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source: XIOS/dev/dev_olga/src/io/nc4_data_output.cpp @ 1030

Last change on this file since 1030 was 1030, checked in by oabramkina, 7 years ago
dev: intermediate commit.
Property copyright set to Software name : XIOS (Xml I/O Server) http://forge.ipsl.jussieu.fr/ioserver Creation date : January 2009 Licence : CeCCIL version2 see license file in root directory : Licence_CeCILL_V2-en.txt or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement) CNRS/IPSL (Institut Pierre Simon Laplace) Project Manager : Yann Meurdesoif yann.meurdesoif@cea.fr Property svn:executable set to ``*
File size: 119.1 KB

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1	#include "nc4_data_output.hpp"
2
3	#include <boost/lexical_cast.hpp>
4	#include "attribute_template.hpp"
5	#include "group_template.hpp"
6
7	#include "file.hpp"
8	#include "calendar.hpp"
9	#include "context.hpp"
10	#include "context_server.hpp"
11	#include "netCdfException.hpp"
12	#include "exception.hpp"
13
14	namespace xios
15	{
16	/// ////////////////////// Dfinitions ////////////////////// ///
17	CNc4DataOutput::CNc4DataOutput
18	(const StdString & filename, bool exist)
19	: SuperClass()
20	, SuperClassWriter(filename, exist)
21	, filename(filename)
22	{
23	SuperClass::type = MULTI_FILE;
24	}
25
26	CNc4DataOutput::CNc4DataOutput
27	(const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
28	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
29	: SuperClass()
30	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
31	, comm_file(comm_file)
32	, filename(filename)
33	, isCollective(isCollective)
34	{
35	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
36	}
37
38	CNc4DataOutput::~CNc4DataOutput(void)
39	{ /* Ne rien faire de plus */ }
40
41	///--------------------------------------------------------------
42
43	const StdString & CNc4DataOutput::getFileName(void) const
44	{
45	return (this->filename);
46	}
47
48	//---------------------------------------------------------------
49
50	void CNc4DataOutput::writeDomain_(CDomain* domain)
51	{
52	if (domain->type == CDomain::type_attr::unstructured)
53	{
54	if (SuperClassWriter::useCFConvention)
55	writeUnstructuredDomain(domain) ;
56	else
57	writeUnstructuredDomainUgrid(domain) ;
58	return ;
59	}
60
61	CContext* context = CContext::getCurrent() ;
62	CContextServer* server=context->server ;
63
64	if (domain->IsWritten(this->filename)) return;
65	domain->checkAttributes();
66
67	if (domain->isEmpty())
68	if (SuperClass::type==MULTI_FILE) return;
69
70	std::vector<StdString> dim0, dim1;
71	StdString domid = domain->getDomainOutputName();
72	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
73	if (isWrittenDomain(domid)) return ;
74	else setWrittenDomain(domid);
75
76	const std::vector<int>& local_size_write = domain->getLocalWriteSize();
77	const std::vector<int>& global_size_write = domain->getGlobalWriteSize();
78	const std::vector<int>& start_write = domain->getStartWriteIndex();
79	const std::vector<int>& count_write = domain->getCountWriteIndex();
80	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
81
82	StdString dimXid, dimYid ;
83
84	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
85	switch (domain->type)
86	{
87	case CDomain::type_attr::curvilinear :
88	dimXid = StdString("x").append(appendDomid);
89	dimYid = StdString("y").append(appendDomid);
90	break ;
91	case CDomain::type_attr::rectilinear :
92	dimXid = StdString("lon").append(appendDomid);
93	dimYid = StdString("lat").append(appendDomid);
94	break;
95	}
96
97	StdString dimVertId = StdString("nvertex").append(appendDomid);
98
99	string lonid,latid,bounds_lonid,bounds_latid ;
100	string areaId = "area" + appendDomid;
101	/*
102	StdString lonid_loc = (server->intraCommSize > 1)
103	? StdString("lon").append(appendDomid).append("_local")
104	: lonid;
105	StdString latid_loc = (server->intraCommSize > 1)
106	? StdString("lat").append(appendDomid).append("_local")
107	: latid;
108	*/
109
110	try
111	{
112	switch (SuperClass::type)
113	{
114	case (MULTI_FILE) :
115	{
116	// if (domain->isEmpty()) return;
117
118	if (server->intraCommSize > 1)
119	{
120	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
121	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
122	}
123
124	switch (domain->type)
125	{
126	case CDomain::type_attr::curvilinear :
127	dim0.push_back(dimYid); dim0.push_back(dimXid);
128	lonid = StdString("nav_lon").append(appendDomid);
129	latid = StdString("nav_lat").append(appendDomid);
130	break ;
131	case CDomain::type_attr::rectilinear :
132	lonid = StdString("lon").append(appendDomid);
133	latid = StdString("lat").append(appendDomid);
134	dim0.push_back(dimYid);
135	dim1.push_back(dimXid);
136	break;
137	}
138
139	bounds_lonid = StdString("bounds_lon").append(appendDomid);
140	bounds_latid = StdString("bounds_lat").append(appendDomid);
141
142	SuperClassWriter::addDimension(dimXid, local_size_write[0]);
143	SuperClassWriter::addDimension(dimYid, local_size_write[1]);
144
145	if (domain->hasBounds)
146	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
147
148	if (server->intraCommSize > 1)
149	{
150	this->writeLocalAttributes(0, count_write[0],
151	0, count_write[1],
152	appendDomid);
153
154	if (singleDomain)
155	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
156	0, count_write[0],
157	0, count_write[1],
158	domain->ni_glo,domain->nj_glo,
159	server->intraCommRank,server->intraCommSize);
160	}
161
162	if (domain->hasLonLat)
163	{
164	switch (domain->type)
165	{
166	case CDomain::type_attr::curvilinear :
167	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
168	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
169	break ;
170	case CDomain::type_attr::rectilinear :
171	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
172	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
173	break ;
174	}
175
176	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
177	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
178
179	if (domain->hasBounds)
180	{
181	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
182	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
183
184	dim0.clear();
185	dim0.push_back(dimYid);
186	dim0.push_back(dimXid);
187	dim0.push_back(dimVertId);
188	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
189	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
190	}
191	}
192
193	dim0.clear();
194	dim0.push_back(dimYid);
195	dim0.push_back(dimXid);
196
197
198	// supress mask if (server->intraCommSize > 1)
199	// supress mask {
200	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
201	// supress mask
202	// supress mask this->writeMaskAttributes(maskid,
203	// supress mask domain->data_dim.getValue()/*,
204	// supress mask domain->data_ni.getValue(),
205	// supress mask domain->data_nj.getValue(),
206	// supress mask domain->data_ibegin.getValue(),
207	// supress mask domain->data_jbegin.getValue()*/);
208	// supress mask }
209
210	//SuperClassWriter::setDefaultValue(maskid, &dvm);
211
212	if (domain->hasArea)
213	{
214	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
215	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
216	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
217	}
218
219	SuperClassWriter::definition_end();
220
221	if (domain->hasLonLat)
222	{
223	switch (domain->type)
224	{
225	case CDomain::type_attr::curvilinear :
226	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
227	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
228	break;
229	case CDomain::type_attr::rectilinear :
230	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,local_size_write[0])) ;
231	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
232	CArray<double,1> lon = domain->lonvalue(Range(0,local_size_write[1])) ;
233	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
234	break;
235	}
236
237	if (domain->hasBounds)
238	{
239	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
240	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
241	}
242	}
243
244	if (domain->hasArea)
245	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
246
247	SuperClassWriter::definition_start();
248
249	break;
250	}
251	case (ONE_FILE) :
252	{
253	SuperClassWriter::addDimension(dimXid, global_size_write[0]);
254	SuperClassWriter::addDimension(dimYid, global_size_write[1]);
255
256	if (domain->hasBounds)
257	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
258
259	if (domain->hasLonLat)
260	{
261	switch (domain->type)
262	{
263	case CDomain::type_attr::curvilinear :
264	dim0.push_back(dimYid); dim0.push_back(dimXid);
265	lonid = StdString("nav_lon").append(appendDomid);
266	latid = StdString("nav_lat").append(appendDomid);
267	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
268	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
269	break;
270
271	case CDomain::type_attr::rectilinear :
272	dim0.push_back(dimYid);
273	dim1.push_back(dimXid);
274	lonid = StdString("lon").append(appendDomid);
275	latid = StdString("lat").append(appendDomid);
276	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
277	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
278	break;
279	}
280
281	bounds_lonid = StdString("bounds_lon").append(appendDomid);
282	bounds_latid = StdString("bounds_lat").append(appendDomid);
283
284	this->writeAxisAttributes
285	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
286	this->writeAxisAttributes
287	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
288
289	if (domain->hasBounds)
290	{
291	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
292	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
293
294	dim0.clear();
295	dim0.push_back(dimYid);
296	dim0.push_back(dimXid);
297	dim0.push_back(dimVertId);
298	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
299	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
300	}
301	}
302
303	if (domain->hasArea)
304	{
305	dim0.clear();
306	dim0.push_back(dimYid); dim0.push_back(dimXid);
307	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
308	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
309	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
310	dim0.clear();
311	}
312
313	SuperClassWriter::definition_end();
314
315	switch (domain->type)
316	{
317	case CDomain::type_attr::curvilinear :
318	{
319	std::vector<StdSize> start(2) ;
320	std::vector<StdSize> count(2) ;
321	if (domain->isEmpty())
322	{
323	start[0]=0 ; start[1]=0 ;
324	count[0]=0 ; count[1]=0 ;
325	}
326	else
327	{
328	// start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
329	// start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
330	// count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
331	start[1]= start_write[0];
332	start[0]= start_write[1];
333	count[1]= count_write[0];
334	count[0]= count_write[1];
335	}
336
337	if (domain->hasLonLat)
338	{
339	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
340	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
341	}
342	break;
343	}
344	case CDomain::type_attr::rectilinear :
345	{
346	if (domain->hasLonLat)
347	{
348	std::vector<StdSize> start(1) ;
349	std::vector<StdSize> count(1) ;
350	if (domain->isEmpty())
351	{
352	start[0]=0 ;
353	count[0]=0 ;
354	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
355	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
356
357	}
358	else
359	{
360	start[0]= start_write[1];
361	count[0]= count_write[1];
362	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,count_write[0])) ;
363	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
364
365	start[0]= start_write[0];
366	count[0]= count_write[0];
367	CArray<double,1> lon=domain->lonvalue(Range(0,count_write[1])) ;
368	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
369	}
370	}
371	break;
372	}
373	}
374
375	if (domain->hasBounds)
376	{
377	std::vector<StdSize> start(3);
378	std::vector<StdSize> count(3);
379	if (domain->isEmpty())
380	{
381	start[2] = start[1] = start[0] = 0;
382	count[2] = count[1] = count[0] = 0;
383	}
384	else
385	{
386	start[2] = 0;
387	start[1] = start_write[0];
388	start[0] = start_write[1];
389	count[2] = nvertex;
390	count[1] = count_write[0];
391	count[0] = count_write[1];
392	}
393
394	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count);
395	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
396	}
397
398	if (domain->hasArea)
399	{
400	std::vector<StdSize> start(2);
401	std::vector<StdSize> count(2);
402
403	if (domain->isEmpty())
404	{
405	start[0] = 0; start[1] = 0;
406	count[0] = 0; count[1] = 0;
407	}
408	else
409	{
410	// start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
411	// start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
412	// count[1] = domain->zoom_ni_srv;
413	// count[0] = domain->zoom_nj_srv;
414
415	start[1]= start_write[0];
416	start[0]= start_write[1];
417	count[1]= count_write[0];
418	count[0]= count_write[1];
419	}
420
421	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
422	}
423
424	SuperClassWriter::definition_start();
425	break;
426	}
427	default :
428	ERROR("CNc4DataOutput::writeDomain(domain)",
429	<< "[ type = " << SuperClass::type << "]"
430	<< " not implemented yet !");
431	}
432	}
433	catch (CNetCdfException& e)
434	{
435	StdString msg("On writing the domain : ");
436	msg.append(domid); msg.append("\n");
437	msg.append("In the context : ");
438	msg.append(context->getId()); msg.append("\n");
439	msg.append(e.what());
440	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
441	}
442
443	domain->addRelFile(this->filename);
444	}
445
446	//--------------------------------------------------------------
447
448	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
449	{
450	CContext* context = CContext::getCurrent() ;
451	CContextServer* server=context->server ;
452
453	if (domain->IsWritten(this->filename)) return;
454	domain->checkAttributes();
455	if (domain->isEmpty())
456	if (SuperClass::type==MULTI_FILE) return ;
457
458	std::vector<StdString> dim0;
459	StdString domid = domain->getDomainOutputName();
460	StdString domainName = domain->name;
461	domain->assignMesh(domainName, domain->nvertex);
462	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
463
464	StdString node_x = domainName + "_node_x";
465	StdString node_y = domainName + "_node_y";
466
467	StdString edge_x = domainName + "_edge_x";
468	StdString edge_y = domainName + "_edge_y";
469	StdString edge_nodes = domainName + "_edge_nodes";
470
471	StdString face_x = domainName + "_face_x";
472	StdString face_y = domainName + "_face_y";
473	StdString face_nodes = domainName + "_face_nodes";
474	StdString face_edges = domainName + "_face_edges";
475	StdString edge_faces = domainName + "_edge_face_links";
476	StdString face_faces = domainName + "_face_links";
477
478	StdString dimNode = "n" + domainName + "_node";
479	StdString dimEdge = "n" + domainName + "_edge";
480	StdString dimFace = "n" + domainName + "_face";
481	StdString dimVertex = "n" + domainName + "_vertex";
482	StdString dimTwo = "Two";
483
484	const std::vector<int>& local_size_write = domain->getLocalWriteSize();
485	const std::vector<int>& global_size_write = domain->getGlobalWriteSize();
486	const std::vector<int>& start_write = domain->getStartWriteIndex();
487	const std::vector<int>& count_write = domain->getCountWriteIndex();
488
489	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
490	if (!isWrittenDomain(domid))
491	{
492	dim0.clear();
493	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
494	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
495	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
496	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
497	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
498	}
499
500	try
501	{
502	switch (SuperClass::type)
503	{
504	case (ONE_FILE) :
505	{
506	// Adding nodes
507	if (domain->nvertex == 1)
508	{
509	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
510	{
511	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
512	dim0.clear();
513	dim0.push_back(dimNode);
514	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
515	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
516	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
517	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
518	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
519	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
520	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
521	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
522	}
523	} // domain->nvertex == 1
524
525	// Adding edges and nodes, if nodes have not been defined previously
526	if (domain->nvertex == 2)
527	{
528	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
529	{
530	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
531	dim0.clear();
532	dim0.push_back(dimNode);
533	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
534	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
535	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
536	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
537	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
538	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
539	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
540	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
541	}
542	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
543	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
544	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
545	dim0.clear();
546	dim0.push_back(dimEdge);
547	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
548	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
549	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
550	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
551	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
552	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
553	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
554	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
555	dim0.clear();
556	dim0.push_back(dimEdge);
557	dim0.push_back(dimTwo);
558	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
559	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
560	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
561	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
562	} // domain->nvertex == 2
563
564	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
565	if (domain->nvertex > 2)
566	{
567	// Nodes
568	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
569	{
570	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
571	dim0.clear();
572	dim0.push_back(dimNode);
573	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
574	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
575	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
576	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
577	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
578	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
579	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
580	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
581	}
582	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
583	{
584	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
585	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
586	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
587	dim0.clear();
588	dim0.push_back(dimEdge);
589	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
590	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
591	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
592	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
593	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
594	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
595	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
596	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
597	dim0.clear();
598	dim0.push_back(dimEdge);
599	dim0.push_back(dimTwo);
600	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
601	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
602	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
603	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
604	}
605	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
606	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
607	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
608	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
609	dim0.clear();
610	dim0.push_back(dimFace);
611	SuperClassWriter::addVariable(face_x, NC_FLOAT, dim0);
612	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
613	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
614	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
615	SuperClassWriter::addVariable(face_y, NC_FLOAT, dim0);
616	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
617	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
618	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
619	dim0.clear();
620	dim0.push_back(dimFace);
621	dim0.push_back(dimVertex);
622	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
623	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
624	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
625	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
626	dim0.clear();
627	dim0.push_back(dimFace);
628	dim0.push_back(dimVertex);
629	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
630	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
631	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
632	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
633	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
634	dim0.clear();
635	dim0.push_back(dimEdge);
636	dim0.push_back(dimTwo);
637	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
638	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
639	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
640	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
641	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
642	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
643	dim0.clear();
644	dim0.push_back(dimFace);
645	dim0.push_back(dimVertex);
646	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
647	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
648	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
649	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
650	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
651	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
652	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
653	} // domain->nvertex > 2
654
655	SuperClassWriter::definition_end();
656
657	std::vector<StdSize> startEdges(1) ;
658	std::vector<StdSize> countEdges(1) ;
659	std::vector<StdSize> startNodes(1) ;
660	std::vector<StdSize> countNodes(1) ;
661	std::vector<StdSize> startFaces(1) ;
662	std::vector<StdSize> countFaces(1) ;
663	std::vector<StdSize> startEdgeNodes(2) ;
664	std::vector<StdSize> countEdgeNodes(2) ;
665	std::vector<StdSize> startEdgeFaces(2) ;
666	std::vector<StdSize> countEdgeFaces(2) ;
667	std::vector<StdSize> startFaceConctv(2) ;
668	std::vector<StdSize> countFaceConctv(2) ;
669
670	if (!isWrittenDomain(domid))
671	{
672	if (domain->nvertex == 1)
673	{
674	if (domain->isEmpty())
675	{
676	startNodes[0]=0 ;
677	countNodes[0]=0 ;
678	}
679	else
680	{
681	startNodes[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
682	countNodes[0] = count_write[0]; //domain->zoom_ni_srv ;
683	}
684
685	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
686	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
687	}
688	else if (domain->nvertex == 2)
689	{
690	if (domain->isEmpty())
691	{
692	startEdges[0]=0 ;
693	countEdges[0]=0 ;
694	startNodes[0]=0 ;
695	countNodes[0]=0 ;
696	startEdgeNodes[0]=0;
697	startEdgeNodes[1]=0;
698	countEdgeNodes[0]=0;
699	countEdgeNodes[1]=0;
700
701	}
702	else
703	{
704	startEdges[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
705	countEdges[0] = count_write[0];
706	startNodes[0] = domain->mesh->node_start;
707	countNodes[0] = domain->mesh->node_count;
708	startEdgeNodes[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
709	startEdgeNodes[1] = 0;
710	countEdgeNodes[0] = count_write[0]; //domain->zoom_ni_srv;
711	countEdgeNodes[1]= 2;
712	}
713	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
714	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
715	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
716	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
717	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
718	}
719	else
720	{
721	if (domain->isEmpty())
722	{
723	startFaces[0] = 0 ;
724	countFaces[0] = 0 ;
725	startNodes[0] = 0;
726	countNodes[0] = 0;
727	startEdges[0] = 0;
728	countEdges[0] = 0;
729	startEdgeFaces[0] = 0;
730	startEdgeFaces[1] = 0;
731	countEdgeFaces[0] = 0;
732	countEdgeFaces[1] = 0;
733	startFaceConctv[0] = 0;
734	startFaceConctv[1] = 0;
735	countFaceConctv[0] = 0;
736	countFaceConctv[1] = 0;
737	}
738	else
739	{
740	startFaces[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
741	countFaces[0] = count_write[0]; //domain->zoom_ni_srv ;
742	startNodes[0] = domain->mesh->node_start;
743	countNodes[0] = domain->mesh->node_count;
744	startEdges[0] = domain->mesh->edge_start;
745	countEdges[0] = domain->mesh->edge_count;
746	startEdgeNodes[0] = domain->mesh->edge_start;
747	startEdgeNodes[1] = 0;
748	countEdgeNodes[0] = domain->mesh->edge_count;
749	countEdgeNodes[1]= 2;
750	startEdgeFaces[0] = domain->mesh->edge_start;
751	startEdgeFaces[1]= 0;
752	countEdgeFaces[0] = domain->mesh->edge_count;
753	countEdgeFaces[1]= 2;
754	startFaceConctv[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
755	startFaceConctv[1] = 0; //0;
756	countFaceConctv[0] = count_write[0]; //domain->zoom_ni_srv;
757	countFaceConctv[1] = domain->nvertex;
758	}
759	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
760	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
761	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
762	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
763	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
764	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
765	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
766	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
767	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
768	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
769	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
770	}
771	setWrittenDomain(domid);
772	} // !isWrittenDomain
773	else
774	{
775	if (domain->nvertex == 2)
776	{
777	startEdges[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
778	countEdges[0] = count_write[0]; //domain->zoom_ni_srv ;
779	startEdgeNodes[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
780	startEdgeNodes[1] = 0; //0;
781	countEdgeNodes[0] = count_write[0]; //domain->zoom_ni_srv;
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	if (domain->nvertex > 2)
788	{
789
790	if (!domain->mesh->edgesAreWritten)
791	{
792	startEdges[0] = domain->mesh->edge_start;
793	countEdges[0] = domain->mesh->edge_count;
794	startEdgeNodes[0] = domain->mesh->edge_start;
795	startEdgeNodes[1] = 0;
796	countEdgeNodes[0] = domain->mesh->edge_count;
797	countEdgeNodes[1]= 2;
798	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
799	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
800	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
801	}
802	startFaces[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
803	countFaces[0] = count_write[0]; //domain->zoom_ni_srv;
804	startEdgeFaces[0] = domain->mesh->edge_start;
805	startEdgeFaces[1]= 0;
806	countEdgeFaces[0] = domain->mesh->edge_count;
807	countEdgeFaces[1]= 2;
808	startFaceConctv[0] = start_write[0]; //domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
809	startFaceConctv[1] = 0; //0;
810	countFaceConctv[0] = count_write[0]; //domain->zoom_ni_srv;
811	countFaceConctv[1]= domain->nvertex;
812	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
813	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
814	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
815	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
816	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
817	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
818	}
819	}// isWrittenDomain
820
821	SuperClassWriter::definition_start();
822
823	break;
824	} // ONE_FILE
825
826	case (MULTI_FILE) :
827	{
828	break;
829	}
830
831	default :
832	ERROR("CNc4DataOutput::writeDomain(domain)",
833	<< "[ type = " << SuperClass::type << "]"
834	<< " not implemented yet !");
835	} // switch
836	} // try
837
838	catch (CNetCdfException& e)
839	{
840	StdString msg("On writing the domain : ");
841	msg.append(domid); msg.append("\n");
842	msg.append("In the context : ");
843	msg.append(context->getId()); msg.append("\n");
844	msg.append(e.what());
845	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
846	}
847
848	domain->addRelFile(this->filename);
849	}
850
851	//--------------------------------------------------------------
852
853	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
854	{
855	CContext* context = CContext::getCurrent() ;
856	CContextServer* server=context->server ;
857
858	if (domain->IsWritten(this->filename)) return;
859	domain->checkAttributes();
860
861	if (domain->isEmpty())
862	if (SuperClass::type==MULTI_FILE) return ;
863
864	std::vector<StdString> dim0, dim1;
865	StdString domid = domain->getDomainOutputName();
866	if (isWrittenDomain(domid)) return ;
867	else setWrittenDomain(domid);
868
869	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
870
871	StdString dimXid = StdString("cell").append(appendDomid);
872	StdString dimVertId = StdString("nvertex").append(appendDomid);
873
874	string lonid,latid,bounds_lonid,bounds_latid ;
875	string areaId = "area" + appendDomid;
876
877	const std::vector<int>& local_size_write = domain->getLocalWriteSize();
878	const std::vector<int>& global_size_write = domain->getGlobalWriteSize();
879	const std::vector<int>& start_write = domain->getStartWriteIndex();
880	const std::vector<int>& count_write = domain->getCountWriteIndex();
881	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
882
883	try
884	{
885	switch (SuperClass::type)
886	{
887	case (MULTI_FILE) :
888	{
889	dim0.push_back(dimXid);
890	SuperClassWriter::addDimension(dimXid, local_size_write[0]);
891
892	lonid = StdString("lon").append(appendDomid);
893	latid = StdString("lat").append(appendDomid);
894	bounds_lonid = StdString("bounds_lon").append(appendDomid);
895	bounds_latid = StdString("bounds_lat").append(appendDomid);
896	if (domain->hasLonLat)
897	{
898	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
899	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
900	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
901	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
902	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
903	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
904	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
905	}
906	dim0.clear();
907	if (domain->hasBounds)
908	{
909	dim0.push_back(dimXid);
910	dim0.push_back(dimVertId);
911	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
912	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
913	}
914
915	dim0.clear();
916	dim0.push_back(dimXid);
917	if (domain->hasArea)
918	{
919	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
920	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
921	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
922	}
923
924	SuperClassWriter::definition_end();
925
926	if (domain->hasLonLat)
927	{
928	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
929	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
930	if (domain->hasBounds)
931	{
932	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
933	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
934	}
935	}
936
937	if (domain->hasArea)
938	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
939
940	SuperClassWriter::definition_start();
941	break ;
942	}
943
944	case (ONE_FILE) :
945	{
946	lonid = StdString("lon").append(appendDomid);
947	latid = StdString("lat").append(appendDomid);
948	bounds_lonid = StdString("bounds_lon").append(appendDomid);
949	bounds_latid = StdString("bounds_lat").append(appendDomid);
950	dim0.push_back(dimXid);
951	SuperClassWriter::addDimension(dimXid, global_size_write[0]);
952	if (domain->hasLonLat)
953	{
954	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
955	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
956
957	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
958	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
959	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
960	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
961	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
962	}
963	dim0.clear();
964
965	if (domain->hasBounds)
966	{
967	dim0.push_back(dimXid);
968	dim0.push_back(dimVertId);
969	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
970	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
971	}
972
973	if (domain->hasArea)
974	{
975	dim0.clear();
976	dim0.push_back(dimXid);
977	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
978	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
979	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
980	}
981
982	SuperClassWriter::definition_end();
983
984	std::vector<StdSize> start(1), startBounds(2) ;
985	std::vector<StdSize> count(1), countBounds(2) ;
986	if (domain->isEmpty())
987	{
988	start[0]=0 ;
989	count[0]=0 ;
990	startBounds[1]=0 ;
991	countBounds[1]=nvertex ;
992	startBounds[0]=0 ;
993	countBounds[0]=0 ;
994	}
995	else
996	{
997	start[0]=start_write[0];
998	count[0]=count_write[0];
999	startBounds[0]=start_write[0];
1000	startBounds[1]=0 ;
1001	countBounds[0]=count_write[0];
1002	countBounds[1]=nvertex ;
1003	}
1004
1005	if (domain->hasLonLat)
1006	{
1007	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
1008	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
1009	if (domain->hasBounds)
1010	{
1011	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1012	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1013	}
1014	}
1015
1016	if (domain->hasArea)
1017	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
1018
1019	SuperClassWriter::definition_start();
1020
1021	break;
1022	}
1023	default :
1024	ERROR("CNc4DataOutput::writeDomain(domain)",
1025	<< "[ type = " << SuperClass::type << "]"
1026	<< " not implemented yet !");
1027	}
1028	}
1029	catch (CNetCdfException& e)
1030	{
1031	StdString msg("On writing the domain : ");
1032	msg.append(domid); msg.append("\n");
1033	msg.append("In the context : ");
1034	msg.append(context->getId()); msg.append("\n");
1035	msg.append(e.what());
1036	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1037	}
1038	domain->addRelFile(this->filename);
1039	}
1040	//--------------------------------------------------------------
1041
1042	void CNc4DataOutput::writeAxis_(CAxis* axis)
1043	{
1044	CContext* context = CContext::getCurrent();
1045
1046	if (axis->IsWritten(this->filename)) return;
1047	axis->checkAttributes();
1048
1049	int local_size_write = axis->getLocalWriteSize();
1050	int global_size_write = axis->getGlobalWriteSize();
1051	int start_write = axis->getStartWriteIndex();
1052	int count_write = axis->getCountWriteIndex();
1053
1054	if ((0 == local_size_write) && (MULTI_FILE == SuperClass::type)) return;
1055
1056	std::vector<StdString> dims;
1057	StdString axisid = axis->getAxisOutputName();
1058	if (isWrittenAxis(axisid)) return ;
1059	else setWrittenAxis(axisid);
1060
1061	try
1062	{
1063	SuperClassWriter::addDimension(axisid, global_size_write);
1064	if (axis->hasValue)
1065	{
1066	dims.push_back(axisid);
1067	SuperClassWriter::addVariable(axisid, NC_FLOAT, dims);
1068
1069	if (!axis->name.isEmpty())
1070	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1071
1072	if (!axis->standard_name.isEmpty())
1073	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1074
1075	if (!axis->long_name.isEmpty())
1076	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1077
1078	if (!axis->unit.isEmpty())
1079	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1080
1081	if (!axis->positive.isEmpty())
1082	{
1083	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1084	SuperClassWriter::addAttribute("positive",
1085	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1086	&axisid);
1087	}
1088
1089	StdString axisBoundsId = axisid + "_bounds";
1090	if (!axis->bounds.isEmpty())
1091	{
1092	dims.push_back("axis_nbounds");
1093	SuperClassWriter::addVariable(axisBoundsId, NC_FLOAT, dims);
1094	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1095	}
1096
1097	SuperClassWriter::definition_end();
1098
1099	switch (SuperClass::type)
1100	{
1101	case MULTI_FILE:
1102	{
1103	CArray<double,1> axis_value(local_size_write);
1104	for (int i = 0; i < local_size_write; i++) axis_value(i) = axis->value(i);
1105	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1106
1107	if (!axis->bounds.isEmpty())
1108	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
1109
1110	SuperClassWriter::definition_start();
1111
1112	break;
1113	}
1114	case ONE_FILE:
1115	{
1116	CArray<double,1> axis_value(count_write);
1117	axis_value = axis->value;
1118
1119	std::vector<StdSize> start(1), startBounds(2) ;
1120	std::vector<StdSize> count(1), countBounds(2) ;
1121	start[0] = startBounds[0] = start_write;
1122	count[0] = countBounds[0] = count_write;
1123	startBounds[1] = 0;
1124	countBounds[1] = 2;
1125	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1126
1127	if (!axis->bounds.isEmpty())
1128	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1129
1130	SuperClassWriter::definition_start();
1131
1132	break;
1133	}
1134	default :
1135	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1136	<< "[ type = " << SuperClass::type << "]"
1137	<< " not implemented yet !");
1138	}
1139	}
1140	}
1141	catch (CNetCdfException& e)
1142	{
1143	StdString msg("On writing the axis : ");
1144	msg.append(axisid); msg.append("\n");
1145	msg.append("In the context : ");
1146	CContext* context = CContext::getCurrent() ;
1147	msg.append(context->getId()); msg.append("\n");
1148	msg.append(e.what());
1149	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1150	}
1151
1152	axis->addRelFile(this->filename);
1153	}
1154
1155	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1156	{
1157	if (scalar->IsWritten(this->filename)) return;
1158	scalar->checkAttributes();
1159	int scalarSize = 1;
1160
1161	StdString scalaId = scalar->getScalarOutputName();
1162	if (isWrittenAxis(scalaId)) return ;
1163	else setWrittenAxis(scalaId);
1164
1165	try
1166	{
1167	if (!scalar->value.isEmpty())
1168	{
1169	// dims.push_back(scalaId);
1170	std::vector<StdString> dims;
1171	SuperClassWriter::addVariable(scalaId, NC_FLOAT, dims);
1172
1173	if (!scalar->name.isEmpty())
1174	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1175
1176	if (!scalar->standard_name.isEmpty())
1177	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1178
1179	if (!scalar->long_name.isEmpty())
1180	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1181
1182	if (!scalar->unit.isEmpty())
1183	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1184
1185	SuperClassWriter::definition_end();
1186
1187	switch (SuperClass::type)
1188	{
1189	case MULTI_FILE:
1190	{
1191	CArray<double,1> scalarValue(scalarSize);
1192	scalarValue(0) = scalar->value;
1193	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1194	SuperClassWriter::definition_start();
1195
1196	break;
1197	}
1198	case ONE_FILE:
1199	{
1200	CArray<double,1> scalarValue(scalarSize);
1201	scalarValue(0) = scalar->value;
1202
1203	std::vector<StdSize> start(1);
1204	std::vector<StdSize> count(1);
1205	start[0] = 0;
1206	count[0] = 1;
1207	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1208	SuperClassWriter::definition_start();
1209
1210	break;
1211	}
1212	default :
1213	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1214	<< "[ type = " << SuperClass::type << "]"
1215	<< " not implemented yet !");
1216	}
1217	}
1218	}
1219	catch (CNetCdfException& e)
1220	{
1221	StdString msg("On writing the scalar : ");
1222	msg.append(scalaId); msg.append("\n");
1223	msg.append("In the context : ");
1224	CContext* context = CContext::getCurrent() ;
1225	msg.append(context->getId()); msg.append("\n");
1226	msg.append(e.what());
1227	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1228	}
1229	scalar->addRelFile(this->filename);
1230	}
1231
1232	//--------------------------------------------------------------
1233
1234	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1235	{
1236	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1237
1238	try
1239	{
1240	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1241	std::vector<StdString> domainList = grid->getDomainList();
1242	std::vector<StdString> axisList = grid->getAxisList();
1243	std::vector<StdString> scalarList = grid->getScalarList();
1244	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1245
1246	std::vector<StdString> dims;
1247
1248	if (grid->isCompressible())
1249	{
1250	StdString varId = grid->getId() + "_points";
1251
1252	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1253	SuperClassWriter::addDimension(varId, nbIndexes);
1254
1255	dims.push_back(varId);
1256	SuperClassWriter::addVariable(varId, NC_INT, dims);
1257
1258	StdOStringStream compress;
1259	for (int i = numElement - 1; i >= 0; --i)
1260	{
1261	if (2 == axisDomainOrder(i))
1262	{
1263	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1264	StdString domId = domain->getDomainOutputName();
1265	StdString appendDomId = singleDomain ? "" : "_" + domId;
1266
1267	switch (domain->type)
1268	{
1269	case CDomain::type_attr::curvilinear:
1270	compress << "y" << appendDomId << " x" << appendDomId;
1271	break;
1272	case CDomain::type_attr::rectilinear:
1273	compress << "lat" << appendDomId << " lon" << appendDomId;
1274	break;
1275	case CDomain::type_attr::unstructured:
1276	compress << "cell" << appendDomId;
1277	break;
1278	}
1279	++idxDomain;
1280	}
1281	else if (1 == axisDomainOrder(i))
1282	{
1283	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1284	compress << axis->getAxisOutputName();
1285	++idxAxis;
1286	}
1287	else
1288	{
1289	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1290	compress << scalar->getScalarOutputName();
1291	++idxScalar;
1292	}
1293
1294	if (i != 0) compress << ' ';
1295	}
1296	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1297
1298	grid->computeCompressedIndex();
1299
1300	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1301	std::map<int, CArray<size_t, 1> >::const_iterator it;
1302	for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
1303	{
1304	const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
1305	for (int i = 0; i < it->second.numElements(); i++)
1306	indexes(compressedIndexes(i)) = it->second(i);
1307	}
1308
1309	switch (SuperClass::type)
1310	{
1311	case (MULTI_FILE):
1312	{
1313	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1314	break;
1315	}
1316	case (ONE_FILE):
1317	{
1318	if (grid->doGridHaveDataDistributed())
1319	grid->getDistributionServer()->computeGlobalIndex(indexes);
1320
1321	std::vector<StdSize> start, count;
1322	start.push_back(grid->getOffsetWrittenIndexes());
1323	count.push_back(grid->getNumberWrittenIndexes());
1324
1325	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1326	break;
1327	}
1328	}
1329	}
1330	else
1331	{
1332	for (int i = 0; i < numElement; ++i)
1333	{
1334	StdString varId, compress;
1335	CArray<int, 1> indexes;
1336	bool isDistributed;
1337	StdSize nbIndexes, totalNbIndexes, offset;
1338	int firstGlobalIndex;
1339
1340	if (2 == axisDomainOrder(i))
1341	{
1342	CDomain* domain = CDomain::get(domainList[idxDomain]);
1343	StdString domId = domain->getDomainOutputName();
1344
1345	if (!domain->isCompressible()
1346	\|\| domain->type == CDomain::type_attr::unstructured
1347	\|\| domain->isWrittenCompressed(this->filename)
1348	\|\| isWrittenCompressedDomain(domId))
1349	continue;
1350
1351	StdString appendDomId = singleDomain ? "" : "_" + domId;
1352
1353	varId = domId + "_points";
1354	switch (domain->type)
1355	{
1356	case CDomain::type_attr::curvilinear:
1357	compress = "y" + appendDomId + " x" + appendDomId;
1358	break;
1359	case CDomain::type_attr::rectilinear:
1360	compress = "lat" + appendDomId + " lon" + appendDomId;
1361	break;
1362	}
1363
1364	const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
1365	indexes.resize(indexesToWrite.size());
1366	for (int n = 0; n < indexes.numElements(); ++n)
1367	indexes(n) = indexesToWrite[n];
1368
1369	isDistributed = domain->isDistributed();
1370	nbIndexes = domain->getNumberWrittenIndexes();
1371	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1372	offset = domain->getOffsetWrittenIndexes();
1373	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1374
1375	domain->addRelFileCompressed(this->filename);
1376	setWrittenCompressedDomain(domId);
1377	++idxDomain;
1378	}
1379	else if (1 == axisDomainOrder(i))
1380	{
1381	CAxis* axis = CAxis::get(axisList[idxAxis]);
1382	StdString axisId = axis->getAxisOutputName();
1383
1384	if (!axis->isCompressible()
1385	\|\| axis->isWrittenCompressed(this->filename)
1386	\|\| isWrittenCompressedAxis(axisId))
1387	continue;
1388
1389	varId = axisId + "_points";
1390	compress = axisId;
1391
1392	const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
1393	indexes.resize(indexesToWrite.size());
1394	for (int n = 0; n < indexes.numElements(); ++n)
1395	indexes(n) = indexesToWrite[n];
1396
1397	isDistributed = axis->isDistributed();
1398	nbIndexes = axis->getNumberWrittenIndexes();
1399	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1400	offset = axis->getOffsetWrittenIndexes();
1401	firstGlobalIndex = axis->begin;
1402
1403	axis->addRelFileCompressed(this->filename);
1404	setWrittenCompressedAxis(axisId);
1405	++idxAxis;
1406	}
1407	else
1408	{
1409	}
1410
1411	if (!varId.empty())
1412	{
1413	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1414
1415	dims.clear();
1416	dims.push_back(varId);
1417	SuperClassWriter::addVariable(varId, NC_INT, dims);
1418
1419	SuperClassWriter::addAttribute("compress", compress, &varId);
1420
1421	switch (SuperClass::type)
1422	{
1423	case (MULTI_FILE):
1424	{
1425	indexes -= firstGlobalIndex;
1426	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1427	break;
1428	}
1429	case (ONE_FILE):
1430	{
1431	std::vector<StdSize> start, count;
1432	start.push_back(offset);
1433	count.push_back(nbIndexes);
1434
1435	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1436	break;
1437	}
1438	}
1439	}
1440	}
1441
1442	if (!dims.empty())
1443	grid->computeCompressedIndex();
1444	}
1445
1446	grid->addRelFileCompressed(this->filename);
1447	}
1448	catch (CNetCdfException& e)
1449	{
1450	StdString msg("On writing compressed grid : ");
1451	msg.append(grid->getId()); msg.append("\n");
1452	msg.append("In the context : ");
1453	CContext* context = CContext::getCurrent();
1454	msg.append(context->getId()); msg.append("\n");
1455	msg.append(e.what());
1456	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1457	}
1458	}
1459
1460	//--------------------------------------------------------------
1461
1462	void CNc4DataOutput::writeTimeDimension_(void)
1463	{
1464	try
1465	{
1466	SuperClassWriter::addDimension(getTimeCounterName());
1467	}
1468	catch (CNetCdfException& e)
1469	{
1470	StdString msg("On writing time dimension : time_couter\n");
1471	msg.append("In the context : ");
1472	CContext* context = CContext::getCurrent() ;
1473	msg.append(context->getId()); msg.append("\n");
1474	msg.append(e.what());
1475	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1476	}
1477	}
1478
1479	//--------------------------------------------------------------
1480
1481	void CNc4DataOutput::writeField_(CField* field)
1482	{
1483	CContext* context = CContext::getCurrent() ;
1484	CContextServer* server=context->server ;
1485
1486	std::vector<StdString> dims, coodinates;
1487	CGrid* grid = field->grid;
1488	if (!grid->doGridHaveDataToWrite())
1489	if (SuperClass::type==MULTI_FILE) return ;
1490
1491	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1492	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1493	std::vector<StdString> domainList = grid->getDomainList();
1494	std::vector<StdString> axisList = grid->getAxisList();
1495	std::vector<StdString> scalarList = grid->getScalarList();
1496
1497	StdString timeid = getTimeCounterName();
1498	StdString dimXid,dimYid;
1499	std::deque<StdString> dimIdList, dimCoordList;
1500	bool hasArea = false;
1501	StdString cellMeasures = "area:";
1502	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1503
1504	for (int i = 0; i < numElement; ++i)
1505	{
1506	if (2 == axisDomainOrder(i))
1507	{
1508	CDomain* domain = CDomain::get(domainList[idxDomain]);
1509	StdString domId = domain->getDomainOutputName();
1510	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1511
1512	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1513	{
1514	dimIdList.push_back(domId + "_points");
1515	field->setUseCompressedOutput();
1516	}
1517
1518	switch (domain->type)
1519	{
1520	case CDomain::type_attr::curvilinear:
1521	if (!compressedOutput \|\| !domain->isCompressible())
1522	{
1523	dimXid = StdString("x").append(appendDomId);
1524	dimIdList.push_back(dimXid);
1525	dimYid = StdString("y").append(appendDomId);
1526	dimIdList.push_back(dimYid);
1527	}
1528	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1529	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1530	break ;
1531	case CDomain::type_attr::rectilinear:
1532	if (!compressedOutput \|\| !domain->isCompressible())
1533	{
1534	dimXid = StdString("lon").append(appendDomId);
1535	dimIdList.push_back(dimXid);
1536	dimYid = StdString("lat").append(appendDomId);
1537	dimIdList.push_back(dimYid);
1538	}
1539	break ;
1540	case CDomain::type_attr::unstructured:
1541	{
1542	if (SuperClassWriter::useCFConvention)
1543	{
1544	dimXid = StdString("cell").append(appendDomId);
1545	dimIdList.push_back(dimXid);
1546	dimCoordList.push_back(StdString("lon").append(appendDomId));
1547	dimCoordList.push_back(StdString("lat").append(appendDomId));
1548	}
1549	else
1550	{
1551	StdString domainName = domain->name;
1552	if (domain->nvertex == 1)
1553	{
1554	dimXid = "n" + domainName + "_node";
1555	dimIdList.push_back(dimXid);
1556	dimCoordList.push_back(StdString(domainName + "_node_x"));
1557	dimCoordList.push_back(StdString(domainName + "_node_y"));
1558	}
1559	else if (domain->nvertex == 2)
1560	{
1561	dimXid = "n" + domainName + "_edge";
1562	dimIdList.push_back(dimXid);
1563	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1564	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1565	}
1566	else
1567	{
1568	dimXid = "n" + domainName + "_face";
1569	dimIdList.push_back(dimXid);
1570	dimCoordList.push_back(StdString(domainName + "_face_x"));
1571	dimCoordList.push_back(StdString(domainName + "_face_y"));
1572	}
1573	} // ugrid convention
1574	} // case unstructured domain
1575	}
1576
1577	if (domain->hasArea)
1578	{
1579	hasArea = true;
1580	cellMeasures += " area" + appendDomId;
1581	}
1582	++idxDomain;
1583	}
1584	else if (1 == axisDomainOrder(i))
1585	{
1586	CAxis* axis = CAxis::get(axisList[idxAxis]);
1587	StdString axisId = axis->getAxisOutputName();
1588
1589	if (compressedOutput && axis->isCompressible())
1590	{
1591	dimIdList.push_back(axisId + "_points");
1592	field->setUseCompressedOutput();
1593	}
1594	else
1595	dimIdList.push_back(axisId);
1596
1597	dimCoordList.push_back(axisId);
1598	++idxAxis;
1599	}
1600	else // scalar
1601	{
1602	/* Do nothing here */
1603	}
1604	}
1605
1606	/*
1607	StdString lonid_loc = (server->intraCommSize > 1)
1608	? StdString("lon").append(appendDomid).append("_local")
1609	: lonid;
1610	StdString latid_loc = (server->intraCommSize > 1)
1611	? StdString("lat").append(appendDomid).append("_local")
1612	: latid;
1613	*/
1614	StdString fieldid = field->getFieldOutputName();
1615
1616	nc_type type ;
1617	if (field->prec.isEmpty()) type = NC_FLOAT ;
1618	else
1619	{
1620	if (field->prec==2) type = NC_SHORT ;
1621	else if (field->prec==4) type = NC_FLOAT ;
1622	else if (field->prec==8) type = NC_DOUBLE ;
1623	}
1624
1625	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1626
1627	if (wtime)
1628	{
1629
1630	//StdOStringStream oss;
1631	// oss << "time_" << field->operation.getValue()
1632	// << "_" << field->getRelFile()->output_freq.getValue();
1633	//oss
1634	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
1635	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
1636	dims.push_back(timeid);
1637	}
1638
1639	if (compressedOutput && grid->isCompressible())
1640	{
1641	dims.push_back(grid->getId() + "_points");
1642	field->setUseCompressedOutput();
1643	}
1644	else
1645	{
1646	while (!dimIdList.empty())
1647	{
1648	dims.push_back(dimIdList.back());
1649	dimIdList.pop_back();
1650	}
1651	}
1652
1653	while (!dimCoordList.empty())
1654	{
1655	coodinates.push_back(dimCoordList.back());
1656	dimCoordList.pop_back();
1657	}
1658
1659	try
1660	{
1661	SuperClassWriter::addVariable(fieldid, type, dims);
1662
1663	if (!field->standard_name.isEmpty())
1664	SuperClassWriter::addAttribute
1665	("standard_name", field->standard_name.getValue(), &fieldid);
1666
1667	if (!field->long_name.isEmpty())
1668	SuperClassWriter::addAttribute
1669	("long_name", field->long_name.getValue(), &fieldid);
1670
1671	if (!field->unit.isEmpty())
1672	SuperClassWriter::addAttribute
1673	("units", field->unit.getValue(), &fieldid);
1674
1675	if (!field->valid_min.isEmpty())
1676	SuperClassWriter::addAttribute
1677	("valid_min", field->valid_min.getValue(), &fieldid);
1678
1679	if (!field->valid_max.isEmpty())
1680	SuperClassWriter::addAttribute
1681	("valid_max", field->valid_max.getValue(), &fieldid);
1682
1683	if (!field->scale_factor.isEmpty())
1684	SuperClassWriter::addAttribute
1685	("scale_factor", field->scale_factor.getValue(), &fieldid);
1686
1687	if (!field->add_offset.isEmpty())
1688	SuperClassWriter::addAttribute
1689	("add_offset", field->add_offset.getValue(), &fieldid);
1690
1691	SuperClassWriter::addAttribute
1692	("online_operation", field->operation.getValue(), &fieldid);
1693
1694	// write child variables as attributes
1695
1696
1697	vector<CVariable*> listVars = field->getAllVariables() ;
1698	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1699
1700	bool alreadyAddCellMethod = false;
1701	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1702	if (!field->cell_methods.isEmpty())
1703	{
1704	StdString cellMethodString = field->cell_methods;
1705	if (field->cell_methods_mode.isEmpty() \|\|
1706	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1707	{
1708	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1709	alreadyAddCellMethod = true;
1710	}
1711	else
1712	{
1713	switch (field->cell_methods_mode)
1714	{
1715	case (CField::cell_methods_mode_attr::prefix):
1716	cellMethodsPrefix = cellMethodString;
1717	cellMethodsPrefix += " ";
1718	break;
1719	case (CField::cell_methods_mode_attr::suffix):
1720	cellMethodsSuffix = " ";
1721	cellMethodsSuffix += cellMethodString;
1722	break;
1723	case (CField::cell_methods_mode_attr::none):
1724	break;
1725	default:
1726	break;
1727	}
1728	}
1729	}
1730
1731
1732	if (wtime)
1733	{
1734	CDuration freqOp = field->freq_op.getValue();
1735	freqOp.solveTimeStep(*context->calendar);
1736	StdString freqOpStr = freqOp.toStringUDUnits();
1737	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1738
1739	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1740	freqOut.solveTimeStep(*context->calendar);
1741	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1742
1743	StdString cellMethods(cellMethodsPrefix + "time: ");
1744	if (field->operation.getValue() == "instant") cellMethods += "point";
1745	else if (field->operation.getValue() == "average") cellMethods += "mean";
1746	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1747	else cellMethods += field->operation;
1748	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1749	cellMethods += " (interval: " + freqOpStr + ")";
1750	cellMethods += cellMethodsSuffix;
1751	if (!alreadyAddCellMethod)
1752	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1753	}
1754
1755	if (hasArea)
1756	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1757
1758	if (!field->default_value.isEmpty())
1759	{
1760	double default_value = field->default_value.getValue();
1761	float fdefault_value = (float)default_value;
1762	if (type == NC_DOUBLE)
1763	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1764	else
1765	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1766	}
1767	else
1768	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1769
1770	if (field->compression_level.isEmpty())
1771	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1772	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1773
1774	{ // Ecriture des coordonnes
1775
1776	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1777	std::vector<StdString>::iterator
1778	itc = coodinates.begin(), endc = coodinates.end();
1779
1780	for (; itc!= endc; itc++)
1781	{
1782	StdString & coord = *itc;
1783	if (itc+1 != endc)
1784	coordstr.append(coord).append(" ");
1785	else coordstr.append(coord);
1786	}
1787
1788	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1789
1790	}
1791	}
1792	catch (CNetCdfException& e)
1793	{
1794	StdString msg("On writing field : ");
1795	msg.append(fieldid); msg.append("\n");
1796	msg.append("In the context : ");
1797	msg.append(context->getId()); msg.append("\n");
1798	msg.append(e.what());
1799	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1800	}
1801	} // writeField_()
1802
1803	//--------------------------------------------------------------
1804
1805	void CNc4DataOutput::writeFile_ (CFile* file)
1806	{
1807	StdString filename = file->getFileOutputName();
1808	StdString description = (!file->description.isEmpty())
1809	? file->description.getValue()
1810	: StdString("Created by xios");
1811
1812	singleDomain = (file->nbDomains == 1);
1813
1814	try
1815	{
1816	if (SuperClassWriter::useCFConvention)
1817	this->writeFileAttributes(filename, description,
1818	StdString("CF-1.5"),
1819	StdString("An IPSL model"),
1820	this->getTimeStamp());
1821	else
1822	this->writeFileAttributes(filename, description,
1823	StdString("UGRID"),
1824	StdString("An IPSL model"),
1825	this->getTimeStamp());
1826
1827
1828	if (!appendMode)
1829	SuperClassWriter::addDimension("axis_nbounds", 2);
1830	}
1831	catch (CNetCdfException& e)
1832	{
1833	StdString msg("On writing file : ");
1834	msg.append(filename); msg.append("\n");
1835	msg.append("In the context : ");
1836	CContext* context = CContext::getCurrent() ;
1837	msg.append(context->getId()); msg.append("\n");
1838	msg.append(e.what());
1839	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1840	}
1841	}
1842
1843	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1844	{
1845	StdString name = var->getVariableOutputName();
1846
1847	try
1848	{
1849	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1850	addAttribute(name, var->getData<int>(), &fieldId);
1851	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1852	addAttribute(name, var->getData<short int>(), &fieldId);
1853	else if (var->type.getValue() == CVariable::type_attr::t_float)
1854	addAttribute(name, var->getData<float>(), &fieldId);
1855	else if (var->type.getValue() == CVariable::type_attr::t_double)
1856	addAttribute(name, var->getData<double>(), &fieldId);
1857	else if (var->type.getValue() == CVariable::type_attr::t_string)
1858	addAttribute(name, var->getData<string>(), &fieldId);
1859	else
1860	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1861	<< "Unsupported variable of type " << var->type.getStringValue());
1862	}
1863	catch (CNetCdfException& e)
1864	{
1865	StdString msg("On writing attributes of variable with name : ");
1866	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1867	msg.append("In the context : ");
1868	CContext* context = CContext::getCurrent() ;
1869	msg.append(context->getId()); msg.append("\n");
1870	msg.append(e.what());
1871	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1872	}
1873	}
1874
1875	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1876	{
1877	StdString name = var->getVariableOutputName();
1878
1879	try
1880	{
1881	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1882	addAttribute(name, var->getData<int>());
1883	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1884	addAttribute(name, var->getData<short int>());
1885	else if (var->type.getValue() == CVariable::type_attr::t_float)
1886	addAttribute(name, var->getData<float>());
1887	else if (var->type.getValue() == CVariable::type_attr::t_double)
1888	addAttribute(name, var->getData<double>());
1889	else if (var->type.getValue() == CVariable::type_attr::t_string)
1890	addAttribute(name, var->getData<string>());
1891	else
1892	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1893	<< "Unsupported variable of type " << var->type.getStringValue());
1894	}
1895	catch (CNetCdfException& e)
1896	{
1897	StdString msg("On writing attributes of variable with name : ");
1898	msg.append(name); msg.append("\n");
1899	msg.append("In the context : ");
1900	CContext* context = CContext::getCurrent() ;
1901	msg.append(context->getId()); msg.append("\n");
1902	msg.append(e.what());
1903	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1904	}
1905	}
1906
1907	void CNc4DataOutput::syncFile_ (void)
1908	{
1909	try
1910	{
1911	SuperClassWriter::sync() ;
1912	}
1913	catch (CNetCdfException& e)
1914	{
1915	StdString msg("On synchronizing the write among processes");
1916	msg.append("In the context : ");
1917	CContext* context = CContext::getCurrent() ;
1918	msg.append(context->getId()); msg.append("\n");
1919	msg.append(e.what());
1920	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1921	}
1922	}
1923
1924	void CNc4DataOutput::closeFile_ (void)
1925	{
1926	try
1927	{
1928	SuperClassWriter::close() ;
1929	}
1930	catch (CNetCdfException& e)
1931	{
1932	StdString msg("On closing file");
1933	msg.append("In the context : ");
1934	CContext* context = CContext::getCurrent() ;
1935	msg.append(context->getId()); msg.append("\n");
1936	msg.append(e.what());
1937	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1938	}
1939
1940	}
1941
1942	//---------------------------------------------------------------
1943
1944	StdString CNc4DataOutput::getTimeStamp(void) const
1945	{
1946	const int buffer_size = 100;
1947	time_t rawtime;
1948	struct tm * timeinfo = NULL;
1949	char buffer [buffer_size];
1950
1951	time ( &rawtime );
1952	timeinfo = localtime ( &rawtime );
1953	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
1954
1955	return (StdString(buffer));
1956	}
1957
1958	//---------------------------------------------------------------
1959
1960	void CNc4DataOutput::writeFieldData_ (CField* field)
1961	{
1962	CContext* context = CContext::getCurrent();
1963	CContextServer* server = context->server;
1964	CGrid* grid = field->grid;
1965
1966	if (field->getNStep()<1) return ;
1967
1968	if (!grid->doGridHaveDataToWrite())
1969	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
1970
1971	StdString fieldid = field->getFieldOutputName();
1972
1973	StdOStringStream oss;
1974	string timeAxisId;
1975	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
1976	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
1977
1978	StdString timeBoundId = getTimeCounterName() + "_bounds";
1979
1980	StdString timeAxisBoundId;
1981	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
1982	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
1983
1984	if (!field->wasWritten())
1985	{
1986	if (appendMode && field->file->record_offset.isEmpty() &&
1987	field->getOperationTimeType() != func::CFunctor::once)
1988	{
1989	field->resetNStep(getRecordFromTime(field->last_Write_srv) + 1);
1990	}
1991
1992	field->setWritten();
1993	}
1994
1995
1996	CArray<double,1> time_data(1);
1997	CArray<double,1> time_data_bound(2);
1998	CArray<double,1> time_counter(1);
1999	CArray<double,1> time_counter_bound(2);
2000
2001	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2002
2003	if (wtime)
2004	{
2005	Time lastWrite = field->last_Write_srv;
2006	Time lastLastWrite = field->lastlast_Write_srv;
2007
2008	if (field->getOperationTimeType() == func::CFunctor::instant)
2009	time_data(0) = lastWrite;
2010	else if (field->getOperationTimeType() == func::CFunctor::centered)
2011	time_data(0) = (lastWrite + lastLastWrite) / 2;
2012
2013	if (field->getOperationTimeType() == func::CFunctor::instant)
2014	time_data_bound(0) = time_data_bound(1) = lastWrite;
2015	else if (field->getOperationTimeType() == func::CFunctor::centered)
2016	{
2017	time_data_bound(0) = lastLastWrite;
2018	time_data_bound(1) = lastWrite;
2019	}
2020
2021	if (field->file->time_counter == CFile::time_counter_attr::instant)
2022	time_counter(0) = lastWrite;
2023	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2024	time_counter(0) = (lastWrite + lastLastWrite) / 2;
2025	else if (field->file->time_counter == CFile::time_counter_attr::record)
2026	time_counter(0) = field->getNStep() - 1;
2027
2028
2029	if (field->file->time_counter == CFile::time_counter_attr::instant)
2030	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
2031	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2032	{
2033	time_counter_bound(0) = lastLastWrite;
2034	time_counter_bound(1) = lastWrite;
2035	}
2036	else if (field->file->time_counter == CFile::time_counter_attr::record)
2037	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2038	}
2039
2040	bool isRoot = (server->intraCommRank == 0);
2041
2042	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2043	{
2044	double scaleFactor = 1.0;
2045	double addOffset = 0.0;
2046	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2047	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2048	field->scaleFactorAddOffset(scaleFactor, addOffset);
2049	}
2050
2051	try
2052	{
2053	size_t writtenSize;
2054	if (field->getUseCompressedOutput())
2055	writtenSize = grid->getNumberWrittenIndexes();
2056	else
2057	writtenSize = grid->getWrittenDataSize();
2058
2059	CArray<double,1> fieldData(writtenSize);
2060	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2061
2062	if (field->getUseCompressedOutput())
2063	field->outputCompressedField(fieldData);
2064	else
2065	field->outputField(fieldData);
2066
2067	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2068
2069	switch (SuperClass::type)
2070	{
2071	case (MULTI_FILE) :
2072	{
2073	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2074	if (wtime)
2075	{
2076	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2077	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2078	if (field->file->time_counter != CFile::time_counter_attr::none)
2079	{
2080	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2081	if (field->file->time_counter != CFile::time_counter_attr::record)
2082	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2083	}
2084	}
2085	break;
2086	}
2087	case (ONE_FILE) :
2088	{
2089	// const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2090	// const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2091	// const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2092
2093	// std::vector<StdSize> start, count;
2094
2095	// if (field->getUseCompressedOutput())
2096	// {
2097	// if (grid->isCompressible())
2098	// {
2099	// start.push_back(grid->getOffsetWrittenIndexes());
2100	// count.push_back(grid->getNumberWrittenIndexes());
2101	// }
2102	// else
2103	// {
2104	// CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2105	// std::vector<StdString> domainList = grid->getDomainList();
2106	// std::vector<StdString> axisList = grid->getAxisList();
2107	// int numElement = axisDomainOrder.numElements();
2108	// int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2109	// int idx = nZoomBeginGlobal.size() - 1;
2110
2111	// start.reserve(nZoomBeginGlobal.size());
2112	// count.reserve(nZoomBeginGlobal.size());
2113
2114
2115	// for (int i = numElement - 1; i >= 0; --i)
2116	// {
2117	// if (2 == axisDomainOrder(i))
2118	// {
2119	// CDomain* domain = CDomain::get(domainList[idxDomain]);
2120
2121	// if (domain->isCompressible())
2122	// {
2123	// start.push_back(domain->getOffsetWrittenIndexes());
2124	// count.push_back(domain->getNumberWrittenIndexes());
2125	// idx -= 2;
2126	// }
2127	// else
2128	// {
2129	// if ((domain->type) != CDomain::type_attr::unstructured)
2130	// {
2131	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2132	// count.push_back(nZoomSizeServer[idx]);
2133	// }
2134	// --idx;
2135	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2136	// count.push_back(nZoomSizeServer[idx]);
2137	// --idx;
2138	// }
2139	// --idxDomain;
2140	// }
2141	// else if (1 == axisDomainOrder(i))
2142	// {
2143	// CAxis* axis = CAxis::get(axisList[idxAxis]);
2144
2145	// if (axis->isCompressible())
2146	// {
2147	// start.push_back(axis->getOffsetWrittenIndexes());
2148	// count.push_back(axis->getNumberWrittenIndexes());
2149	// }
2150	// else
2151	// {
2152	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2153	// count.push_back(nZoomSizeServer[idx]);
2154	// }
2155
2156	// --idxAxis;
2157	// --idx;
2158	// }
2159	// }
2160	// }
2161	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2162	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2163	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2164
2165	std::vector<StdSize> start, count;
2166
2167	if (field->getUseCompressedOutput())
2168	{
2169	if (grid->isCompressible())
2170	{
2171	start.push_back(grid->getOffsetWrittenIndexes());
2172	count.push_back(grid->getNumberWrittenIndexes());
2173	}
2174	else
2175	{
2176	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2177	std::vector<StdString> domainList = grid->getDomainList();
2178	std::vector<StdString> axisList = grid->getAxisList();
2179	int numElement = axisDomainOrder.numElements();
2180	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2181	int idx = nZoomBeginGlobal.size() - 1;
2182
2183	start.reserve(nZoomBeginGlobal.size());
2184	count.reserve(nZoomBeginGlobal.size());
2185
2186
2187	for (int i = numElement - 1; i >= 0; --i)
2188	{
2189	if (2 == axisDomainOrder(i))
2190	{
2191	CDomain* domain = CDomain::get(domainList[idxDomain]);
2192
2193	if (domain->isCompressible())
2194	{
2195	start.push_back(domain->getOffsetWrittenIndexes());
2196	count.push_back(domain->getNumberWrittenIndexes());
2197	idx -= 2;
2198	}
2199	else
2200	{
2201	if ((domain->type) != CDomain::type_attr::unstructured)
2202	{
2203	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2204	count.push_back(nZoomSizeServer[idx]);
2205	}
2206	--idx;
2207	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2208	count.push_back(nZoomSizeServer[idx]);
2209	--idx;
2210	}
2211	--idxDomain;
2212	}
2213	else if (1 == axisDomainOrder(i))
2214	{
2215	CAxis* axis = CAxis::get(axisList[idxAxis]);
2216
2217	if (axis->isCompressible())
2218	{
2219	start.push_back(axis->getOffsetWrittenIndexes());
2220	count.push_back(axis->getNumberWrittenIndexes());
2221	}
2222	else
2223	{
2224	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2225	count.push_back(nZoomSizeServer[idx]);
2226	}
2227
2228	--idxAxis;
2229	--idx;
2230	}
2231	}
2232	}
2233	}
2234	else
2235	{
2236	// CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2237	// std::vector<StdString> domainList = grid->getDomainList();
2238	// std::vector<StdString> axisList = grid->getAxisList();
2239	// int numElement = axisDomainOrder.numElements();
2240	// int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2241	// int idx = nZoomBeginGlobal.size() - 1;
2242
2243	// start.reserve(nZoomBeginGlobal.size());
2244	// count.reserve(nZoomBeginGlobal.size());
2245
2246	// for (int i = numElement - 1; i >= 0; --i)
2247	// {
2248	// if (2 == axisDomainOrder(i))
2249	// {
2250	// CDomain* domain = CDomain::get(domainList[idxDomain]);
2251	// if ((domain->type) != CDomain::type_attr::unstructured)
2252	// {
2253	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2254	// count.push_back(nZoomSizeServer[idx]);
2255	// }
2256	// --idx ;
2257	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2258	// count.push_back(nZoomSizeServer[idx]);
2259	// --idx ;
2260	// --idxDomain;
2261	// }
2262	// else if (1 == axisDomainOrder(i))
2263	// {
2264	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2265	// count.push_back(nZoomSizeServer[idx]);
2266	// --idx;
2267	// }
2268	// else
2269	// {
2270	// if (1 == axisDomainOrder.numElements())
2271	// {
2272	// start.push_back(0);
2273	// count.push_back(1);
2274	// }
2275	// --idx;
2276	// }
2277	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2278	std::vector<StdString> domainList = grid->getDomainList();
2279	std::vector<StdString> axisList = grid->getAxisList();
2280	int numElement = axisDomainOrder.numElements();
2281	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2282	int idx = domainList.size() * 2 + axisList.size() - 1;// nZoomBeginGlobal.size() - 1;
2283
2284	start.reserve(nZoomBeginGlobal.size());
2285	count.reserve(nZoomBeginGlobal.size());
2286
2287	for (int i = numElement - 1; i >= 0; --i)
2288	{
2289	if (2 == axisDomainOrder(i))
2290	{
2291	CDomain* domain = CDomain::get(domainList[idxDomain]);
2292	if ((domain->type) != CDomain::type_attr::unstructured)
2293	{
2294	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2295	// count.push_back(nZoomSizeServer[idx]);
2296	start.push_back((domain->getStartWriteIndex())[idx]);
2297	count.push_back((domain->getCountWriteIndex())[idx]);
2298	}
2299	--idx ;
2300	// start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2301	// count.push_back(nZoomSizeServer[idx]);
2302	start.push_back((domain->getStartWriteIndex())[idx]);
2303	count.push_back((domain->getCountWriteIndex())[idx]);
2304	--idx ;
2305	--idxDomain;
2306	}
2307	else if (1 == axisDomainOrder(i))
2308	{
2309	CAxis* axis = CAxis::get(axisList[idxAxis]);
2310	start.push_back(axis->getStartWriteIndex());
2311	count.push_back(axis->getCountWriteIndex());
2312	--idx;
2313	--idxAxis;
2314	}
2315	else
2316	{
2317	if (1 == axisDomainOrder.numElements())
2318	{
2319	start.push_back(0);
2320	count.push_back(1);
2321	}
2322	--idx;
2323	}
2324	}
2325	}
2326
2327	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2328	if (wtime)
2329	{
2330	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2331	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2332	if (field->file->time_counter != CFile::time_counter_attr::none)
2333	{
2334	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
2335	if (field->file->time_counter != CFile::time_counter_attr::record)
2336	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2337	}
2338	}
2339
2340	break;
2341	}
2342	}
2343	}
2344	catch (CNetCdfException& e)
2345	{
2346	StdString msg("On writing field data: ");
2347	msg.append(fieldid); msg.append("\n");
2348	msg.append("In the context : ");
2349	msg.append(context->getId()); msg.append("\n");
2350	msg.append(e.what());
2351	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2352	}
2353	}
2354
2355	//---------------------------------------------------------------
2356
2357	void CNc4DataOutput::writeTimeAxis_
2358	(CField* field,
2359	const boost::shared_ptr<CCalendar> cal)
2360	{
2361	StdOStringStream oss;
2362
2363	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2364
2365	// oss << "time_" << field->operation.getValue()
2366	// << "_" << field->getRelFile()->output_freq.getValue();
2367
2368	// StdString axisid = oss.str();
2369	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
2370	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
2371
2372	StdString axisid("time_centered") ;
2373	StdString axisBoundId("time_centered_bounds");
2374	StdString timeid(getTimeCounterName());
2375	StdString timeBoundId("axis_nbounds");
2376
2377	if (field->getOperationTimeType() == func::CFunctor::instant)
2378	{
2379	axisid = "time_instant";
2380	axisBoundId = "time_instant_bounds";
2381	}
2382
2383	try
2384	{
2385	// Adding time_instant or time_centered
2386	std::vector<StdString> dims;
2387	dims.push_back(timeid);
2388	if (!SuperClassWriter::varExist(axisid))
2389	{
2390	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2391
2392	CDate timeOrigin=cal->getTimeOrigin() ;
2393	StdOStringStream oss2;
2394	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
2395	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
2396	StdString strInitdate=oss2.str() ;
2397	StdString strTimeOrigin=timeOrigin.toString() ;
2398	this->writeTimeAxisAttributes
2399	(axisid, cal->getType(),
2400	StdString("seconds since ").append(strTimeOrigin),
2401	strTimeOrigin, axisBoundId);
2402	}
2403
2404	// Adding time_instant_bounds or time_centered_bounds variables
2405	if (!SuperClassWriter::varExist(axisBoundId))
2406	{
2407	dims.clear() ;
2408	dims.push_back(timeid);
2409	dims.push_back(timeBoundId);
2410	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2411	}
2412
2413	if (field->file->time_counter != CFile::time_counter_attr::none)
2414	{
2415	// Adding time_counter
2416	axisid = getTimeCounterName();
2417	axisBoundId = getTimeCounterName() + "_bounds";
2418	dims.clear();
2419	dims.push_back(timeid);
2420	if (!SuperClassWriter::varExist(axisid))
2421	{
2422	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2423	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
2424
2425	if (field->file->time_counter != CFile::time_counter_attr::record)
2426	{
2427	CDate timeOrigin = cal->getTimeOrigin();
2428	StdString strTimeOrigin = timeOrigin.toString();
2429
2430	this->writeTimeAxisAttributes(axisid, cal->getType(),
2431	StdString("seconds since ").append(strTimeOrigin),
2432	strTimeOrigin, axisBoundId);
2433	}
2434	}
2435
2436	// Adding time_counter_bound dimension
2437	if (field->file->time_counter != CFile::time_counter_attr::record)
2438	{
2439	if (!SuperClassWriter::varExist(axisBoundId))
2440	{
2441	dims.clear();
2442	dims.push_back(timeid);
2443	dims.push_back(timeBoundId);
2444	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2445	}
2446	}
2447	}
2448	}
2449	catch (CNetCdfException& e)
2450	{
2451	StdString msg("On writing time axis data: ");
2452	msg.append("In the context : ");
2453	CContext* context = CContext::getCurrent() ;
2454	msg.append(context->getId()); msg.append("\n");
2455	msg.append(e.what());
2456	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2457	const boost::shared_ptr<CCalendar> cal)", << msg);
2458	}
2459	}
2460
2461	//---------------------------------------------------------------
2462
2463	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2464	const StdString & calendar,
2465	const StdString & units,
2466	const StdString & time_origin,
2467	const StdString & time_bounds,
2468	const StdString & standard_name,
2469	const StdString & long_name)
2470	{
2471	try
2472	{
2473	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2474	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2475	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2476	SuperClassWriter::addAttribute("units", units , &axis_name);
2477	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2478	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2479	}
2480	catch (CNetCdfException& e)
2481	{
2482	StdString msg("On writing time axis Attribute: ");
2483	msg.append("In the context : ");
2484	CContext* context = CContext::getCurrent() ;
2485	msg.append(context->getId()); msg.append("\n");
2486	msg.append(e.what());
2487	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2488	const StdString & calendar,\
2489	const StdString & units, \
2490	const StdString & time_origin, \
2491	const StdString & time_bounds, \
2492	const StdString & standard_name, \
2493	const StdString & long_name)", << msg);
2494	}
2495	}
2496
2497	//---------------------------------------------------------------
2498
2499	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2500	const StdString & axis,
2501	const StdString & standard_name,
2502	const StdString & long_name,
2503	const StdString & units,
2504	const StdString & nav_model)
2505	{
2506	try
2507	{
2508	if (!axis.empty())
2509	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2510
2511	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2512	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2513	SuperClassWriter::addAttribute("units" , units , &axis_name);
2514	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2515	}
2516	catch (CNetCdfException& e)
2517	{
2518	StdString msg("On writing Axis Attribute: ");
2519	msg.append("In the context : ");
2520	CContext* context = CContext::getCurrent() ;
2521	msg.append(context->getId()); msg.append("\n");
2522	msg.append(e.what());
2523	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2524	const StdString & axis, \
2525	const StdString & standard_name, \
2526	const StdString & long_name, \
2527	const StdString & units, \
2528	const StdString & nav_model)", << msg);
2529	}
2530	}
2531
2532	//---------------------------------------------------------------
2533
2534	void CNc4DataOutput::writeLocalAttributes
2535	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2536	{
2537	try
2538	{
2539	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2540	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2541	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2542	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2543	}
2544	catch (CNetCdfException& e)
2545	{
2546	StdString msg("On writing Local Attributes: ");
2547	msg.append("In the context : ");
2548	CContext* context = CContext::getCurrent() ;
2549	msg.append(context->getId()); msg.append("\n");
2550	msg.append(e.what());
2551	ERROR("CNc4DataOutput::writeLocalAttributes \
2552	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2553	}
2554
2555	}
2556
2557	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2558	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2559	{
2560	CArray<int,1> array(2) ;
2561
2562	try
2563	{
2564	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2565	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2566	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2567	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2568	array=ni_glo,nj_glo ;
2569	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2570	array=ni,nj ;
2571	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2572	array=ibegin+1,jbegin+1 ;
2573	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2574	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2575	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2576	array=0,0 ;
2577	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2578	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2579	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2580	/*
2581	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2582	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2583	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2584	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2585	*/
2586	}
2587	catch (CNetCdfException& e)
2588	{
2589	StdString msg("On writing Local Attributes IOIPSL \n");
2590	msg.append("In the context : ");
2591	CContext* context = CContext::getCurrent() ;
2592	msg.append(context->getId()); msg.append("\n");
2593	msg.append(e.what());
2594	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2595	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2596	}
2597	}
2598	//---------------------------------------------------------------
2599
2600	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2601	const StdString & description,
2602	const StdString & conventions,
2603	const StdString & production,
2604	const StdString & timeStamp)
2605	{
2606	try
2607	{
2608	SuperClassWriter::addAttribute("name" , name);
2609	SuperClassWriter::addAttribute("description", description);
2610	SuperClassWriter::addAttribute("title" , description);
2611	SuperClassWriter::addAttribute("Conventions", conventions);
2612	SuperClassWriter::addAttribute("production" , production);
2613	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
2614	}
2615	catch (CNetCdfException& e)
2616	{
2617	StdString msg("On writing File Attributes \n ");
2618	msg.append("In the context : ");
2619	CContext* context = CContext::getCurrent() ;
2620	msg.append(context->getId()); msg.append("\n");
2621	msg.append(e.what());
2622	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2623	const StdString & description, \
2624	const StdString & conventions, \
2625	const StdString & production, \
2626	const StdString & timeStamp)", << msg);
2627	}
2628	}
2629
2630	//---------------------------------------------------------------
2631
2632	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2633	int data_dim,
2634	int data_ni,
2635	int data_nj,
2636	int data_ibegin,
2637	int data_jbegin)
2638	{
2639	try
2640	{
2641	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2642	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2643	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2644	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2645	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2646	}
2647	catch (CNetCdfException& e)
2648	{
2649	StdString msg("On writing Mask Attributes \n ");
2650	msg.append("In the context : ");
2651	CContext* context = CContext::getCurrent() ;
2652	msg.append(context->getId()); msg.append("\n");
2653	msg.append(e.what());
2654	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2655	int data_dim, \
2656	int data_ni, \
2657	int data_nj, \
2658	int data_ibegin, \
2659	int data_jbegin)", << msg);
2660	}
2661	}
2662
2663	///--------------------------------------------------------------
2664
2665	StdSize CNc4DataOutput::getRecordFromTime(Time time)
2666	{
2667	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2668	if (it == timeToRecordCache.end())
2669	{
2670	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2671	if (!SuperClassWriter::varExist(timeAxisBoundsId))
2672	timeAxisBoundsId = "time_instant_bounds";
2673
2674	CArray<double,2> timeAxisBounds;
2675	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
2676
2677	StdSize record = 0;
2678	double dtime(time);
2679	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
2680	{
2681	if (timeAxisBounds(1, n) < dtime)
2682	{
2683	record = n + 1;
2684	break;
2685	}
2686	}
2687	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2688	}
2689	return it->second;
2690	}
2691
2692	///--------------------------------------------------------------
2693
2694	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2695	{
2696	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2697	}
2698
2699	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2700	{
2701	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2702	}
2703
2704	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2705	{
2706	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2707	}
2708
2709	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2710	{
2711	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2712	}
2713
2714	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2715	{
2716	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2717	}
2718
2719	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2720	{
2721	this->writtenDomains.insert(domainName);
2722	}
2723
2724	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2725	{
2726	this->writtenCompressedDomains.insert(domainName);
2727	}
2728
2729	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2730	{
2731	this->writtenAxis.insert(axisName);
2732	}
2733
2734	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2735	{
2736	this->writtenCompressedAxis.insert(axisName);
2737	}
2738
2739	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2740	{
2741	this->writtenScalar.insert(scalarName);
2742	}
2743	} // namespace xios

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