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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 881

Last change on this file since 881 was 881, checked in by oabramkina, 8 years ago
Commit for UGRID norms: bad allocations have been taken care of.
Property copyright set to Software name : XIOS (Xml I/O Server) http://forge.ipsl.jussieu.fr/ioserver Creation date : January 2009 Licence : CeCCIL version2 see license file in root directory : Licence_CeCILL_V2-en.txt or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement) CNRS/IPSL (Institut Pierre Simon Laplace) Project Manager : Yann Meurdesoif yann.meurdesoif@cea.fr Property svn:executable set to ``*
File size: 100.0 KB

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

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