var->getData<int>());
1952	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1953	addAttribute(name, var->getData<short int>());
1954	else if (var->type.getValue() == CVariable::type_attr::t_float)
1955	addAttribute(name, var->getData<float>());
1956	else if (var->type.getValue() == CVariable::type_attr::t_double)
1957	addAttribute(name, var->getData<double>());
1958	else if (var->type.getValue() == CVariable::type_attr::t_string)
1959	addAttribute(name, var->getData<string>());
1960	else
1961	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1962	<< "Unsupported variable of type " << var->type.getStringValue());
1963	}
1964	catch (CNetCdfException& e)
1965	{
1966	StdString msg("On writing attributes of variable with name : ");
1967	msg.append(name); msg.append("\n");
1968	msg.append("In the context : ");
1969	CContext* context = CContext::getCurrent() ;
1970	msg.append(context->getId()); msg.append("\n");
1971	msg.append(e.what());
1972	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1973	}
1974	}
1975
1976	void CNc4DataOutput::syncFile_ (void)
1977	{
1978	try
1979	{
1980	SuperClassWriter::sync() ;
1981	}
1982	catch (CNetCdfException& e)
1983	{
1984	StdString msg("On synchronizing the write among processes");
1985	msg.append("In the context : ");
1986	CContext* context = CContext::getCurrent() ;
1987	msg.append(context->getId()); msg.append("\n");
1988	msg.append(e.what());
1989	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1990	}
1991	}
1992
1993	void CNc4DataOutput::closeFile_ (void)
1994	{
1995	try
1996	{
1997	SuperClassWriter::close() ;
1998	}
1999	catch (CNetCdfException& e)
2000	{
2001	StdString msg("On closing file");
2002	msg.append("In the context : ");
2003	CContext* context = CContext::getCurrent() ;
2004	msg.append(context->getId()); msg.append("\n");
2005	msg.append(e.what());
2006	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2007	}
2008
2009	}
2010
2011	//---------------------------------------------------------------
2012
2013	StdString CNc4DataOutput::getTimeStamp(void) const
2014	{
2015	const int buffer_size = 100;
2016	time_t rawtime;
2017	struct tm * timeinfo = NULL;
2018	char buffer [buffer_size];
2019
2020	time ( &rawtime );
2021	timeinfo = localtime ( &rawtime );
2022	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
2023
2024	return (StdString(buffer));
2025	}
2026
2027	//---------------------------------------------------------------
2028
2029	void CNc4DataOutput::writeFieldData_ (CField* field)
2030	{
2031	CContext* context = CContext::getCurrent();
2032	CContextServer* server = context->server;
2033	CGrid* grid = field->grid;
2034
2035	if (field->getNStep()<1) return ;
2036
2037	if (!grid->doGridHaveDataToWrite())
2038	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
2039
2040	StdString fieldid = field->getFieldOutputName();
2041
2042	StdOStringStream oss;
2043	string timeAxisId;
2044	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
2045	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
2046
2047	StdString timeBoundId = getTimeCounterName() + "_bounds";
2048
2049	StdString timeAxisBoundId;
2050	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
2051	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
2052
2053	if (!field->wasWritten())
2054	{
2055	if (appendMode && field->file->record_offset.isEmpty() &&
2056	field->getOperationTimeType() != func::CFunctor::once)
2057	{
2058	field->resetNStep(getRecordFromTime(field->last_Write_srv) + 1);
2059	}
2060
2061	field->setWritten();
2062	}
2063
2064
2065	CArray<double,1> time_data(1);
2066	CArray<double,1> time_data_bound(2);
2067	CArray<double,1> time_counter(1);
2068	CArray<double,1> time_counter_bound(2);
2069
2070	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2071
2072	if (wtime)
2073	{
2074	Time lastWrite = field->last_Write_srv;
2075	Time lastLastWrite = field->lastlast_Write_srv;
2076
2077	if (field->getOperationTimeType() == func::CFunctor::instant)
2078	time_data(0) = lastWrite;
2079	else if (field->getOperationTimeType() == func::CFunctor::centered)
2080	time_data(0) = (lastWrite + lastLastWrite) / 2;
2081
2082	if (field->getOperationTimeType() == func::CFunctor::instant)
2083	time_data_bound(0) = time_data_bound(1) = lastWrite;
2084	else if (field->getOperationTimeType() == func::CFunctor::centered)
2085	{
2086	time_data_bound(0) = lastLastWrite;
2087	time_data_bound(1) = lastWrite;
2088	}
2089
2090	if (field->file->time_counter == CFile::time_counter_attr::instant)
2091	time_counter(0) = lastWrite;
2092	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2093	time_counter(0) = (lastWrite + lastLastWrite) / 2;
2094	else if (field->file->time_counter == CFile::time_counter_attr::record)
2095	time_counter(0) = field->getNStep() - 1;
2096
2097
2098	if (field->file->time_counter == CFile::time_counter_attr::instant)
2099	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
2100	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2101	{
2102	time_counter_bound(0) = lastLastWrite;
2103	time_counter_bound(1) = lastWrite;
2104	}
2105	else if (field->file->time_counter == CFile::time_counter_attr::record)
2106	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2107	}
2108
2109	bool isRoot = (server->intraCommRank == 0);
2110
2111	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2112	{
2113	double scaleFactor = 1.0;
2114	double addOffset = 0.0;
2115	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2116	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2117	field->scaleFactorAddOffset(scaleFactor, addOffset);
2118	}
2119
2120	try
2121	{
2122	size_t writtenSize;
2123	if (field->getUseCompressedOutput())
2124	writtenSize = grid->getNumberWrittenIndexes();
2125	else
2126	writtenSize = grid->getWrittenDataSize();
2127
2128	CArray<double,1> fieldData(writtenSize);
2129	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2130
2131	if (field->getUseCompressedOutput())
2132	field->outputCompressedField(fieldData);
2133	else
2134	field->outputField(fieldData);
2135
2136	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2137
2138	switch (SuperClass::type)
2139	{
2140	case (MULTI_FILE) :
2141	{
2142	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2143	if (wtime)
2144	{
2145	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2146	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2147	if (field->file->time_counter != CFile::time_counter_attr::none)
2148	{
2149	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2150	if (field->file->time_counter != CFile::time_counter_attr::record)
2151	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2152	}
2153	}
2154	break;
2155	}
2156	case (ONE_FILE) :
2157	{
2158	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2159	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2160	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2161
2162	std::vector<StdSize> start, count;
2163
2164	if (field->getUseCompressedOutput())
2165	{
2166	if (grid->isCompressible())
2167	{
2168	start.push_back(grid->getOffsetWrittenIndexes());
2169	count.push_back(grid->getNumberWrittenIndexes());
2170	}
2171	else
2172	{
2173	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2174	std::vector<StdString> domainList = grid->getDomainList();
2175	std::vector<StdString> axisList = grid->getAxisList();
2176	int numElement = axisDomainOrder.numElements();
2177	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2178	int idx = nZoomBeginGlobal.size() - 1;
2179
2180	start.reserve(nZoomBeginGlobal.size());
2181	count.reserve(nZoomBeginGlobal.size());
2182
2183
2184	for (int i = numElement - 1; i >= 0; --i)
2185	{
2186	if (2 == axisDomainOrder(i))
2187	{
2188	CDomain* domain = CDomain::get(domainList[idxDomain]);
2189
2190	if (domain->isCompressible())
2191	{
2192	start.push_back(domain->getOffsetWrittenIndexes());
2193	count.push_back(domain->getNumberWrittenIndexes());
2194	idx -= 2;
2195	}
2196	else
2197	{
2198	if ((domain->type) != CDomain::type_attr::unstructured)
2199	{
2200	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2201	count.push_back(nZoomSizeServer[idx]);
2202	}
2203	--idx;
2204	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2205	count.push_back(nZoomSizeServer[idx]);
2206	--idx;
2207	}
2208	--idxDomain;
2209	}
2210	else if (1 == axisDomainOrder(i))
2211	{
2212	CAxis* axis = CAxis::get(axisList[idxAxis]);
2213
2214	if (axis->isCompressible())
2215	{
2216	start.push_back(axis->getOffsetWrittenIndexes());
2217	count.push_back(axis->getNumberWrittenIndexes());
2218	}
2219	else
2220	{
2221	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2222	count.push_back(nZoomSizeServer[idx]);
2223	}
2224
2225	--idxAxis;
2226	--idx;
2227	}
2228	}
2229	}
2230	}
2231	else
2232	{
2233	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2234	std::vector<StdString> domainList = grid->getDomainList();
2235	std::vector<StdString> axisList = grid->getAxisList();
2236	int numElement = axisDomainOrder.numElements();
2237	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2238	int idx = domainList.size() * 2 + axisList.size() - 1;// nZoomBeginGlobal.size() - 1;
2239
2240	start.reserve(nZoomBeginGlobal.size());
2241	count.reserve(nZoomBeginGlobal.size());
2242
2243	for (int i = numElement - 1; i >= 0; --i)
2244	{
2245	if (2 == axisDomainOrder(i))
2246	{
2247	CDomain* domain = CDomain::get(domainList[idxDomain]);
2248	if ((domain->type) != CDomain::type_attr::unstructured)
2249	{
2250	start.push_back(domain->zoom_jbegin - domain->global_zoom_jbegin);
2251	count.push_back(domain->zoom_nj);
2252	}
2253	--idx ;
2254
2255	start.push_back(domain->zoom_ibegin - domain->global_zoom_ibegin);
2256	count.push_back(domain->zoom_ni);
2257	--idx ;
2258	--idxDomain;
2259	}
2260	else if (1 == axisDomainOrder(i))
2261	{
2262	CAxis* axis = CAxis::get(axisList[idxAxis]);
2263	start.push_back(axis->zoom_begin - axis->global_zoom_begin);
2264	count.push_back(axis->zoom_n);
2265	--idx;
2266	--idxAxis;
2267	}
2268	else
2269	{
2270	if (1 == axisDomainOrder.numElements())
2271	{
2272	start.push_back(0);
2273	count.push_back(1);
2274	}
2275	--idx;
2276	}
2277	}
2278	}
2279
2280	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2281	if (wtime)
2282	{
2283	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2284	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2285	if (field->file->time_counter != CFile::time_counter_attr::none)
2286	{
2287	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
2288	if (field->file->time_counter != CFile::time_counter_attr::record)
2289	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2290	}
2291	}
2292
2293	break;
2294	}
2295	}
2296	}
2297	catch (CNetCdfException& e)
2298	{
2299	StdString msg("On writing field data: ");
2300	msg.append(fieldid); msg.append("\n");
2301	msg.append("In the context : ");
2302	msg.append(context->getId()); msg.append("\n");
2303	msg.append(e.what());
2304	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2305	}
2306	}
2307
2308	//---------------------------------------------------------------
2309
2310	void CNc4DataOutput::writeTimeAxis_
2311	(CField* field,
2312	const boost::shared_ptr<CCalendar> cal)
2313	{
2314	StdOStringStream oss;
2315
2316	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2317
2318	// oss << "time_" << field->operation.getValue()
2319	// << "_" << field->getRelFile()->output_freq.getValue();
2320
2321	// StdString axisid = oss.str();
2322	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
2323	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
2324
2325	StdString axisid("time_centered") ;
2326	StdString axisBoundId("time_centered_bounds");
2327	StdString timeid(getTimeCounterName());
2328	StdString timeBoundId("axis_nbounds");
2329
2330	if (field->getOperationTimeType() == func::CFunctor::instant)
2331	{
2332	axisid = "time_instant";
2333	axisBoundId = "time_instant_bounds";
2334	}
2335
2336	try
2337	{
2338	// Adding time_instant or time_centered
2339	std::vector<StdString> dims;
2340	dims.push_back(timeid);
2341	if (!SuperClassWriter::varExist(axisid))
2342	{
2343	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2344
2345	CDate timeOrigin=cal->getTimeOrigin() ;
2346	StdOStringStream oss2;
2347	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
2348	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
2349	StdString strInitdate=oss2.str() ;
2350	StdString strTimeOrigin=timeOrigin.toString() ;
2351	this->writeTimeAxisAttributes
2352	(axisid, cal->getType(),
2353	StdString("seconds since ").append(strTimeOrigin),
2354	strTimeOrigin, axisBoundId);
2355	}
2356
2357	// Adding time_instant_bounds or time_centered_bounds variables
2358	if (!SuperClassWriter::varExist(axisBoundId))
2359	{
2360	dims.clear() ;
2361	dims.push_back(timeid);
2362	dims.push_back(timeBoundId);
2363	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2364	}
2365
2366	if (field->file->time_counter != CFile::time_counter_attr::none)
2367	{
2368	// Adding time_counter
2369	axisid = getTimeCounterName();
2370	axisBoundId = getTimeCounterName() + "_bounds";
2371	dims.clear();
2372	dims.push_back(timeid);
2373	if (!SuperClassWriter::varExist(axisid))
2374	{
2375	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2376	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
2377
2378	if (field->file->time_counter != CFile::time_counter_attr::record)
2379	{
2380	CDate timeOrigin = cal->getTimeOrigin();
2381	StdString strTimeOrigin = timeOrigin.toString();
2382
2383	this->writeTimeAxisAttributes(axisid, cal->getType(),
2384	StdString("seconds since ").append(strTimeOrigin),
2385	strTimeOrigin, axisBoundId);
2386	}
2387	}
2388
2389	// Adding time_counter_bound dimension
2390	if (field->file->time_counter != CFile::time_counter_attr::record)
2391	{
2392	if (!SuperClassWriter::varExist(axisBoundId))
2393	{
2394	dims.clear();
2395	dims.push_back(timeid);
2396	dims.push_back(timeBoundId);
2397	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2398	}
2399	}
2400	}
2401	}
2402	catch (CNetCdfException& e)
2403	{
2404	StdString msg("On writing time axis data: ");
2405	msg.append("In the context : ");
2406	CContext* context = CContext::getCurrent() ;
2407	msg.append(context->getId()); msg.append("\n");
2408	msg.append(e.what());
2409	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2410	const boost::shared_ptr<CCalendar> cal)", << msg);
2411	}
2412	}
2413
2414	//---------------------------------------------------------------
2415
2416	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2417	const StdString & calendar,
2418	const StdString & units,
2419	const StdString & time_origin,
2420	const StdString & time_bounds,
2421	const StdString & standard_name,
2422	const StdString & long_name)
2423	{
2424	try
2425	{
2426	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2427	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2428	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2429	SuperClassWriter::addAttribute("units", units , &axis_name);
2430	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2431	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2432	}
2433	catch (CNetCdfException& e)
2434	{
2435	StdString msg("On writing time axis Attribute: ");
2436	msg.append("In the context : ");
2437	CContext* context = CContext::getCurrent() ;
2438	msg.append(context->getId()); msg.append("\n");
2439	msg.append(e.what());
2440	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2441	const StdString & calendar,\
2442	const StdString & units, \
2443	const StdString & time_origin, \
2444	const StdString & time_bounds, \
2445	const StdString & standard_name, \
2446	const StdString & long_name)", << msg);
2447	}
2448	}
2449
2450	//---------------------------------------------------------------
2451
2452	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2453	const StdString & axis,
2454	const StdString & standard_name,
2455	const StdString & long_name,
2456	const StdString & units,
2457	const StdString & nav_model)
2458	{
2459	try
2460	{
2461	if (!axis.empty())
2462	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2463
2464	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2465	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2466	SuperClassWriter::addAttribute("units" , units , &axis_name);
2467	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2468	}
2469	catch (CNetCdfException& e)
2470	{
2471	StdString msg("On writing Axis Attribute: ");
2472	msg.append("In the context : ");
2473	CContext* context = CContext::getCurrent() ;
2474	msg.append(context->getId()); msg.append("\n");
2475	msg.append(e.what());
2476	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2477	const StdString & axis, \
2478	const StdString & standard_name, \
2479	const StdString & long_name, \
2480	const StdString & units, \
2481	const StdString & nav_model)", << msg);
2482	}
2483	}
2484
2485	//---------------------------------------------------------------
2486
2487	void CNc4DataOutput::writeLocalAttributes
2488	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2489	{
2490	try
2491	{
2492	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2493	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2494	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2495	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2496	}
2497	catch (CNetCdfException& e)
2498	{
2499	StdString msg("On writing Local Attributes: ");
2500	msg.append("In the context : ");
2501	CContext* context = CContext::getCurrent() ;
2502	msg.append(context->getId()); msg.append("\n");
2503	msg.append(e.what());
2504	ERROR("CNc4DataOutput::writeLocalAttributes \
2505	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2506	}
2507
2508	}
2509
2510	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2511	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2512	{
2513	CArray<int,1> array(2) ;
2514
2515	try
2516	{
2517	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2518	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2519	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2520	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2521	array=ni_glo,nj_glo ;
2522	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2523	array=ni,nj ;
2524	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2525	array=ibegin+1,jbegin+1 ;
2526	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2527	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2528	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2529	array=0,0 ;
2530	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2531	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2532	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2533	/*
2534	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2535	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2536	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2537	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2538	*/
2539	}
2540	catch (CNetCdfException& e)
2541	{
2542	StdString msg("On writing Local Attributes IOIPSL \n");
2543	msg.append("In the context : ");
2544	CContext* context = CContext::getCurrent() ;
2545	msg.append(context->getId()); msg.append("\n");
2546	msg.append(e.what());
2547	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2548	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2549	}
2550	}
2551	//---------------------------------------------------------------
2552
2553	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2554	const StdString & description,
2555	const StdString & conventions,
2556	const StdString & production,
2557	const StdString & timeStamp)
2558	{
2559	try
2560	{
2561	SuperClassWriter::addAttribute("name" , name);
2562	SuperClassWriter::addAttribute("description", description);
2563	SuperClassWriter::addAttribute("title" , description);
2564	SuperClassWriter::addAttribute("Conventions", conventions);
2565	SuperClassWriter::addAttribute("production" , production);
2566	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
2567	}
2568	catch (CNetCdfException& e)
2569	{
2570	StdString msg("On writing File Attributes \n ");
2571	msg.append("In the context : ");
2572	CContext* context = CContext::getCurrent() ;
2573	msg.append(context->getId()); msg.append("\n");
2574	msg.append(e.what());
2575	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2576	const StdString & description, \
2577	const StdString & conventions, \
2578	const StdString & production, \
2579	const StdString & timeStamp)", << msg);
2580	}
2581	}
2582
2583	//---------------------------------------------------------------
2584
2585	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2586	int data_dim,
2587	int data_ni,
2588	int data_nj,
2589	int data_ibegin,
2590	int data_jbegin)
2591	{
2592	try
2593	{
2594	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2595	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2596	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2597	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2598	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2599	}
2600	catch (CNetCdfException& e)
2601	{
2602	StdString msg("On writing Mask Attributes \n ");
2603	msg.append("In the context : ");
2604	CContext* context = CContext::getCurrent() ;
2605	msg.append(context->getId()); msg.append("\n");
2606	msg.append(e.what());
2607	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2608	int data_dim, \
2609	int data_ni, \
2610	int data_nj, \
2611	int data_ibegin, \
2612	int data_jbegin)", << msg);
2613	}
2614	}
2615
2616	///--------------------------------------------------------------
2617
2618	StdSize CNc4DataOutput::getRecordFromTime(Time time)
2619	{
2620	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2621	if (it == timeToRecordCache.end())
2622	{
2623	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2624	if (!SuperClassWriter::varExist(timeAxisBoundsId))
2625	timeAxisBoundsId = "time_instant_bounds";
2626
2627	CArray<double,2> timeAxisBounds;
2628	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
2629
2630	StdSize record = 0;
2631	double dtime(time);
2632	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
2633	{
2634	if (timeAxisBounds(1, n) < dtime)
2635	{
2636	record = n + 1;
2637	break;
2638	}
2639	}
2640	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2641	}
2642	return it->second;
2643	}
2644
2645	///--------------------------------------------------------------
2646
2647	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2648	{
2649	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2650	}
2651
2652	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2653	{
2654	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2655	}
2656
2657	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2658	{
2659	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2660	}
2661
2662	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2663	{
2664	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2665	}
2666
2667	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2668	{
2669	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2670	}
2671
2672	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2673	{
2674	this->writtenDomains.insert(domainName);
2675	}
2676
2677	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2678	{
2679	this->writtenCompressedDomains.insert(domainName);
2680	}
2681
2682	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2683	{
2684	this->writtenAxis.insert(axisName);
2685	}
2686
2687	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2688	{
2689	this->writtenCompressedAxis.insert(axisName);
2690	}
2691
2692	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2693	{
2694	this->writtenScalar.insert(scalarName);
2695	}
2696	} // namespace xios

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