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nc4_data_output.cpp @ 1169

Last change on this file since 1169 was 1169, checked in by mhnguyen, 7 years ago

Non-continuous zoom on axis
Zoomed points are defined by array index of zoom_axis

+) Update axis with new type of zoom

Test
+) On Curie
+) Work
+) Update test_complete with this new zoom.

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: 121.1 KB

Line
1	#include "nc4_data_output.hpp"
2
3	#include <boost/lexical_cast.hpp>
4	#include "attribute_template.hpp"
5	#include "group_template.hpp"
6
7	#include "file.hpp"
8	#include "calendar.hpp"
9	#include "context.hpp"
10	#include "context_server.hpp"
11	#include "netCdfException.hpp"
12	#include "exception.hpp"
13	#include "timer.hpp"
14	#include "uuid.hpp"
15	namespace xios
16	{
17	/// ////////////////////// Dfinitions ////////////////////// ///
18	CNc4DataOutput::CNc4DataOutput
19	(CFile* file, const StdString & filename, bool exist)
20	: SuperClass()
21	, SuperClassWriter(filename, exist)
22	, filename(filename)
23	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
24	{
25	SuperClass::type = MULTI_FILE;
26	}
27
28	CNc4DataOutput::CNc4DataOutput
29	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
30	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
31	: SuperClass()
32	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
33	, comm_file(comm_file)
34	, filename(filename)
35	, isCollective(isCollective)
36	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none)
37	{
38	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
39	}
40
41	CNc4DataOutput::~CNc4DataOutput(void)
42	{ /* Ne rien faire de plus */ }
43
44	///--------------------------------------------------------------
45
46	const StdString & CNc4DataOutput::getFileName(void) const
47	{
48	return (this->filename);
49	}
50
51	//---------------------------------------------------------------
52
53	void CNc4DataOutput::writeDomain_(CDomain* domain)
54	{
55	if (domain->type == CDomain::type_attr::unstructured)
56	{
57	if (SuperClassWriter::useCFConvention)
58	writeUnstructuredDomain(domain) ;
59	else
60	writeUnstructuredDomainUgrid(domain) ;
61	return ;
62	}
63
64	CContext* context = CContext::getCurrent() ;
65	CContextServer* server=context->server ;
66
67	if (domain->IsWritten(this->filename)) return;
68	domain->checkAttributes();
69
70	if (domain->isEmpty())
71	if (SuperClass::type==MULTI_FILE) return;
72
73	std::vector<StdString> dim0, dim1;
74	StdString domid = domain->getDomainOutputName();
75	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
76	if (isWrittenDomain(domid)) return ;
77	else setWrittenDomain(domid);
78
79
80	StdString dimXid, dimYid ;
81
82	nc_type typePrec ;
83	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
84	else if (domain->prec==4) typePrec = NC_FLOAT ;
85	else if (domain->prec==8) typePrec = NC_DOUBLE ;
86
87	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
88	switch (domain->type)
89	{
90	case CDomain::type_attr::curvilinear :
91	dimXid = StdString("x").append(appendDomid);
92	dimYid = StdString("y").append(appendDomid);
93	break ;
94	case CDomain::type_attr::rectilinear :
95	dimXid = StdString("lon").append(appendDomid);
96	dimYid = StdString("lat").append(appendDomid);
97	break;
98	}
99
100	StdString dimVertId = StdString("nvertex").append(appendDomid);
101
102	string lonid,latid,bounds_lonid,bounds_latid ;
103	string areaId = "area" + appendDomid;
104	/*
105	StdString lonid_loc = (server->intraCommSize > 1)
106	? StdString("lon").append(appendDomid).append("_local")
107	: lonid;
108	StdString latid_loc = (server->intraCommSize > 1)
109	? StdString("lat").append(appendDomid).append("_local")
110	: latid;
111	*/
112
113	try
114	{
115	switch (SuperClass::type)
116	{
117	case (MULTI_FILE) :
118	{
119	// if (domain->isEmpty()) return;
120
121	if (server->intraCommSize > 1)
122	{
123	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
124	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
125	}
126
127	switch (domain->type)
128	{
129	case CDomain::type_attr::curvilinear :
130	dim0.push_back(dimYid); dim0.push_back(dimXid);
131	lonid = StdString("nav_lon").append(appendDomid);
132	latid = StdString("nav_lat").append(appendDomid);
133	break ;
134	case CDomain::type_attr::rectilinear :
135	lonid = StdString("lon").append(appendDomid);
136	latid = StdString("lat").append(appendDomid);
137	dim0.push_back(dimYid);
138	dim1.push_back(dimXid);
139	break;
140	}
141
142	bounds_lonid = StdString("bounds_lon").append(appendDomid);
143	bounds_latid = StdString("bounds_lat").append(appendDomid);
144
145	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
146	SuperClassWriter::addDimension(dimYid, domain->zoom_nj_srv);
147
148	if (domain->hasBounds)
149	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
150
151	if (server->intraCommSize > 1)
152	{
153	this->writeLocalAttributes(domain->zoom_ibegin_srv,
154	domain->zoom_ni_srv,
155	domain->zoom_jbegin_srv,
156	domain->zoom_nj_srv,
157	appendDomid);
158
159	if (singleDomain)
160	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
161	domain->zoom_ibegin_srv,
162	domain->zoom_ni_srv,
163	domain->zoom_jbegin_srv,
164	domain->zoom_nj_srv,
165	domain->ni_glo,domain->nj_glo,
166	server->intraCommRank,server->intraCommSize);
167	}
168
169	if (domain->hasLonLat)
170	{
171	switch (domain->type)
172	{
173	case CDomain::type_attr::curvilinear :
174	SuperClassWriter::addVariable(latid, typePrec, dim0);
175	SuperClassWriter::addVariable(lonid, typePrec, dim0);
176	break ;
177	case CDomain::type_attr::rectilinear :
178	SuperClassWriter::addVariable(latid, typePrec, dim0);
179	SuperClassWriter::addVariable(lonid, typePrec, dim1);
180	break ;
181	}
182
183	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
184	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
185
186	if (domain->hasBounds)
187	{
188	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
189	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
190
191	dim0.clear();
192	dim0.push_back(dimYid);
193	dim0.push_back(dimXid);
194	dim0.push_back(dimVertId);
195	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
196	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
197	}
198	}
199
200	dim0.clear();
201	dim0.push_back(dimYid);
202	dim0.push_back(dimXid);
203
204
205	// supress mask if (server->intraCommSize > 1)
206	// supress mask {
207	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
208	// supress mask
209	// supress mask this->writeMaskAttributes(maskid,
210	// supress mask domain->data_dim.getValue()/*,
211	// supress mask domain->data_ni.getValue(),
212	// supress mask domain->data_nj.getValue(),
213	// supress mask domain->data_ibegin.getValue(),
214	// supress mask domain->data_jbegin.getValue()*/);
215	// supress mask }
216
217	//SuperClassWriter::setDefaultValue(maskid, &dvm);
218
219	if (domain->hasArea)
220	{
221	SuperClassWriter::addVariable(areaId, typePrec, dim0);
222	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
223	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
224	}
225
226	SuperClassWriter::definition_end();
227
228	if (domain->hasLonLat)
229	{
230	switch (domain->type)
231	{
232	case CDomain::type_attr::curvilinear :
233	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
234	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
235	break;
236	case CDomain::type_attr::rectilinear :
237	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
238	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
239	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
240	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
241	break;
242	}
243
244	if (domain->hasBounds)
245	{
246	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
247	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
248	}
249	}
250
251	if (domain->hasArea)
252	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
253
254	SuperClassWriter::definition_start();
255
256	break;
257	}
258	case (ONE_FILE) :
259	{
260	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
261	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
262
263	if (domain->hasBounds)
264	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
265
266	if (domain->hasLonLat)
267	{
268	switch (domain->type)
269	{
270	case CDomain::type_attr::curvilinear :
271	dim0.push_back(dimYid); dim0.push_back(dimXid);
272	lonid = StdString("nav_lon").append(appendDomid);
273	latid = StdString("nav_lat").append(appendDomid);
274	SuperClassWriter::addVariable(latid, typePrec, dim0);
275	SuperClassWriter::addVariable(lonid, typePrec, dim0);
276	break;
277
278	case CDomain::type_attr::rectilinear :
279	dim0.push_back(dimYid);
280	dim1.push_back(dimXid);
281	lonid = StdString("lon").append(appendDomid);
282	latid = StdString("lat").append(appendDomid);
283	SuperClassWriter::addVariable(latid, typePrec, dim0);
284	SuperClassWriter::addVariable(lonid, typePrec, dim1);
285	break;
286	}
287
288	bounds_lonid = StdString("bounds_lon").append(appendDomid);
289	bounds_latid = StdString("bounds_lat").append(appendDomid);
290
291	this->writeAxisAttributes
292	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
293	this->writeAxisAttributes
294	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
295
296	if (domain->hasBounds)
297	{
298	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
299	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
300
301	dim0.clear();
302	dim0.push_back(dimYid);
303	dim0.push_back(dimXid);
304	dim0.push_back(dimVertId);
305	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
306	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
307	}
308	}
309
310	if (domain->hasArea)
311	{
312	dim0.clear();
313	dim0.push_back(dimYid); dim0.push_back(dimXid);
314	SuperClassWriter::addVariable(areaId, typePrec, dim0);
315	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
316	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
317	dim0.clear();
318	}
319
320	SuperClassWriter::definition_end();
321
322	switch (domain->type)
323	{
324	case CDomain::type_attr::curvilinear :
325	{
326	std::vector<StdSize> start(2) ;
327	std::vector<StdSize> count(2) ;
328	if (domain->isEmpty())
329	{
330	start[0]=0 ; start[1]=0 ;
331	count[0]=0 ; count[1]=0 ;
332	}
333	else
334	{
335	start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
336	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
337	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
338	}
339
340	if (domain->hasLonLat)
341	{
342	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
343	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
344	}
345	break;
346	}
347	case CDomain::type_attr::rectilinear :
348	{
349	if (domain->hasLonLat)
350	{
351	std::vector<StdSize> start(1) ;
352	std::vector<StdSize> count(1) ;
353	if (domain->isEmpty())
354	{
355	start[0]=0 ;
356	count[0]=0 ;
357	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
358	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
359
360	}
361	else
362	{
363	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
364	count[0]=domain->zoom_nj_srv ;
365	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
366	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
367
368	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
369	count[0]=domain->zoom_ni_srv ;
370	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
371	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
372	}
373	}
374	break;
375	}
376	}
377
378	if (domain->hasBounds)
379	{
380	std::vector<StdSize> start(3);
381	std::vector<StdSize> count(3);
382	if (domain->isEmpty())
383	{
384	start[2] = start[1] = start[0] = 0;
385	count[2] = count[1] = count[0] = 0;
386	}
387	else
388	{
389	start[2] = 0;
390	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
391	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
392	count[2] = domain->nvertex;
393	count[1] = domain->zoom_ni_srv;
394	count[0] = domain->zoom_nj_srv;
395	}
396
397	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0, &start, &count);
398	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0, &start, &count);
399	}
400
401	if (domain->hasArea)
402	{
403	std::vector<StdSize> start(2);
404	std::vector<StdSize> count(2);
405
406	if (domain->isEmpty())
407	{
408	start[0] = 0; start[1] = 0;
409	count[0] = 0; count[1] = 0;
410	}
411	else
412	{
413	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
414	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
415	count[1] = domain->zoom_ni_srv;
416	count[0] = domain->zoom_nj_srv;
417	}
418
419	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
420	}
421
422	SuperClassWriter::definition_start();
423	break;
424	}
425	default :
426	ERROR("CNc4DataOutput::writeDomain(domain)",
427	<< "[ type = " << SuperClass::type << "]"
428	<< " not implemented yet !");
429	}
430	}
431	catch (CNetCdfException& e)
432	{
433	StdString msg("On writing the domain : ");
434	msg.append(domid); msg.append("\n");
435	msg.append("In the context : ");
436	msg.append(context->getId()); msg.append("\n");
437	msg.append(e.what());
438	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
439	}
440
441	domain->addRelFile(this->filename);
442	}
443
444	//--------------------------------------------------------------
445
446	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
447	{
448	CContext* context = CContext::getCurrent() ;
449	CContextServer* server=context->server ;
450
451	if (domain->IsWritten(this->filename)) return;
452	domain->checkAttributes();
453	if (domain->isEmpty())
454	if (SuperClass::type==MULTI_FILE) return ;
455
456	nc_type typePrec ;
457	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
458	else if (domain->prec==4) typePrec = NC_FLOAT ;
459	else if (domain->prec==8) typePrec = NC_DOUBLE ;
460
461	std::vector<StdString> dim0;
462	StdString domid = domain->getDomainOutputName();
463	StdString domainName = domain->name;
464	domain->assignMesh(domainName, domain->nvertex);
465	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
466
467	StdString node_x = domainName + "_node_x";
468	StdString node_y = domainName + "_node_y";
469
470	StdString edge_x = domainName + "_edge_x";
471	StdString edge_y = domainName + "_edge_y";
472	StdString edge_nodes = domainName + "_edge_nodes";
473
474	StdString face_x = domainName + "_face_x";
475	StdString face_y = domainName + "_face_y";
476	StdString face_nodes = domainName + "_face_nodes";
477	StdString face_edges = domainName + "_face_edges";
478	StdString edge_faces = domainName + "_edge_face_links";
479	StdString face_faces = domainName + "_face_links";
480
481	StdString dimNode = "n" + domainName + "_node";
482	StdString dimEdge = "n" + domainName + "_edge";
483	StdString dimFace = "n" + domainName + "_face";
484	StdString dimVertex = "n" + domainName + "_vertex";
485	StdString dimTwo = "Two";
486
487	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
488	if (!isWrittenDomain(domid))
489	{
490	dim0.clear();
491	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
492	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
493	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
494	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
495	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
496	}
497
498	try
499	{
500	switch (SuperClass::type)
501	{
502	case (ONE_FILE) :
503	{
504	// Adding nodes
505	if (domain->nvertex == 1)
506	{
507	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
508	{
509	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
510	dim0.clear();
511	dim0.push_back(dimNode);
512	SuperClassWriter::addVariable(node_x, typePrec, dim0);
513	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
514	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
515	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
516	SuperClassWriter::addVariable(node_y, typePrec, dim0);
517	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
518	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
519	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
520	}
521	} // domain->nvertex == 1
522
523	// Adding edges and nodes, if nodes have not been defined previously
524	if (domain->nvertex == 2)
525	{
526	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
527	{
528	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
529	dim0.clear();
530	dim0.push_back(dimNode);
531	SuperClassWriter::addVariable(node_x, typePrec, dim0);
532	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
533	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
534	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
535	SuperClassWriter::addVariable(node_y, typePrec, dim0);
536	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
537	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
538	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
539	}
540	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
541	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
542	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
543	dim0.clear();
544	dim0.push_back(dimEdge);
545	SuperClassWriter::addVariable(edge_x, typePrec, dim0);
546	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
547	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
548	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
549	SuperClassWriter::addVariable(edge_y, typePrec, dim0);
550	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
551	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
552	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
553	dim0.clear();
554	dim0.push_back(dimEdge);
555	dim0.push_back(dimTwo);
556	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
557	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
558	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
559	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
560	} // domain->nvertex == 2
561
562	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
563	if (domain->nvertex > 2)
564	{
565	// Nodes
566	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
567	{
568	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
569	dim0.clear();
570	dim0.push_back(dimNode);
571	SuperClassWriter::addVariable(node_x, typePrec, dim0);
572	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
573	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
574	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
575	SuperClassWriter::addVariable(node_y, typePrec, dim0);
576	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
577	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
578	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
579	}
580	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
581	{
582	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
583	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
584	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
585	dim0.clear();
586	dim0.push_back(dimEdge);
587	SuperClassWriter::addVariable(edge_x, typePrec, dim0);
588	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
589	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
590	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
591	SuperClassWriter::addVariable(edge_y, typePrec, dim0);
592	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
593	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
594	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
595	dim0.clear();
596	dim0.push_back(dimEdge);
597	dim0.push_back(dimTwo);
598	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
599	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
600	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
601	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
602	}
603	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
604	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
605	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
606	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
607	dim0.clear();
608	dim0.push_back(dimFace);
609	SuperClassWriter::addVariable(face_x, typePrec, dim0);
610	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
611	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
612	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
613	SuperClassWriter::addVariable(face_y, typePrec, dim0);
614	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
615	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
616	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
617	dim0.clear();
618	dim0.push_back(dimFace);
619	dim0.push_back(dimVertex);
620	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
621	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
622	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
623	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
624	dim0.clear();
625	dim0.push_back(dimFace);
626	dim0.push_back(dimVertex);
627	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
628	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
629	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
630	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
631	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
632	dim0.clear();
633	dim0.push_back(dimEdge);
634	dim0.push_back(dimTwo);
635	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
636	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
637	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
638	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
639	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
640	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
641	dim0.clear();
642	dim0.push_back(dimFace);
643	dim0.push_back(dimVertex);
644	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
645	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
646	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
647	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
648	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
649	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
650	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
651	} // domain->nvertex > 2
652
653	SuperClassWriter::definition_end();
654
655	std::vector<StdSize> startEdges(1) ;
656	std::vector<StdSize> countEdges(1) ;
657	std::vector<StdSize> startNodes(1) ;
658	std::vector<StdSize> countNodes(1) ;
659	std::vector<StdSize> startFaces(1) ;
660	std::vector<StdSize> countFaces(1) ;
661	std::vector<StdSize> startEdgeNodes(2) ;
662	std::vector<StdSize> countEdgeNodes(2) ;
663	std::vector<StdSize> startEdgeFaces(2) ;
664	std::vector<StdSize> countEdgeFaces(2) ;
665	std::vector<StdSize> startFaceConctv(2) ;
666	std::vector<StdSize> countFaceConctv(2) ;
667
668	if (!isWrittenDomain(domid))
669	{
670	if (domain->nvertex == 1)
671	{
672	if (domain->isEmpty())
673	{
674	startNodes[0]=0 ;
675	countNodes[0]=0 ;
676	}
677	else
678	{
679	startNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
680	countNodes[0] = domain->zoom_ni_srv ;
681	}
682
683	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
684	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
685	}
686	else if (domain->nvertex == 2)
687	{
688	if (domain->isEmpty())
689	{
690	startEdges[0]=0 ;
691	countEdges[0]=0 ;
692	startNodes[0]=0 ;
693	countNodes[0]=0 ;
694	startEdgeNodes[0]=0;
695	startEdgeNodes[1]=0;
696	countEdgeNodes[0]=0;
697	countEdgeNodes[1]=0;
698
699	}
700	else
701	{
702	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
703	countEdges[0] = domain->zoom_ni_srv ;
704	startNodes[0] = domain->mesh->node_start;
705	countNodes[0] = domain->mesh->node_count;
706	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
707	startEdgeNodes[1] = 0;
708	countEdgeNodes[0] = domain->zoom_ni_srv;
709	countEdgeNodes[1]= 2;
710	}
711	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
712	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
713	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
714	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
715	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
716	}
717	else
718	{
719	if (domain->isEmpty())
720	{
721	startFaces[0] = 0 ;
722	countFaces[0] = 0 ;
723	startNodes[0] = 0;
724	countNodes[0] = 0;
725	startEdges[0] = 0;
726	countEdges[0] = 0;
727	startEdgeFaces[0] = 0;
728	startEdgeFaces[1] = 0;
729	countEdgeFaces[0] = 0;
730	countEdgeFaces[1] = 0;
731	startFaceConctv[0] = 0;
732	startFaceConctv[1] = 0;
733	countFaceConctv[0] = 0;
734	countFaceConctv[1] = 0;
735	}
736	else
737	{
738	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
739	countFaces[0] = domain->zoom_ni_srv ;
740	startNodes[0] = domain->mesh->node_start;
741	countNodes[0] = domain->mesh->node_count;
742	startEdges[0] = domain->mesh->edge_start;
743	countEdges[0] = domain->mesh->edge_count;
744	startEdgeNodes[0] = domain->mesh->edge_start;
745	startEdgeNodes[1] = 0;
746	countEdgeNodes[0] = domain->mesh->edge_count;
747	countEdgeNodes[1]= 2;
748	startEdgeFaces[0] = domain->mesh->edge_start;
749	startEdgeFaces[1]= 0;
750	countEdgeFaces[0] = domain->mesh->edge_count;
751	countEdgeFaces[1]= 2;
752	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
753	startFaceConctv[1] = 0;
754	countFaceConctv[0] = domain->zoom_ni_srv;
755	countFaceConctv[1] = domain->nvertex;
756	}
757	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
758	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
759	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
760	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
761	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
762	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
763	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
764	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
765	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
766	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
767	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
768	}
769	setWrittenDomain(domid);
770	} // !isWrittenDomain
771	else
772	{
773	if (domain->nvertex == 2)
774	{
775	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
776	countEdges[0] = domain->zoom_ni_srv ;
777	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
778	startEdgeNodes[1] = 0;
779	countEdgeNodes[0] = domain->zoom_ni_srv;
780	countEdgeNodes[1]= 2;
781	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
782	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
783	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
784	}
785	if (domain->nvertex > 2)
786	{
787
788	if (!domain->mesh->edgesAreWritten)
789	{
790	startEdges[0] = domain->mesh->edge_start;
791	countEdges[0] = domain->mesh->edge_count;
792	startEdgeNodes[0] = domain->mesh->edge_start;
793	startEdgeNodes[1] = 0;
794	countEdgeNodes[0] = domain->mesh->edge_count;
795	countEdgeNodes[1]= 2;
796	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
797	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
798	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
799	}
800	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
801	countFaces[0] = domain->zoom_ni_srv;
802	startEdgeFaces[0] = domain->mesh->edge_start;
803	startEdgeFaces[1]= 0;
804	countEdgeFaces[0] = domain->mesh->edge_count;
805	countEdgeFaces[1]= 2;
806	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
807	startFaceConctv[1] = 0;
808	countFaceConctv[0] = domain->zoom_ni_srv;
809	countFaceConctv[1]= domain->nvertex;
810	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
811	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
812	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
813	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
814	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
815	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
816	}
817	}// isWrittenDomain
818
819	SuperClassWriter::definition_start();
820
821	break;
822	} // ONE_FILE
823
824	case (MULTI_FILE) :
825	{
826	break;
827	}
828
829	default :
830	ERROR("CNc4DataOutput::writeDomain(domain)",
831	<< "[ type = " << SuperClass::type << "]"
832	<< " not implemented yet !");
833	} // switch
834	} // try
835
836	catch (CNetCdfException& e)
837	{
838	StdString msg("On writing the domain : ");
839	msg.append(domid); msg.append("\n");
840	msg.append("In the context : ");
841	msg.append(context->getId()); msg.append("\n");
842	msg.append(e.what());
843	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
844	}
845
846	domain->addRelFile(this->filename);
847	}
848
849	//--------------------------------------------------------------
850
851	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
852	{
853	CContext* context = CContext::getCurrent() ;
854	CContextServer* server=context->server ;
855
856	if (domain->IsWritten(this->filename)) return;
857	domain->checkAttributes();
858
859	if (domain->isEmpty())
860	if (SuperClass::type==MULTI_FILE) return ;
861
862	std::vector<StdString> dim0, dim1;
863	StdString domid = domain->getDomainOutputName();
864	if (isWrittenDomain(domid)) return ;
865	else setWrittenDomain(domid);
866
867	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
868
869	StdString dimXid = StdString("cell").append(appendDomid);
870	StdString dimVertId = StdString("nvertex").append(appendDomid);
871
872	string lonid,latid,bounds_lonid,bounds_latid ;
873	string areaId = "area" + appendDomid;
874
875	nc_type typePrec ;
876	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
877	else if (domain->prec==4) typePrec = NC_FLOAT ;
878	else if (domain->prec==8) typePrec = NC_DOUBLE ;
879
880	try
881	{
882	switch (SuperClass::type)
883	{
884	case (MULTI_FILE) :
885	{
886	dim0.push_back(dimXid);
887	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
888
889	lonid = StdString("lon").append(appendDomid);
890	latid = StdString("lat").append(appendDomid);
891	bounds_lonid = StdString("bounds_lon").append(appendDomid);
892	bounds_latid = StdString("bounds_lat").append(appendDomid);
893	if (domain->hasLonLat)
894	{
895	SuperClassWriter::addVariable(latid, typePrec, dim0);
896	SuperClassWriter::addVariable(lonid, typePrec, dim0);
897	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
898	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
899	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
900	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
901	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
902	}
903	dim0.clear();
904	if (domain->hasBounds)
905	{
906	dim0.push_back(dimXid);
907	dim0.push_back(dimVertId);
908	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
909	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
910	}
911
912	dim0.clear();
913	dim0.push_back(dimXid);
914	if (domain->hasArea)
915	{
916	SuperClassWriter::addVariable(areaId, typePrec, dim0);
917	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
918	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
919	}
920
921	SuperClassWriter::definition_end();
922
923	if (domain->hasLonLat)
924	{
925	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
926	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
927	if (domain->hasBounds)
928	{
929	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
930	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
931	}
932	}
933
934	if (domain->hasArea)
935	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
936
937	SuperClassWriter::definition_start();
938	break ;
939	}
940
941	case (ONE_FILE) :
942	{
943	lonid = StdString("lon").append(appendDomid);
944	latid = StdString("lat").append(appendDomid);
945	bounds_lonid = StdString("bounds_lon").append(appendDomid);
946	bounds_latid = StdString("bounds_lat").append(appendDomid);
947	dim0.push_back(dimXid);
948	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
949	if (domain->hasLonLat)
950	{
951	SuperClassWriter::addVariable(latid, typePrec, dim0);
952	SuperClassWriter::addVariable(lonid, typePrec, dim0);
953
954	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
955	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
956	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
957	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
958	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
959	}
960	dim0.clear();
961
962	if (domain->hasBounds)
963	{
964	dim0.push_back(dimXid);
965	dim0.push_back(dimVertId);
966	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
967	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
968	}
969
970	if (domain->hasArea)
971	{
972	dim0.clear();
973	dim0.push_back(dimXid);
974	SuperClassWriter::addVariable(areaId, typePrec, dim0);
975	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
976	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
977	}
978
979	SuperClassWriter::definition_end();
980
981	std::vector<StdSize> start(1), startBounds(2) ;
982	std::vector<StdSize> count(1), countBounds(2) ;
983	if (domain->isEmpty())
984	{
985	start[0]=0 ;
986	count[0]=0 ;
987	startBounds[1]=0 ;
988	countBounds[1]=domain->nvertex ;
989	startBounds[0]=0 ;
990	countBounds[0]=0 ;
991	}
992	else
993	{
994	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
995	count[0]=domain->zoom_ni_srv ;
996	startBounds[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
997	startBounds[1]=0 ;
998	countBounds[0]=domain->zoom_ni_srv ;
999	countBounds[1]=domain->nvertex ;
1000	}
1001
1002	if (domain->hasLonLat)
1003	{
1004	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
1005	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
1006	if (domain->hasBounds)
1007	{
1008	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1009	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1010	}
1011	}
1012
1013	if (domain->hasArea)
1014	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
1015
1016	SuperClassWriter::definition_start();
1017
1018	break;
1019	}
1020	default :
1021	ERROR("CNc4DataOutput::writeDomain(domain)",
1022	<< "[ type = " << SuperClass::type << "]"
1023	<< " not implemented yet !");
1024	}
1025	}
1026	catch (CNetCdfException& e)
1027	{
1028	StdString msg("On writing the domain : ");
1029	msg.append(domid); msg.append("\n");
1030	msg.append("In the context : ");
1031	msg.append(context->getId()); msg.append("\n");
1032	msg.append(e.what());
1033	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1034	}
1035	domain->addRelFile(this->filename);
1036	}
1037	//--------------------------------------------------------------
1038
1039	void CNc4DataOutput::writeAxis_(CAxis* axis)
1040	{
1041	if (axis->IsWritten(this->filename)) return;
1042	axis->checkAttributes();
1043	int zoom_size_srv = axis->zoom_size_srv;
1044	int zoom_begin_srv = axis->zoom_begin_srv;
1045	int zoom_size = (MULTI_FILE == SuperClass::type) ? zoom_size_srv
1046	: axis->global_zoom_size_srv;
1047
1048	if ((0 == zoom_size_srv) && (MULTI_FILE == SuperClass::type)) return;
1049
1050	std::vector<StdString> dims;
1051	StdString axisid = axis->getAxisOutputName();
1052	if (isWrittenAxis(axisid)) return ;
1053	else setWrittenAxis(axisid);
1054
1055	nc_type typePrec ;
1056	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1057	else if (axis->prec==4) typePrec = NC_FLOAT ;
1058	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1059
1060	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
1061	string strId="str_len" ;
1062	try
1063	{
1064	SuperClassWriter::addDimension(axisid, zoom_size);
1065	if (!axis->label.isEmpty()) SuperClassWriter::addDimension(strId, stringArrayLen);
1066	if (axis->hasValue)
1067	{
1068	dims.push_back(axisid);
1069	if (!axis->label.isEmpty()) dims.push_back(strId);
1070	SuperClassWriter::addVariable(axisid, typePrec, dims);
1071
1072	if (!axis->name.isEmpty())
1073	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1074
1075	if (!axis->standard_name.isEmpty())
1076	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1077
1078	if (!axis->long_name.isEmpty())
1079	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1080
1081	if (!axis->unit.isEmpty())
1082	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1083
1084	if (!axis->positive.isEmpty())
1085	{
1086	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1087	SuperClassWriter::addAttribute("positive",
1088	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1089	&axisid);
1090	}
1091
1092	StdString axisBoundsId = axisid + "_bounds";
1093	if (!axis->bounds.isEmpty())
1094	{
1095	dims.push_back("axis_nbounds");
1096	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims);
1097	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1098	}
1099
1100	SuperClassWriter::definition_end();
1101
1102	switch (SuperClass::type)
1103	{
1104	case MULTI_FILE:
1105	{
1106	CArray<double,1> axis_value(zoom_size_srv);
1107	for (int i = 0; i < zoom_size_srv; i++) axis_value(i) = axis->value_srv(i);
1108	if (axis->label.isEmpty()) SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1109
1110	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
1111	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0);
1112
1113	if (! axis->label.isEmpty()) SuperClassWriter::writeData(axis->label_srv, axisid, isCollective, 0);
1114
1115	SuperClassWriter::definition_start();
1116	break;
1117	}
1118	case ONE_FILE:
1119	{
1120	CArray<double,1> axis_value(zoom_size_srv);
1121	axis_value = axis->value_srv;
1122
1123	std::vector<StdSize> start(1), startBounds(2) ;
1124	std::vector<StdSize> count(1), countBounds(2) ;
1125	start[0] = startBounds[0] = zoom_begin_srv-axis->global_zoom_begin_srv;
1126	count[0] = countBounds[0] = zoom_size_srv;
1127	startBounds[1] = 0;
1128	countBounds[1] = 2;
1129	if (axis->label.isEmpty()) SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1130
1131	if (!axis->bounds.isEmpty()&& axis->label.isEmpty())
1132	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1133
1134	if (! axis->label.isEmpty()) SuperClassWriter::writeData(axis->label_srv, axisid, isCollective, 0);
1135
1136	SuperClassWriter::definition_start();
1137
1138	break;
1139	}
1140	default :
1141	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1142	<< "[ type = " << SuperClass::type << "]"
1143	<< " not implemented yet !");
1144	}
1145	}
1146	}
1147	catch (CNetCdfException& e)
1148	{
1149	StdString msg("On writing the axis : ");
1150	msg.append(axisid); msg.append("\n");
1151	msg.append("In the context : ");
1152	CContext* context = CContext::getCurrent() ;
1153	msg.append(context->getId()); msg.append("\n");
1154	msg.append(e.what());
1155	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1156	}
1157	axis->addRelFile(this->filename);
1158	}
1159
1160	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1161	{
1162	if (scalar->IsWritten(this->filename)) return;
1163	scalar->checkAttributes();
1164	int scalarSize = 1;
1165
1166	StdString scalaId = scalar->getScalarOutputName();
1167	if (isWrittenAxis(scalaId)) return ;
1168	else setWrittenAxis(scalaId);
1169
1170	nc_type typePrec ;
1171	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1172	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1173	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1174
1175
1176	try
1177	{
1178	if (!scalar->value.isEmpty())
1179	{
1180	// dims.push_back(scalaId);
1181	std::vector<StdString> dims;
1182	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1183
1184	if (!scalar->name.isEmpty())
1185	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1186
1187	if (!scalar->standard_name.isEmpty())
1188	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1189
1190	if (!scalar->long_name.isEmpty())
1191	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1192
1193	if (!scalar->unit.isEmpty())
1194	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1195
1196	SuperClassWriter::definition_end();
1197
1198	switch (SuperClass::type)
1199	{
1200	case MULTI_FILE:
1201	{
1202	CArray<double,1> scalarValue(scalarSize);
1203	scalarValue(0) = scalar->value;
1204	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1205	SuperClassWriter::definition_start();
1206
1207	break;
1208	}
1209	case ONE_FILE:
1210	{
1211	CArray<double,1> scalarValue(scalarSize);
1212	scalarValue(0) = scalar->value;
1213
1214	std::vector<StdSize> start(1);
1215	std::vector<StdSize> count(1);
1216	start[0] = 0;
1217	count[0] = 1;
1218	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1219	SuperClassWriter::definition_start();
1220
1221	break;
1222	}
1223	default :
1224	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1225	<< "[ type = " << SuperClass::type << "]"
1226	<< " not implemented yet !");
1227	}
1228	}
1229	}
1230	catch (CNetCdfException& e)
1231	{
1232	StdString msg("On writing the scalar : ");
1233	msg.append(scalaId); msg.append("\n");
1234	msg.append("In the context : ");
1235	CContext* context = CContext::getCurrent() ;
1236	msg.append(context->getId()); msg.append("\n");
1237	msg.append(e.what());
1238	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1239	}
1240	scalar->addRelFile(this->filename);
1241	}
1242
1243	//--------------------------------------------------------------
1244
1245	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1246	{
1247	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1248
1249	try
1250	{
1251	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1252	std::vector<StdString> domainList = grid->getDomainList();
1253	std::vector<StdString> axisList = grid->getAxisList();
1254	std::vector<StdString> scalarList = grid->getScalarList();
1255	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1256
1257	std::vector<StdString> dims;
1258
1259	if (grid->isCompressible())
1260	{
1261	StdString varId = grid->getId() + "_points";
1262
1263	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1264	SuperClassWriter::addDimension(varId, nbIndexes);
1265
1266	dims.push_back(varId);
1267	SuperClassWriter::addVariable(varId, NC_INT, dims);
1268
1269	StdOStringStream compress;
1270	for (int i = numElement - 1; i >= 0; --i)
1271	{
1272	if (2 == axisDomainOrder(i))
1273	{
1274	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1275	StdString domId = domain->getDomainOutputName();
1276	StdString appendDomId = singleDomain ? "" : "_" + domId;
1277
1278	switch (domain->type)
1279	{
1280	case CDomain::type_attr::curvilinear:
1281	compress << "y" << appendDomId << " x" << appendDomId;
1282	break;
1283	case CDomain::type_attr::rectilinear:
1284	compress << "lat" << appendDomId << " lon" << appendDomId;
1285	break;
1286	case CDomain::type_attr::unstructured:
1287	compress << "cell" << appendDomId;
1288	break;
1289	}
1290	++idxDomain;
1291	}
1292	else if (1 == axisDomainOrder(i))
1293	{
1294	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1295	compress << axis->getAxisOutputName();
1296	++idxAxis;
1297	}
1298	else
1299	{
1300	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1301	compress << scalar->getScalarOutputName();
1302	++idxScalar;
1303	}
1304
1305	if (i != 0) compress << ' ';
1306	}
1307	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1308
1309	grid->computeCompressedIndex();
1310
1311	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1312	std::map<int, CArray<size_t, 1> >::const_iterator it;
1313	for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
1314	{
1315	const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
1316	for (int i = 0; i < it->second.numElements(); i++)
1317	indexes(compressedIndexes(i)) = it->second(i);
1318	}
1319
1320	switch (SuperClass::type)
1321	{
1322	case (MULTI_FILE):
1323	{
1324	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1325	break;
1326	}
1327	case (ONE_FILE):
1328	{
1329	if (grid->doGridHaveDataDistributed())
1330	grid->getDistributionServer()->computeGlobalIndex(indexes);
1331
1332	std::vector<StdSize> start, count;
1333	start.push_back(grid->getOffsetWrittenIndexes());
1334	count.push_back(grid->getNumberWrittenIndexes());
1335
1336	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1337	break;
1338	}
1339	}
1340	}
1341	else
1342	{
1343	for (int i = 0; i < numElement; ++i)
1344	{
1345	StdString varId, compress;
1346	CArray<int, 1> indexes;
1347	bool isDistributed;
1348	StdSize nbIndexes, totalNbIndexes, offset;
1349	int firstGlobalIndex;
1350
1351	if (2 == axisDomainOrder(i))
1352	{
1353	CDomain* domain = CDomain::get(domainList[idxDomain]);
1354	StdString domId = domain->getDomainOutputName();
1355
1356	if (!domain->isCompressible()
1357	\|\| domain->type == CDomain::type_attr::unstructured
1358	\|\| domain->isWrittenCompressed(this->filename)
1359	\|\| isWrittenCompressedDomain(domId))
1360	continue;
1361
1362	StdString appendDomId = singleDomain ? "" : "_" + domId;
1363
1364	varId = domId + "_points";
1365	switch (domain->type)
1366	{
1367	case CDomain::type_attr::curvilinear:
1368	compress = "y" + appendDomId + " x" + appendDomId;
1369	break;
1370	case CDomain::type_attr::rectilinear:
1371	compress = "lat" + appendDomId + " lon" + appendDomId;
1372	break;
1373	}
1374
1375	const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
1376	indexes.resize(indexesToWrite.size());
1377	for (int n = 0; n < indexes.numElements(); ++n)
1378	indexes(n) = indexesToWrite[n];
1379
1380	isDistributed = domain->isDistributed();
1381	nbIndexes = domain->getNumberWrittenIndexes();
1382	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1383	offset = domain->getOffsetWrittenIndexes();
1384	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1385
1386	domain->addRelFileCompressed(this->filename);
1387	setWrittenCompressedDomain(domId);
1388	++idxDomain;
1389	}
1390	else if (1 == axisDomainOrder(i))
1391	{
1392	CAxis* axis = CAxis::get(axisList[idxAxis]);
1393	StdString axisId = axis->getAxisOutputName();
1394
1395	if (!axis->isCompressible()
1396	\|\| axis->isWrittenCompressed(this->filename)
1397	\|\| isWrittenCompressedAxis(axisId))
1398	continue;
1399
1400	varId = axisId + "_points";
1401	compress = axisId;
1402
1403	const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
1404	indexes.resize(indexesToWrite.size());
1405	for (int n = 0; n < indexes.numElements(); ++n)
1406	indexes(n) = indexesToWrite[n];
1407
1408	isDistributed = axis->isDistributed();
1409	nbIndexes = axis->getNumberWrittenIndexes();
1410	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1411	offset = axis->getOffsetWrittenIndexes();
1412	firstGlobalIndex = axis->begin;
1413
1414	axis->addRelFileCompressed(this->filename);
1415	setWrittenCompressedAxis(axisId);
1416	++idxAxis;
1417	}
1418	else
1419	{
1420	}
1421
1422	if (!varId.empty())
1423	{
1424	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1425
1426	dims.clear();
1427	dims.push_back(varId);
1428	SuperClassWriter::addVariable(varId, NC_INT, dims);
1429
1430	SuperClassWriter::addAttribute("compress", compress, &varId);
1431
1432	switch (SuperClass::type)
1433	{
1434	case (MULTI_FILE):
1435	{
1436	indexes -= firstGlobalIndex;
1437	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1438	break;
1439	}
1440	case (ONE_FILE):
1441	{
1442	std::vector<StdSize> start, count;
1443	start.push_back(offset);
1444	count.push_back(nbIndexes);
1445
1446	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1447	break;
1448	}
1449	}
1450	}
1451	}
1452
1453	if (!dims.empty())
1454	grid->computeCompressedIndex();
1455	}
1456
1457	grid->addRelFileCompressed(this->filename);
1458	}
1459	catch (CNetCdfException& e)
1460	{
1461	StdString msg("On writing compressed grid : ");
1462	msg.append(grid->getId()); msg.append("\n");
1463	msg.append("In the context : ");
1464	CContext* context = CContext::getCurrent();
1465	msg.append(context->getId()); msg.append("\n");
1466	msg.append(e.what());
1467	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1468	}
1469	}
1470
1471	//--------------------------------------------------------------
1472
1473	void CNc4DataOutput::writeTimeDimension_(void)
1474	{
1475	try
1476	{
1477	SuperClassWriter::addDimension(getTimeCounterName());
1478	}
1479	catch (CNetCdfException& e)
1480	{
1481	StdString msg("On writing time dimension : time_couter\n");
1482	msg.append("In the context : ");
1483	CContext* context = CContext::getCurrent() ;
1484	msg.append(context->getId()); msg.append("\n");
1485	msg.append(e.what());
1486	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1487	}
1488	}
1489
1490	//--------------------------------------------------------------
1491
1492	void CNc4DataOutput::writeField_(CField* field)
1493	{
1494	CContext* context = CContext::getCurrent() ;
1495	CContextServer* server=context->server ;
1496
1497	std::vector<StdString> dims, coodinates;
1498	CGrid* grid = field->grid;
1499	if (!grid->doGridHaveDataToWrite())
1500	if (SuperClass::type==MULTI_FILE) return ;
1501
1502	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1503	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1504	std::vector<StdString> domainList = grid->getDomainList();
1505	std::vector<StdString> axisList = grid->getAxisList();
1506	std::vector<StdString> scalarList = grid->getScalarList();
1507
1508	StdString timeid = getTimeCounterName();
1509	StdString dimXid,dimYid;
1510	std::deque<StdString> dimIdList, dimCoordList;
1511	bool hasArea = false;
1512	StdString cellMeasures = "area:";
1513	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1514
1515	for (int i = 0; i < numElement; ++i)
1516	{
1517	if (2 == axisDomainOrder(i))
1518	{
1519	CDomain* domain = CDomain::get(domainList[idxDomain]);
1520	StdString domId = domain->getDomainOutputName();
1521	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1522
1523	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1524	{
1525	dimIdList.push_back(domId + "_points");
1526	field->setUseCompressedOutput();
1527	}
1528
1529	switch (domain->type)
1530	{
1531	case CDomain::type_attr::curvilinear:
1532	if (!compressedOutput \|\| !domain->isCompressible())
1533	{
1534	dimXid = StdString("x").append(appendDomId);
1535	dimIdList.push_back(dimXid);
1536	dimYid = StdString("y").append(appendDomId);
1537	dimIdList.push_back(dimYid);
1538	}
1539	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1540	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1541	break ;
1542	case CDomain::type_attr::rectilinear:
1543	if (!compressedOutput \|\| !domain->isCompressible())
1544	{
1545	dimXid = StdString("lon").append(appendDomId);
1546	dimIdList.push_back(dimXid);
1547	dimYid = StdString("lat").append(appendDomId);
1548	dimIdList.push_back(dimYid);
1549	}
1550	break ;
1551	case CDomain::type_attr::unstructured:
1552	{
1553	if (SuperClassWriter::useCFConvention)
1554	{
1555	dimXid = StdString("cell").append(appendDomId);
1556	dimIdList.push_back(dimXid);
1557	dimCoordList.push_back(StdString("lon").append(appendDomId));
1558	dimCoordList.push_back(StdString("lat").append(appendDomId));
1559	}
1560	else
1561	{
1562	StdString domainName = domain->name;
1563	if (domain->nvertex == 1)
1564	{
1565	dimXid = "n" + domainName + "_node";
1566	dimIdList.push_back(dimXid);
1567	dimCoordList.push_back(StdString(domainName + "_node_x"));
1568	dimCoordList.push_back(StdString(domainName + "_node_y"));
1569	}
1570	else if (domain->nvertex == 2)
1571	{
1572	dimXid = "n" + domainName + "_edge";
1573	dimIdList.push_back(dimXid);
1574	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1575	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1576	}
1577	else
1578	{
1579	dimXid = "n" + domainName + "_face";
1580	dimIdList.push_back(dimXid);
1581	dimCoordList.push_back(StdString(domainName + "_face_x"));
1582	dimCoordList.push_back(StdString(domainName + "_face_y"));
1583	}
1584	} // ugrid convention
1585	} // case unstructured domain
1586	}
1587
1588	if (domain->hasArea)
1589	{
1590	hasArea = true;
1591	cellMeasures += " area" + appendDomId;
1592	}
1593	++idxDomain;
1594	}
1595	else if (1 == axisDomainOrder(i))
1596	{
1597	CAxis* axis = CAxis::get(axisList[idxAxis]);
1598	StdString axisId = axis->getAxisOutputName();
1599
1600	if (compressedOutput && axis->isCompressible())
1601	{
1602	dimIdList.push_back(axisId + "_points");
1603	field->setUseCompressedOutput();
1604	}
1605	else
1606	dimIdList.push_back(axisId);
1607
1608	dimCoordList.push_back(axisId);
1609	++idxAxis;
1610	}
1611	else // scalar
1612	{
1613	/* Do nothing here */
1614	}
1615	}
1616
1617	StdString fieldid = field->getFieldOutputName();
1618
1619	nc_type type ;
1620	if (field->prec.isEmpty()) type = NC_FLOAT ;
1621	else
1622	{
1623	if (field->prec==2) type = NC_SHORT ;
1624	else if (field->prec==4) type = NC_FLOAT ;
1625	else if (field->prec==8) type = NC_DOUBLE ;
1626	}
1627
1628	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1629
1630	if (wtime)
1631	{
1632	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
1633	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
1634	dims.push_back(timeid);
1635	}
1636
1637	if (compressedOutput && grid->isCompressible())
1638	{
1639	dims.push_back(grid->getId() + "_points");
1640	field->setUseCompressedOutput();
1641	}
1642	else
1643	{
1644	while (!dimIdList.empty())
1645	{
1646	dims.push_back(dimIdList.back());
1647	dimIdList.pop_back();
1648	}
1649	}
1650
1651	while (!dimCoordList.empty())
1652	{
1653	coodinates.push_back(dimCoordList.back());
1654	dimCoordList.pop_back();
1655	}
1656
1657	try
1658	{
1659	SuperClassWriter::addVariable(fieldid, type, dims);
1660
1661	if (!field->standard_name.isEmpty())
1662	SuperClassWriter::addAttribute
1663	("standard_name", field->standard_name.getValue(), &fieldid);
1664
1665	if (!field->long_name.isEmpty())
1666	SuperClassWriter::addAttribute
1667	("long_name", field->long_name.getValue(), &fieldid);
1668
1669	if (!field->unit.isEmpty())
1670	SuperClassWriter::addAttribute
1671	("units", field->unit.getValue(), &fieldid);
1672
1673	// Ugrid field attributes "mesh" and "location"
1674	if (!SuperClassWriter::useCFConvention)
1675	{
1676	if (!domainList.empty())
1677	{
1678	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
1679	StdString mesh = domain->name;
1680	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
1681	StdString location;
1682	if (domain->nvertex == 1)
1683	location = "node";
1684	else if (domain->nvertex == 2)
1685	location = "edge";
1686	else if (domain->nvertex > 2)
1687	location = "face";
1688	SuperClassWriter::addAttribute("location", location, &fieldid);
1689	}
1690
1691	}
1692
1693	if (!field->valid_min.isEmpty())
1694	SuperClassWriter::addAttribute
1695	("valid_min", field->valid_min.getValue(), &fieldid);
1696
1697	if (!field->valid_max.isEmpty())
1698	SuperClassWriter::addAttribute
1699	("valid_max", field->valid_max.getValue(), &fieldid);
1700
1701	if (!field->scale_factor.isEmpty())
1702	SuperClassWriter::addAttribute
1703	("scale_factor", field->scale_factor.getValue(), &fieldid);
1704
1705	if (!field->add_offset.isEmpty())
1706	SuperClassWriter::addAttribute
1707	("add_offset", field->add_offset.getValue(), &fieldid);
1708
1709	SuperClassWriter::addAttribute
1710	("online_operation", field->operation.getValue(), &fieldid);
1711
1712	// write child variables as attributes
1713
1714
1715	vector<CVariable*> listVars = field->getAllVariables() ;
1716	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1717
1718	bool alreadyAddCellMethod = false;
1719	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1720	if (!field->cell_methods.isEmpty())
1721	{
1722	StdString cellMethodString = field->cell_methods;
1723	if (field->cell_methods_mode.isEmpty() \|\|
1724	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1725	{
1726	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1727	alreadyAddCellMethod = true;
1728	}
1729	else
1730	{
1731	switch (field->cell_methods_mode)
1732	{
1733	case (CField::cell_methods_mode_attr::prefix):
1734	cellMethodsPrefix = cellMethodString;
1735	cellMethodsPrefix += " ";
1736	break;
1737	case (CField::cell_methods_mode_attr::suffix):
1738	cellMethodsSuffix = " ";
1739	cellMethodsSuffix += cellMethodString;
1740	break;
1741	case (CField::cell_methods_mode_attr::none):
1742	break;
1743	default:
1744	break;
1745	}
1746	}
1747	}
1748
1749
1750	if (wtime)
1751	{
1752	CDuration freqOp = field->freq_op.getValue();
1753	freqOp.solveTimeStep(*context->calendar);
1754	StdString freqOpStr = freqOp.toStringUDUnits();
1755	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1756
1757	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1758	freqOut.solveTimeStep(*context->calendar);
1759	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1760
1761	StdString cellMethods(cellMethodsPrefix + "time: ");
1762	if (field->operation.getValue() == "instant") cellMethods += "point";
1763	else if (field->operation.getValue() == "average") cellMethods += "mean";
1764	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1765	else cellMethods += field->operation;
1766	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1767	cellMethods += " (interval: " + freqOpStr + ")";
1768	cellMethods += cellMethodsSuffix;
1769	if (!alreadyAddCellMethod)
1770	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1771	}
1772
1773	if (hasArea)
1774	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1775
1776	if (!field->default_value.isEmpty())
1777	{
1778	double default_value = field->default_value.getValue();
1779	float fdefault_value = (float)default_value;
1780	if (type == NC_DOUBLE)
1781	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1782	else
1783	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1784	}
1785	else
1786	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1787
1788	if (field->compression_level.isEmpty())
1789	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1790	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1791
1792	{ // Ecriture des coordonnes
1793
1794	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1795	std::vector<StdString>::iterator
1796	itc = coodinates.begin(), endc = coodinates.end();
1797
1798	for (; itc!= endc; itc++)
1799	{
1800	StdString & coord = *itc;
1801	if (itc+1 != endc)
1802	coordstr.append(coord).append(" ");
1803	else coordstr.append(coord);
1804	}
1805
1806	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1807
1808	}
1809	}
1810	catch (CNetCdfException& e)
1811	{
1812	StdString msg("On writing field : ");
1813	msg.append(fieldid); msg.append("\n");
1814	msg.append("In the context : ");
1815	msg.append(context->getId()); msg.append("\n");
1816	msg.append(e.what());
1817	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1818	}
1819	} // writeField_()
1820
1821	//--------------------------------------------------------------
1822
1823	void CNc4DataOutput::writeFile_ (CFile* file)
1824	{
1825	StdString filename = file->getFileOutputName();
1826	StdString description = (!file->description.isEmpty())
1827	? file->description.getValue()
1828	: StdString("Created by xios");
1829
1830	singleDomain = (file->nbDomains == 1);
1831
1832	StdString conv_str ;
1833	if (file->convention_str.isEmpty())
1834	{
1835	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
1836	else conv_str="UGRID" ;
1837	}
1838	else conv_str=file->convention_str ;
1839
1840	try
1841	{
1842	this->writeFileAttributes(filename, description,
1843	conv_str,
1844	StdString("An IPSL model"),
1845	this->getTimeStamp());
1846
1847	if (!appendMode)
1848	SuperClassWriter::addDimension("axis_nbounds", 2);
1849	}
1850	catch (CNetCdfException& e)
1851	{
1852	StdString msg("On writing file : ");
1853	msg.append(filename); msg.append("\n");
1854	msg.append("In the context : ");
1855	CContext* context = CContext::getCurrent() ;
1856	msg.append(context->getId()); msg.append("\n");
1857	msg.append(e.what());
1858	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1859	}
1860	}
1861
1862	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1863	{
1864	StdString name = var->getVariableOutputName();
1865
1866	try
1867	{
1868	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1869	addAttribute(name, var->getData<int>(), &fieldId);
1870	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1871	addAttribute(name, var->getData<short int>(), &fieldId);
1872	else if (var->type.getValue() == CVariable::type_attr::t_float)
1873	addAttribute(name, var->getData<float>(), &fieldId);
1874	else if (var->type.getValue() == CVariable::type_attr::t_double)
1875	addAttribute(name, var->getData<double>(), &fieldId);
1876	else if (var->type.getValue() == CVariable::type_attr::t_string)
1877	addAttribute(name, var->getData<string>(), &fieldId);
1878	else
1879	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1880	<< "Unsupported variable of type " << var->type.getStringValue());
1881	}
1882	catch (CNetCdfException& e)
1883	{
1884	StdString msg("On writing attributes of variable with name : ");
1885	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1886	msg.append("In the context : ");
1887	CContext* context = CContext::getCurrent() ;
1888	msg.append(context->getId()); msg.append("\n");
1889	msg.append(e.what());
1890	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1891	}
1892	}
1893
1894	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1895	{
1896	StdString name = var->getVariableOutputName();
1897
1898	try
1899	{
1900	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1901	addAttribute(name, var->getData<int>());
1902	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1903	addAttribute(name, var->getData<short int>());
1904	else if (var->type.getValue() == CVariable::type_attr::t_float)
1905	addAttribute(name, var->getData<float>());
1906	else if (var->type.getValue() == CVariable::type_attr::t_double)
1907	addAttribute(name, var->getData<double>());
1908	else if (var->type.getValue() == CVariable::type_attr::t_string)
1909	addAttribute(name, var->getData<string>());
1910	else
1911	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1912	<< "Unsupported variable of type " << var->type.getStringValue());
1913	}
1914	catch (CNetCdfException& e)
1915	{
1916	StdString msg("On writing attributes of variable with name : ");
1917	msg.append(name); msg.append("\n");
1918	msg.append("In the context : ");
1919	CContext* context = CContext::getCurrent() ;
1920	msg.append(context->getId()); msg.append("\n");
1921	msg.append(e.what());
1922	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1923	}
1924	}
1925
1926	void CNc4DataOutput::syncFile_ (void)
1927	{
1928	try
1929	{
1930	SuperClassWriter::sync() ;
1931	}
1932	catch (CNetCdfException& e)
1933	{
1934	StdString msg("On synchronizing the write among processes");
1935	msg.append("In the context : ");
1936	CContext* context = CContext::getCurrent() ;
1937	msg.append(context->getId()); msg.append("\n");
1938	msg.append(e.what());
1939	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1940	}
1941	}
1942
1943	void CNc4DataOutput::closeFile_ (void)
1944	{
1945	try
1946	{
1947	SuperClassWriter::close() ;
1948	}
1949	catch (CNetCdfException& e)
1950	{
1951	StdString msg("On closing file");
1952	msg.append("In the context : ");
1953	CContext* context = CContext::getCurrent() ;
1954	msg.append(context->getId()); msg.append("\n");
1955	msg.append(e.what());
1956	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1957	}
1958
1959	}
1960
1961	//---------------------------------------------------------------
1962
1963	StdString CNc4DataOutput::getTimeStamp(void) const
1964	{
1965	const int buffer_size = 100;
1966	time_t rawtime;
1967	struct tm * timeinfo = NULL;
1968	char buffer [buffer_size];
1969	StdString formatStr;
1970	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
1971	else formatStr=file->time_stamp_format;
1972
1973	// time ( &rawtime );
1974	// timeinfo = localtime ( &rawtime );
1975	time ( &rawtime );
1976	timeinfo = gmtime ( &rawtime );
1977	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
1978
1979	return (StdString(buffer));
1980	}
1981
1982	//---------------------------------------------------------------
1983
1984	void CNc4DataOutput::writeFieldData_ (CField* field)
1985	{
1986	CContext* context = CContext::getCurrent();
1987	CContextServer* server = context->server;
1988	CGrid* grid = field->grid;
1989
1990	if (field->getNStep()<1)
1991	{
1992	return;
1993	}
1994
1995	if (!grid->doGridHaveDataToWrite())
1996	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
1997	{
1998	return;
1999	}
2000
2001
2002	StdString fieldid = field->getFieldOutputName();
2003
2004	StdOStringStream oss;
2005	string timeAxisId;
2006	if (field->hasTimeInstant) timeAxisId = "time_instant";
2007	else if (field->hasTimeCentered) timeAxisId = "time_centered";
2008
2009	StdString timeBoundId = getTimeCounterName() + "_bounds";
2010
2011	StdString timeAxisBoundId;
2012	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
2013	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
2014
2015	if (!field->wasWritten())
2016	{
2017	if (appendMode && field->file->record_offset.isEmpty() &&
2018	field->getOperationTimeType() != func::CFunctor::once)
2019	{
2020	double factorUnit;
2021	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2022	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2023	else factorUnit=1 ;
2024	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2025	}
2026
2027	field->setWritten();
2028	}
2029
2030
2031	CArray<double,1> time_data(1);
2032	CArray<double,1> time_data_bound(2);
2033	CArray<double,1> time_counter(1);
2034	CArray<double,1> time_counter_bound(2);
2035
2036	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2037	bool wtimeCounter =false ;
2038	bool wtimeData =false ;
2039
2040
2041	if (wtime)
2042	{
2043
2044	Time lastWrite = field->last_Write_srv;
2045	Time lastLastWrite = field->lastlast_Write_srv;
2046
2047
2048	if (field->hasTimeInstant)
2049	{
2050	time_data(0) = time_data_bound(1) = lastWrite;
2051	time_data_bound(0) = time_data_bound(1) = lastWrite;
2052	if (timeCounterType==instant)
2053	{
2054	time_counter(0) = time_data(0);
2055	time_counter_bound(0) = time_data_bound(0);
2056	time_counter_bound(1) = time_data_bound(1);
2057	wtimeCounter=true ;
2058	}
2059	if (hasTimeInstant) wtimeData=true ;
2060	}
2061	else if (field->hasTimeCentered)
2062	{
2063	time_data(0) = (lastWrite + lastLastWrite) / 2;
2064	time_data_bound(0) = lastLastWrite;
2065	time_data_bound(1) = lastWrite;
2066	if (timeCounterType==centered)
2067	{
2068	time_counter(0) = time_data(0) ;
2069	time_counter_bound(0) = time_data_bound(0) ;
2070	time_counter_bound(1) = time_data_bound(1) ;
2071	wtimeCounter=true ;
2072	}
2073	if (hasTimeCentered) wtimeData=true ;
2074	}
2075
2076	if (timeCounterType==record)
2077	{
2078	time_counter(0) = field->getNStep() - 1;
2079	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2080	wtimeCounter=true ;
2081	}
2082
2083	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2084	{
2085	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2086	time_data/=secByDay;
2087	time_data_bound/=secByDay;
2088	time_counter/=secByDay;
2089	time_counter_bound/=secByDay;
2090	}
2091	}
2092
2093	bool isRoot = (server->intraCommRank == 0);
2094
2095	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2096	{
2097	double scaleFactor = 1.0;
2098	double addOffset = 0.0;
2099	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2100	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2101	field->scaleFactorAddOffset(scaleFactor, addOffset);
2102	}
2103
2104	try
2105	{
2106	size_t writtenSize;
2107	if (field->getUseCompressedOutput())
2108	writtenSize = grid->getNumberWrittenIndexes();
2109	else
2110	writtenSize = grid->getWrittenDataSize();
2111
2112	CArray<double,1> fieldData(writtenSize);
2113	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2114
2115	if (field->getUseCompressedOutput())
2116	field->outputCompressedField(fieldData);
2117	else
2118	field->outputField(fieldData);
2119
2120	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2121
2122	switch (SuperClass::type)
2123	{
2124	case (MULTI_FILE) :
2125	{
2126	CTimer::get("Files : writing data").resume();
2127	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2128	CTimer::get("Files : writing data").suspend();
2129	if (wtime)
2130	{
2131	CTimer::get("Files : writing time axis").resume();
2132	if ( wtimeData)
2133	{
2134	// SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2135	// SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2136	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2137	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2138	}
2139	if (wtimeCounter)
2140	{
2141	// SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2142	// if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2143	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2144	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2145	}
2146	CTimer::get("Files : writing time axis").suspend();
2147	}
2148	break;
2149	}
2150	case (ONE_FILE) :
2151	{
2152	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2153	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2154	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2155
2156	std::vector<StdSize> start, count;
2157
2158	if (field->getUseCompressedOutput())
2159	{
2160	if (grid->isCompressible())
2161	{
2162	start.push_back(grid->getOffsetWrittenIndexes());
2163	count.push_back(grid->getNumberWrittenIndexes());
2164	}
2165	else
2166	{
2167	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2168	std::vector<StdString> domainList = grid->getDomainList();
2169	std::vector<StdString> axisList = grid->getAxisList();
2170	int numElement = axisDomainOrder.numElements();
2171	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2172	int idx = nZoomBeginGlobal.size() - 1;
2173
2174	start.reserve(nZoomBeginGlobal.size());
2175	count.reserve(nZoomBeginGlobal.size());
2176
2177
2178	for (int i = numElement - 1; i >= 0; --i)
2179	{
2180	if (2 == axisDomainOrder(i))
2181	{
2182	CDomain* domain = CDomain::get(domainList[idxDomain]);
2183
2184	if (domain->isCompressible())
2185	{
2186	start.push_back(domain->getOffsetWrittenIndexes());
2187	count.push_back(domain->getNumberWrittenIndexes());
2188	idx -= 2;
2189	}
2190	else
2191	{
2192	if ((domain->type) != CDomain::type_attr::unstructured)
2193	{
2194	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2195	count.push_back(nZoomSizeServer[idx]);
2196	}
2197	--idx;
2198	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2199	count.push_back(nZoomSizeServer[idx]);
2200	--idx;
2201	}
2202	--idxDomain;
2203	}
2204	else if (1 == axisDomainOrder(i))
2205	{
2206	CAxis* axis = CAxis::get(axisList[idxAxis]);
2207
2208	if (axis->isCompressible())
2209	{
2210	start.push_back(axis->getOffsetWrittenIndexes());
2211	count.push_back(axis->getNumberWrittenIndexes());
2212	}
2213	else
2214	{
2215	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2216	count.push_back(nZoomSizeServer[idx]);
2217	}
2218
2219	--idxAxis;
2220	--idx;
2221	}
2222	}
2223	}
2224	}
2225	else
2226	{
2227
2228	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2229	std::vector<StdString> domainList = grid->getDomainList();
2230	std::vector<StdString> axisList = grid->getAxisList();
2231	int numElement = axisDomainOrder.numElements();
2232	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2233	int idx = nZoomBeginGlobal.size() - 1;
2234
2235	start.reserve(nZoomBeginGlobal.size());
2236	count.reserve(nZoomBeginGlobal.size());
2237
2238	for (int i = numElement - 1; i >= 0; --i)
2239	{
2240	if (2 == axisDomainOrder(i))
2241	{
2242	CDomain* domain = CDomain::get(domainList[idxDomain]);
2243	if ((domain->type) != CDomain::type_attr::unstructured)
2244	{
2245	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2246	count.push_back(nZoomSizeServer[idx]);
2247	}
2248	--idx ;
2249	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2250	count.push_back(nZoomSizeServer[idx]);
2251	--idx ;
2252	--idxDomain;
2253	}
2254	else if (1 == axisDomainOrder(i))
2255	{
2256	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2257	count.push_back(nZoomSizeServer[idx]);
2258	--idx;
2259	}
2260	else
2261	{
2262	if (1 == axisDomainOrder.numElements())
2263	{
2264	start.push_back(0);
2265	count.push_back(1);
2266	}
2267	--idx;
2268	}
2269	}
2270	}
2271
2272
2273	CTimer::get("Files : writing data").resume();
2274	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2275	CTimer::get("Files : writing data").suspend();
2276
2277	if (wtime)
2278	{
2279	CTimer::get("Files : writing time axis").resume();
2280	if ( wtimeData)
2281	{
2282	// SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2283	// SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2284	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2285	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2286	}
2287	if (wtimeCounter)
2288	{
2289	// SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2290	// if (timeCounterType!=record) SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2291	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1,isRoot);
2292	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2293
2294	}
2295	CTimer::get("Files : writing time axis").suspend();
2296	}
2297
2298	break;
2299	}
2300	}
2301	}
2302	catch (CNetCdfException& e)
2303	{
2304	StdString msg("On writing field data: ");
2305	msg.append(fieldid); msg.append("\n");
2306	msg.append("In the context : ");
2307	msg.append(context->getId()); msg.append("\n");
2308	msg.append(e.what());
2309	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2310	}
2311	}
2312
2313	//---------------------------------------------------------------
2314
2315	void CNc4DataOutput::writeTimeAxis_
2316	(CField* field,
2317	const boost::shared_ptr<CCalendar> cal)
2318	{
2319	StdOStringStream oss;
2320	bool createInstantAxis=false ;
2321	bool createCenteredAxis=false ;
2322	bool createTimeCounterAxis=false ;
2323
2324	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2325
2326
2327	StdString axisId ;
2328	StdString axisBoundId;
2329	StdString timeid(getTimeCounterName());
2330	StdString timeBoundId("axis_nbounds");
2331
2332	StdString strTimeUnits ;
2333	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2334	else strTimeUnits="seconds since " ;
2335
2336	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
2337	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
2338
2339
2340	if (field->file->time_counter.isEmpty())
2341	{
2342	if (timeCounterType==none) createTimeCounterAxis=true ;
2343	if (field->hasTimeCentered)
2344	{
2345	timeCounterType=centered ;
2346	if (!hasTimeCentered) createCenteredAxis=true ;
2347	}
2348	if (field->hasTimeInstant)
2349	{
2350	if (timeCounterType==none) timeCounterType=instant ;
2351	if (!hasTimeInstant) createInstantAxis=true ;
2352	}
2353	}
2354	else if (field->file->time_counter==CFile::time_counter_attr::instant)
2355	{
2356	if (field->hasTimeCentered)
2357	{
2358	if (!hasTimeCentered) createCenteredAxis=true ;
2359	}
2360	if (field->hasTimeInstant)
2361	{
2362	if (timeCounterType==none) createTimeCounterAxis=true ;
2363	timeCounterType=instant ;
2364	if (!hasTimeInstant) createInstantAxis=true ;
2365	}
2366	}
2367	else if (field->file->time_counter==CFile::time_counter_attr::centered)
2368	{
2369	if (field->hasTimeCentered)
2370	{
2371	if (timeCounterType==none) createTimeCounterAxis=true ;
2372	timeCounterType=centered ;
2373	if (!hasTimeCentered) createCenteredAxis=true ;
2374	}
2375	if (field->hasTimeInstant)
2376	{
2377	if (!hasTimeInstant) createInstantAxis=true ;
2378	}
2379	}
2380	else if (field->file->time_counter==CFile::time_counter_attr::instant_exclusive)
2381	{
2382	if (field->hasTimeCentered)
2383	{
2384	if (!hasTimeCentered) createCenteredAxis=true ;
2385	}
2386	if (field->hasTimeInstant)
2387	{
2388	if (timeCounterType==none) createTimeCounterAxis=true ;
2389	timeCounterType=instant ;
2390	}
2391	}
2392	else if (field->file->time_counter==CFile::time_counter_attr::centered_exclusive)
2393	{
2394	if (field->hasTimeCentered)
2395	{
2396	if (timeCounterType==none) createTimeCounterAxis=true ;
2397	timeCounterType=centered ;
2398	}
2399	if (field->hasTimeInstant)
2400	{
2401	if (!hasTimeInstant) createInstantAxis=true ;
2402	}
2403	}
2404	else if (field->file->time_counter==CFile::time_counter_attr::exclusive)
2405	{
2406	if (field->hasTimeCentered)
2407	{
2408	if (timeCounterType==none) createTimeCounterAxis=true ;
2409	if (timeCounterType==instant) createInstantAxis=true ;
2410	timeCounterType=centered ;
2411	}
2412	if (field->hasTimeInstant)
2413	{
2414	if (timeCounterType==none)
2415	{
2416	createTimeCounterAxis=true ;
2417	timeCounterType=instant ;
2418	}
2419	if (timeCounterType==centered)
2420	{
2421	if (!hasTimeInstant) createInstantAxis=true ;
2422	}
2423	}
2424	}
2425	else if (field->file->time_counter==CFile::time_counter_attr::none)
2426	{
2427	if (field->hasTimeCentered)
2428	{
2429	if (!hasTimeCentered) createCenteredAxis=true ;
2430	}
2431	if (field->hasTimeInstant)
2432	{
2433	if (!hasTimeInstant) createInstantAxis=true ;
2434	}
2435	}
2436	else if (field->file->time_counter==CFile::time_counter_attr::record)
2437	{
2438	if (timeCounterType==none) createTimeCounterAxis=true ;
2439	timeCounterType=record ;
2440	if (field->hasTimeCentered)
2441	{
2442	if (!hasTimeCentered) createCenteredAxis=true ;
2443	}
2444	if (field->hasTimeInstant)
2445	{
2446	if (!hasTimeInstant) createInstantAxis=true ;
2447	}
2448	}
2449
2450	if (createInstantAxis)
2451	{
2452	axisId="time_instant" ;
2453	axisBoundId="time_instant_bounds";
2454	hasTimeInstant=true ;
2455	}
2456
2457	if (createCenteredAxis)
2458	{
2459	axisId="time_centered" ;
2460	axisBoundId="time_centered_bounds";
2461	hasTimeCentered=true ;
2462	}
2463
2464
2465	try
2466	{
2467	std::vector<StdString> dims;
2468
2469	if (createInstantAxis \|\| createCenteredAxis)
2470	{
2471	// Adding time_instant or time_centered
2472	dims.push_back(timeid);
2473	if (!SuperClassWriter::varExist(axisId))
2474	{
2475	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2476
2477	CDate timeOrigin=cal->getTimeOrigin() ;
2478	StdOStringStream oss2;
2479	StdString strInitdate=oss2.str() ;
2480	StdString strTimeOrigin=timeOrigin.toString() ;
2481	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
2482	strTimeOrigin, axisBoundId);
2483	}
2484
2485	// Adding time_instant_bounds or time_centered_bounds variables
2486	if (!SuperClassWriter::varExist(axisBoundId))
2487	{
2488	dims.clear() ;
2489	dims.push_back(timeid);
2490	dims.push_back(timeBoundId);
2491	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2492	}
2493	}
2494
2495	if (createTimeCounterAxis)
2496	{
2497	// Adding time_counter
2498	axisId = getTimeCounterName();
2499	axisBoundId = getTimeCounterName() + "_bounds";
2500	dims.clear();
2501	dims.push_back(timeid);
2502	if (!SuperClassWriter::varExist(axisId))
2503	{
2504	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
2505	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
2506
2507	if (field->file->time_counter.isEmpty() \|\|
2508	(field->file->time_counter != CFile::time_counter_attr::record))
2509	{
2510	CDate timeOrigin = cal->getTimeOrigin();
2511	StdString strTimeOrigin = timeOrigin.toString();
2512
2513	this->writeTimeAxisAttributes(axisId, cal->getType(),
2514	strTimeUnits+strTimeOrigin,
2515	strTimeOrigin, axisBoundId);
2516	}
2517	}
2518
2519	// Adding time_counter_bound dimension
2520	if (field->file->time_counter.isEmpty() \|\| (field->file->time_counter != CFile::time_counter_attr::record))
2521	{
2522	if (!SuperClassWriter::varExist(axisBoundId))
2523	{
2524	dims.clear();
2525	dims.push_back(timeid);
2526	dims.push_back(timeBoundId);
2527	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2528	}
2529	}
2530	}
2531	}
2532	catch (CNetCdfException& e)
2533	{
2534	StdString msg("On writing time axis data: ");
2535	msg.append("In the context : ");
2536	CContext* context = CContext::getCurrent() ;
2537	msg.append(context->getId()); msg.append("\n");
2538	msg.append(e.what());
2539	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2540	const boost::shared_ptr<CCalendar> cal)", << msg);
2541	}
2542	}
2543
2544	//---------------------------------------------------------------
2545
2546	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2547	const StdString & calendar,
2548	const StdString & units,
2549	const StdString & time_origin,
2550	const StdString & time_bounds,
2551	const StdString & standard_name,
2552	const StdString & long_name)
2553	{
2554	try
2555	{
2556	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2557	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2558	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2559	SuperClassWriter::addAttribute("units", units , &axis_name);
2560	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2561	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2562	}
2563	catch (CNetCdfException& e)
2564	{
2565	StdString msg("On writing time axis Attribute: ");
2566	msg.append("In the context : ");
2567	CContext* context = CContext::getCurrent() ;
2568	msg.append(context->getId()); msg.append("\n");
2569	msg.append(e.what());
2570	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2571	const StdString & calendar,\
2572	const StdString & units, \
2573	const StdString & time_origin, \
2574	const StdString & time_bounds, \
2575	const StdString & standard_name, \
2576	const StdString & long_name)", << msg);
2577	}
2578	}
2579
2580	//---------------------------------------------------------------
2581
2582	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2583	const StdString & axis,
2584	const StdString & standard_name,
2585	const StdString & long_name,
2586	const StdString & units,
2587	const StdString & nav_model)
2588	{
2589	try
2590	{
2591	if (!axis.empty())
2592	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2593
2594	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2595	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2596	SuperClassWriter::addAttribute("units" , units , &axis_name);
2597	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2598	}
2599	catch (CNetCdfException& e)
2600	{
2601	StdString msg("On writing Axis Attribute: ");
2602	msg.append("In the context : ");
2603	CContext* context = CContext::getCurrent() ;
2604	msg.append(context->getId()); msg.append("\n");
2605	msg.append(e.what());
2606	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2607	const StdString & axis, \
2608	const StdString & standard_name, \
2609	const StdString & long_name, \
2610	const StdString & units, \
2611	const StdString & nav_model)", << msg);
2612	}
2613	}
2614
2615	//---------------------------------------------------------------
2616
2617	void CNc4DataOutput::writeLocalAttributes
2618	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2619	{
2620	try
2621	{
2622	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2623	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2624	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2625	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2626	}
2627	catch (CNetCdfException& e)
2628	{
2629	StdString msg("On writing Local Attributes: ");
2630	msg.append("In the context : ");
2631	CContext* context = CContext::getCurrent() ;
2632	msg.append(context->getId()); msg.append("\n");
2633	msg.append(e.what());
2634	ERROR("CNc4DataOutput::writeLocalAttributes \
2635	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2636	}
2637
2638	}
2639
2640	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2641	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2642	{
2643	CArray<int,1> array(2) ;
2644
2645	try
2646	{
2647	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2648	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2649	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2650	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2651	array=ni_glo,nj_glo ;
2652	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2653	array=ni,nj ;
2654	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2655	array=ibegin+1,jbegin+1 ;
2656	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2657	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2658	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2659	array=0,0 ;
2660	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2661	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2662	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2663	/*
2664	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2665	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2666	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2667	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2668	*/
2669	}
2670	catch (CNetCdfException& e)
2671	{
2672	StdString msg("On writing Local Attributes IOIPSL \n");
2673	msg.append("In the context : ");
2674	CContext* context = CContext::getCurrent() ;
2675	msg.append(context->getId()); msg.append("\n");
2676	msg.append(e.what());
2677	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2678	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2679	}
2680	}
2681	//---------------------------------------------------------------
2682
2683	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2684	const StdString & description,
2685	const StdString & conventions,
2686	const StdString & production,
2687	const StdString & timeStamp)
2688	{
2689	try
2690	{
2691	SuperClassWriter::addAttribute("name" , name);
2692	SuperClassWriter::addAttribute("description", description);
2693	SuperClassWriter::addAttribute("title" , description);
2694	SuperClassWriter::addAttribute("Conventions", conventions);
2695	// SuperClassWriter::addAttribute("production" , production);
2696
2697	StdString timeStampStr ;
2698	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
2699	else timeStampStr=file->time_stamp_name ;
2700	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
2701
2702	StdString uuidName ;
2703	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
2704	else uuidName=file->uuid_name ;
2705
2706	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
2707	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
2708
2709	}
2710	catch (CNetCdfException& e)
2711	{
2712	StdString msg("On writing File Attributes \n ");
2713	msg.append("In the context : ");
2714	CContext* context = CContext::getCurrent() ;
2715	msg.append(context->getId()); msg.append("\n");
2716	msg.append(e.what());
2717	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2718	const StdString & description, \
2719	const StdString & conventions, \
2720	const StdString & production, \
2721	const StdString & timeStamp)", << msg);
2722	}
2723	}
2724
2725	//---------------------------------------------------------------
2726
2727	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2728	int data_dim,
2729	int data_ni,
2730	int data_nj,
2731	int data_ibegin,
2732	int data_jbegin)
2733	{
2734	try
2735	{
2736	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2737	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2738	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2739	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2740	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2741	}
2742	catch (CNetCdfException& e)
2743	{
2744	StdString msg("On writing Mask Attributes \n ");
2745	msg.append("In the context : ");
2746	CContext* context = CContext::getCurrent() ;
2747	msg.append(context->getId()); msg.append("\n");
2748	msg.append(e.what());
2749	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2750	int data_dim, \
2751	int data_ni, \
2752	int data_nj, \
2753	int data_ibegin, \
2754	int data_jbegin)", << msg);
2755	}
2756	}
2757
2758	///--------------------------------------------------------------
2759
2760	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
2761	{
2762	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2763	if (it == timeToRecordCache.end())
2764	{
2765	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2766	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
2767	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
2768
2769	CArray<double,2> timeAxisBounds;
2770	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
2771
2772	StdSize record = 0;
2773	double dtime(time);
2774	for (int n = dimSize[0] - 1; n >= 0; n--)
2775	{
2776	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
2777	timeAxisBounds*=factorUnit ;
2778	if (timeAxisBounds(1, 0) < dtime)
2779	{
2780	record = n + 1;
2781	break;
2782	}
2783	}
2784	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2785	}
2786	return it->second;
2787	}
2788
2789	///--------------------------------------------------------------
2790
2791	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2792	{
2793	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2794	}
2795
2796	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2797	{
2798	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2799	}
2800
2801	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2802	{
2803	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2804	}
2805
2806	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2807	{
2808	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2809	}
2810
2811	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2812	{
2813	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2814	}
2815
2816	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2817	{
2818	this->writtenDomains.insert(domainName);
2819	}
2820
2821	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2822	{
2823	this->writtenCompressedDomains.insert(domainName);
2824	}
2825
2826	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2827	{
2828	this->writtenAxis.insert(axisName);
2829	}
2830
2831	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2832	{
2833	this->writtenCompressedAxis.insert(axisName);
2834	}
2835
2836	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2837	{
2838	this->writtenScalar.insert(scalarName);
2839	}
2840	} // namespace xios

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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 1169

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