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nc4_data_output.cpp @ 1143

Last change on this file since 1143 was 1143, checked in by mhnguyen, 7 years ago

Updating compressed index output on using 2-level server

+) Update compressed index output with new grid distribution

Test
+) On Curie
+) test_complete:

Mode: classical and 2 level server
config: 4 clients + 4 servers
passed

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: 116.6 KB

Line
1	#include "nc4_data_output.hpp"
2
3	#include <boost/lexical_cast.hpp>
4	#include "attribute_template.hpp"
5	#include "group_template.hpp"
6
7	#include "file.hpp"
8	#include "calendar.hpp"
9	#include "context.hpp"
10	#include "context_server.hpp"
11	#include "netCdfException.hpp"
12	#include "exception.hpp"
13
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	// grid->computeCompressedIndex();
1383
1384	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1385	indexes = grid->localIndexToWriteOnServer;
1386	// std::map<int, CArray<size_t, 1> >::const_iterator it;
1387	// for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
1388	// {
1389	// const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
1390	// for (int i = 0; i < it->second.numElements(); i++)
1391	// indexes(compressedIndexes(i)) = it->second(i);
1392	// }
1393
1394	switch (SuperClass::type)
1395	{
1396	case (MULTI_FILE):
1397	{
1398	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1399	break;
1400	}
1401	case (ONE_FILE):
1402	{
1403	if (grid->doGridHaveDataDistributed())
1404	grid->getDistributionServer()->computeGlobalIndex(indexes);
1405
1406	std::vector<StdSize> start, count;
1407	start.push_back(grid->getOffsetWrittenIndexes());
1408	count.push_back(grid->getNumberWrittenIndexes());
1409
1410	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1411	break;
1412	}
1413	}
1414	}
1415	else
1416	{
1417	for (int i = 0; i < numElement; ++i)
1418	{
1419	StdString varId, compress;
1420	CArray<int, 1> indexes;
1421	bool isDistributed;
1422	StdSize nbIndexes, totalNbIndexes, offset;
1423	int firstGlobalIndex;
1424
1425	if (2 == axisDomainOrder(i))
1426	{
1427	CDomain* domain = CDomain::get(domainList[idxDomain]);
1428	StdString domId = domain->getDomainOutputName();
1429
1430	if (!domain->isCompressible()
1431	\|\| domain->type == CDomain::type_attr::unstructured
1432	\|\| domain->isWrittenCompressed(this->filename)
1433	\|\| isWrittenCompressedDomain(domId))
1434	continue;
1435
1436	StdString appendDomId = singleDomain ? "" : "_" + domId;
1437
1438	varId = domId + "_points";
1439	switch (domain->type)
1440	{
1441	case CDomain::type_attr::curvilinear:
1442	compress = "y" + appendDomId + " x" + appendDomId;
1443	break;
1444	case CDomain::type_attr::rectilinear:
1445	compress = "lat" + appendDomId + " lon" + appendDomId;
1446	break;
1447	}
1448
1449	// const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
1450	// indexes.resize(indexesToWrite.size());
1451	// for (int n = 0; n < indexes.numElements(); ++n)
1452	// indexes(n) = indexesToWrite[n];
1453
1454	indexes.resize(domain->compressedIndexToWriteOnServer.numElements());
1455	indexes = domain->compressedIndexToWriteOnServer;
1456
1457	isDistributed = domain->isDistributed();
1458	nbIndexes = domain->getNumberWrittenIndexes();
1459	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1460	offset = domain->getOffsetWrittenIndexes();
1461	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1462
1463	domain->addRelFileCompressed(this->filename);
1464	setWrittenCompressedDomain(domId);
1465	++idxDomain;
1466	}
1467	else if (1 == axisDomainOrder(i))
1468	{
1469	CAxis* axis = CAxis::get(axisList[idxAxis]);
1470	StdString axisId = axis->getAxisOutputName();
1471
1472	if (!axis->isCompressible()
1473	\|\| axis->isWrittenCompressed(this->filename)
1474	\|\| isWrittenCompressedAxis(axisId))
1475	continue;
1476
1477	varId = axisId + "_points";
1478	compress = axisId;
1479
1480	// const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
1481	// indexes.resize(indexesToWrite.size());
1482	// for (int n = 0; n < indexes.numElements(); ++n)
1483	// indexes(n) = indexesToWrite[n];
1484
1485	indexes.resize(axis->compressedIndexToWriteOnServer.numElements());
1486	indexes = axis->compressedIndexToWriteOnServer;
1487
1488	isDistributed = axis->isDistributed();
1489	nbIndexes = axis->getNumberWrittenIndexes();
1490	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1491	offset = axis->getOffsetWrittenIndexes();
1492	firstGlobalIndex = axis->begin;
1493
1494	axis->addRelFileCompressed(this->filename);
1495	setWrittenCompressedAxis(axisId);
1496	++idxAxis;
1497	}
1498	else
1499	{
1500	}
1501
1502	if (!varId.empty())
1503	{
1504	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1505
1506	dims.clear();
1507	dims.push_back(varId);
1508	SuperClassWriter::addVariable(varId, NC_INT, dims);
1509
1510	SuperClassWriter::addAttribute("compress", compress, &varId);
1511
1512	switch (SuperClass::type)
1513	{
1514	case (MULTI_FILE):
1515	{
1516	indexes -= firstGlobalIndex;
1517	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1518	break;
1519	}
1520	case (ONE_FILE):
1521	{
1522	std::vector<StdSize> start, count;
1523	start.push_back(offset);
1524	count.push_back(nbIndexes);
1525
1526	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1527	break;
1528	}
1529	}
1530	}
1531	}
1532
1533	// if (!dims.empty())
1534	// grid->computeCompressedIndex();
1535	}
1536
1537	grid->addRelFileCompressed(this->filename);
1538	}
1539	catch (CNetCdfException& e)
1540	{
1541	StdString msg("On writing compressed grid : ");
1542	msg.append(grid->getId()); msg.append("\n");
1543	msg.append("In the context : ");
1544	CContext* context = CContext::getCurrent();
1545	msg.append(context->getId()); msg.append("\n");
1546	msg.append(e.what());
1547	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1548	}
1549	}
1550
1551	//--------------------------------------------------------------
1552
1553	void CNc4DataOutput::writeTimeDimension_(void)
1554	{
1555	try
1556	{
1557	SuperClassWriter::addDimension(getTimeCounterName());
1558	}
1559	catch (CNetCdfException& e)
1560	{
1561	StdString msg("On writing time dimension : time_couter\n");
1562	msg.append("In the context : ");
1563	CContext* context = CContext::getCurrent() ;
1564	msg.append(context->getId()); msg.append("\n");
1565	msg.append(e.what());
1566	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1567	}
1568	}
1569
1570	//--------------------------------------------------------------
1571
1572	void CNc4DataOutput::writeField_(CField* field)
1573	{
1574	CContext* context = CContext::getCurrent() ;
1575	CContextServer* server=context->server ;
1576
1577	std::vector<StdString> dims, coodinates;
1578	CGrid* grid = field->grid;
1579	if (!grid->doGridHaveDataToWrite())
1580	if (SuperClass::type==MULTI_FILE) return ;
1581
1582	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1583	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1584	std::vector<StdString> domainList = grid->getDomainList();
1585	std::vector<StdString> axisList = grid->getAxisList();
1586	std::vector<StdString> scalarList = grid->getScalarList();
1587
1588	StdString timeid = getTimeCounterName();
1589	StdString dimXid,dimYid;
1590	std::deque<StdString> dimIdList, dimCoordList;
1591	bool hasArea = false;
1592	StdString cellMeasures = "area:";
1593	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1594
1595	for (int i = 0; i < numElement; ++i)
1596	{
1597	if (2 == axisDomainOrder(i))
1598	{
1599	CDomain* domain = CDomain::get(domainList[idxDomain]);
1600	StdString domId = domain->getDomainOutputName();
1601	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1602
1603	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1604	{
1605	dimIdList.push_back(domId + "_points");
1606	field->setUseCompressedOutput();
1607	}
1608
1609	switch (domain->type)
1610	{
1611	case CDomain::type_attr::curvilinear:
1612	if (!compressedOutput \|\| !domain->isCompressible())
1613	{
1614	dimXid = StdString("x").append(appendDomId);
1615	dimIdList.push_back(dimXid);
1616	dimYid = StdString("y").append(appendDomId);
1617	dimIdList.push_back(dimYid);
1618	}
1619	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1620	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1621	break ;
1622	case CDomain::type_attr::rectilinear:
1623	if (!compressedOutput \|\| !domain->isCompressible())
1624	{
1625	dimXid = StdString("lon").append(appendDomId);
1626	dimIdList.push_back(dimXid);
1627	dimYid = StdString("lat").append(appendDomId);
1628	dimIdList.push_back(dimYid);
1629	}
1630	break ;
1631	case CDomain::type_attr::unstructured:
1632	{
1633	if (SuperClassWriter::useCFConvention)
1634	{
1635	dimXid = StdString("cell").append(appendDomId);
1636	dimIdList.push_back(dimXid);
1637	dimCoordList.push_back(StdString("lon").append(appendDomId));
1638	dimCoordList.push_back(StdString("lat").append(appendDomId));
1639	}
1640	else
1641	{
1642	StdString domainName = domain->name;
1643	if (domain->nvertex == 1)
1644	{
1645	dimXid = "n" + domainName + "_node";
1646	dimIdList.push_back(dimXid);
1647	dimCoordList.push_back(StdString(domainName + "_node_x"));
1648	dimCoordList.push_back(StdString(domainName + "_node_y"));
1649	}
1650	else if (domain->nvertex == 2)
1651	{
1652	dimXid = "n" + domainName + "_edge";
1653	dimIdList.push_back(dimXid);
1654	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1655	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1656	}
1657	else
1658	{
1659	dimXid = "n" + domainName + "_face";
1660	dimIdList.push_back(dimXid);
1661	dimCoordList.push_back(StdString(domainName + "_face_x"));
1662	dimCoordList.push_back(StdString(domainName + "_face_y"));
1663	}
1664	} // ugrid convention
1665	} // case unstructured domain
1666	}
1667
1668	if (domain->hasArea)
1669	{
1670	hasArea = true;
1671	cellMeasures += " area" + appendDomId;
1672	}
1673	++idxDomain;
1674	}
1675	else if (1 == axisDomainOrder(i))
1676	{
1677	CAxis* axis = CAxis::get(axisList[idxAxis]);
1678	StdString axisId = axis->getAxisOutputName();
1679
1680	if (compressedOutput && axis->isCompressible())
1681	{
1682	dimIdList.push_back(axisId + "_points");
1683	field->setUseCompressedOutput();
1684	}
1685	else
1686	dimIdList.push_back(axisId);
1687
1688	dimCoordList.push_back(axisId);
1689	++idxAxis;
1690	}
1691	else // scalar
1692	{
1693	/* Do nothing here */
1694	}
1695	}
1696
1697	/*
1698	StdString lonid_loc = (server->intraCommSize > 1)
1699	? StdString("lon").append(appendDomid).append("_local")
1700	: lonid;
1701	StdString latid_loc = (server->intraCommSize > 1)
1702	? StdString("lat").append(appendDomid).append("_local")
1703	: latid;
1704	*/
1705	StdString fieldid = field->getFieldOutputName();
1706
1707	nc_type type ;
1708	if (field->prec.isEmpty()) type = NC_FLOAT ;
1709	else
1710	{
1711	if (field->prec==2) type = NC_SHORT ;
1712	else if (field->prec==4) type = NC_FLOAT ;
1713	else if (field->prec==8) type = NC_DOUBLE ;
1714	}
1715
1716	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1717
1718	if (wtime)
1719	{
1720
1721	//StdOStringStream oss;
1722	// oss << "time_" << field->operation.getValue()
1723	// << "_" << field->getRelFile()->output_freq.getValue();
1724	//oss
1725	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
1726	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
1727	dims.push_back(timeid);
1728	}
1729
1730	if (compressedOutput && grid->isCompressible())
1731	{
1732	dims.push_back(grid->getId() + "_points");
1733	field->setUseCompressedOutput();
1734	}
1735	else
1736	{
1737	while (!dimIdList.empty())
1738	{
1739	dims.push_back(dimIdList.back());
1740	dimIdList.pop_back();
1741	}
1742	}
1743
1744	while (!dimCoordList.empty())
1745	{
1746	coodinates.push_back(dimCoordList.back());
1747	dimCoordList.pop_back();
1748	}
1749
1750	try
1751	{
1752	SuperClassWriter::addVariable(fieldid, type, dims);
1753
1754	if (!field->standard_name.isEmpty())
1755	SuperClassWriter::addAttribute
1756	("standard_name", field->standard_name.getValue(), &fieldid);
1757
1758	if (!field->long_name.isEmpty())
1759	SuperClassWriter::addAttribute
1760	("long_name", field->long_name.getValue(), &fieldid);
1761
1762	if (!field->unit.isEmpty())
1763	SuperClassWriter::addAttribute
1764	("units", field->unit.getValue(), &fieldid);
1765
1766	if (!field->valid_min.isEmpty())
1767	SuperClassWriter::addAttribute
1768	("valid_min", field->valid_min.getValue(), &fieldid);
1769
1770	if (!field->valid_max.isEmpty())
1771	SuperClassWriter::addAttribute
1772	("valid_max", field->valid_max.getValue(), &fieldid);
1773
1774	if (!field->scale_factor.isEmpty())
1775	SuperClassWriter::addAttribute
1776	("scale_factor", field->scale_factor.getValue(), &fieldid);
1777
1778	if (!field->add_offset.isEmpty())
1779	SuperClassWriter::addAttribute
1780	("add_offset", field->add_offset.getValue(), &fieldid);
1781
1782	SuperClassWriter::addAttribute
1783	("online_operation", field->operation.getValue(), &fieldid);
1784
1785	// write child variables as attributes
1786
1787
1788	vector<CVariable*> listVars = field->getAllVariables() ;
1789	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1790
1791	bool alreadyAddCellMethod = false;
1792	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1793	if (!field->cell_methods.isEmpty())
1794	{
1795	StdString cellMethodString = field->cell_methods;
1796	if (field->cell_methods_mode.isEmpty() \|\|
1797	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1798	{
1799	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1800	alreadyAddCellMethod = true;
1801	}
1802	else
1803	{
1804	switch (field->cell_methods_mode)
1805	{
1806	case (CField::cell_methods_mode_attr::prefix):
1807	cellMethodsPrefix = cellMethodString;
1808	cellMethodsPrefix += " ";
1809	break;
1810	case (CField::cell_methods_mode_attr::suffix):
1811	cellMethodsSuffix = " ";
1812	cellMethodsSuffix += cellMethodString;
1813	break;
1814	case (CField::cell_methods_mode_attr::none):
1815	break;
1816	default:
1817	break;
1818	}
1819	}
1820	}
1821
1822
1823	if (wtime)
1824	{
1825	CDuration freqOp = field->freq_op.getValue();
1826	freqOp.solveTimeStep(*context->calendar);
1827	StdString freqOpStr = freqOp.toStringUDUnits();
1828	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1829
1830	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1831	freqOut.solveTimeStep(*context->calendar);
1832	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1833
1834	StdString cellMethods(cellMethodsPrefix + "time: ");
1835	if (field->operation.getValue() == "instant") cellMethods += "point";
1836	else if (field->operation.getValue() == "average") cellMethods += "mean";
1837	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1838	else cellMethods += field->operation;
1839	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1840	cellMethods += " (interval: " + freqOpStr + ")";
1841	cellMethods += cellMethodsSuffix;
1842	if (!alreadyAddCellMethod)
1843	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1844	}
1845
1846	if (hasArea)
1847	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1848
1849	if (!field->default_value.isEmpty())
1850	{
1851	double default_value = field->default_value.getValue();
1852	float fdefault_value = (float)default_value;
1853	if (type == NC_DOUBLE)
1854	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1855	else
1856	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1857	}
1858	else
1859	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1860
1861	if (field->compression_level.isEmpty())
1862	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1863	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1864
1865	{ // Ecriture des coordonnes
1866
1867	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1868	std::vector<StdString>::iterator
1869	itc = coodinates.begin(), endc = coodinates.end();
1870
1871	for (; itc!= endc; itc++)
1872	{
1873	StdString & coord = *itc;
1874	if (itc+1 != endc)
1875	coordstr.append(coord).append(" ");
1876	else coordstr.append(coord);
1877	}
1878
1879	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1880
1881	}
1882	}
1883	catch (CNetCdfException& e)
1884	{
1885	StdString msg("On writing field : ");
1886	msg.append(fieldid); msg.append("\n");
1887	msg.append("In the context : ");
1888	msg.append(context->getId()); msg.append("\n");
1889	msg.append(e.what());
1890	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1891	}
1892	} // writeField_()
1893
1894	//--------------------------------------------------------------
1895
1896	void CNc4DataOutput::writeFile_ (CFile* file)
1897	{
1898	StdString filename = file->getFileOutputName();
1899	StdString description = (!file->description.isEmpty())
1900	? file->description.getValue()
1901	: StdString("Created by xios");
1902
1903	singleDomain = (file->nbDomains == 1);
1904
1905	try
1906	{
1907	if (SuperClassWriter::useCFConvention)
1908	this->writeFileAttributes(filename, description,
1909	StdString("CF-1.5"),
1910	StdString("An IPSL model"),
1911	this->getTimeStamp());
1912	else
1913	this->writeFileAttributes(filename, description,
1914	StdString("UGRID"),
1915	StdString("An IPSL model"),
1916	this->getTimeStamp());
1917
1918
1919	if (!appendMode)
1920	SuperClassWriter::addDimension("axis_nbounds", 2);
1921	}
1922	catch (CNetCdfException& e)
1923	{
1924	StdString msg("On writing file : ");
1925	msg.append(filename); msg.append("\n");
1926	msg.append("In the context : ");
1927	CContext* context = CContext::getCurrent() ;
1928	msg.append(context->getId()); msg.append("\n");
1929	msg.append(e.what());
1930	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1931	}
1932	}
1933
1934	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1935	{
1936	StdString name = var->getVariableOutputName();
1937
1938	try
1939	{
1940	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1941	addAttribute(name, var->getData<int>(), &fieldId);
1942	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1943	addAttribute(name, var->getData<short int>(), &fieldId);
1944	else if (var->type.getValue() == CVariable::type_attr::t_float)
1945	addAttribute(name, var->getData<float>(), &fieldId);
1946	else if (var->type.getValue() == CVariable::type_attr::t_double)
1947	addAttribute(name, var->getData<double>(), &fieldId);
1948	else if (var->type.getValue() == CVariable::type_attr::t_string)
1949	addAttribute(name, var->getData<string>(), &fieldId);
1950	else
1951	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1952	<< "Unsupported variable of type " << var->type.getStringValue());
1953	}
1954	catch (CNetCdfException& e)
1955	{
1956	StdString msg("On writing attributes of variable with name : ");
1957	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1958	msg.append("In the context : ");
1959	CContext* context = CContext::getCurrent() ;
1960	msg.append(context->getId()); msg.append("\n");
1961	msg.append(e.what());
1962	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1963	}
1964	}
1965
1966	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1967	{
1968	StdString name = var->getVariableOutputName();
1969
1970	try
1971	{
1972	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1973	addAttribute(name, var->getData<int>());
1974	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1975	addAttribute(name, var->getData<short int>());
1976	else if (var->type.getValue() == CVariable::type_attr::t_float)
1977	addAttribute(name, var->getData<float>());
1978	else if (var->type.getValue() == CVariable::type_attr::t_double)
1979	addAttribute(name, var->getData<double>());
1980	else if (var->type.getValue() == CVariable::type_attr::t_string)
1981	addAttribute(name, var->getData<string>());
1982	else
1983	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1984	<< "Unsupported variable of type " << var->type.getStringValue());
1985	}
1986	catch (CNetCdfException& e)
1987	{
1988	StdString msg("On writing attributes of variable with name : ");
1989	msg.append(name); msg.append("\n");
1990	msg.append("In the context : ");
1991	CContext* context = CContext::getCurrent() ;
1992	msg.append(context->getId()); msg.append("\n");
1993	msg.append(e.what());
1994	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1995	}
1996	}
1997
1998	void CNc4DataOutput::syncFile_ (void)
1999	{
2000	try
2001	{
2002	SuperClassWriter::sync() ;
2003	}
2004	catch (CNetCdfException& e)
2005	{
2006	StdString msg("On synchronizing the write among processes");
2007	msg.append("In the context : ");
2008	CContext* context = CContext::getCurrent() ;
2009	msg.append(context->getId()); msg.append("\n");
2010	msg.append(e.what());
2011	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2012	}
2013	}
2014
2015	void CNc4DataOutput::closeFile_ (void)
2016	{
2017	try
2018	{
2019	SuperClassWriter::close() ;
2020	}
2021	catch (CNetCdfException& e)
2022	{
2023	StdString msg("On closing file");
2024	msg.append("In the context : ");
2025	CContext* context = CContext::getCurrent() ;
2026	msg.append(context->getId()); msg.append("\n");
2027	msg.append(e.what());
2028	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
2029	}
2030
2031	}
2032
2033	//---------------------------------------------------------------
2034
2035	StdString CNc4DataOutput::getTimeStamp(void) const
2036	{
2037	const int buffer_size = 100;
2038	time_t rawtime;
2039	struct tm * timeinfo = NULL;
2040	char buffer [buffer_size];
2041
2042	time ( &rawtime );
2043	timeinfo = localtime ( &rawtime );
2044	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
2045
2046	return (StdString(buffer));
2047	}
2048
2049	//---------------------------------------------------------------
2050
2051	void CNc4DataOutput::writeFieldData_ (CField* field)
2052	{
2053	CContext* context = CContext::getCurrent();
2054	CContextServer* server = context->server;
2055	CGrid* grid = field->grid;
2056
2057	if (field->getNStep()<1) return ;
2058
2059	if (!grid->doGridHaveDataToWrite())
2060	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
2061
2062	StdString fieldid = field->getFieldOutputName();
2063
2064	StdOStringStream oss;
2065	string timeAxisId;
2066	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
2067	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
2068
2069	StdString timeBoundId = getTimeCounterName() + "_bounds";
2070
2071	StdString timeAxisBoundId;
2072	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
2073	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
2074
2075	if (!field->wasWritten())
2076	{
2077	if (appendMode && field->file->record_offset.isEmpty() &&
2078	field->getOperationTimeType() != func::CFunctor::once)
2079	{
2080	field->resetNStep(getRecordFromTime(field->last_Write_srv) + 1);
2081	}
2082
2083	field->setWritten();
2084	}
2085
2086
2087	CArray<double,1> time_data(1);
2088	CArray<double,1> time_data_bound(2);
2089	CArray<double,1> time_counter(1);
2090	CArray<double,1> time_counter_bound(2);
2091
2092	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2093
2094	if (wtime)
2095	{
2096	Time lastWrite = field->last_Write_srv;
2097	Time lastLastWrite = field->lastlast_Write_srv;
2098
2099	if (field->getOperationTimeType() == func::CFunctor::instant)
2100	time_data(0) = lastWrite;
2101	else if (field->getOperationTimeType() == func::CFunctor::centered)
2102	time_data(0) = (lastWrite + lastLastWrite) / 2;
2103
2104	if (field->getOperationTimeType() == func::CFunctor::instant)
2105	time_data_bound(0) = time_data_bound(1) = lastWrite;
2106	else if (field->getOperationTimeType() == func::CFunctor::centered)
2107	{
2108	time_data_bound(0) = lastLastWrite;
2109	time_data_bound(1) = lastWrite;
2110	}
2111
2112	if (field->file->time_counter == CFile::time_counter_attr::instant)
2113	time_counter(0) = lastWrite;
2114	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2115	time_counter(0) = (lastWrite + lastLastWrite) / 2;
2116	else if (field->file->time_counter == CFile::time_counter_attr::record)
2117	time_counter(0) = field->getNStep() - 1;
2118
2119
2120	if (field->file->time_counter == CFile::time_counter_attr::instant)
2121	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
2122	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2123	{
2124	time_counter_bound(0) = lastLastWrite;
2125	time_counter_bound(1) = lastWrite;
2126	}
2127	else if (field->file->time_counter == CFile::time_counter_attr::record)
2128	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2129	}
2130
2131	bool isRoot = (server->intraCommRank == 0);
2132
2133	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2134	{
2135	double scaleFactor = 1.0;
2136	double addOffset = 0.0;
2137	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2138	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2139	field->scaleFactorAddOffset(scaleFactor, addOffset);
2140	}
2141
2142	try
2143	{
2144	size_t writtenSize;
2145	if (field->getUseCompressedOutput())
2146	writtenSize = grid->getNumberWrittenIndexes();
2147	else
2148	writtenSize = grid->getWrittenDataSize();
2149
2150	CArray<double,1> fieldData(writtenSize);
2151	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2152
2153	if (field->getUseCompressedOutput())
2154	field->outputCompressedField(fieldData);
2155	else
2156	field->outputField(fieldData);
2157
2158	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2159
2160	switch (SuperClass::type)
2161	{
2162	case (MULTI_FILE) :
2163	{
2164	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2165	if (wtime)
2166	{
2167	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2168	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2169	if (field->file->time_counter != CFile::time_counter_attr::none)
2170	{
2171	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2172	if (field->file->time_counter != CFile::time_counter_attr::record)
2173	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2174	}
2175	}
2176	break;
2177	}
2178	case (ONE_FILE) :
2179	{
2180	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2181	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2182	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2183
2184	std::vector<StdSize> start, count;
2185
2186	if (field->getUseCompressedOutput())
2187	{
2188	if (grid->isCompressible())
2189	{
2190	start.push_back(grid->getOffsetWrittenIndexes());
2191	count.push_back(grid->getNumberWrittenIndexes());
2192	}
2193	else
2194	{
2195	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2196	std::vector<StdString> domainList = grid->getDomainList();
2197	std::vector<StdString> axisList = grid->getAxisList();
2198	int numElement = axisDomainOrder.numElements();
2199	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2200	int idx = nZoomBeginGlobal.size() - 1;
2201
2202	start.reserve(nZoomBeginGlobal.size());
2203	count.reserve(nZoomBeginGlobal.size());
2204
2205
2206	for (int i = numElement - 1; i >= 0; --i)
2207	{
2208	if (2 == axisDomainOrder(i))
2209	{
2210	CDomain* domain = CDomain::get(domainList[idxDomain]);
2211
2212	if (domain->isCompressible())
2213	{
2214	start.push_back(domain->getOffsetWrittenIndexes());
2215	count.push_back(domain->getNumberWrittenIndexes());
2216	idx -= 2;
2217	}
2218	else
2219	{
2220	if ((domain->type) != CDomain::type_attr::unstructured)
2221	{
2222	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2223	count.push_back(nZoomSizeServer[idx]);
2224	}
2225	--idx;
2226	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2227	count.push_back(nZoomSizeServer[idx]);
2228	--idx;
2229	}
2230	--idxDomain;
2231	}
2232	else if (1 == axisDomainOrder(i))
2233	{
2234	CAxis* axis = CAxis::get(axisList[idxAxis]);
2235
2236	if (axis->isCompressible())
2237	{
2238	start.push_back(axis->getOffsetWrittenIndexes());
2239	count.push_back(axis->getNumberWrittenIndexes());
2240	}
2241	else
2242	{
2243	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2244	count.push_back(nZoomSizeServer[idx]);
2245	}
2246
2247	--idxAxis;
2248	--idx;
2249	}
2250	}
2251	}
2252	}
2253	else
2254	{
2255	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2256	std::vector<StdString> domainList = grid->getDomainList();
2257	std::vector<StdString> axisList = grid->getAxisList();
2258	int numElement = axisDomainOrder.numElements();
2259	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2260	int idx = domainList.size() * 2 + axisList.size() - 1;// nZoomBeginGlobal.size() - 1;
2261
2262	start.reserve(nZoomBeginGlobal.size());
2263	count.reserve(nZoomBeginGlobal.size());
2264
2265	for (int i = numElement - 1; i >= 0; --i)
2266	{
2267	if (2 == axisDomainOrder(i))
2268	{
2269	CDomain* domain = CDomain::get(domainList[idxDomain]);
2270	if ((domain->type) != CDomain::type_attr::unstructured)
2271	{
2272	start.push_back(domain->zoom_jbegin - domain->global_zoom_jbegin);
2273	count.push_back(domain->zoom_nj);
2274	}
2275	--idx ;
2276
2277	start.push_back(domain->zoom_ibegin - domain->global_zoom_ibegin);
2278	count.push_back(domain->zoom_ni);
2279	--idx ;
2280	--idxDomain;
2281	}
2282	else if (1 == axisDomainOrder(i))
2283	{
2284	CAxis* axis = CAxis::get(axisList[idxAxis]);
2285	start.push_back(axis->zoom_begin - axis->global_zoom_begin);
2286	count.push_back(axis->zoom_n);
2287	--idx;
2288	--idxAxis;
2289	}
2290	else
2291	{
2292	if (1 == axisDomainOrder.numElements())
2293	{
2294	start.push_back(0);
2295	count.push_back(1);
2296	}
2297	--idx;
2298	}
2299	}
2300	}
2301
2302	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2303	if (wtime)
2304	{
2305	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2306	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2307	if (field->file->time_counter != CFile::time_counter_attr::none)
2308	{
2309	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
2310	if (field->file->time_counter != CFile::time_counter_attr::record)
2311	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2312	}
2313	}
2314
2315	break;
2316	}
2317	}
2318	}
2319	catch (CNetCdfException& e)
2320	{
2321	StdString msg("On writing field data: ");
2322	msg.append(fieldid); msg.append("\n");
2323	msg.append("In the context : ");
2324	msg.append(context->getId()); msg.append("\n");
2325	msg.append(e.what());
2326	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2327	}
2328	}
2329
2330	//---------------------------------------------------------------
2331
2332	void CNc4DataOutput::writeTimeAxis_
2333	(CField* field,
2334	const boost::shared_ptr<CCalendar> cal)
2335	{
2336	StdOStringStream oss;
2337
2338	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2339
2340	// oss << "time_" << field->operation.getValue()
2341	// << "_" << field->getRelFile()->output_freq.getValue();
2342
2343	// StdString axisid = oss.str();
2344	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
2345	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
2346
2347	StdString axisid("time_centered") ;
2348	StdString axisBoundId("time_centered_bounds");
2349	StdString timeid(getTimeCounterName());
2350	StdString timeBoundId("axis_nbounds");
2351
2352	if (field->getOperationTimeType() == func::CFunctor::instant)
2353	{
2354	axisid = "time_instant";
2355	axisBoundId = "time_instant_bounds";
2356	}
2357
2358	try
2359	{
2360	// Adding time_instant or time_centered
2361	std::vector<StdString> dims;
2362	dims.push_back(timeid);
2363	if (!SuperClassWriter::varExist(axisid))
2364	{
2365	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2366
2367	CDate timeOrigin=cal->getTimeOrigin() ;
2368	StdOStringStream oss2;
2369	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
2370	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
2371	StdString strInitdate=oss2.str() ;
2372	StdString strTimeOrigin=timeOrigin.toString() ;
2373	this->writeTimeAxisAttributes
2374	(axisid, cal->getType(),
2375	StdString("seconds since ").append(strTimeOrigin),
2376	strTimeOrigin, axisBoundId);
2377	}
2378
2379	// Adding time_instant_bounds or time_centered_bounds variables
2380	if (!SuperClassWriter::varExist(axisBoundId))
2381	{
2382	dims.clear() ;
2383	dims.push_back(timeid);
2384	dims.push_back(timeBoundId);
2385	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2386	}
2387
2388	if (field->file->time_counter != CFile::time_counter_attr::none)
2389	{
2390	// Adding time_counter
2391	axisid = getTimeCounterName();
2392	axisBoundId = getTimeCounterName() + "_bounds";
2393	dims.clear();
2394	dims.push_back(timeid);
2395	if (!SuperClassWriter::varExist(axisid))
2396	{
2397	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2398	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
2399
2400	if (field->file->time_counter != CFile::time_counter_attr::record)
2401	{
2402	CDate timeOrigin = cal->getTimeOrigin();
2403	StdString strTimeOrigin = timeOrigin.toString();
2404
2405	this->writeTimeAxisAttributes(axisid, cal->getType(),
2406	StdString("seconds since ").append(strTimeOrigin),
2407	strTimeOrigin, axisBoundId);
2408	}
2409	}
2410
2411	// Adding time_counter_bound dimension
2412	if (field->file->time_counter != CFile::time_counter_attr::record)
2413	{
2414	if (!SuperClassWriter::varExist(axisBoundId))
2415	{
2416	dims.clear();
2417	dims.push_back(timeid);
2418	dims.push_back(timeBoundId);
2419	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2420	}
2421	}
2422	}
2423	}
2424	catch (CNetCdfException& e)
2425	{
2426	StdString msg("On writing time axis data: ");
2427	msg.append("In the context : ");
2428	CContext* context = CContext::getCurrent() ;
2429	msg.append(context->getId()); msg.append("\n");
2430	msg.append(e.what());
2431	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2432	const boost::shared_ptr<CCalendar> cal)", << msg);
2433	}
2434	}
2435
2436	//---------------------------------------------------------------
2437
2438	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2439	const StdString & calendar,
2440	const StdString & units,
2441	const StdString & time_origin,
2442	const StdString & time_bounds,
2443	const StdString & standard_name,
2444	const StdString & long_name)
2445	{
2446	try
2447	{
2448	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2449	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2450	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2451	SuperClassWriter::addAttribute("units", units , &axis_name);
2452	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2453	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2454	}
2455	catch (CNetCdfException& e)
2456	{
2457	StdString msg("On writing time axis Attribute: ");
2458	msg.append("In the context : ");
2459	CContext* context = CContext::getCurrent() ;
2460	msg.append(context->getId()); msg.append("\n");
2461	msg.append(e.what());
2462	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2463	const StdString & calendar,\
2464	const StdString & units, \
2465	const StdString & time_origin, \
2466	const StdString & time_bounds, \
2467	const StdString & standard_name, \
2468	const StdString & long_name)", << msg);
2469	}
2470	}
2471
2472	//---------------------------------------------------------------
2473
2474	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2475	const StdString & axis,
2476	const StdString & standard_name,
2477	const StdString & long_name,
2478	const StdString & units,
2479	const StdString & nav_model)
2480	{
2481	try
2482	{
2483	if (!axis.empty())
2484	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2485
2486	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2487	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2488	SuperClassWriter::addAttribute("units" , units , &axis_name);
2489	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2490	}
2491	catch (CNetCdfException& e)
2492	{
2493	StdString msg("On writing Axis Attribute: ");
2494	msg.append("In the context : ");
2495	CContext* context = CContext::getCurrent() ;
2496	msg.append(context->getId()); msg.append("\n");
2497	msg.append(e.what());
2498	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2499	const StdString & axis, \
2500	const StdString & standard_name, \
2501	const StdString & long_name, \
2502	const StdString & units, \
2503	const StdString & nav_model)", << msg);
2504	}
2505	}
2506
2507	//---------------------------------------------------------------
2508
2509	void CNc4DataOutput::writeLocalAttributes
2510	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2511	{
2512	try
2513	{
2514	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2515	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2516	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2517	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2518	}
2519	catch (CNetCdfException& e)
2520	{
2521	StdString msg("On writing Local Attributes: ");
2522	msg.append("In the context : ");
2523	CContext* context = CContext::getCurrent() ;
2524	msg.append(context->getId()); msg.append("\n");
2525	msg.append(e.what());
2526	ERROR("CNc4DataOutput::writeLocalAttributes \
2527	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2528	}
2529
2530	}
2531
2532	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2533	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2534	{
2535	CArray<int,1> array(2) ;
2536
2537	try
2538	{
2539	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2540	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2541	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2542	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2543	array=ni_glo,nj_glo ;
2544	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2545	array=ni,nj ;
2546	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2547	array=ibegin+1,jbegin+1 ;
2548	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2549	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2550	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2551	array=0,0 ;
2552	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2553	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2554	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2555	/*
2556	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2557	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2558	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2559	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2560	*/
2561	}
2562	catch (CNetCdfException& e)
2563	{
2564	StdString msg("On writing Local Attributes IOIPSL \n");
2565	msg.append("In the context : ");
2566	CContext* context = CContext::getCurrent() ;
2567	msg.append(context->getId()); msg.append("\n");
2568	msg.append(e.what());
2569	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2570	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2571	}
2572	}
2573	//---------------------------------------------------------------
2574
2575	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2576	const StdString & description,
2577	const StdString & conventions,
2578	const StdString & production,
2579	const StdString & timeStamp)
2580	{
2581	try
2582	{
2583	SuperClassWriter::addAttribute("name" , name);
2584	SuperClassWriter::addAttribute("description", description);
2585	SuperClassWriter::addAttribute("title" , description);
2586	SuperClassWriter::addAttribute("Conventions", conventions);
2587	SuperClassWriter::addAttribute("production" , production);
2588	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
2589	}
2590	catch (CNetCdfException& e)
2591	{
2592	StdString msg("On writing File Attributes \n ");
2593	msg.append("In the context : ");
2594	CContext* context = CContext::getCurrent() ;
2595	msg.append(context->getId()); msg.append("\n");
2596	msg.append(e.what());
2597	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2598	const StdString & description, \
2599	const StdString & conventions, \
2600	const StdString & production, \
2601	const StdString & timeStamp)", << msg);
2602	}
2603	}
2604
2605	//---------------------------------------------------------------
2606
2607	void 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)
2613	{
2614	try
2615	{
2616	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2617	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2618	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2619	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2620	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2621	}
2622	catch (CNetCdfException& e)
2623	{
2624	StdString msg("On writing Mask Attributes \n ");
2625	msg.append("In the context : ");
2626	CContext* context = CContext::getCurrent() ;
2627	msg.append(context->getId()); msg.append("\n");
2628	msg.append(e.what());
2629	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2630	int data_dim, \
2631	int data_ni, \
2632	int data_nj, \
2633	int data_ibegin, \
2634	int data_jbegin)", << msg);
2635	}
2636	}
2637
2638	///--------------------------------------------------------------
2639
2640	StdSize CNc4DataOutput::getRecordFromTime(Time time)
2641	{
2642	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2643	if (it == timeToRecordCache.end())
2644	{
2645	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2646	if (!SuperClassWriter::varExist(timeAxisBoundsId))
2647	timeAxisBoundsId = "time_instant_bounds";
2648
2649	CArray<double,2> timeAxisBounds;
2650	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
2651
2652	StdSize record = 0;
2653	double dtime(time);
2654	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
2655	{
2656	if (timeAxisBounds(1, n) < dtime)
2657	{
2658	record = n + 1;
2659	break;
2660	}
2661	}
2662	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2663	}
2664	return it->second;
2665	}
2666
2667	///--------------------------------------------------------------
2668
2669	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2670	{
2671	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2672	}
2673
2674	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2675	{
2676	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2677	}
2678
2679	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2680	{
2681	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2682	}
2683
2684	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2685	{
2686	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2687	}
2688
2689	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2690	{
2691	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2692	}
2693
2694	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2695	{
2696	this->writtenDomains.insert(domainName);
2697	}
2698
2699	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2700	{
2701	this->writtenCompressedDomains.insert(domainName);
2702	}
2703
2704	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2705	{
2706	this->writtenAxis.insert(axisName);
2707	}
2708
2709	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2710	{
2711	this->writtenCompressedAxis.insert(axisName);
2712	}
2713
2714	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2715	{
2716	this->writtenScalar.insert(scalarName);
2717	}
2718	} // namespace xios

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source: XIOS/dev/dev_olga/src/io/nc4_data_output.cpp @ 1143

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