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nc4_data_output.cpp @ 1012

Last change on this file since 1012 was 1012, checked in by mhnguyen, 7 years ago

Modifying behavior of file append: If ALL fields in file have operation="once", append mode will be ignored

+) Only read timestep for field whose operation is different from once.

Test
+) On Curie
+) OK

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: 114.5 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	if (domain->type == CDomain::type_attr::unstructured)
53	{
54	if (SuperClassWriter::useCFConvention)
55	writeUnstructuredDomain(domain) ;
56	else
57	writeUnstructuredDomainUgrid(domain) ;
58	return ;
59	}
60
61	CContext* context = CContext::getCurrent() ;
62	CContextServer* server=context->server ;
63
64	if (domain->IsWritten(this->filename)) return;
65	domain->checkAttributes();
66
67	if (domain->isEmpty())
68	if (SuperClass::type==MULTI_FILE) return;
69
70	std::vector<StdString> dim0, dim1;
71	StdString domid = domain->getDomainOutputName();
72	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
73	if (isWrittenDomain(domid)) return ;
74	else setWrittenDomain(domid);
75
76
77	StdString dimXid, dimYid ;
78
79	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
80	switch (domain->type)
81	{
82	case CDomain::type_attr::curvilinear :
83	dimXid = StdString("x").append(appendDomid);
84	dimYid = StdString("y").append(appendDomid);
85	break ;
86	case CDomain::type_attr::rectilinear :
87	dimXid = StdString("lon").append(appendDomid);
88	dimYid = StdString("lat").append(appendDomid);
89	break;
90	}
91
92	StdString dimVertId = StdString("nvertex").append(appendDomid);
93
94	string lonid,latid,bounds_lonid,bounds_latid ;
95	string areaId = "area" + appendDomid;
96	/*
97	StdString lonid_loc = (server->intraCommSize > 1)
98	? StdString("lon").append(appendDomid).append("_local")
99	: lonid;
100	StdString latid_loc = (server->intraCommSize > 1)
101	? StdString("lat").append(appendDomid).append("_local")
102	: latid;
103	*/
104
105	try
106	{
107	switch (SuperClass::type)
108	{
109	case (MULTI_FILE) :
110	{
111	// if (domain->isEmpty()) return;
112
113	if (server->intraCommSize > 1)
114	{
115	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
116	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
117	}
118
119	switch (domain->type)
120	{
121	case CDomain::type_attr::curvilinear :
122	dim0.push_back(dimYid); dim0.push_back(dimXid);
123	lonid = StdString("nav_lon").append(appendDomid);
124	latid = StdString("nav_lat").append(appendDomid);
125	break ;
126	case CDomain::type_attr::rectilinear :
127	lonid = StdString("lon").append(appendDomid);
128	latid = StdString("lat").append(appendDomid);
129	dim0.push_back(dimYid);
130	dim1.push_back(dimXid);
131	break;
132	}
133
134	bounds_lonid = StdString("bounds_lon").append(appendDomid);
135	bounds_latid = StdString("bounds_lat").append(appendDomid);
136
137	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
138	SuperClassWriter::addDimension(dimYid, domain->zoom_nj_srv);
139
140	if (domain->hasBounds)
141	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
142
143	if (server->intraCommSize > 1)
144	{
145	this->writeLocalAttributes(domain->zoom_ibegin_srv,
146	domain->zoom_ni_srv,
147	domain->zoom_jbegin_srv,
148	domain->zoom_nj_srv,
149	appendDomid);
150
151	if (singleDomain)
152	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
153	domain->zoom_ibegin_srv,
154	domain->zoom_ni_srv,
155	domain->zoom_jbegin_srv,
156	domain->zoom_nj_srv,
157	domain->ni_glo,domain->nj_glo,
158	server->intraCommRank,server->intraCommSize);
159	}
160
161	if (domain->hasLonLat)
162	{
163	switch (domain->type)
164	{
165	case CDomain::type_attr::curvilinear :
166	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
167	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
168	break ;
169	case CDomain::type_attr::rectilinear :
170	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
171	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
172	break ;
173	}
174
175	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
176	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
177
178	if (domain->hasBounds)
179	{
180	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
181	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
182
183	dim0.clear();
184	dim0.push_back(dimYid);
185	dim0.push_back(dimXid);
186	dim0.push_back(dimVertId);
187	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
188	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
189	}
190	}
191
192	dim0.clear();
193	dim0.push_back(dimYid);
194	dim0.push_back(dimXid);
195
196
197	// supress mask if (server->intraCommSize > 1)
198	// supress mask {
199	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
200	// supress mask
201	// supress mask this->writeMaskAttributes(maskid,
202	// supress mask domain->data_dim.getValue()/*,
203	// supress mask domain->data_ni.getValue(),
204	// supress mask domain->data_nj.getValue(),
205	// supress mask domain->data_ibegin.getValue(),
206	// supress mask domain->data_jbegin.getValue()*/);
207	// supress mask }
208
209	//SuperClassWriter::setDefaultValue(maskid, &dvm);
210
211	if (domain->hasArea)
212	{
213	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
214	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
215	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
216	}
217
218	SuperClassWriter::definition_end();
219
220	if (domain->hasLonLat)
221	{
222	switch (domain->type)
223	{
224	case CDomain::type_attr::curvilinear :
225	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
226	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
227	break;
228	case CDomain::type_attr::rectilinear :
229	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
230	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
231	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
232	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
233	break;
234	}
235
236	if (domain->hasBounds)
237	{
238	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
239	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
240	}
241	}
242
243	if (domain->hasArea)
244	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
245
246	SuperClassWriter::definition_start();
247
248	break;
249	}
250	case (ONE_FILE) :
251	{
252	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
253	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
254
255	if (domain->hasBounds)
256	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
257
258	if (domain->hasLonLat)
259	{
260	switch (domain->type)
261	{
262	case CDomain::type_attr::curvilinear :
263	dim0.push_back(dimYid); dim0.push_back(dimXid);
264	lonid = StdString("nav_lon").append(appendDomid);
265	latid = StdString("nav_lat").append(appendDomid);
266	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
267	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
268	break;
269
270	case CDomain::type_attr::rectilinear :
271	dim0.push_back(dimYid);
272	dim1.push_back(dimXid);
273	lonid = StdString("lon").append(appendDomid);
274	latid = StdString("lat").append(appendDomid);
275	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
276	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
277	break;
278	}
279
280	bounds_lonid = StdString("bounds_lon").append(appendDomid);
281	bounds_latid = StdString("bounds_lat").append(appendDomid);
282
283	this->writeAxisAttributes
284	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
285	this->writeAxisAttributes
286	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
287
288	if (domain->hasBounds)
289	{
290	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
291	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
292
293	dim0.clear();
294	dim0.push_back(dimYid);
295	dim0.push_back(dimXid);
296	dim0.push_back(dimVertId);
297	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
298	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
299	}
300	}
301
302	if (domain->hasArea)
303	{
304	dim0.clear();
305	dim0.push_back(dimYid); dim0.push_back(dimXid);
306	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
307	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
308	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
309	dim0.clear();
310	}
311
312	SuperClassWriter::definition_end();
313
314	switch (domain->type)
315	{
316	case CDomain::type_attr::curvilinear :
317	{
318	std::vector<StdSize> start(2) ;
319	std::vector<StdSize> count(2) ;
320	if (domain->isEmpty())
321	{
322	start[0]=0 ; start[1]=0 ;
323	count[0]=0 ; count[1]=0 ;
324	}
325	else
326	{
327	start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
328	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
329	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
330	}
331
332	if (domain->hasLonLat)
333	{
334	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
335	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
336	}
337	break;
338	}
339	case CDomain::type_attr::rectilinear :
340	{
341	if (domain->hasLonLat)
342	{
343	std::vector<StdSize> start(1) ;
344	std::vector<StdSize> count(1) ;
345	if (domain->isEmpty())
346	{
347	start[0]=0 ;
348	count[0]=0 ;
349	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
350	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
351
352	}
353	else
354	{
355	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
356	count[0]=domain->zoom_nj_srv ;
357	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
358	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
359
360	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
361	count[0]=domain->zoom_ni_srv ;
362	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
363	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
364	}
365	}
366	break;
367	}
368	}
369
370	if (domain->hasBounds)
371	{
372	std::vector<StdSize> start(3);
373	std::vector<StdSize> count(3);
374	if (domain->isEmpty())
375	{
376	start[2] = start[1] = start[0] = 0;
377	count[2] = count[1] = count[0] = 0;
378	}
379	else
380	{
381	start[2] = 0;
382	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
383	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
384	count[2] = domain->nvertex;
385	count[1] = domain->zoom_ni_srv;
386	count[0] = domain->zoom_nj_srv;
387	}
388
389	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0, &start, &count);
390	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0, &start, &count);
391	}
392
393	if (domain->hasArea)
394	{
395	std::vector<StdSize> start(2);
396	std::vector<StdSize> count(2);
397
398	if (domain->isEmpty())
399	{
400	start[0] = 0; start[1] = 0;
401	count[0] = 0; count[1] = 0;
402	}
403	else
404	{
405	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
406	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
407	count[1] = domain->zoom_ni_srv;
408	count[0] = domain->zoom_nj_srv;
409	}
410
411	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
412	}
413
414	SuperClassWriter::definition_start();
415	break;
416	}
417	default :
418	ERROR("CNc4DataOutput::writeDomain(domain)",
419	<< "[ type = " << SuperClass::type << "]"
420	<< " not implemented yet !");
421	}
422	}
423	catch (CNetCdfException& e)
424	{
425	StdString msg("On writing the domain : ");
426	msg.append(domid); msg.append("\n");
427	msg.append("In the context : ");
428	msg.append(context->getId()); msg.append("\n");
429	msg.append(e.what());
430	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
431	}
432
433	domain->addRelFile(this->filename);
434	}
435
436	//--------------------------------------------------------------
437
438	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
439	{
440	CContext* context = CContext::getCurrent() ;
441	CContextServer* server=context->server ;
442
443	if (domain->IsWritten(this->filename)) return;
444	domain->checkAttributes();
445	if (domain->isEmpty())
446	if (SuperClass::type==MULTI_FILE) return ;
447
448	std::vector<StdString> dim0;
449	StdString domid = domain->getDomainOutputName();
450	StdString domainName = domain->name;
451	domain->assignMesh(domainName, domain->nvertex);
452	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
453
454	StdString node_x = domainName + "_node_x";
455	StdString node_y = domainName + "_node_y";
456
457	StdString edge_x = domainName + "_edge_x";
458	StdString edge_y = domainName + "_edge_y";
459	StdString edge_nodes = domainName + "_edge_nodes";
460
461	StdString face_x = domainName + "_face_x";
462	StdString face_y = domainName + "_face_y";
463	StdString face_nodes = domainName + "_face_nodes";
464	StdString face_edges = domainName + "_face_edges";
465	StdString edge_faces = domainName + "_edge_face_links";
466	StdString face_faces = domainName + "_face_links";
467
468	StdString dimNode = "n" + domainName + "_node";
469	StdString dimEdge = "n" + domainName + "_edge";
470	StdString dimFace = "n" + domainName + "_face";
471	StdString dimVertex = "n" + domainName + "_vertex";
472	StdString dimTwo = "Two";
473
474	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
475	if (!isWrittenDomain(domid))
476	{
477	dim0.clear();
478	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
479	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
480	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
481	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
482	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
483	}
484
485	try
486	{
487	switch (SuperClass::type)
488	{
489	case (ONE_FILE) :
490	{
491	// Adding nodes
492	if (domain->nvertex == 1)
493	{
494	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
495	{
496	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
497	dim0.clear();
498	dim0.push_back(dimNode);
499	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
500	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
501	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
502	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
503	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
504	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
505	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
506	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
507	}
508	} // domain->nvertex == 1
509
510	// Adding edges and nodes, if nodes have not been defined previously
511	if (domain->nvertex == 2)
512	{
513	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
514	{
515	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
516	dim0.clear();
517	dim0.push_back(dimNode);
518	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
519	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
520	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
521	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
522	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
523	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
524	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
525	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
526	}
527	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
528	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
529	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
530	dim0.clear();
531	dim0.push_back(dimEdge);
532	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
533	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
534	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
535	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
536	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
537	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
538	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
539	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
540	dim0.clear();
541	dim0.push_back(dimEdge);
542	dim0.push_back(dimTwo);
543	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
544	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
545	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
546	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
547	} // domain->nvertex == 2
548
549	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
550	if (domain->nvertex > 2)
551	{
552	// Nodes
553	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
554	{
555	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
556	dim0.clear();
557	dim0.push_back(dimNode);
558	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
559	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
560	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
561	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
562	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
563	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
564	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
565	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
566	}
567	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
568	{
569	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
570	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
571	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
572	dim0.clear();
573	dim0.push_back(dimEdge);
574	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
575	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
576	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
577	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
578	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
579	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
580	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
581	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
582	dim0.clear();
583	dim0.push_back(dimEdge);
584	dim0.push_back(dimTwo);
585	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
586	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
587	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
588	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
589	}
590	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
591	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
592	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
593	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
594	dim0.clear();
595	dim0.push_back(dimFace);
596	SuperClassWriter::addVariable(face_x, NC_FLOAT, dim0);
597	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
598	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
599	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
600	SuperClassWriter::addVariable(face_y, NC_FLOAT, dim0);
601	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
602	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
603	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
604	dim0.clear();
605	dim0.push_back(dimFace);
606	dim0.push_back(dimVertex);
607	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
608	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
609	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
610	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
611	dim0.clear();
612	dim0.push_back(dimFace);
613	dim0.push_back(dimVertex);
614	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
615	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
616	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
617	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
618	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
619	dim0.clear();
620	dim0.push_back(dimEdge);
621	dim0.push_back(dimTwo);
622	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
623	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
624	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
625	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
626	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
627	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
628	dim0.clear();
629	dim0.push_back(dimFace);
630	dim0.push_back(dimVertex);
631	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
632	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
633	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
634	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
635	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
636	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
637	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
638	} // domain->nvertex > 2
639
640	SuperClassWriter::definition_end();
641
642	std::vector<StdSize> startEdges(1) ;
643	std::vector<StdSize> countEdges(1) ;
644	std::vector<StdSize> startNodes(1) ;
645	std::vector<StdSize> countNodes(1) ;
646	std::vector<StdSize> startFaces(1) ;
647	std::vector<StdSize> countFaces(1) ;
648	std::vector<StdSize> startEdgeNodes(2) ;
649	std::vector<StdSize> countEdgeNodes(2) ;
650	std::vector<StdSize> startEdgeFaces(2) ;
651	std::vector<StdSize> countEdgeFaces(2) ;
652	std::vector<StdSize> startFaceConctv(2) ;
653	std::vector<StdSize> countFaceConctv(2) ;
654
655	if (!isWrittenDomain(domid))
656	{
657	if (domain->nvertex == 1)
658	{
659	if (domain->isEmpty())
660	{
661	startNodes[0]=0 ;
662	countNodes[0]=0 ;
663	}
664	else
665	{
666	startNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
667	countNodes[0] = domain->zoom_ni_srv ;
668	}
669
670	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
671	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
672	}
673	else if (domain->nvertex == 2)
674	{
675	if (domain->isEmpty())
676	{
677	startEdges[0]=0 ;
678	countEdges[0]=0 ;
679	startNodes[0]=0 ;
680	countNodes[0]=0 ;
681	startEdgeNodes[0]=0;
682	startEdgeNodes[1]=0;
683	countEdgeNodes[0]=0;
684	countEdgeNodes[1]=0;
685
686	}
687	else
688	{
689	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
690	countEdges[0] = domain->zoom_ni_srv ;
691	startNodes[0] = domain->mesh->node_start;
692	countNodes[0] = domain->mesh->node_count;
693	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
694	startEdgeNodes[1] = 0;
695	countEdgeNodes[0] = domain->zoom_ni_srv;
696	countEdgeNodes[1]= 2;
697	}
698	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
699	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
700	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
701	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
702	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
703	}
704	else
705	{
706	if (domain->isEmpty())
707	{
708	startFaces[0] = 0 ;
709	countFaces[0] = 0 ;
710	startNodes[0] = 0;
711	countNodes[0] = 0;
712	startEdges[0] = 0;
713	countEdges[0] = 0;
714	startEdgeFaces[0] = 0;
715	startEdgeFaces[1] = 0;
716	countEdgeFaces[0] = 0;
717	countEdgeFaces[1] = 0;
718	startFaceConctv[0] = 0;
719	startFaceConctv[1] = 0;
720	countFaceConctv[0] = 0;
721	countFaceConctv[1] = 0;
722	}
723	else
724	{
725	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
726	countFaces[0] = domain->zoom_ni_srv ;
727	startNodes[0] = domain->mesh->node_start;
728	countNodes[0] = domain->mesh->node_count;
729	startEdges[0] = domain->mesh->edge_start;
730	countEdges[0] = domain->mesh->edge_count;
731	startEdgeNodes[0] = domain->mesh->edge_start;
732	startEdgeNodes[1] = 0;
733	countEdgeNodes[0] = domain->mesh->edge_count;
734	countEdgeNodes[1]= 2;
735	startEdgeFaces[0] = domain->mesh->edge_start;
736	startEdgeFaces[1]= 0;
737	countEdgeFaces[0] = domain->mesh->edge_count;
738	countEdgeFaces[1]= 2;
739	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
740	startFaceConctv[1] = 0;
741	countFaceConctv[0] = domain->zoom_ni_srv;
742	countFaceConctv[1] = domain->nvertex;
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	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
750	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
751	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
752	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
753	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
754	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
755	}
756	setWrittenDomain(domid);
757	} // !isWrittenDomain
758	else
759	{
760	if (domain->nvertex == 2)
761	{
762	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
763	countEdges[0] = domain->zoom_ni_srv ;
764	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
765	startEdgeNodes[1] = 0;
766	countEdgeNodes[0] = domain->zoom_ni_srv;
767	countEdgeNodes[1]= 2;
768	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
769	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
770	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
771	}
772	if (domain->nvertex > 2)
773	{
774
775	if (!domain->mesh->edgesAreWritten)
776	{
777	startEdges[0] = domain->mesh->edge_start;
778	countEdges[0] = domain->mesh->edge_count;
779	startEdgeNodes[0] = domain->mesh->edge_start;
780	startEdgeNodes[1] = 0;
781	countEdgeNodes[0] = domain->mesh->edge_count;
782	countEdgeNodes[1]= 2;
783	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
784	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
785	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
786	}
787	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
788	countFaces[0] = domain->zoom_ni_srv;
789	startEdgeFaces[0] = domain->mesh->edge_start;
790	startEdgeFaces[1]= 0;
791	countEdgeFaces[0] = domain->mesh->edge_count;
792	countEdgeFaces[1]= 2;
793	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
794	startFaceConctv[1] = 0;
795	countFaceConctv[0] = domain->zoom_ni_srv;
796	countFaceConctv[1]= domain->nvertex;
797	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
798	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
799	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
800	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
801	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
802	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
803	}
804	}// isWrittenDomain
805
806	SuperClassWriter::definition_start();
807
808	break;
809	} // ONE_FILE
810
811	case (MULTI_FILE) :
812	{
813	break;
814	}
815
816	default :
817	ERROR("CNc4DataOutput::writeDomain(domain)",
818	<< "[ type = " << SuperClass::type << "]"
819	<< " not implemented yet !");
820	} // switch
821	} // try
822
823	catch (CNetCdfException& e)
824	{
825	StdString msg("On writing the domain : ");
826	msg.append(domid); msg.append("\n");
827	msg.append("In the context : ");
828	msg.append(context->getId()); msg.append("\n");
829	msg.append(e.what());
830	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
831	}
832
833	domain->addRelFile(this->filename);
834	}
835
836	//--------------------------------------------------------------
837
838	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
839	{
840	CContext* context = CContext::getCurrent() ;
841	CContextServer* server=context->server ;
842
843	if (domain->IsWritten(this->filename)) return;
844	domain->checkAttributes();
845
846	if (domain->isEmpty())
847	if (SuperClass::type==MULTI_FILE) return ;
848
849	std::vector<StdString> dim0, dim1;
850	StdString domid = domain->getDomainOutputName();
851	if (isWrittenDomain(domid)) return ;
852	else setWrittenDomain(domid);
853
854	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
855
856	StdString dimXid = StdString("cell").append(appendDomid);
857	StdString dimVertId = StdString("nvertex").append(appendDomid);
858
859	string lonid,latid,bounds_lonid,bounds_latid ;
860	string areaId = "area" + appendDomid;
861
862	try
863	{
864	switch (SuperClass::type)
865	{
866	case (MULTI_FILE) :
867	{
868	dim0.push_back(dimXid);
869	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
870
871	lonid = StdString("lon").append(appendDomid);
872	latid = StdString("lat").append(appendDomid);
873	bounds_lonid = StdString("bounds_lon").append(appendDomid);
874	bounds_latid = StdString("bounds_lat").append(appendDomid);
875	if (domain->hasLonLat)
876	{
877	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
878	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
879	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
880	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
881	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
882	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
883	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
884	}
885	dim0.clear();
886	if (domain->hasBounds)
887	{
888	dim0.push_back(dimXid);
889	dim0.push_back(dimVertId);
890	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
891	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
892	}
893
894	dim0.clear();
895	dim0.push_back(dimXid);
896	if (domain->hasArea)
897	{
898	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
899	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
900	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
901	}
902
903	SuperClassWriter::definition_end();
904
905	if (domain->hasLonLat)
906	{
907	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
908	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
909	if (domain->hasBounds)
910	{
911	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
912	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
913	}
914	}
915
916	if (domain->hasArea)
917	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
918
919	SuperClassWriter::definition_start();
920	break ;
921	}
922
923	case (ONE_FILE) :
924	{
925	lonid = StdString("lon").append(appendDomid);
926	latid = StdString("lat").append(appendDomid);
927	bounds_lonid = StdString("bounds_lon").append(appendDomid);
928	bounds_latid = StdString("bounds_lat").append(appendDomid);
929	dim0.push_back(dimXid);
930	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
931	if (domain->hasLonLat)
932	{
933	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
934	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
935
936	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
937	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
938	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
939	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
940	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
941	}
942	dim0.clear();
943
944	if (domain->hasBounds)
945	{
946	dim0.push_back(dimXid);
947	dim0.push_back(dimVertId);
948	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
949	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
950	}
951
952	if (domain->hasArea)
953	{
954	dim0.clear();
955	dim0.push_back(dimXid);
956	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
957	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
958	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
959	}
960
961	SuperClassWriter::definition_end();
962
963	std::vector<StdSize> start(1), startBounds(2) ;
964	std::vector<StdSize> count(1), countBounds(2) ;
965	if (domain->isEmpty())
966	{
967	start[0]=0 ;
968	count[0]=0 ;
969	startBounds[1]=0 ;
970	countBounds[1]=domain->nvertex ;
971	startBounds[0]=0 ;
972	countBounds[0]=0 ;
973	}
974	else
975	{
976	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
977	count[0]=domain->zoom_ni_srv ;
978	startBounds[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
979	startBounds[1]=0 ;
980	countBounds[0]=domain->zoom_ni_srv ;
981	countBounds[1]=domain->nvertex ;
982	}
983
984	if (domain->hasLonLat)
985	{
986	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
987	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
988	if (domain->hasBounds)
989	{
990	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
991	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0,&startBounds,&countBounds);
992	}
993	}
994
995	if (domain->hasArea)
996	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
997
998	SuperClassWriter::definition_start();
999
1000	break;
1001	}
1002	default :
1003	ERROR("CNc4DataOutput::writeDomain(domain)",
1004	<< "[ type = " << SuperClass::type << "]"
1005	<< " not implemented yet !");
1006	}
1007	}
1008	catch (CNetCdfException& e)
1009	{
1010	StdString msg("On writing the domain : ");
1011	msg.append(domid); msg.append("\n");
1012	msg.append("In the context : ");
1013	msg.append(context->getId()); msg.append("\n");
1014	msg.append(e.what());
1015	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1016	}
1017	domain->addRelFile(this->filename);
1018	}
1019	//--------------------------------------------------------------
1020
1021	void CNc4DataOutput::writeAxis_(CAxis* axis)
1022	{
1023	if (axis->IsWritten(this->filename)) return;
1024	axis->checkAttributes();
1025	int zoom_size_srv = axis->zoom_size_srv;
1026	int zoom_begin_srv = axis->zoom_begin_srv;
1027	int zoom_size = (MULTI_FILE == SuperClass::type) ? zoom_size_srv
1028	: axis->global_zoom_n;
1029	int zoom_begin = (MULTI_FILE == SuperClass::type) ? zoom_begin_srv
1030	: axis->global_zoom_begin;
1031
1032	if ((0 == zoom_size_srv) && (MULTI_FILE == SuperClass::type)) return;
1033
1034	std::vector<StdString> dims;
1035	StdString axisid = axis->getAxisOutputName();
1036	if (isWrittenAxis(axisid)) return ;
1037	else setWrittenAxis(axisid);
1038
1039	try
1040	{
1041	SuperClassWriter::addDimension(axisid, zoom_size);
1042	if (axis->hasValue)
1043	{
1044	dims.push_back(axisid);
1045	SuperClassWriter::addVariable(axisid, NC_FLOAT, dims);
1046
1047	if (!axis->name.isEmpty())
1048	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1049
1050	if (!axis->standard_name.isEmpty())
1051	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1052
1053	if (!axis->long_name.isEmpty())
1054	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1055
1056	if (!axis->unit.isEmpty())
1057	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1058
1059	if (!axis->positive.isEmpty())
1060	{
1061	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1062	SuperClassWriter::addAttribute("positive",
1063	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1064	&axisid);
1065	}
1066
1067	StdString axisBoundsId = axisid + "_bounds";
1068	if (!axis->bounds.isEmpty())
1069	{
1070	dims.push_back("axis_nbounds");
1071	SuperClassWriter::addVariable(axisBoundsId, NC_FLOAT, dims);
1072	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1073	}
1074
1075	SuperClassWriter::definition_end();
1076
1077	switch (SuperClass::type)
1078	{
1079	case MULTI_FILE:
1080	{
1081	CArray<double,1> axis_value(zoom_size_srv);
1082	for (int i = 0; i < zoom_size_srv; i++) axis_value(i) = axis->value_srv(i);
1083	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1084
1085	if (!axis->bounds.isEmpty())
1086	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0);
1087
1088	SuperClassWriter::definition_start();
1089
1090	break;
1091	}
1092	case ONE_FILE:
1093	{
1094	CArray<double,1> axis_value(zoom_size_srv);
1095	axis_value = axis->value_srv;
1096
1097	std::vector<StdSize> start(1), startBounds(2) ;
1098	std::vector<StdSize> count(1), countBounds(2) ;
1099	start[0] = startBounds[0] = zoom_begin_srv-axis->global_zoom_begin;
1100	count[0] = countBounds[0] = zoom_size_srv;
1101	startBounds[1] = 0;
1102	countBounds[1] = 2;
1103	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1104
1105	if (!axis->bounds.isEmpty())
1106	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1107
1108	SuperClassWriter::definition_start();
1109
1110	break;
1111	}
1112	default :
1113	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1114	<< "[ type = " << SuperClass::type << "]"
1115	<< " not implemented yet !");
1116	}
1117	}
1118	}
1119	catch (CNetCdfException& e)
1120	{
1121	StdString msg("On writing the axis : ");
1122	msg.append(axisid); msg.append("\n");
1123	msg.append("In the context : ");
1124	CContext* context = CContext::getCurrent() ;
1125	msg.append(context->getId()); msg.append("\n");
1126	msg.append(e.what());
1127	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1128	}
1129	axis->addRelFile(this->filename);
1130	}
1131
1132	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1133	{
1134	if (scalar->IsWritten(this->filename)) return;
1135	scalar->checkAttributes();
1136	int scalarSize = 1;
1137
1138	StdString scalaId = scalar->getScalarOutputName();
1139	if (isWrittenAxis(scalaId)) return ;
1140	else setWrittenAxis(scalaId);
1141
1142	try
1143	{
1144	if (!scalar->value.isEmpty())
1145	{
1146	// dims.push_back(scalaId);
1147	std::vector<StdString> dims;
1148	SuperClassWriter::addVariable(scalaId, NC_FLOAT, dims);
1149
1150	if (!scalar->name.isEmpty())
1151	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1152
1153	if (!scalar->standard_name.isEmpty())
1154	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1155
1156	if (!scalar->long_name.isEmpty())
1157	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1158
1159	if (!scalar->unit.isEmpty())
1160	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1161
1162	SuperClassWriter::definition_end();
1163
1164	switch (SuperClass::type)
1165	{
1166	case MULTI_FILE:
1167	{
1168	CArray<double,1> scalarValue(scalarSize);
1169	scalarValue(0) = scalar->value;
1170	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1171	SuperClassWriter::definition_start();
1172
1173	break;
1174	}
1175	case ONE_FILE:
1176	{
1177	CArray<double,1> scalarValue(scalarSize);
1178	scalarValue(0) = scalar->value;
1179
1180	std::vector<StdSize> start(1);
1181	std::vector<StdSize> count(1);
1182	start[0] = 0;
1183	count[0] = 1;
1184	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1185	SuperClassWriter::definition_start();
1186
1187	break;
1188	}
1189	default :
1190	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1191	<< "[ type = " << SuperClass::type << "]"
1192	<< " not implemented yet !");
1193	}
1194	}
1195	}
1196	catch (CNetCdfException& e)
1197	{
1198	StdString msg("On writing the scalar : ");
1199	msg.append(scalaId); msg.append("\n");
1200	msg.append("In the context : ");
1201	CContext* context = CContext::getCurrent() ;
1202	msg.append(context->getId()); msg.append("\n");
1203	msg.append(e.what());
1204	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1205	}
1206	scalar->addRelFile(this->filename);
1207	}
1208
1209	//--------------------------------------------------------------
1210
1211	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1212	{
1213	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1214
1215	try
1216	{
1217	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1218	std::vector<StdString> domainList = grid->getDomainList();
1219	std::vector<StdString> axisList = grid->getAxisList();
1220	std::vector<StdString> scalarList = grid->getScalarList();
1221	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1222
1223	std::vector<StdString> dims;
1224
1225	if (grid->isCompressible())
1226	{
1227	StdString varId = grid->getId() + "_points";
1228
1229	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1230	SuperClassWriter::addDimension(varId, nbIndexes);
1231
1232	dims.push_back(varId);
1233	SuperClassWriter::addVariable(varId, NC_INT, dims);
1234
1235	StdOStringStream compress;
1236	for (int i = numElement - 1; i >= 0; --i)
1237	{
1238	if (2 == axisDomainOrder(i))
1239	{
1240	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1241	StdString domId = domain->getDomainOutputName();
1242	StdString appendDomId = singleDomain ? "" : "_" + domId;
1243
1244	switch (domain->type)
1245	{
1246	case CDomain::type_attr::curvilinear:
1247	compress << "y" << appendDomId << " x" << appendDomId;
1248	break;
1249	case CDomain::type_attr::rectilinear:
1250	compress << "lat" << appendDomId << " lon" << appendDomId;
1251	break;
1252	case CDomain::type_attr::unstructured:
1253	compress << "cell" << appendDomId;
1254	break;
1255	}
1256	++idxDomain;
1257	}
1258	else if (1 == axisDomainOrder(i))
1259	{
1260	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1261	compress << axis->getAxisOutputName();
1262	++idxAxis;
1263	}
1264	else
1265	{
1266	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1267	compress << scalar->getScalarOutputName();
1268	++idxScalar;
1269	}
1270
1271	if (i != 0) compress << ' ';
1272	}
1273	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1274
1275	grid->computeCompressedIndex();
1276
1277	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1278	std::map<int, CArray<size_t, 1> >::const_iterator it;
1279	for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
1280	{
1281	const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
1282	for (int i = 0; i < it->second.numElements(); i++)
1283	indexes(compressedIndexes(i)) = it->second(i);
1284	}
1285
1286	switch (SuperClass::type)
1287	{
1288	case (MULTI_FILE):
1289	{
1290	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1291	break;
1292	}
1293	case (ONE_FILE):
1294	{
1295	if (grid->doGridHaveDataDistributed())
1296	grid->getDistributionServer()->computeGlobalIndex(indexes);
1297
1298	std::vector<StdSize> start, count;
1299	start.push_back(grid->getOffsetWrittenIndexes());
1300	count.push_back(grid->getNumberWrittenIndexes());
1301
1302	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1303	break;
1304	}
1305	}
1306	}
1307	else
1308	{
1309	for (int i = 0; i < numElement; ++i)
1310	{
1311	StdString varId, compress;
1312	CArray<int, 1> indexes;
1313	bool isDistributed;
1314	StdSize nbIndexes, totalNbIndexes, offset;
1315	int firstGlobalIndex;
1316
1317	if (2 == axisDomainOrder(i))
1318	{
1319	CDomain* domain = CDomain::get(domainList[idxDomain]);
1320	StdString domId = domain->getDomainOutputName();
1321
1322	if (!domain->isCompressible()
1323	\|\| domain->type == CDomain::type_attr::unstructured
1324	\|\| domain->isWrittenCompressed(this->filename)
1325	\|\| isWrittenCompressedDomain(domId))
1326	continue;
1327
1328	StdString appendDomId = singleDomain ? "" : "_" + domId;
1329
1330	varId = domId + "_points";
1331	switch (domain->type)
1332	{
1333	case CDomain::type_attr::curvilinear:
1334	compress = "y" + appendDomId + " x" + appendDomId;
1335	break;
1336	case CDomain::type_attr::rectilinear:
1337	compress = "lat" + appendDomId + " lon" + appendDomId;
1338	break;
1339	}
1340
1341	const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
1342	indexes.resize(indexesToWrite.size());
1343	for (int n = 0; n < indexes.numElements(); ++n)
1344	indexes(n) = indexesToWrite[n];
1345
1346	isDistributed = domain->isDistributed();
1347	nbIndexes = domain->getNumberWrittenIndexes();
1348	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1349	offset = domain->getOffsetWrittenIndexes();
1350	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1351
1352	domain->addRelFileCompressed(this->filename);
1353	setWrittenCompressedDomain(domId);
1354	++idxDomain;
1355	}
1356	else if (1 == axisDomainOrder(i))
1357	{
1358	CAxis* axis = CAxis::get(axisList[idxAxis]);
1359	StdString axisId = axis->getAxisOutputName();
1360
1361	if (!axis->isCompressible()
1362	\|\| axis->isWrittenCompressed(this->filename)
1363	\|\| isWrittenCompressedAxis(axisId))
1364	continue;
1365
1366	varId = axisId + "_points";
1367	compress = axisId;
1368
1369	const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
1370	indexes.resize(indexesToWrite.size());
1371	for (int n = 0; n < indexes.numElements(); ++n)
1372	indexes(n) = indexesToWrite[n];
1373
1374	isDistributed = axis->isDistributed();
1375	nbIndexes = axis->getNumberWrittenIndexes();
1376	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1377	offset = axis->getOffsetWrittenIndexes();
1378	firstGlobalIndex = axis->begin;
1379
1380	axis->addRelFileCompressed(this->filename);
1381	setWrittenCompressedAxis(axisId);
1382	++idxAxis;
1383	}
1384	else
1385	{
1386	}
1387
1388	if (!varId.empty())
1389	{
1390	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1391
1392	dims.clear();
1393	dims.push_back(varId);
1394	SuperClassWriter::addVariable(varId, NC_INT, dims);
1395
1396	SuperClassWriter::addAttribute("compress", compress, &varId);
1397
1398	switch (SuperClass::type)
1399	{
1400	case (MULTI_FILE):
1401	{
1402	indexes -= firstGlobalIndex;
1403	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1404	break;
1405	}
1406	case (ONE_FILE):
1407	{
1408	std::vector<StdSize> start, count;
1409	start.push_back(offset);
1410	count.push_back(nbIndexes);
1411
1412	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1413	break;
1414	}
1415	}
1416	}
1417	}
1418
1419	if (!dims.empty())
1420	grid->computeCompressedIndex();
1421	}
1422
1423	grid->addRelFileCompressed(this->filename);
1424	}
1425	catch (CNetCdfException& e)
1426	{
1427	StdString msg("On writing compressed grid : ");
1428	msg.append(grid->getId()); msg.append("\n");
1429	msg.append("In the context : ");
1430	CContext* context = CContext::getCurrent();
1431	msg.append(context->getId()); msg.append("\n");
1432	msg.append(e.what());
1433	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1434	}
1435	}
1436
1437	//--------------------------------------------------------------
1438
1439	void CNc4DataOutput::writeTimeDimension_(void)
1440	{
1441	try
1442	{
1443	SuperClassWriter::addDimension(getTimeCounterName());
1444	}
1445	catch (CNetCdfException& e)
1446	{
1447	StdString msg("On writing time dimension : time_couter\n");
1448	msg.append("In the context : ");
1449	CContext* context = CContext::getCurrent() ;
1450	msg.append(context->getId()); msg.append("\n");
1451	msg.append(e.what());
1452	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1453	}
1454	}
1455
1456	//--------------------------------------------------------------
1457
1458	void CNc4DataOutput::writeField_(CField* field)
1459	{
1460	CContext* context = CContext::getCurrent() ;
1461	CContextServer* server=context->server ;
1462
1463	std::vector<StdString> dims, coodinates;
1464	CGrid* grid = field->grid;
1465	if (!grid->doGridHaveDataToWrite())
1466	if (SuperClass::type==MULTI_FILE) return ;
1467
1468	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1469	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1470	std::vector<StdString> domainList = grid->getDomainList();
1471	std::vector<StdString> axisList = grid->getAxisList();
1472	std::vector<StdString> scalarList = grid->getScalarList();
1473
1474	StdString timeid = getTimeCounterName();
1475	StdString dimXid,dimYid;
1476	std::deque<StdString> dimIdList, dimCoordList;
1477	bool hasArea = false;
1478	StdString cellMeasures = "area:";
1479	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1480
1481	for (int i = 0; i < numElement; ++i)
1482	{
1483	if (2 == axisDomainOrder(i))
1484	{
1485	CDomain* domain = CDomain::get(domainList[idxDomain]);
1486	StdString domId = domain->getDomainOutputName();
1487	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1488
1489	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1490	{
1491	dimIdList.push_back(domId + "_points");
1492	field->setUseCompressedOutput();
1493	}
1494
1495	switch (domain->type)
1496	{
1497	case CDomain::type_attr::curvilinear:
1498	if (!compressedOutput \|\| !domain->isCompressible())
1499	{
1500	dimXid = StdString("x").append(appendDomId);
1501	dimIdList.push_back(dimXid);
1502	dimYid = StdString("y").append(appendDomId);
1503	dimIdList.push_back(dimYid);
1504	}
1505	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1506	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1507	break ;
1508	case CDomain::type_attr::rectilinear:
1509	if (!compressedOutput \|\| !domain->isCompressible())
1510	{
1511	dimXid = StdString("lon").append(appendDomId);
1512	dimIdList.push_back(dimXid);
1513	dimYid = StdString("lat").append(appendDomId);
1514	dimIdList.push_back(dimYid);
1515	}
1516	break ;
1517	case CDomain::type_attr::unstructured:
1518	{
1519	if (SuperClassWriter::useCFConvention)
1520	{
1521	dimXid = StdString("cell").append(appendDomId);
1522	dimIdList.push_back(dimXid);
1523	dimCoordList.push_back(StdString("lon").append(appendDomId));
1524	dimCoordList.push_back(StdString("lat").append(appendDomId));
1525	}
1526	else
1527	{
1528	StdString domainName = domain->name;
1529	if (domain->nvertex == 1)
1530	{
1531	dimXid = "n" + domainName + "_node";
1532	dimIdList.push_back(dimXid);
1533	dimCoordList.push_back(StdString(domainName + "_node_x"));
1534	dimCoordList.push_back(StdString(domainName + "_node_y"));
1535	}
1536	else if (domain->nvertex == 2)
1537	{
1538	dimXid = "n" + domainName + "_edge";
1539	dimIdList.push_back(dimXid);
1540	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1541	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1542	}
1543	else
1544	{
1545	dimXid = "n" + domainName + "_face";
1546	dimIdList.push_back(dimXid);
1547	dimCoordList.push_back(StdString(domainName + "_face_x"));
1548	dimCoordList.push_back(StdString(domainName + "_face_y"));
1549	}
1550	} // ugrid convention
1551	} // case unstructured domain
1552	}
1553
1554	if (domain->hasArea)
1555	{
1556	hasArea = true;
1557	cellMeasures += " area" + appendDomId;
1558	}
1559	++idxDomain;
1560	}
1561	else if (1 == axisDomainOrder(i))
1562	{
1563	CAxis* axis = CAxis::get(axisList[idxAxis]);
1564	StdString axisId = axis->getAxisOutputName();
1565
1566	if (compressedOutput && axis->isCompressible())
1567	{
1568	dimIdList.push_back(axisId + "_points");
1569	field->setUseCompressedOutput();
1570	}
1571	else
1572	dimIdList.push_back(axisId);
1573
1574	dimCoordList.push_back(axisId);
1575	++idxAxis;
1576	}
1577	else // scalar
1578	{
1579	/* Do nothing here */
1580	}
1581	}
1582
1583	/*
1584	StdString lonid_loc = (server->intraCommSize > 1)
1585	? StdString("lon").append(appendDomid).append("_local")
1586	: lonid;
1587	StdString latid_loc = (server->intraCommSize > 1)
1588	? StdString("lat").append(appendDomid).append("_local")
1589	: latid;
1590	*/
1591	StdString fieldid = field->getFieldOutputName();
1592
1593	nc_type type ;
1594	if (field->prec.isEmpty()) type = NC_FLOAT ;
1595	else
1596	{
1597	if (field->prec==2) type = NC_SHORT ;
1598	else if (field->prec==4) type = NC_FLOAT ;
1599	else if (field->prec==8) type = NC_DOUBLE ;
1600	}
1601
1602	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1603
1604	if (wtime)
1605	{
1606
1607	//StdOStringStream oss;
1608	// oss << "time_" << field->operation.getValue()
1609	// << "_" << field->getRelFile()->output_freq.getValue();
1610	//oss
1611	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
1612	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
1613	dims.push_back(timeid);
1614	}
1615
1616	if (compressedOutput && grid->isCompressible())
1617	{
1618	dims.push_back(grid->getId() + "_points");
1619	field->setUseCompressedOutput();
1620	}
1621	else
1622	{
1623	while (!dimIdList.empty())
1624	{
1625	dims.push_back(dimIdList.back());
1626	dimIdList.pop_back();
1627	}
1628	}
1629
1630	while (!dimCoordList.empty())
1631	{
1632	coodinates.push_back(dimCoordList.back());
1633	dimCoordList.pop_back();
1634	}
1635
1636	try
1637	{
1638	SuperClassWriter::addVariable(fieldid, type, dims);
1639
1640	if (!field->standard_name.isEmpty())
1641	SuperClassWriter::addAttribute
1642	("standard_name", field->standard_name.getValue(), &fieldid);
1643
1644	if (!field->long_name.isEmpty())
1645	SuperClassWriter::addAttribute
1646	("long_name", field->long_name.getValue(), &fieldid);
1647
1648	if (!field->unit.isEmpty())
1649	SuperClassWriter::addAttribute
1650	("units", field->unit.getValue(), &fieldid);
1651
1652	// Ugrid field attributes "mesh" and "location"
1653	if (!SuperClassWriter::useCFConvention)
1654	{
1655	if (!domainList.empty())
1656	{
1657	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
1658	StdString mesh = domain->name;
1659	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
1660	StdString location;
1661	if (domain->nvertex == 1)
1662	location = "node";
1663	else if (domain->nvertex == 2)
1664	location = "edge";
1665	else if (domain->nvertex > 2)
1666	location = "face";
1667	SuperClassWriter::addAttribute("location", location, &fieldid);
1668	}
1669
1670	}
1671
1672	if (!field->valid_min.isEmpty())
1673	SuperClassWriter::addAttribute
1674	("valid_min", field->valid_min.getValue(), &fieldid);
1675
1676	if (!field->valid_max.isEmpty())
1677	SuperClassWriter::addAttribute
1678	("valid_max", field->valid_max.getValue(), &fieldid);
1679
1680	if (!field->scale_factor.isEmpty())
1681	SuperClassWriter::addAttribute
1682	("scale_factor", field->scale_factor.getValue(), &fieldid);
1683
1684	if (!field->add_offset.isEmpty())
1685	SuperClassWriter::addAttribute
1686	("add_offset", field->add_offset.getValue(), &fieldid);
1687
1688	SuperClassWriter::addAttribute
1689	("online_operation", field->operation.getValue(), &fieldid);
1690
1691	// write child variables as attributes
1692
1693
1694	vector<CVariable*> listVars = field->getAllVariables() ;
1695	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1696
1697	bool alreadyAddCellMethod = false;
1698	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1699	if (!field->cell_methods.isEmpty())
1700	{
1701	StdString cellMethodString = field->cell_methods;
1702	if (field->cell_methods_mode.isEmpty() \|\|
1703	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1704	{
1705	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1706	alreadyAddCellMethod = true;
1707	}
1708	else
1709	{
1710	switch (field->cell_methods_mode)
1711	{
1712	case (CField::cell_methods_mode_attr::prefix):
1713	cellMethodsPrefix = cellMethodString;
1714	cellMethodsPrefix += " ";
1715	break;
1716	case (CField::cell_methods_mode_attr::suffix):
1717	cellMethodsSuffix = " ";
1718	cellMethodsSuffix += cellMethodString;
1719	break;
1720	case (CField::cell_methods_mode_attr::none):
1721	break;
1722	default:
1723	break;
1724	}
1725	}
1726	}
1727
1728
1729	if (wtime)
1730	{
1731	CDuration freqOp = field->freq_op.getValue();
1732	freqOp.solveTimeStep(*context->calendar);
1733	StdString freqOpStr = freqOp.toStringUDUnits();
1734	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1735
1736	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1737	freqOut.solveTimeStep(*context->calendar);
1738	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1739
1740	StdString cellMethods(cellMethodsPrefix + "time: ");
1741	if (field->operation.getValue() == "instant") cellMethods += "point";
1742	else if (field->operation.getValue() == "average") cellMethods += "mean";
1743	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1744	else cellMethods += field->operation;
1745	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1746	cellMethods += " (interval: " + freqOpStr + ")";
1747	cellMethods += cellMethodsSuffix;
1748	if (!alreadyAddCellMethod)
1749	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1750	}
1751
1752	if (hasArea)
1753	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1754
1755	if (!field->default_value.isEmpty())
1756	{
1757	double default_value = field->default_value.getValue();
1758	float fdefault_value = (float)default_value;
1759	if (type == NC_DOUBLE)
1760	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1761	else
1762	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1763	}
1764	else
1765	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1766
1767	if (field->compression_level.isEmpty())
1768	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1769	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1770
1771	{ // Ecriture des coordonnes
1772
1773	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1774	std::vector<StdString>::iterator
1775	itc = coodinates.begin(), endc = coodinates.end();
1776
1777	for (; itc!= endc; itc++)
1778	{
1779	StdString & coord = *itc;
1780	if (itc+1 != endc)
1781	coordstr.append(coord).append(" ");
1782	else coordstr.append(coord);
1783	}
1784
1785	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1786
1787	}
1788	}
1789	catch (CNetCdfException& e)
1790	{
1791	StdString msg("On writing field : ");
1792	msg.append(fieldid); msg.append("\n");
1793	msg.append("In the context : ");
1794	msg.append(context->getId()); msg.append("\n");
1795	msg.append(e.what());
1796	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1797	}
1798	} // writeField_()
1799
1800	//--------------------------------------------------------------
1801
1802	void CNc4DataOutput::writeFile_ (CFile* file)
1803	{
1804	StdString filename = file->getFileOutputName();
1805	StdString description = (!file->description.isEmpty())
1806	? file->description.getValue()
1807	: StdString("Created by xios");
1808
1809	singleDomain = (file->nbDomains == 1);
1810
1811	try
1812	{
1813	if (SuperClassWriter::useCFConvention)
1814	this->writeFileAttributes(filename, description,
1815	StdString("CF-1.6"),
1816	StdString("An IPSL model"),
1817	this->getTimeStamp());
1818	else
1819	this->writeFileAttributes(filename, description,
1820	StdString("UGRID"),
1821	StdString("An IPSL model"),
1822	this->getTimeStamp());
1823
1824
1825	if (!appendMode)
1826	SuperClassWriter::addDimension("axis_nbounds", 2);
1827	}
1828	catch (CNetCdfException& e)
1829	{
1830	StdString msg("On writing file : ");
1831	msg.append(filename); msg.append("\n");
1832	msg.append("In the context : ");
1833	CContext* context = CContext::getCurrent() ;
1834	msg.append(context->getId()); msg.append("\n");
1835	msg.append(e.what());
1836	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1837	}
1838	}
1839
1840	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1841	{
1842	StdString name = var->getVariableOutputName();
1843
1844	try
1845	{
1846	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1847	addAttribute(name, var->getData<int>(), &fieldId);
1848	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1849	addAttribute(name, var->getData<short int>(), &fieldId);
1850	else if (var->type.getValue() == CVariable::type_attr::t_float)
1851	addAttribute(name, var->getData<float>(), &fieldId);
1852	else if (var->type.getValue() == CVariable::type_attr::t_double)
1853	addAttribute(name, var->getData<double>(), &fieldId);
1854	else if (var->type.getValue() == CVariable::type_attr::t_string)
1855	addAttribute(name, var->getData<string>(), &fieldId);
1856	else
1857	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1858	<< "Unsupported variable of type " << var->type.getStringValue());
1859	}
1860	catch (CNetCdfException& e)
1861	{
1862	StdString msg("On writing attributes of variable with name : ");
1863	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1864	msg.append("In the context : ");
1865	CContext* context = CContext::getCurrent() ;
1866	msg.append(context->getId()); msg.append("\n");
1867	msg.append(e.what());
1868	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1869	}
1870	}
1871
1872	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1873	{
1874	StdString name = var->getVariableOutputName();
1875
1876	try
1877	{
1878	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1879	addAttribute(name, var->getData<int>());
1880	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1881	addAttribute(name, var->getData<short int>());
1882	else if (var->type.getValue() == CVariable::type_attr::t_float)
1883	addAttribute(name, var->getData<float>());
1884	else if (var->type.getValue() == CVariable::type_attr::t_double)
1885	addAttribute(name, var->getData<double>());
1886	else if (var->type.getValue() == CVariable::type_attr::t_string)
1887	addAttribute(name, var->getData<string>());
1888	else
1889	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1890	<< "Unsupported variable of type " << var->type.getStringValue());
1891	}
1892	catch (CNetCdfException& e)
1893	{
1894	StdString msg("On writing attributes of variable with name : ");
1895	msg.append(name); msg.append("\n");
1896	msg.append("In the context : ");
1897	CContext* context = CContext::getCurrent() ;
1898	msg.append(context->getId()); msg.append("\n");
1899	msg.append(e.what());
1900	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1901	}
1902	}
1903
1904	void CNc4DataOutput::syncFile_ (void)
1905	{
1906	try
1907	{
1908	SuperClassWriter::sync() ;
1909	}
1910	catch (CNetCdfException& e)
1911	{
1912	StdString msg("On synchronizing the write among processes");
1913	msg.append("In the context : ");
1914	CContext* context = CContext::getCurrent() ;
1915	msg.append(context->getId()); msg.append("\n");
1916	msg.append(e.what());
1917	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1918	}
1919	}
1920
1921	void CNc4DataOutput::closeFile_ (void)
1922	{
1923	try
1924	{
1925	SuperClassWriter::close() ;
1926	}
1927	catch (CNetCdfException& e)
1928	{
1929	StdString msg("On closing file");
1930	msg.append("In the context : ");
1931	CContext* context = CContext::getCurrent() ;
1932	msg.append(context->getId()); msg.append("\n");
1933	msg.append(e.what());
1934	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1935	}
1936
1937	}
1938
1939	//---------------------------------------------------------------
1940
1941	StdString CNc4DataOutput::getTimeStamp(void) const
1942	{
1943	const int buffer_size = 100;
1944	time_t rawtime;
1945	struct tm * timeinfo = NULL;
1946	char buffer [buffer_size];
1947
1948	time ( &rawtime );
1949	timeinfo = localtime ( &rawtime );
1950	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
1951
1952	return (StdString(buffer));
1953	}
1954
1955	//---------------------------------------------------------------
1956
1957	void CNc4DataOutput::writeFieldData_ (CField* field)
1958	{
1959	CContext* context = CContext::getCurrent();
1960	CContextServer* server = context->server;
1961	CGrid* grid = field->grid;
1962
1963	if (field->getNStep()<1) return ;
1964
1965	if (!grid->doGridHaveDataToWrite())
1966	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
1967
1968	StdString fieldid = field->getFieldOutputName();
1969
1970	StdOStringStream oss;
1971	string timeAxisId;
1972	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
1973	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
1974
1975	StdString timeBoundId = getTimeCounterName() + "_bounds";
1976
1977	StdString timeAxisBoundId;
1978	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
1979	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
1980
1981	if (!field->wasWritten())
1982	{
1983	if (appendMode && field->file->record_offset.isEmpty() &&
1984	field->getOperationTimeType() != func::CFunctor::once)
1985	{
1986	field->resetNStep(getRecordFromTime(field->last_Write_srv) + 1);
1987	}
1988
1989	field->setWritten();
1990	}
1991
1992
1993	CArray<double,1> time_data(1);
1994	CArray<double,1> time_data_bound(2);
1995	CArray<double,1> time_counter(1);
1996	CArray<double,1> time_counter_bound(2);
1997
1998	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
1999
2000	if (wtime)
2001	{
2002	Time lastWrite = field->last_Write_srv;
2003	Time lastLastWrite = field->lastlast_Write_srv;
2004
2005	if (field->getOperationTimeType() == func::CFunctor::instant)
2006	time_data(0) = lastWrite;
2007	else if (field->getOperationTimeType() == func::CFunctor::centered)
2008	time_data(0) = (lastWrite + lastLastWrite) / 2;
2009
2010	if (field->getOperationTimeType() == func::CFunctor::instant)
2011	time_data_bound(0) = time_data_bound(1) = lastWrite;
2012	else if (field->getOperationTimeType() == func::CFunctor::centered)
2013	{
2014	time_data_bound(0) = lastLastWrite;
2015	time_data_bound(1) = lastWrite;
2016	}
2017
2018	if (field->file->time_counter.isEmpty())
2019	if (field->hasTimeInstant && !field->hasTimeCentered)
2020	time_counter(0) = lastWrite;
2021	else
2022	time_counter(0) = (lastWrite + lastLastWrite) / 2;
2023
2024	else if (field->file->time_counter == CFile::time_counter_attr::instant)
2025	time_counter(0) = lastWrite;
2026	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2027	time_counter(0) = (lastWrite + lastLastWrite) / 2;
2028	else if (field->file->time_counter == CFile::time_counter_attr::record)
2029	time_counter(0) = field->getNStep() - 1;
2030
2031
2032	if (field->file->time_counter.isEmpty())
2033	if (field->hasTimeInstant && !field->hasTimeCentered)
2034	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
2035	else
2036	{
2037	time_counter_bound(0) = lastLastWrite;
2038	time_counter_bound(1) = lastWrite;
2039	}
2040	else if (field->file->time_counter == CFile::time_counter_attr::instant)
2041	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
2042	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2043	{
2044	time_counter_bound(0) = lastLastWrite;
2045	time_counter_bound(1) = lastWrite;
2046	}
2047	else if (field->file->time_counter == CFile::time_counter_attr::record)
2048	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2049	}
2050
2051	bool isRoot = (server->intraCommRank == 0);
2052
2053	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2054	{
2055	double scaleFactor = 1.0;
2056	double addOffset = 0.0;
2057	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2058	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2059	field->scaleFactorAddOffset(scaleFactor, addOffset);
2060	}
2061
2062	try
2063	{
2064	size_t writtenSize;
2065	if (field->getUseCompressedOutput())
2066	writtenSize = grid->getNumberWrittenIndexes();
2067	else
2068	writtenSize = grid->getWrittenDataSize();
2069
2070	CArray<double,1> fieldData(writtenSize);
2071	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2072
2073	if (field->getUseCompressedOutput())
2074	field->outputCompressedField(fieldData);
2075	else
2076	field->outputField(fieldData);
2077
2078	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2079
2080	switch (SuperClass::type)
2081	{
2082	case (MULTI_FILE) :
2083	{
2084	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2085	if (wtime)
2086	{
2087	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2088	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2089	if (field->file->time_counter.isEmpty() \|\|
2090	(field->file->time_counter != CFile::time_counter_attr::none))
2091	{
2092	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2093	if (field->file->time_counter.isEmpty() \|\|
2094	(field->file->time_counter != CFile::time_counter_attr::record))
2095	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2096	}
2097	}
2098	break;
2099	}
2100	case (ONE_FILE) :
2101	{
2102	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2103	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2104	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2105
2106	std::vector<StdSize> start, count;
2107
2108	if (field->getUseCompressedOutput())
2109	{
2110	if (grid->isCompressible())
2111	{
2112	start.push_back(grid->getOffsetWrittenIndexes());
2113	count.push_back(grid->getNumberWrittenIndexes());
2114	}
2115	else
2116	{
2117	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2118	std::vector<StdString> domainList = grid->getDomainList();
2119	std::vector<StdString> axisList = grid->getAxisList();
2120	int numElement = axisDomainOrder.numElements();
2121	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2122	int idx = nZoomBeginGlobal.size() - 1;
2123
2124	start.reserve(nZoomBeginGlobal.size());
2125	count.reserve(nZoomBeginGlobal.size());
2126
2127
2128	for (int i = numElement - 1; i >= 0; --i)
2129	{
2130	if (2 == axisDomainOrder(i))
2131	{
2132	CDomain* domain = CDomain::get(domainList[idxDomain]);
2133
2134	if (domain->isCompressible())
2135	{
2136	start.push_back(domain->getOffsetWrittenIndexes());
2137	count.push_back(domain->getNumberWrittenIndexes());
2138	idx -= 2;
2139	}
2140	else
2141	{
2142	if ((domain->type) != CDomain::type_attr::unstructured)
2143	{
2144	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2145	count.push_back(nZoomSizeServer[idx]);
2146	}
2147	--idx;
2148	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2149	count.push_back(nZoomSizeServer[idx]);
2150	--idx;
2151	}
2152	--idxDomain;
2153	}
2154	else if (1 == axisDomainOrder(i))
2155	{
2156	CAxis* axis = CAxis::get(axisList[idxAxis]);
2157
2158	if (axis->isCompressible())
2159	{
2160	start.push_back(axis->getOffsetWrittenIndexes());
2161	count.push_back(axis->getNumberWrittenIndexes());
2162	}
2163	else
2164	{
2165	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2166	count.push_back(nZoomSizeServer[idx]);
2167	}
2168
2169	--idxAxis;
2170	--idx;
2171	}
2172	}
2173	}
2174	}
2175	else
2176	{
2177
2178	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2179	std::vector<StdString> domainList = grid->getDomainList();
2180	std::vector<StdString> axisList = grid->getAxisList();
2181	int numElement = axisDomainOrder.numElements();
2182	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2183	int idx = nZoomBeginGlobal.size() - 1;
2184
2185	start.reserve(nZoomBeginGlobal.size());
2186	count.reserve(nZoomBeginGlobal.size());
2187
2188	for (int i = numElement - 1; i >= 0; --i)
2189	{
2190	if (2 == axisDomainOrder(i))
2191	{
2192	CDomain* domain = CDomain::get(domainList[idxDomain]);
2193	if ((domain->type) != CDomain::type_attr::unstructured)
2194	{
2195	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2196	count.push_back(nZoomSizeServer[idx]);
2197	}
2198	--idx ;
2199	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2200	count.push_back(nZoomSizeServer[idx]);
2201	--idx ;
2202	--idxDomain;
2203	}
2204	else if (1 == axisDomainOrder(i))
2205	{
2206	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2207	count.push_back(nZoomSizeServer[idx]);
2208	--idx;
2209	}
2210	else
2211	{
2212	if (1 == axisDomainOrder.numElements())
2213	{
2214	start.push_back(0);
2215	count.push_back(1);
2216	}
2217	--idx;
2218	}
2219	}
2220	}
2221
2222	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2223	if (wtime)
2224	{
2225	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2226	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2227	if (field->file->time_counter.isEmpty() \|\|
2228	(field->file->time_counter != CFile::time_counter_attr::none))
2229	{
2230	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
2231	if (field->file->time_counter.isEmpty() \|\|
2232	(field->file->time_counter != CFile::time_counter_attr::record))
2233	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2234	}
2235	}
2236
2237	break;
2238	}
2239	}
2240	}
2241	catch (CNetCdfException& e)
2242	{
2243	StdString msg("On writing field data: ");
2244	msg.append(fieldid); msg.append("\n");
2245	msg.append("In the context : ");
2246	msg.append(context->getId()); msg.append("\n");
2247	msg.append(e.what());
2248	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2249	}
2250	}
2251
2252	//---------------------------------------------------------------
2253
2254	void CNc4DataOutput::writeTimeAxis_
2255	(CField* field,
2256	const boost::shared_ptr<CCalendar> cal)
2257	{
2258	StdOStringStream oss;
2259
2260	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2261
2262	// oss << "time_" << field->operation.getValue()
2263	// << "_" << field->getRelFile()->output_freq.getValue();
2264
2265	// StdString axisid = oss.str();
2266	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
2267	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
2268
2269	StdString axisid("time_centered") ;
2270	StdString axisBoundId("time_centered_bounds");
2271	StdString timeid(getTimeCounterName());
2272	StdString timeBoundId("axis_nbounds");
2273
2274	if (field->getOperationTimeType() == func::CFunctor::instant)
2275	{
2276	axisid = "time_instant";
2277	axisBoundId = "time_instant_bounds";
2278	field->hasTimeInstant = true;
2279	}
2280
2281	if (field->getOperationTimeType() == func::CFunctor::centered)
2282	{
2283	field->hasTimeCentered = true;
2284	}
2285
2286	try
2287	{
2288	// Adding time_instant or time_centered
2289	std::vector<StdString> dims;
2290	dims.push_back(timeid);
2291	if (!SuperClassWriter::varExist(axisid))
2292	{
2293	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2294
2295	CDate timeOrigin=cal->getTimeOrigin() ;
2296	StdOStringStream oss2;
2297	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
2298	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
2299	StdString strInitdate=oss2.str() ;
2300	StdString strTimeOrigin=timeOrigin.toString() ;
2301	this->writeTimeAxisAttributes
2302	(axisid, cal->getType(),
2303	StdString("seconds since ").append(strTimeOrigin),
2304	strTimeOrigin, axisBoundId);
2305	}
2306
2307	// Adding time_instant_bounds or time_centered_bounds variables
2308	if (!SuperClassWriter::varExist(axisBoundId))
2309	{
2310	dims.clear() ;
2311	dims.push_back(timeid);
2312	dims.push_back(timeBoundId);
2313	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2314	}
2315
2316	if (field->file->time_counter.isEmpty() \|\|
2317	(field->file->time_counter != CFile::time_counter_attr::none))
2318	{
2319	// Adding time_counter
2320	axisid = getTimeCounterName();
2321	axisBoundId = getTimeCounterName() + "_bounds";
2322	dims.clear();
2323	dims.push_back(timeid);
2324	if (!SuperClassWriter::varExist(axisid))
2325	{
2326	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2327	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
2328
2329	if (field->file->time_counter.isEmpty() \|\|
2330	(field->file->time_counter != CFile::time_counter_attr::record))
2331	{
2332	CDate timeOrigin = cal->getTimeOrigin();
2333	StdString strTimeOrigin = timeOrigin.toString();
2334
2335	this->writeTimeAxisAttributes(axisid, cal->getType(),
2336	StdString("seconds since ").append(strTimeOrigin),
2337	strTimeOrigin, axisBoundId);
2338	}
2339	}
2340
2341	// Adding time_counter_bound dimension
2342	if (field->file->time_counter.isEmpty() \|\|
2343	(field->file->time_counter != CFile::time_counter_attr::record))
2344	{
2345	if (!SuperClassWriter::varExist(axisBoundId))
2346	{
2347	dims.clear();
2348	dims.push_back(timeid);
2349	dims.push_back(timeBoundId);
2350	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2351	}
2352	}
2353	}
2354	}
2355	catch (CNetCdfException& e)
2356	{
2357	StdString msg("On writing time axis data: ");
2358	msg.append("In the context : ");
2359	CContext* context = CContext::getCurrent() ;
2360	msg.append(context->getId()); msg.append("\n");
2361	msg.append(e.what());
2362	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2363	const boost::shared_ptr<CCalendar> cal)", << msg);
2364	}
2365	}
2366
2367	//---------------------------------------------------------------
2368
2369	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2370	const StdString & calendar,
2371	const StdString & units,
2372	const StdString & time_origin,
2373	const StdString & time_bounds,
2374	const StdString & standard_name,
2375	const StdString & long_name)
2376	{
2377	try
2378	{
2379	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2380	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2381	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2382	SuperClassWriter::addAttribute("units", units , &axis_name);
2383	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2384	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2385	}
2386	catch (CNetCdfException& e)
2387	{
2388	StdString msg("On writing time axis Attribute: ");
2389	msg.append("In the context : ");
2390	CContext* context = CContext::getCurrent() ;
2391	msg.append(context->getId()); msg.append("\n");
2392	msg.append(e.what());
2393	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2394	const StdString & calendar,\
2395	const StdString & units, \
2396	const StdString & time_origin, \
2397	const StdString & time_bounds, \
2398	const StdString & standard_name, \
2399	const StdString & long_name)", << msg);
2400	}
2401	}
2402
2403	//---------------------------------------------------------------
2404
2405	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2406	const StdString & axis,
2407	const StdString & standard_name,
2408	const StdString & long_name,
2409	const StdString & units,
2410	const StdString & nav_model)
2411	{
2412	try
2413	{
2414	if (!axis.empty())
2415	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2416
2417	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2418	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2419	SuperClassWriter::addAttribute("units" , units , &axis_name);
2420	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2421	}
2422	catch (CNetCdfException& e)
2423	{
2424	StdString msg("On writing Axis Attribute: ");
2425	msg.append("In the context : ");
2426	CContext* context = CContext::getCurrent() ;
2427	msg.append(context->getId()); msg.append("\n");
2428	msg.append(e.what());
2429	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2430	const StdString & axis, \
2431	const StdString & standard_name, \
2432	const StdString & long_name, \
2433	const StdString & units, \
2434	const StdString & nav_model)", << msg);
2435	}
2436	}
2437
2438	//---------------------------------------------------------------
2439
2440	void CNc4DataOutput::writeLocalAttributes
2441	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2442	{
2443	try
2444	{
2445	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2446	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2447	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2448	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2449	}
2450	catch (CNetCdfException& e)
2451	{
2452	StdString msg("On writing Local Attributes: ");
2453	msg.append("In the context : ");
2454	CContext* context = CContext::getCurrent() ;
2455	msg.append(context->getId()); msg.append("\n");
2456	msg.append(e.what());
2457	ERROR("CNc4DataOutput::writeLocalAttributes \
2458	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2459	}
2460
2461	}
2462
2463	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2464	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2465	{
2466	CArray<int,1> array(2) ;
2467
2468	try
2469	{
2470	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2471	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2472	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2473	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2474	array=ni_glo,nj_glo ;
2475	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2476	array=ni,nj ;
2477	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2478	array=ibegin+1,jbegin+1 ;
2479	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2480	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2481	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2482	array=0,0 ;
2483	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2484	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2485	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2486	/*
2487	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2488	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2489	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2490	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2491	*/
2492	}
2493	catch (CNetCdfException& e)
2494	{
2495	StdString msg("On writing Local Attributes IOIPSL \n");
2496	msg.append("In the context : ");
2497	CContext* context = CContext::getCurrent() ;
2498	msg.append(context->getId()); msg.append("\n");
2499	msg.append(e.what());
2500	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2501	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2502	}
2503	}
2504	//---------------------------------------------------------------
2505
2506	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2507	const StdString & description,
2508	const StdString & conventions,
2509	const StdString & production,
2510	const StdString & timeStamp)
2511	{
2512	try
2513	{
2514	SuperClassWriter::addAttribute("name" , name);
2515	SuperClassWriter::addAttribute("description", description);
2516	SuperClassWriter::addAttribute("title" , description);
2517	SuperClassWriter::addAttribute("Conventions", conventions);
2518	// SuperClassWriter::addAttribute("production" , production);
2519	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
2520	}
2521	catch (CNetCdfException& e)
2522	{
2523	StdString msg("On writing File Attributes \n ");
2524	msg.append("In the context : ");
2525	CContext* context = CContext::getCurrent() ;
2526	msg.append(context->getId()); msg.append("\n");
2527	msg.append(e.what());
2528	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2529	const StdString & description, \
2530	const StdString & conventions, \
2531	const StdString & production, \
2532	const StdString & timeStamp)", << msg);
2533	}
2534	}
2535
2536	//---------------------------------------------------------------
2537
2538	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2539	int data_dim,
2540	int data_ni,
2541	int data_nj,
2542	int data_ibegin,
2543	int data_jbegin)
2544	{
2545	try
2546	{
2547	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2548	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2549	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2550	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2551	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2552	}
2553	catch (CNetCdfException& e)
2554	{
2555	StdString msg("On writing Mask Attributes \n ");
2556	msg.append("In the context : ");
2557	CContext* context = CContext::getCurrent() ;
2558	msg.append(context->getId()); msg.append("\n");
2559	msg.append(e.what());
2560	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2561	int data_dim, \
2562	int data_ni, \
2563	int data_nj, \
2564	int data_ibegin, \
2565	int data_jbegin)", << msg);
2566	}
2567	}
2568
2569	///--------------------------------------------------------------
2570
2571	StdSize CNc4DataOutput::getRecordFromTime(Time time)
2572	{
2573	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2574	if (it == timeToRecordCache.end())
2575	{
2576	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2577	if (!SuperClassWriter::varExist(timeAxisBoundsId))
2578	timeAxisBoundsId = "time_instant_bounds";
2579
2580	CArray<double,2> timeAxisBounds;
2581	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
2582
2583	StdSize record = 0;
2584	double dtime(time);
2585	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
2586	{
2587	if (timeAxisBounds(1, n) < dtime)
2588	{
2589	record = n + 1;
2590	break;
2591	}
2592	}
2593	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2594	}
2595	return it->second;
2596	}
2597
2598	///--------------------------------------------------------------
2599
2600	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2601	{
2602	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2603	}
2604
2605	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2606	{
2607	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2608	}
2609
2610	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2611	{
2612	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2613	}
2614
2615	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2616	{
2617	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2618	}
2619
2620	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2621	{
2622	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2623	}
2624
2625	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2626	{
2627	this->writtenDomains.insert(domainName);
2628	}
2629
2630	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2631	{
2632	this->writtenCompressedDomains.insert(domainName);
2633	}
2634
2635	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2636	{
2637	this->writtenAxis.insert(axisName);
2638	}
2639
2640	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2641	{
2642	this->writtenCompressedAxis.insert(axisName);
2643	}
2644
2645	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2646	{
2647	this->writtenScalar.insert(scalarName);
2648	}
2649	} // namespace xios

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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 1012

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