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nc4_data_output.cpp @ 929

Last change on this file since 929 was 929, checked in by oabramkina, 8 years ago

Mesh connectivity:

Fixing a bug for UGRID in case meshes containing cells with different number of vertexes.

Function for determining face neighbors of a local domain added.

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: 111.1 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
14	namespace xios
15	{
16	/// ////////////////////// Dfinitions ////////////////////// ///
17	CNc4DataOutput::CNc4DataOutput
18	(const StdString & filename, bool exist)
19	: SuperClass()
20	, SuperClassWriter(filename, exist)
21	, filename(filename)
22	{
23	SuperClass::type = MULTI_FILE;
24	}
25
26	CNc4DataOutput::CNc4DataOutput
27	(const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
28	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
29	: SuperClass()
30	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
31	, comm_file(comm_file)
32	, filename(filename)
33	, isCollective(isCollective)
34	{
35	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
36	}
37
38	CNc4DataOutput::~CNc4DataOutput(void)
39	{ /* Ne rien faire de plus */ }
40
41	///--------------------------------------------------------------
42
43	const StdString & CNc4DataOutput::getFileName(void) const
44	{
45	return (this->filename);
46	}
47
48	//---------------------------------------------------------------
49
50	void CNc4DataOutput::writeDomain_(CDomain* domain)
51	{
52	if (domain->type == CDomain::type_attr::unstructured)
53	{
54	if (SuperClassWriter::useCFConvention)
55	writeUnstructuredDomain(domain) ;
56	else
57	writeUnstructuredDomainUgrid(domain) ;
58	return ;
59	}
60
61	CContext* context = CContext::getCurrent() ;
62	CContextServer* server=context->server ;
63
64	if (domain->IsWritten(this->filename)) return;
65	domain->checkAttributes();
66
67	if (domain->isEmpty())
68	if (SuperClass::type==MULTI_FILE) return;
69
70	std::vector<StdString> dim0, dim1;
71	StdString domid = domain->getDomainOutputName();
72	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
73	if (isWrittenDomain(domid)) return ;
74	else setWrittenDomain(domid);
75
76
77	StdString dimXid, dimYid ;
78
79	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
80	switch (domain->type)
81	{
82	case CDomain::type_attr::curvilinear :
83	dimXid = StdString("x").append(appendDomid);
84	dimYid = StdString("y").append(appendDomid);
85	break ;
86	case CDomain::type_attr::rectilinear :
87	dimXid = StdString("lon").append(appendDomid);
88	dimYid = StdString("lat").append(appendDomid);
89	break;
90	}
91
92	StdString dimVertId = StdString("nvertex").append(appendDomid);
93
94	string lonid,latid,bounds_lonid,bounds_latid ;
95	string areaId = "area" + appendDomid;
96	/*
97	StdString lonid_loc = (server->intraCommSize > 1)
98	? StdString("lon").append(appendDomid).append("_local")
99	: lonid;
100	StdString latid_loc = (server->intraCommSize > 1)
101	? StdString("lat").append(appendDomid).append("_local")
102	: latid;
103	*/
104
105	try
106	{
107	switch (SuperClass::type)
108	{
109	case (MULTI_FILE) :
110	{
111	// if (domain->isEmpty()) return;
112
113	if (server->intraCommSize > 1)
114	{
115	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
116	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
117	}
118
119	switch (domain->type)
120	{
121	case CDomain::type_attr::curvilinear :
122	dim0.push_back(dimYid); dim0.push_back(dimXid);
123	lonid = StdString("nav_lon").append(appendDomid);
124	latid = StdString("nav_lat").append(appendDomid);
125	break ;
126	case CDomain::type_attr::rectilinear :
127	lonid = StdString("lon").append(appendDomid);
128	latid = StdString("lat").append(appendDomid);
129	dim0.push_back(dimYid);
130	dim1.push_back(dimXid);
131	break;
132	}
133
134	bounds_lonid = StdString("bounds_lon").append(appendDomid);
135	bounds_latid = StdString("bounds_lat").append(appendDomid);
136
137	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
138	SuperClassWriter::addDimension(dimYid, domain->zoom_nj_srv);
139
140	if (domain->hasBounds)
141	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
142
143	if (server->intraCommSize > 1)
144	{
145	this->writeLocalAttributes(domain->zoom_ibegin_srv,
146	domain->zoom_ni_srv,
147	domain->zoom_jbegin_srv,
148	domain->zoom_nj_srv,
149	appendDomid);
150
151	if (singleDomain)
152	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
153	domain->zoom_ibegin_srv,
154	domain->zoom_ni_srv,
155	domain->zoom_jbegin_srv,
156	domain->zoom_nj_srv,
157	domain->ni_glo,domain->nj_glo,
158	server->intraCommRank,server->intraCommSize);
159	}
160
161	if (domain->hasLonLat)
162	{
163	switch (domain->type)
164	{
165	case CDomain::type_attr::curvilinear :
166	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
167	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
168	break ;
169	case CDomain::type_attr::rectilinear :
170	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
171	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
172	break ;
173	}
174
175	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
176	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
177
178	if (domain->hasBounds)
179	{
180	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
181	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
182
183	dim0.clear();
184	dim0.push_back(dimYid);
185	dim0.push_back(dimXid);
186	dim0.push_back(dimVertId);
187	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
188	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
189	}
190	}
191
192	dim0.clear();
193	dim0.push_back(dimYid);
194	dim0.push_back(dimXid);
195
196
197	// supress mask if (server->intraCommSize > 1)
198	// supress mask {
199	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
200	// supress mask
201	// supress mask this->writeMaskAttributes(maskid,
202	// supress mask domain->data_dim.getValue()/*,
203	// supress mask domain->data_ni.getValue(),
204	// supress mask domain->data_nj.getValue(),
205	// supress mask domain->data_ibegin.getValue(),
206	// supress mask domain->data_jbegin.getValue()*/);
207	// supress mask }
208
209	//SuperClassWriter::setDefaultValue(maskid, &dvm);
210
211	if (domain->hasArea)
212	{
213	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
214	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
215	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
216	}
217
218	SuperClassWriter::definition_end();
219
220	if (domain->hasLonLat)
221	{
222	switch (domain->type)
223	{
224	case CDomain::type_attr::curvilinear :
225	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
226	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
227	break;
228	case CDomain::type_attr::rectilinear :
229	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
230	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
231	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
232	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
233	break;
234	}
235
236	if (domain->hasBounds)
237	{
238	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
239	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
240	}
241	}
242
243	if (domain->hasArea)
244	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
245
246	SuperClassWriter::definition_start();
247
248	break;
249	}
250	case (ONE_FILE) :
251	{
252	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
253	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
254
255	if (domain->hasBounds)
256	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
257
258	if (domain->hasLonLat)
259	{
260	switch (domain->type)
261	{
262	case CDomain::type_attr::curvilinear :
263	dim0.push_back(dimYid); dim0.push_back(dimXid);
264	lonid = StdString("nav_lon").append(appendDomid);
265	latid = StdString("nav_lat").append(appendDomid);
266	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
267	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
268	break;
269
270	case CDomain::type_attr::rectilinear :
271	dim0.push_back(dimYid);
272	dim1.push_back(dimXid);
273	lonid = StdString("lon").append(appendDomid);
274	latid = StdString("lat").append(appendDomid);
275	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
276	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
277	break;
278	}
279
280	bounds_lonid = StdString("bounds_lon").append(appendDomid);
281	bounds_latid = StdString("bounds_lat").append(appendDomid);
282
283	this->writeAxisAttributes
284	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
285	this->writeAxisAttributes
286	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
287
288	if (domain->hasBounds)
289	{
290	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
291	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
292
293	dim0.clear();
294	dim0.push_back(dimYid);
295	dim0.push_back(dimXid);
296	dim0.push_back(dimVertId);
297	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
298	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
299	}
300	}
301
302	if (domain->hasArea)
303	{
304	dim0.clear();
305	dim0.push_back(dimYid); dim0.push_back(dimXid);
306	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
307	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
308	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
309	dim0.clear();
310	}
311
312	SuperClassWriter::definition_end();
313
314	switch (domain->type)
315	{
316	case CDomain::type_attr::curvilinear :
317	{
318	std::vector<StdSize> start(2) ;
319	std::vector<StdSize> count(2) ;
320	if (domain->isEmpty())
321	{
322	start[0]=0 ; start[1]=0 ;
323	count[0]=0 ; count[1]=0 ;
324	}
325	else
326	{
327	start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
328	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
329	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
330	}
331
332	if (domain->hasLonLat)
333	{
334	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
335	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
336	}
337	break;
338	}
339	case CDomain::type_attr::rectilinear :
340	{
341	if (domain->hasLonLat)
342	{
343	std::vector<StdSize> start(1) ;
344	std::vector<StdSize> count(1) ;
345	if (domain->isEmpty())
346	{
347	start[0]=0 ;
348	count[0]=0 ;
349	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
350	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
351
352	}
353	else
354	{
355	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
356	count[0]=domain->zoom_nj_srv ;
357	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
358	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
359
360	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
361	count[0]=domain->zoom_ni_srv ;
362	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
363	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
364	}
365	}
366	break;
367	}
368	}
369
370	if (domain->hasBounds)
371	{
372	std::vector<StdSize> start(3);
373	std::vector<StdSize> count(3);
374	if (domain->isEmpty())
375	{
376	start[2] = start[1] = start[0] = 0;
377	count[2] = count[1] = count[0] = 0;
378	}
379	else
380	{
381	start[2] = 0;
382	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
383	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
384	count[2] = domain->nvertex;
385	count[1] = domain->zoom_ni_srv;
386	count[0] = domain->zoom_nj_srv;
387	}
388
389	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0, &start, &count);
390	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0, &start, &count);
391	}
392
393	if (domain->hasArea)
394	{
395	std::vector<StdSize> start(2);
396	std::vector<StdSize> count(2);
397
398	if (domain->isEmpty())
399	{
400	start[0] = 0; start[1] = 0;
401	count[0] = 0; count[1] = 0;
402	}
403	else
404	{
405	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
406	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
407	count[1] = domain->zoom_ni_srv;
408	count[0] = domain->zoom_nj_srv;
409	}
410
411	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
412	}
413
414	SuperClassWriter::definition_start();
415	break;
416	}
417	default :
418	ERROR("CNc4DataOutput::writeDomain(domain)",
419	<< "[ type = " << SuperClass::type << "]"
420	<< " not implemented yet !");
421	}
422	}
423	catch (CNetCdfException& e)
424	{
425	StdString msg("On writing the domain : ");
426	msg.append(domid); msg.append("\n");
427	msg.append("In the context : ");
428	msg.append(context->getId()); msg.append("\n");
429	msg.append(e.what());
430	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
431	}
432
433	domain->addRelFile(this->filename);
434	}
435
436	//--------------------------------------------------------------
437
438	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
439	{
440	CContext* context = CContext::getCurrent() ;
441	CContextServer* server=context->server ;
442
443	if (domain->IsWritten(this->filename)) return;
444	domain->checkAttributes();
445	if (domain->isEmpty())
446	if (SuperClass::type==MULTI_FILE) return ;
447
448	std::vector<StdString> dim0;
449	StdString domid = domain->getDomainOutputName();
450	StdString domainName = domain->name;
451	domain->assignMesh(domainName, domain->nvertex);
452	//domain->mesh->createMesh(domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
453	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
454
455	StdString node_x = domainName + "_node_x";
456	StdString node_y = domainName + "_node_y";
457
458	StdString edge_x = domainName + "_edge_x";
459	StdString edge_y = domainName + "_edge_y";
460	StdString edge_nodes = domainName + "_edge_nodes";
461
462	StdString face_x = domainName + "_face_x";
463	StdString face_y = domainName + "_face_y";
464	StdString face_nodes = domainName + "_face_nodes";
465	StdString face_edges = domainName + "_face_edges";
466	StdString edge_faces = domainName + "_edge_face_links";
467	StdString face_faces = domainName + "_face_links";
468
469	StdString dimNode = "n" + domainName + "_node";
470	StdString dimEdge = "n" + domainName + "_edge";
471	StdString dimFace = "n" + domainName + "_face";
472	StdString dimVertex = "n" + domainName + "_vertex";
473	StdString dimTwo = "Two";
474
475	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
476	if (!isWrittenDomain(domid))
477	{
478	dim0.clear();
479	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
480	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
481	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
482	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
483	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
484	}
485
486	try
487	{
488	switch (SuperClass::type)
489	{
490	case (ONE_FILE) :
491	{
492	// Adding nodes
493	if (domain->nvertex == 1)
494	{
495	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
496	{
497	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
498	dim0.clear();
499	dim0.push_back(dimNode);
500	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
501	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
502	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
503	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
504	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
505	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
506	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
507	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
508	}
509	} // domain->nvertex == 1
510
511	// Adding edges and nodes, if nodes have not been defined previously
512	if (domain->nvertex == 2)
513	{
514	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
515	{
516	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
517	dim0.clear();
518	dim0.push_back(dimNode);
519	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
520	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
521	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
522	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
523	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
524	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
525	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
526	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
527	}
528	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
529	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
530	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
531	dim0.clear();
532	dim0.push_back(dimEdge);
533	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
534	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
535	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
536	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
537	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
538	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
539	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
540	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
541	dim0.clear();
542	dim0.push_back(dimEdge);
543	dim0.push_back(dimTwo);
544	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
545	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
546	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
547	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
548	} // domain->nvertex == 2
549
550	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
551	if (domain->nvertex > 2)
552	{
553	// Nodes
554	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
555	{
556	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
557	dim0.clear();
558	dim0.push_back(dimNode);
559	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
560	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
561	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
562	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
563	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
564	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
565	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
566	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
567	}
568	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
569	{
570	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
571	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
572	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
573	dim0.clear();
574	dim0.push_back(dimEdge);
575	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
576	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
577	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
578	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
579	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
580	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
581	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
582	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
583	dim0.clear();
584	dim0.push_back(dimEdge);
585	dim0.push_back(dimTwo);
586	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
587	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
588	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
589	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
590	}
591	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
592	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
593	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
594	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
595	dim0.clear();
596	dim0.push_back(dimFace);
597	SuperClassWriter::addVariable(face_x, NC_FLOAT, dim0);
598	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
599	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
600	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
601	SuperClassWriter::addVariable(face_y, NC_FLOAT, dim0);
602	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
603	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
604	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
605	dim0.clear();
606	dim0.push_back(dimFace);
607	dim0.push_back(dimVertex);
608	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
609	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
610	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
611	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
612	dim0.clear();
613	dim0.push_back(dimFace);
614	dim0.push_back(dimVertex);
615	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
616	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
617	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
618	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
619	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
620	dim0.clear();
621	dim0.push_back(dimEdge);
622	dim0.push_back(dimTwo);
623	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
624	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
625	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
626	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
627	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
628	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
629	dim0.clear();
630	dim0.push_back(dimFace);
631	dim0.push_back(dimVertex);
632	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
633	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
634	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
635	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
636	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
637	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
638	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
639	} // domain->nvertex > 2
640
641	SuperClassWriter::definition_end();
642
643	std::vector<StdSize> startEdges(1) ;
644	std::vector<StdSize> countEdges(1) ;
645	std::vector<StdSize> startNodes(1) ;
646	std::vector<StdSize> countNodes(1) ;
647	std::vector<StdSize> startFaces(1) ;
648	std::vector<StdSize> countFaces(1) ;
649	std::vector<StdSize> startEdgeNodes(2) ;
650	std::vector<StdSize> countEdgeNodes(2) ;
651	std::vector<StdSize> startEdgeFaces(2) ;
652	std::vector<StdSize> countEdgeFaces(2) ;
653	std::vector<StdSize> startFaceConctv(2) ;
654	std::vector<StdSize> countFaceConctv(2) ;
655
656	if (!isWrittenDomain(domid))
657	{
658	if (domain->nvertex == 1)
659	{
660	if (domain->isEmpty())
661	{
662	startNodes[0]=0 ;
663	countNodes[0]=0 ;
664	}
665	else
666	{
667	startNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
668	countNodes[0] = domain->zoom_ni_srv ;
669	}
670
671	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
672	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
673	}
674	else if (domain->nvertex == 2)
675	{
676	if (domain->isEmpty())
677	{
678	startEdges[0]=0 ;
679	countEdges[0]=0 ;
680	startNodes[0]=0 ;
681	countNodes[0]=0 ;
682	startEdgeNodes[0]=0;
683	startEdgeNodes[1]=0;
684	countEdgeNodes[0]=0;
685	countEdgeNodes[1]=0;
686
687	}
688	else
689	{
690	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
691	countEdges[0] = domain->zoom_ni_srv ;
692	startNodes[0] = domain->mesh->node_start;
693	countNodes[0] = domain->mesh->node_count;
694	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
695	startEdgeNodes[1] = 0;
696	countEdgeNodes[0] = domain->zoom_ni_srv;
697	countEdgeNodes[1]= 2;
698	}
699	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
700	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
701	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
702	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
703	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
704	}
705	else
706	{
707	if (domain->isEmpty())
708	{
709	startFaces[0] = 0 ;
710	countFaces[0] = 0 ;
711	startNodes[0] = 0;
712	countNodes[0] = 0;
713	startEdges[0] = 0;
714	countEdges[0] = 0;
715	startEdgeFaces[0] = 0;
716	startEdgeFaces[1] = 0;
717	countEdgeFaces[0] = 0;
718	countEdgeFaces[1] = 0;
719	startFaceConctv[0] = 0;
720	startFaceConctv[1] = 0;
721	countFaceConctv[0] = 0;
722	countFaceConctv[1] = 0;
723	}
724	else
725	{
726	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
727	countFaces[0] = domain->zoom_ni_srv ;
728	startNodes[0] = domain->mesh->node_start;
729	countNodes[0] = domain->mesh->node_count;
730	startEdges[0] = domain->mesh->edge_start;
731	countEdges[0] = domain->mesh->edge_count;
732	startEdgeNodes[0] = domain->mesh->edge_start;
733	startEdgeNodes[1] = 0;
734	countEdgeNodes[0] = domain->mesh->edge_count;
735	countEdgeNodes[1]= 2;
736	startEdgeFaces[0] = domain->mesh->edge_start;
737	startEdgeFaces[1]= 0;
738	countEdgeFaces[0] = domain->mesh->edge_count;
739	countEdgeFaces[1]= 2;
740	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
741	startFaceConctv[1] = 0;
742	countFaceConctv[0] = domain->zoom_ni_srv;
743	countFaceConctv[1] = domain->nvertex;
744	}
745	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
746	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
747	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
748	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
749	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
750	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
751	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
752	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
753	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
754	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
755	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
756	}
757	setWrittenDomain(domid);
758	} // !isWrittenDomain
759	else
760	{
761	if (domain->nvertex == 2)
762	{
763	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
764	countEdges[0] = domain->zoom_ni_srv ;
765	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
766	startEdgeNodes[1] = 0;
767	countEdgeNodes[0] = domain->zoom_ni_srv;
768	countEdgeNodes[1]= 2;
769	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
770	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
771	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
772	}
773	if (domain->nvertex > 2)
774	{
775
776	if (!domain->mesh->edgesAreWritten)
777	{
778	startEdges[0] = domain->mesh->edge_start;
779	countEdges[0] = domain->mesh->edge_count;
780	startEdgeNodes[0] = domain->mesh->edge_start;
781	startEdgeNodes[1] = 0;
782	countEdgeNodes[0] = domain->mesh->edge_count;
783	countEdgeNodes[1]= 2;
784	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
785	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
786	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
787	}
788	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
789	countFaces[0] = domain->zoom_ni_srv;
790	startEdgeFaces[0] = domain->mesh->edge_start;
791	startEdgeFaces[1]= 0;
792	countEdgeFaces[0] = domain->mesh->edge_count;
793	countEdgeFaces[1]= 2;
794	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
795	startFaceConctv[1] = 0;
796	countFaceConctv[0] = domain->zoom_ni_srv;
797	countFaceConctv[1]= domain->nvertex;
798	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
799	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
800	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
801	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
802	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
803	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
804	}
805	}// isWrittenDomain
806
807	SuperClassWriter::definition_start();
808
809	break;
810	} // ONE_FILE
811
812	case (MULTI_FILE) :
813	{
814	break;
815	}
816
817	default :
818	ERROR("CNc4DataOutput::writeDomain(domain)",
819	<< "[ type = " << SuperClass::type << "]"
820	<< " not implemented yet !");
821	} // switch
822	} // try
823
824	catch (CNetCdfException& e)
825	{
826	StdString msg("On writing the domain : ");
827	msg.append(domid); msg.append("\n");
828	msg.append("In the context : ");
829	msg.append(context->getId()); msg.append("\n");
830	msg.append(e.what());
831	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
832	}
833
834	domain->addRelFile(this->filename);
835	}
836
837	//--------------------------------------------------------------
838
839	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
840	{
841	CContext* context = CContext::getCurrent() ;
842	CContextServer* server=context->server ;
843
844	if (domain->IsWritten(this->filename)) return;
845	domain->checkAttributes();
846
847	if (domain->isEmpty())
848	if (SuperClass::type==MULTI_FILE) return ;
849
850	std::vector<StdString> dim0, dim1;
851	StdString domid = domain->getDomainOutputName();
852	if (isWrittenDomain(domid)) return ;
853	else setWrittenDomain(domid);
854
855	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
856
857	StdString dimXid = StdString("cell").append(appendDomid);
858	StdString dimVertId = StdString("nvertex").append(appendDomid);
859
860	string lonid,latid,bounds_lonid,bounds_latid ;
861	string areaId = "area" + appendDomid;
862
863	try
864	{
865	switch (SuperClass::type)
866	{
867	case (MULTI_FILE) :
868	{
869	dim0.push_back(dimXid);
870	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
871
872	lonid = StdString("lon").append(appendDomid);
873	latid = StdString("lat").append(appendDomid);
874	bounds_lonid = StdString("bounds_lon").append(appendDomid);
875	bounds_latid = StdString("bounds_lat").append(appendDomid);
876	if (domain->hasLonLat)
877	{
878	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
879	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
880	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
881	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
882	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
883	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
884	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
885	}
886	dim0.clear();
887	if (domain->hasBounds)
888	{
889	dim0.push_back(dimXid);
890	dim0.push_back(dimVertId);
891	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
892	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
893	}
894
895	dim0.clear();
896	dim0.push_back(dimXid);
897	if (domain->hasArea)
898	{
899	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
900	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
901	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
902	}
903
904	SuperClassWriter::definition_end();
905
906	if (domain->hasLonLat)
907	{
908	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
909	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
910	if (domain->hasBounds)
911	{
912	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
913	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
914	}
915	}
916
917	if (domain->hasArea)
918	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
919
920	SuperClassWriter::definition_start();
921	break ;
922	}
923
924	case (ONE_FILE) :
925	{
926	lonid = StdString("lon").append(appendDomid);
927	latid = StdString("lat").append(appendDomid);
928	bounds_lonid = StdString("bounds_lon").append(appendDomid);
929	bounds_latid = StdString("bounds_lat").append(appendDomid);
930	dim0.push_back(dimXid);
931	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
932	if (domain->hasLonLat)
933	{
934	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
935	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
936
937	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
938	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
939	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
940	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
941	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
942	}
943	dim0.clear();
944
945	if (domain->hasBounds)
946	{
947	dim0.push_back(dimXid);
948	dim0.push_back(dimVertId);
949	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
950	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
951	}
952
953	if (domain->hasArea)
954	{
955	dim0.clear();
956	dim0.push_back(dimXid);
957	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
958	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
959	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
960	}
961
962	SuperClassWriter::definition_end();
963
964	std::vector<StdSize> start(1), startBounds(2) ;
965	std::vector<StdSize> count(1), countBounds(2) ;
966	if (domain->isEmpty())
967	{
968	start[0]=0 ;
969	count[0]=0 ;
970	startBounds[1]=0 ;
971	countBounds[1]=domain->nvertex ;
972	startBounds[0]=0 ;
973	countBounds[0]=0 ;
974	}
975	else
976	{
977	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
978	count[0]=domain->zoom_ni_srv ;
979	startBounds[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
980	startBounds[1]=0 ;
981	countBounds[0]=domain->zoom_ni_srv ;
982	countBounds[1]=domain->nvertex ;
983	}
984
985	if (domain->hasLonLat)
986	{
987	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
988	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
989	if (domain->hasBounds)
990	{
991	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
992	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0,&startBounds,&countBounds);
993	}
994	}
995
996	if (domain->hasArea)
997	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
998
999	SuperClassWriter::definition_start();
1000
1001	break;
1002	}
1003	default :
1004	ERROR("CNc4DataOutput::writeDomain(domain)",
1005	<< "[ type = " << SuperClass::type << "]"
1006	<< " not implemented yet !");
1007	}
1008	}
1009	catch (CNetCdfException& e)
1010	{
1011	StdString msg("On writing the domain : ");
1012	msg.append(domid); msg.append("\n");
1013	msg.append("In the context : ");
1014	msg.append(context->getId()); msg.append("\n");
1015	msg.append(e.what());
1016	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1017	}
1018	domain->addRelFile(this->filename);
1019	}
1020	//--------------------------------------------------------------
1021
1022	void CNc4DataOutput::writeAxis_(CAxis* axis)
1023	{
1024	if (axis->IsWritten(this->filename)) return;
1025	axis->checkAttributes();
1026	int zoom_size_srv = axis->zoom_size_srv;
1027	int zoom_begin_srv = axis->zoom_begin_srv;
1028	int zoom_size = (MULTI_FILE == SuperClass::type) ? zoom_size_srv
1029	: axis->global_zoom_n;
1030	int zoom_begin = (MULTI_FILE == SuperClass::type) ? zoom_begin_srv
1031	: axis->global_zoom_begin;
1032
1033	if ((0 == zoom_size_srv) && (MULTI_FILE == SuperClass::type)) return;
1034
1035	std::vector<StdString> dims;
1036	StdString axisid = axis->getAxisOutputName();
1037	if (isWrittenAxis(axisid)) return ;
1038	else setWrittenAxis(axisid);
1039
1040	try
1041	{
1042	SuperClassWriter::addDimension(axisid, zoom_size);
1043	if (axis->hasValue)
1044	{
1045	dims.push_back(axisid);
1046	SuperClassWriter::addVariable(axisid, NC_FLOAT, dims);
1047
1048	if (!axis->name.isEmpty())
1049	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1050
1051	if (!axis->standard_name.isEmpty())
1052	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1053
1054	if (!axis->long_name.isEmpty())
1055	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1056
1057	if (!axis->unit.isEmpty())
1058	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1059
1060	if (!axis->positive.isEmpty())
1061	{
1062	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1063	SuperClassWriter::addAttribute("positive",
1064	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1065	&axisid);
1066	}
1067
1068	StdString axisBoundsId = axisid + "_bounds";
1069	if (!axis->bounds.isEmpty())
1070	{
1071	dims.push_back("axis_nbounds");
1072	SuperClassWriter::addVariable(axisBoundsId, NC_FLOAT, dims);
1073	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1074	}
1075
1076	SuperClassWriter::definition_end();
1077
1078	switch (SuperClass::type)
1079	{
1080	case MULTI_FILE:
1081	{
1082	CArray<double,1> axis_value(zoom_size_srv);
1083	for (int i = 0; i < zoom_size_srv; i++) axis_value(i) = axis->value_srv(i);
1084	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1085
1086	if (!axis->bounds.isEmpty())
1087	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0);
1088
1089	SuperClassWriter::definition_start();
1090
1091	break;
1092	}
1093	case ONE_FILE:
1094	{
1095	CArray<double,1> axis_value(zoom_size_srv);
1096	axis_value = axis->value_srv;
1097
1098	std::vector<StdSize> start(1), startBounds(2) ;
1099	std::vector<StdSize> count(1), countBounds(2) ;
1100	start[0] = startBounds[0] = zoom_begin_srv-axis->global_zoom_begin;
1101	count[0] = countBounds[0] = zoom_size_srv;
1102	startBounds[1] = 0;
1103	countBounds[1] = 2;
1104	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1105
1106	if (!axis->bounds.isEmpty())
1107	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1108
1109	SuperClassWriter::definition_start();
1110
1111	break;
1112	}
1113	default :
1114	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1115	<< "[ type = " << SuperClass::type << "]"
1116	<< " not implemented yet !");
1117	}
1118	}
1119	}
1120	catch (CNetCdfException& e)
1121	{
1122	StdString msg("On writing the axis : ");
1123	msg.append(axisid); msg.append("\n");
1124	msg.append("In the context : ");
1125	CContext* context = CContext::getCurrent() ;
1126	msg.append(context->getId()); msg.append("\n");
1127	msg.append(e.what());
1128	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1129	}
1130	axis->addRelFile(this->filename);
1131	}
1132
1133	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1134	{
1135	if (scalar->IsWritten(this->filename)) return;
1136	scalar->checkAttributes();
1137	int scalarSize = 1;
1138
1139	StdString scalaId = scalar->getScalarOutputName();
1140	if (isWrittenAxis(scalaId)) return ;
1141	else setWrittenAxis(scalaId);
1142
1143	try
1144	{
1145	if (!scalar->value.isEmpty())
1146	{
1147	// dims.push_back(scalaId);
1148	std::vector<StdString> dims;
1149	SuperClassWriter::addVariable(scalaId, NC_FLOAT, dims);
1150
1151	if (!scalar->name.isEmpty())
1152	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1153
1154	if (!scalar->standard_name.isEmpty())
1155	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1156
1157	if (!scalar->long_name.isEmpty())
1158	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1159
1160	if (!scalar->unit.isEmpty())
1161	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1162
1163	SuperClassWriter::definition_end();
1164
1165	switch (SuperClass::type)
1166	{
1167	case MULTI_FILE:
1168	{
1169	CArray<double,1> scalarValue(scalarSize);
1170	scalarValue(0) = scalar->value;
1171	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1172	SuperClassWriter::definition_start();
1173
1174	break;
1175	}
1176	case ONE_FILE:
1177	{
1178	CArray<double,1> scalarValue(scalarSize);
1179	scalarValue(0) = scalar->value;
1180
1181	std::vector<StdSize> start(1);
1182	std::vector<StdSize> count(1);
1183	start[0] = 0;
1184	count[0] = 1;
1185	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1186	SuperClassWriter::definition_start();
1187
1188	break;
1189	}
1190	default :
1191	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1192	<< "[ type = " << SuperClass::type << "]"
1193	<< " not implemented yet !");
1194	}
1195	}
1196	}
1197	catch (CNetCdfException& e)
1198	{
1199	StdString msg("On writing the scalar : ");
1200	msg.append(scalaId); msg.append("\n");
1201	msg.append("In the context : ");
1202	CContext* context = CContext::getCurrent() ;
1203	msg.append(context->getId()); msg.append("\n");
1204	msg.append(e.what());
1205	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1206	}
1207	scalar->addRelFile(this->filename);
1208	}
1209
1210	//--------------------------------------------------------------
1211
1212	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1213	{
1214	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1215
1216	try
1217	{
1218	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1219	std::vector<StdString> domainList = grid->getDomainList();
1220	std::vector<StdString> axisList = grid->getAxisList();
1221	std::vector<StdString> scalarList = grid->getScalarList();
1222	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1223
1224	std::vector<StdString> dims;
1225
1226	if (grid->isCompressible())
1227	{
1228	StdString varId = grid->getId() + "_points";
1229
1230	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1231	SuperClassWriter::addDimension(varId, nbIndexes);
1232
1233	dims.push_back(varId);
1234	SuperClassWriter::addVariable(varId, NC_INT, dims);
1235
1236	StdOStringStream compress;
1237	for (int i = numElement - 1; i >= 0; --i)
1238	{
1239	if (2 == axisDomainOrder(i))
1240	{
1241	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1242	StdString domId = domain->getDomainOutputName();
1243	StdString appendDomId = singleDomain ? "" : "_" + domId;
1244
1245	switch (domain->type)
1246	{
1247	case CDomain::type_attr::curvilinear:
1248	compress << "y" << appendDomId << " x" << appendDomId;
1249	break;
1250	case CDomain::type_attr::rectilinear:
1251	compress << "lat" << appendDomId << " lon" << appendDomId;
1252	break;
1253	case CDomain::type_attr::unstructured:
1254	compress << "cell" << appendDomId;
1255	break;
1256	}
1257	++idxDomain;
1258	}
1259	else if (1 == axisDomainOrder(i))
1260	{
1261	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1262	compress << axis->getAxisOutputName();
1263	++idxAxis;
1264	}
1265	else
1266	{
1267	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1268	compress << scalar->getScalarOutputName();
1269	++idxScalar;
1270	}
1271
1272	if (i != 0) compress << ' ';
1273	}
1274	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1275
1276	grid->computeCompressedIndex();
1277
1278	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1279	std::map<int, CArray<size_t, 1> >::const_iterator it;
1280	for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
1281	{
1282	const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
1283	for (int i = 0; i < it->second.numElements(); i++)
1284	indexes(compressedIndexes(i)) = it->second(i);
1285	}
1286
1287	switch (SuperClass::type)
1288	{
1289	case (MULTI_FILE):
1290	{
1291	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1292	break;
1293	}
1294	case (ONE_FILE):
1295	{
1296	if (grid->doGridHaveDataDistributed())
1297	grid->getDistributionServer()->computeGlobalIndex(indexes);
1298
1299	std::vector<StdSize> start, count;
1300	start.push_back(grid->getOffsetWrittenIndexes());
1301	count.push_back(grid->getNumberWrittenIndexes());
1302
1303	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1304	break;
1305	}
1306	}
1307	}
1308	else
1309	{
1310	for (int i = 0; i < numElement; ++i)
1311	{
1312	StdString varId, compress;
1313	CArray<int, 1> indexes;
1314	bool isDistributed;
1315	StdSize nbIndexes, totalNbIndexes, offset;
1316	int firstGlobalIndex;
1317
1318	if (2 == axisDomainOrder(i))
1319	{
1320	CDomain* domain = CDomain::get(domainList[idxDomain]);
1321	StdString domId = domain->getDomainOutputName();
1322
1323	if (!domain->isCompressible()
1324	\|\| domain->type == CDomain::type_attr::unstructured
1325	\|\| domain->isWrittenCompressed(this->filename)
1326	\|\| isWrittenCompressedDomain(domId))
1327	continue;
1328
1329	StdString appendDomId = singleDomain ? "" : "_" + domId;
1330
1331	varId = domId + "_points";
1332	switch (domain->type)
1333	{
1334	case CDomain::type_attr::curvilinear:
1335	compress = "y" + appendDomId + " x" + appendDomId;
1336	break;
1337	case CDomain::type_attr::rectilinear:
1338	compress = "lat" + appendDomId + " lon" + appendDomId;
1339	break;
1340	}
1341
1342	const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
1343	indexes.resize(indexesToWrite.size());
1344	for (int n = 0; n < indexes.numElements(); ++n)
1345	indexes(n) = indexesToWrite[n];
1346
1347	isDistributed = domain->isDistributed();
1348	nbIndexes = domain->getNumberWrittenIndexes();
1349	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1350	offset = domain->getOffsetWrittenIndexes();
1351	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1352
1353	domain->addRelFileCompressed(this->filename);
1354	setWrittenCompressedDomain(domId);
1355	++idxDomain;
1356	}
1357	else if (1 == axisDomainOrder(i))
1358	{
1359	CAxis* axis = CAxis::get(axisList[idxAxis]);
1360	StdString axisId = axis->getAxisOutputName();
1361
1362	if (!axis->isCompressible()
1363	\|\| axis->isWrittenCompressed(this->filename)
1364	\|\| isWrittenCompressedAxis(axisId))
1365	continue;
1366
1367	varId = axisId + "_points";
1368	compress = axisId;
1369
1370	const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
1371	indexes.resize(indexesToWrite.size());
1372	for (int n = 0; n < indexes.numElements(); ++n)
1373	indexes(n) = indexesToWrite[n];
1374
1375	isDistributed = axis->isDistributed();
1376	nbIndexes = axis->getNumberWrittenIndexes();
1377	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1378	offset = axis->getOffsetWrittenIndexes();
1379	firstGlobalIndex = axis->begin;
1380
1381	axis->addRelFileCompressed(this->filename);
1382	setWrittenCompressedAxis(axisId);
1383	++idxAxis;
1384	}
1385	else
1386	{
1387	}
1388
1389	if (!varId.empty())
1390	{
1391	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1392
1393	dims.clear();
1394	dims.push_back(varId);
1395	SuperClassWriter::addVariable(varId, NC_INT, dims);
1396
1397	SuperClassWriter::addAttribute("compress", compress, &varId);
1398
1399	switch (SuperClass::type)
1400	{
1401	case (MULTI_FILE):
1402	{
1403	indexes -= firstGlobalIndex;
1404	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1405	break;
1406	}
1407	case (ONE_FILE):
1408	{
1409	std::vector<StdSize> start, count;
1410	start.push_back(offset);
1411	count.push_back(nbIndexes);
1412
1413	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1414	break;
1415	}
1416	}
1417	}
1418	}
1419
1420	if (!dims.empty())
1421	grid->computeCompressedIndex();
1422	}
1423
1424	grid->addRelFileCompressed(this->filename);
1425	}
1426	catch (CNetCdfException& e)
1427	{
1428	StdString msg("On writing compressed grid : ");
1429	msg.append(grid->getId()); msg.append("\n");
1430	msg.append("In the context : ");
1431	CContext* context = CContext::getCurrent();
1432	msg.append(context->getId()); msg.append("\n");
1433	msg.append(e.what());
1434	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1435	}
1436	}
1437
1438	//--------------------------------------------------------------
1439
1440	void CNc4DataOutput::writeTimeDimension_(void)
1441	{
1442	try
1443	{
1444	SuperClassWriter::addDimension(getTimeCounterName());
1445	}
1446	catch (CNetCdfException& e)
1447	{
1448	StdString msg("On writing time dimension : time_couter\n");
1449	msg.append("In the context : ");
1450	CContext* context = CContext::getCurrent() ;
1451	msg.append(context->getId()); msg.append("\n");
1452	msg.append(e.what());
1453	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1454	}
1455	}
1456
1457	//--------------------------------------------------------------
1458
1459	void CNc4DataOutput::writeField_(CField* field)
1460	{
1461	CContext* context = CContext::getCurrent() ;
1462	CContextServer* server=context->server ;
1463
1464	std::vector<StdString> dims, coodinates;
1465	CGrid* grid = field->grid;
1466	if (!grid->doGridHaveDataToWrite())
1467	if (SuperClass::type==MULTI_FILE) return ;
1468
1469	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1470	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1471	std::vector<StdString> domainList = grid->getDomainList();
1472	std::vector<StdString> axisList = grid->getAxisList();
1473	std::vector<StdString> scalarList = grid->getScalarList();
1474
1475	StdString timeid = getTimeCounterName();
1476	StdString dimXid,dimYid;
1477	std::deque<StdString> dimIdList, dimCoordList;
1478	bool hasArea = false;
1479	StdString cellMeasures = "area:";
1480	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1481
1482	for (int i = 0; i < numElement; ++i)
1483	{
1484	if (2 == axisDomainOrder(i))
1485	{
1486	CDomain* domain = CDomain::get(domainList[idxDomain]);
1487	StdString domId = domain->getDomainOutputName();
1488	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1489
1490	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1491	{
1492	dimIdList.push_back(domId + "_points");
1493	field->setUseCompressedOutput();
1494	}
1495
1496	switch (domain->type)
1497	{
1498	case CDomain::type_attr::curvilinear:
1499	if (!compressedOutput \|\| !domain->isCompressible())
1500	{
1501	dimXid = StdString("x").append(appendDomId);
1502	dimIdList.push_back(dimXid);
1503	dimYid = StdString("y").append(appendDomId);
1504	dimIdList.push_back(dimYid);
1505	}
1506	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1507	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1508	break ;
1509	case CDomain::type_attr::rectilinear:
1510	if (!compressedOutput \|\| !domain->isCompressible())
1511	{
1512	dimXid = StdString("lon").append(appendDomId);
1513	dimIdList.push_back(dimXid);
1514	dimYid = StdString("lat").append(appendDomId);
1515	dimIdList.push_back(dimYid);
1516	}
1517	break ;
1518	case CDomain::type_attr::unstructured:
1519	{
1520	if (SuperClassWriter::useCFConvention)
1521	{
1522	dimXid = StdString("cell").append(appendDomId);
1523	dimIdList.push_back(dimXid);
1524	dimCoordList.push_back(StdString("lon").append(appendDomId));
1525	dimCoordList.push_back(StdString("lat").append(appendDomId));
1526	}
1527	else
1528	{
1529	StdString domainName = domain->name;
1530	if (domain->nvertex == 1)
1531	{
1532	dimXid = "n" + domainName + "_node";
1533	dimIdList.push_back(dimXid);
1534	dimCoordList.push_back(StdString(domainName + "_node_x"));
1535	dimCoordList.push_back(StdString(domainName + "_node_y"));
1536	}
1537	else if (domain->nvertex == 2)
1538	{
1539	dimXid = "n" + domainName + "_edge";
1540	dimIdList.push_back(dimXid);
1541	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1542	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1543	}
1544	else
1545	{
1546	dimXid = "n" + domainName + "_face";
1547	dimIdList.push_back(dimXid);
1548	dimCoordList.push_back(StdString(domainName + "_face_x"));
1549	dimCoordList.push_back(StdString(domainName + "_face_y"));
1550	}
1551	} // ugrid convention
1552	} // case unstructured domain
1553	}
1554
1555	if (domain->hasArea)
1556	{
1557	hasArea = true;
1558	cellMeasures += " area" + appendDomId;
1559	}
1560	++idxDomain;
1561	}
1562	else if (1 == axisDomainOrder(i))
1563	{
1564	CAxis* axis = CAxis::get(axisList[idxAxis]);
1565	StdString axisId = axis->getAxisOutputName();
1566
1567	if (compressedOutput && axis->isCompressible())
1568	{
1569	dimIdList.push_back(axisId + "_points");
1570	field->setUseCompressedOutput();
1571	}
1572	else
1573	dimIdList.push_back(axisId);
1574
1575	dimCoordList.push_back(axisId);
1576	++idxAxis;
1577	}
1578	else // scalar
1579	{
1580	/* Do nothing here */
1581	}
1582	}
1583
1584	/*
1585	StdString lonid_loc = (server->intraCommSize > 1)
1586	? StdString("lon").append(appendDomid).append("_local")
1587	: lonid;
1588	StdString latid_loc = (server->intraCommSize > 1)
1589	? StdString("lat").append(appendDomid).append("_local")
1590	: latid;
1591	*/
1592	StdString fieldid = field->getFieldOutputName();
1593
1594	nc_type type ;
1595	if (field->prec.isEmpty()) type = NC_FLOAT ;
1596	else
1597	{
1598	if (field->prec==2) type = NC_SHORT ;
1599	else if (field->prec==4) type = NC_FLOAT ;
1600	else if (field->prec==8) type = NC_DOUBLE ;
1601	}
1602
1603	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1604
1605	if (wtime)
1606	{
1607
1608	//StdOStringStream oss;
1609	// oss << "time_" << field->operation.getValue()
1610	// << "_" << field->getRelFile()->output_freq.getValue();
1611	//oss
1612	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
1613	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
1614	dims.push_back(timeid);
1615	}
1616
1617	if (compressedOutput && grid->isCompressible())
1618	{
1619	dims.push_back(grid->getId() + "_points");
1620	field->setUseCompressedOutput();
1621	}
1622	else
1623	{
1624	while (!dimIdList.empty())
1625	{
1626	dims.push_back(dimIdList.back());
1627	dimIdList.pop_back();
1628	}
1629	}
1630
1631	while (!dimCoordList.empty())
1632	{
1633	coodinates.push_back(dimCoordList.back());
1634	dimCoordList.pop_back();
1635	}
1636
1637	try
1638	{
1639	SuperClassWriter::addVariable(fieldid, type, dims);
1640
1641	if (!field->standard_name.isEmpty())
1642	SuperClassWriter::addAttribute
1643	("standard_name", field->standard_name.getValue(), &fieldid);
1644
1645	if (!field->long_name.isEmpty())
1646	SuperClassWriter::addAttribute
1647	("long_name", field->long_name.getValue(), &fieldid);
1648
1649	if (!field->unit.isEmpty())
1650	SuperClassWriter::addAttribute
1651	("units", field->unit.getValue(), &fieldid);
1652
1653	if (!field->valid_min.isEmpty())
1654	SuperClassWriter::addAttribute
1655	("valid_min", field->valid_min.getValue(), &fieldid);
1656
1657	if (!field->valid_max.isEmpty())
1658	SuperClassWriter::addAttribute
1659	("valid_max", field->valid_max.getValue(), &fieldid);
1660
1661	if (!field->scale_factor.isEmpty())
1662	SuperClassWriter::addAttribute
1663	("scale_factor", field->scale_factor.getValue(), &fieldid);
1664
1665	if (!field->add_offset.isEmpty())
1666	SuperClassWriter::addAttribute
1667	("add_offset", field->add_offset.getValue(), &fieldid);
1668
1669	SuperClassWriter::addAttribute
1670	("online_operation", field->operation.getValue(), &fieldid);
1671
1672	// write child variables as attributes
1673
1674
1675	vector<CVariable*> listVars = field->getAllVariables() ;
1676	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1677
1678
1679	if (wtime)
1680	{
1681	CDuration freqOp = field->freq_op.getValue();
1682	freqOp.solveTimeStep(*context->calendar);
1683	StdString freqOpStr = freqOp.toStringUDUnits();
1684	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1685
1686	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1687	freqOut.solveTimeStep(*context->calendar);
1688	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1689
1690	StdString cellMethods = "time: ";
1691	if (field->operation.getValue() == "instant") cellMethods += "point";
1692	else if (field->operation.getValue() == "average") cellMethods += "mean";
1693	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1694	else cellMethods += field->operation;
1695	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1696	cellMethods += " (interval: " + freqOpStr + ")";
1697	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1698	}
1699
1700	if (hasArea)
1701	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1702
1703	if (!field->default_value.isEmpty())
1704	{
1705	double default_value = field->default_value.getValue();
1706	float fdefault_value = (float)default_value;
1707	if (type == NC_DOUBLE)
1708	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1709	else
1710	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1711	}
1712	else
1713	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1714
1715	if (field->compression_level.isEmpty())
1716	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1717	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1718
1719	{ // Ecriture des coordonnes
1720
1721	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1722	std::vector<StdString>::iterator
1723	itc = coodinates.begin(), endc = coodinates.end();
1724
1725	for (; itc!= endc; itc++)
1726	{
1727	StdString & coord = *itc;
1728	if (itc+1 != endc)
1729	coordstr.append(coord).append(" ");
1730	else coordstr.append(coord);
1731	}
1732
1733	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1734
1735	}
1736	}
1737	catch (CNetCdfException& e)
1738	{
1739	StdString msg("On writing field : ");
1740	msg.append(fieldid); msg.append("\n");
1741	msg.append("In the context : ");
1742	msg.append(context->getId()); msg.append("\n");
1743	msg.append(e.what());
1744	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1745	}
1746	} // writeField_()
1747
1748	//--------------------------------------------------------------
1749
1750	void CNc4DataOutput::writeFile_ (CFile* file)
1751	{
1752	StdString filename = file->getFileOutputName();
1753	StdString description = (!file->description.isEmpty())
1754	? file->description.getValue()
1755	: StdString("Created by xios");
1756
1757	singleDomain = (file->nbDomains == 1);
1758
1759	try
1760	{
1761	if (SuperClassWriter::useCFConvention)
1762	this->writeFileAttributes(filename, description,
1763	StdString("CF-1.5"),
1764	StdString("An IPSL model"),
1765	this->getTimeStamp());
1766	else
1767	this->writeFileAttributes(filename, description,
1768	StdString("UGRID"),
1769	StdString("An IPSL model"),
1770	this->getTimeStamp());
1771
1772
1773	if (!appendMode)
1774	SuperClassWriter::addDimension("axis_nbounds", 2);
1775	}
1776	catch (CNetCdfException& e)
1777	{
1778	StdString msg("On writing file : ");
1779	msg.append(filename); msg.append("\n");
1780	msg.append("In the context : ");
1781	CContext* context = CContext::getCurrent() ;
1782	msg.append(context->getId()); msg.append("\n");
1783	msg.append(e.what());
1784	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1785	}
1786	}
1787
1788	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1789	{
1790	StdString name = var->getVariableOutputName();
1791
1792	try
1793	{
1794	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1795	addAttribute(name, var->getData<int>(), &fieldId);
1796	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1797	addAttribute(name, var->getData<short int>(), &fieldId);
1798	else if (var->type.getValue() == CVariable::type_attr::t_float)
1799	addAttribute(name, var->getData<float>(), &fieldId);
1800	else if (var->type.getValue() == CVariable::type_attr::t_double)
1801	addAttribute(name, var->getData<double>(), &fieldId);
1802	else if (var->type.getValue() == CVariable::type_attr::t_string)
1803	addAttribute(name, var->getData<string>(), &fieldId);
1804	else
1805	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1806	<< "Unsupported variable of type " << var->type.getStringValue());
1807	}
1808	catch (CNetCdfException& e)
1809	{
1810	StdString msg("On writing attributes of variable with name : ");
1811	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1812	msg.append("In the context : ");
1813	CContext* context = CContext::getCurrent() ;
1814	msg.append(context->getId()); msg.append("\n");
1815	msg.append(e.what());
1816	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1817	}
1818	}
1819
1820	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1821	{
1822	StdString name = var->getVariableOutputName();
1823
1824	try
1825	{
1826	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1827	addAttribute(name, var->getData<int>());
1828	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1829	addAttribute(name, var->getData<short int>());
1830	else if (var->type.getValue() == CVariable::type_attr::t_float)
1831	addAttribute(name, var->getData<float>());
1832	else if (var->type.getValue() == CVariable::type_attr::t_double)
1833	addAttribute(name, var->getData<double>());
1834	else if (var->type.getValue() == CVariable::type_attr::t_string)
1835	addAttribute(name, var->getData<string>());
1836	else
1837	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1838	<< "Unsupported variable of type " << var->type.getStringValue());
1839	}
1840	catch (CNetCdfException& e)
1841	{
1842	StdString msg("On writing attributes of variable with name : ");
1843	msg.append(name); msg.append("\n");
1844	msg.append("In the context : ");
1845	CContext* context = CContext::getCurrent() ;
1846	msg.append(context->getId()); msg.append("\n");
1847	msg.append(e.what());
1848	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1849	}
1850	}
1851
1852	void CNc4DataOutput::syncFile_ (void)
1853	{
1854	try
1855	{
1856	SuperClassWriter::sync() ;
1857	}
1858	catch (CNetCdfException& e)
1859	{
1860	StdString msg("On synchronizing the write among processes");
1861	msg.append("In the context : ");
1862	CContext* context = CContext::getCurrent() ;
1863	msg.append(context->getId()); msg.append("\n");
1864	msg.append(e.what());
1865	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1866	}
1867	}
1868
1869	void CNc4DataOutput::closeFile_ (void)
1870	{
1871	try
1872	{
1873	SuperClassWriter::close() ;
1874	}
1875	catch (CNetCdfException& e)
1876	{
1877	StdString msg("On closing file");
1878	msg.append("In the context : ");
1879	CContext* context = CContext::getCurrent() ;
1880	msg.append(context->getId()); msg.append("\n");
1881	msg.append(e.what());
1882	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1883	}
1884
1885	}
1886
1887	//---------------------------------------------------------------
1888
1889	StdString CNc4DataOutput::getTimeStamp(void) const
1890	{
1891	const int buffer_size = 100;
1892	time_t rawtime;
1893	struct tm * timeinfo = NULL;
1894	char buffer [buffer_size];
1895
1896	time ( &rawtime );
1897	timeinfo = localtime ( &rawtime );
1898	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
1899
1900	return (StdString(buffer));
1901	}
1902
1903	//---------------------------------------------------------------
1904
1905	void CNc4DataOutput::writeFieldData_ (CField* field)
1906	{
1907	CContext* context = CContext::getCurrent();
1908	CContextServer* server = context->server;
1909	CGrid* grid = field->grid;
1910
1911	if (!grid->doGridHaveDataToWrite())
1912	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
1913
1914	StdString fieldid = field->getFieldOutputName();
1915
1916	StdOStringStream oss;
1917	string timeAxisId;
1918	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
1919	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
1920
1921	StdString timeBoundId = getTimeCounterName() + "_bounds";
1922
1923	StdString timeAxisBoundId;
1924	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
1925	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
1926
1927	if (!field->wasWritten())
1928	{
1929	if (appendMode && field->file->record_offset.isEmpty())
1930	{
1931	field->resetNStep(getRecordFromTime(field->last_Write_srv) + 1);
1932	}
1933
1934	field->setWritten();
1935	}
1936
1937
1938	CArray<double,1> time_data(1);
1939	CArray<double,1> time_data_bound(2);
1940	CArray<double,1> time_counter(1);
1941	CArray<double,1> time_counter_bound(2);
1942
1943	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
1944
1945	if (wtime)
1946	{
1947	Time lastWrite = field->last_Write_srv;
1948	Time lastLastWrite = field->lastlast_Write_srv;
1949
1950	if (field->getOperationTimeType() == func::CFunctor::instant)
1951	time_data(0) = lastWrite;
1952	else if (field->getOperationTimeType() == func::CFunctor::centered)
1953	time_data(0) = (lastWrite + lastLastWrite) / 2;
1954
1955	if (field->getOperationTimeType() == func::CFunctor::instant)
1956	time_data_bound(0) = time_data_bound(1) = lastWrite;
1957	else if (field->getOperationTimeType() == func::CFunctor::centered)
1958	{
1959	time_data_bound(0) = lastLastWrite;
1960	time_data_bound(1) = lastWrite;
1961	}
1962
1963	if (field->file->time_counter == CFile::time_counter_attr::instant)
1964	time_counter(0) = lastWrite;
1965	else if (field->file->time_counter == CFile::time_counter_attr::centered)
1966	time_counter(0) = (lastWrite + lastLastWrite) / 2;
1967	else if (field->file->time_counter == CFile::time_counter_attr::record)
1968	time_counter(0) = field->getNStep() - 1;
1969
1970
1971	if (field->file->time_counter == CFile::time_counter_attr::instant)
1972	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
1973	else if (field->file->time_counter == CFile::time_counter_attr::centered)
1974	{
1975	time_counter_bound(0) = lastLastWrite;
1976	time_counter_bound(1) = lastWrite;
1977	}
1978	else if (field->file->time_counter == CFile::time_counter_attr::record)
1979	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
1980	}
1981
1982	bool isRoot = (server->intraCommRank == 0);
1983
1984	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
1985	{
1986	double scaleFactor = 1.0;
1987	double addOffset = 0.0;
1988	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
1989	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
1990	field->scaleFactorAddOffset(scaleFactor, addOffset);
1991	}
1992
1993	try
1994	{
1995	size_t writtenSize;
1996	if (field->getUseCompressedOutput())
1997	writtenSize = grid->getNumberWrittenIndexes();
1998	else
1999	writtenSize = grid->getWrittenDataSize();
2000
2001	CArray<double,1> fieldData(writtenSize);
2002	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2003
2004	if (field->getUseCompressedOutput())
2005	field->outputCompressedField(fieldData);
2006	else
2007	field->outputField(fieldData);
2008
2009	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2010
2011	switch (SuperClass::type)
2012	{
2013	case (MULTI_FILE) :
2014	{
2015	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2016	if (wtime)
2017	{
2018	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2019	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2020	if (field->file->time_counter != CFile::time_counter_attr::none)
2021	{
2022	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2023	if (field->file->time_counter != CFile::time_counter_attr::record)
2024	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2025	}
2026	}
2027	break;
2028	}
2029	case (ONE_FILE) :
2030	{
2031	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2032	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2033	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2034
2035	std::vector<StdSize> start, count;
2036
2037	if (field->getUseCompressedOutput())
2038	{
2039	if (grid->isCompressible())
2040	{
2041	start.push_back(grid->getOffsetWrittenIndexes());
2042	count.push_back(grid->getNumberWrittenIndexes());
2043	}
2044	else
2045	{
2046	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2047	std::vector<StdString> domainList = grid->getDomainList();
2048	std::vector<StdString> axisList = grid->getAxisList();
2049	int numElement = axisDomainOrder.numElements();
2050	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2051	int idx = nZoomBeginGlobal.size() - 1;
2052
2053	start.reserve(nZoomBeginGlobal.size());
2054	count.reserve(nZoomBeginGlobal.size());
2055
2056
2057	for (int i = numElement - 1; i >= 0; --i)
2058	{
2059	if (2 == axisDomainOrder(i))
2060	{
2061	CDomain* domain = CDomain::get(domainList[idxDomain]);
2062
2063	if (domain->isCompressible())
2064	{
2065	start.push_back(domain->getOffsetWrittenIndexes());
2066	count.push_back(domain->getNumberWrittenIndexes());
2067	idx -= 2;
2068	}
2069	else
2070	{
2071	if ((domain->type) != CDomain::type_attr::unstructured)
2072	{
2073	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2074	count.push_back(nZoomSizeServer[idx]);
2075	}
2076	--idx;
2077	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2078	count.push_back(nZoomSizeServer[idx]);
2079	--idx;
2080	}
2081	--idxDomain;
2082	}
2083	else if (1 == axisDomainOrder(i))
2084	{
2085	CAxis* axis = CAxis::get(axisList[idxAxis]);
2086
2087	if (axis->isCompressible())
2088	{
2089	start.push_back(axis->getOffsetWrittenIndexes());
2090	count.push_back(axis->getNumberWrittenIndexes());
2091	}
2092	else
2093	{
2094	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2095	count.push_back(nZoomSizeServer[idx]);
2096	}
2097
2098	--idxAxis;
2099	--idx;
2100	}
2101	}
2102	}
2103	}
2104	else
2105	{
2106
2107	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2108	std::vector<StdString> domainList = grid->getDomainList();
2109	std::vector<StdString> axisList = grid->getAxisList();
2110	int numElement = axisDomainOrder.numElements();
2111	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2112	int idx = nZoomBeginGlobal.size() - 1;
2113
2114	start.reserve(nZoomBeginGlobal.size());
2115	count.reserve(nZoomBeginGlobal.size());
2116
2117	for (int i = numElement - 1; i >= 0; --i)
2118	{
2119	if (2 == axisDomainOrder(i))
2120	{
2121	CDomain* domain = CDomain::get(domainList[idxDomain]);
2122	if ((domain->type) != CDomain::type_attr::unstructured)
2123	{
2124	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2125	count.push_back(nZoomSizeServer[idx]);
2126	}
2127	--idx ;
2128	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2129	count.push_back(nZoomSizeServer[idx]);
2130	--idx ;
2131	--idxDomain;
2132	}
2133	else if (1 == axisDomainOrder(i))
2134	{
2135	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2136	count.push_back(nZoomSizeServer[idx]);
2137	--idx;
2138	}
2139	else
2140	{
2141	if (1 == axisDomainOrder.numElements())
2142	{
2143	start.push_back(0);
2144	count.push_back(1);
2145	}
2146	--idx;
2147	}
2148	}
2149	}
2150
2151	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2152	if (wtime)
2153	{
2154	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2155	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2156	if (field->file->time_counter != CFile::time_counter_attr::none)
2157	{
2158	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
2159	if (field->file->time_counter != CFile::time_counter_attr::record)
2160	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2161	}
2162	}
2163
2164	break;
2165	}
2166	}
2167	}
2168	catch (CNetCdfException& e)
2169	{
2170	StdString msg("On writing field data: ");
2171	msg.append(fieldid); msg.append("\n");
2172	msg.append("In the context : ");
2173	msg.append(context->getId()); msg.append("\n");
2174	msg.append(e.what());
2175	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2176	}
2177	}
2178
2179	//---------------------------------------------------------------
2180
2181	void CNc4DataOutput::writeTimeAxis_
2182	(CField* field,
2183	const boost::shared_ptr<CCalendar> cal)
2184	{
2185	StdOStringStream oss;
2186
2187	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2188
2189	// oss << "time_" << field->operation.getValue()
2190	// << "_" << field->getRelFile()->output_freq.getValue();
2191
2192	// StdString axisid = oss.str();
2193	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
2194	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
2195
2196	StdString axisid("time_centered") ;
2197	StdString axisBoundId("time_centered_bounds");
2198	StdString timeid(getTimeCounterName());
2199	StdString timeBoundId("axis_nbounds");
2200
2201	if (field->getOperationTimeType() == func::CFunctor::instant)
2202	{
2203	axisid = "time_instant";
2204	axisBoundId = "time_instant_bounds";
2205	}
2206
2207	try
2208	{
2209	// Adding time_instant or time_centered
2210	std::vector<StdString> dims;
2211	dims.push_back(timeid);
2212	if (!SuperClassWriter::varExist(axisid))
2213	{
2214	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2215
2216	CDate timeOrigin=cal->getTimeOrigin() ;
2217	StdOStringStream oss2;
2218	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
2219	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
2220	StdString strInitdate=oss2.str() ;
2221	StdString strTimeOrigin=timeOrigin.toString() ;
2222	this->writeTimeAxisAttributes
2223	(axisid, cal->getType(),
2224	StdString("seconds since ").append(strTimeOrigin),
2225	strTimeOrigin, axisBoundId);
2226	}
2227
2228	// Adding time_instant_bounds or time_centered_bounds variables
2229	if (!SuperClassWriter::varExist(axisBoundId))
2230	{
2231	dims.clear() ;
2232	dims.push_back(timeid);
2233	dims.push_back(timeBoundId);
2234	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2235	}
2236
2237	if (field->file->time_counter != CFile::time_counter_attr::none)
2238	{
2239	// Adding time_counter
2240	axisid = getTimeCounterName();
2241	axisBoundId = getTimeCounterName() + "_bounds";
2242	dims.clear();
2243	dims.push_back(timeid);
2244	if (!SuperClassWriter::varExist(axisid))
2245	{
2246	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2247	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
2248
2249	if (field->file->time_counter != CFile::time_counter_attr::record)
2250	{
2251	CDate timeOrigin = cal->getTimeOrigin();
2252	StdString strTimeOrigin = timeOrigin.toString();
2253
2254	this->writeTimeAxisAttributes(axisid, cal->getType(),
2255	StdString("seconds since ").append(strTimeOrigin),
2256	strTimeOrigin, axisBoundId);
2257	}
2258	}
2259
2260	// Adding time_counter_bound dimension
2261	if (field->file->time_counter != CFile::time_counter_attr::record)
2262	{
2263	if (!SuperClassWriter::varExist(axisBoundId))
2264	{
2265	dims.clear();
2266	dims.push_back(timeid);
2267	dims.push_back(timeBoundId);
2268	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2269	}
2270	}
2271	}
2272	}
2273	catch (CNetCdfException& e)
2274	{
2275	StdString msg("On writing time axis data: ");
2276	msg.append("In the context : ");
2277	CContext* context = CContext::getCurrent() ;
2278	msg.append(context->getId()); msg.append("\n");
2279	msg.append(e.what());
2280	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2281	const boost::shared_ptr<CCalendar> cal)", << msg);
2282	}
2283	}
2284
2285	//---------------------------------------------------------------
2286
2287	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2288	const StdString & calendar,
2289	const StdString & units,
2290	const StdString & time_origin,
2291	const StdString & time_bounds,
2292	const StdString & standard_name,
2293	const StdString & long_name)
2294	{
2295	try
2296	{
2297	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2298	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2299	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2300	SuperClassWriter::addAttribute("units", units , &axis_name);
2301	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2302	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2303	}
2304	catch (CNetCdfException& e)
2305	{
2306	StdString msg("On writing time axis Attribute: ");
2307	msg.append("In the context : ");
2308	CContext* context = CContext::getCurrent() ;
2309	msg.append(context->getId()); msg.append("\n");
2310	msg.append(e.what());
2311	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2312	const StdString & calendar,\
2313	const StdString & units, \
2314	const StdString & time_origin, \
2315	const StdString & time_bounds, \
2316	const StdString & standard_name, \
2317	const StdString & long_name)", << msg);
2318	}
2319	}
2320
2321	//---------------------------------------------------------------
2322
2323	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2324	const StdString & axis,
2325	const StdString & standard_name,
2326	const StdString & long_name,
2327	const StdString & units,
2328	const StdString & nav_model)
2329	{
2330	try
2331	{
2332	if (!axis.empty())
2333	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2334
2335	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2336	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2337	SuperClassWriter::addAttribute("units" , units , &axis_name);
2338	SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2339	}
2340	catch (CNetCdfException& e)
2341	{
2342	StdString msg("On writing Axis Attribute: ");
2343	msg.append("In the context : ");
2344	CContext* context = CContext::getCurrent() ;
2345	msg.append(context->getId()); msg.append("\n");
2346	msg.append(e.what());
2347	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2348	const StdString & axis, \
2349	const StdString & standard_name, \
2350	const StdString & long_name, \
2351	const StdString & units, \
2352	const StdString & nav_model)", << msg);
2353	}
2354	}
2355
2356	//---------------------------------------------------------------
2357
2358	void CNc4DataOutput::writeLocalAttributes
2359	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2360	{
2361	try
2362	{
2363	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2364	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2365	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2366	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2367	}
2368	catch (CNetCdfException& e)
2369	{
2370	StdString msg("On writing Local Attributes: ");
2371	msg.append("In the context : ");
2372	CContext* context = CContext::getCurrent() ;
2373	msg.append(context->getId()); msg.append("\n");
2374	msg.append(e.what());
2375	ERROR("CNc4DataOutput::writeLocalAttributes \
2376	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2377	}
2378
2379	}
2380
2381	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2382	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2383	{
2384	CArray<int,1> array(2) ;
2385
2386	try
2387	{
2388	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2389	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2390	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2391	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2392	array=ni_glo,nj_glo ;
2393	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2394	array=ni,nj ;
2395	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2396	array=ibegin+1,jbegin+1 ;
2397	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2398	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2399	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2400	array=0,0 ;
2401	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2402	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2403	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2404	/*
2405	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2406	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2407	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2408	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2409	*/
2410	}
2411	catch (CNetCdfException& e)
2412	{
2413	StdString msg("On writing Local Attributes IOIPSL \n");
2414	msg.append("In the context : ");
2415	CContext* context = CContext::getCurrent() ;
2416	msg.append(context->getId()); msg.append("\n");
2417	msg.append(e.what());
2418	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2419	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2420	}
2421	}
2422	//---------------------------------------------------------------
2423
2424	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2425	const StdString & description,
2426	const StdString & conventions,
2427	const StdString & production,
2428	const StdString & timeStamp)
2429	{
2430	try
2431	{
2432	SuperClassWriter::addAttribute("name" , name);
2433	SuperClassWriter::addAttribute("description", description);
2434	SuperClassWriter::addAttribute("title" , description);
2435	SuperClassWriter::addAttribute("Conventions", conventions);
2436	SuperClassWriter::addAttribute("production" , production);
2437	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
2438	}
2439	catch (CNetCdfException& e)
2440	{
2441	StdString msg("On writing File Attributes \n ");
2442	msg.append("In the context : ");
2443	CContext* context = CContext::getCurrent() ;
2444	msg.append(context->getId()); msg.append("\n");
2445	msg.append(e.what());
2446	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2447	const StdString & description, \
2448	const StdString & conventions, \
2449	const StdString & production, \
2450	const StdString & timeStamp)", << msg);
2451	}
2452	}
2453
2454	//---------------------------------------------------------------
2455
2456	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2457	int data_dim,
2458	int data_ni,
2459	int data_nj,
2460	int data_ibegin,
2461	int data_jbegin)
2462	{
2463	try
2464	{
2465	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2466	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2467	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2468	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2469	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2470	}
2471	catch (CNetCdfException& e)
2472	{
2473	StdString msg("On writing Mask Attributes \n ");
2474	msg.append("In the context : ");
2475	CContext* context = CContext::getCurrent() ;
2476	msg.append(context->getId()); msg.append("\n");
2477	msg.append(e.what());
2478	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2479	int data_dim, \
2480	int data_ni, \
2481	int data_nj, \
2482	int data_ibegin, \
2483	int data_jbegin)", << msg);
2484	}
2485	}
2486
2487	///--------------------------------------------------------------
2488
2489	StdSize CNc4DataOutput::getRecordFromTime(Time time)
2490	{
2491	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2492	if (it == timeToRecordCache.end())
2493	{
2494	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2495	if (!SuperClassWriter::varExist(timeAxisBoundsId))
2496	timeAxisBoundsId = "time_instant_bounds";
2497
2498	CArray<double,2> timeAxisBounds;
2499	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
2500
2501	StdSize record = 0;
2502	double dtime(time);
2503	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
2504	{
2505	if (timeAxisBounds(1, n) < dtime)
2506	{
2507	record = n + 1;
2508	break;
2509	}
2510	}
2511	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2512	}
2513	return it->second;
2514	}
2515
2516	///--------------------------------------------------------------
2517
2518	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2519	{
2520	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2521	}
2522
2523	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2524	{
2525	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2526	}
2527
2528	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2529	{
2530	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2531	}
2532
2533	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2534	{
2535	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2536	}
2537
2538	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2539	{
2540	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2541	}
2542
2543	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2544	{
2545	this->writtenDomains.insert(domainName);
2546	}
2547
2548	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2549	{
2550	this->writtenCompressedDomains.insert(domainName);
2551	}
2552
2553	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2554	{
2555	this->writtenAxis.insert(axisName);
2556	}
2557
2558	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2559	{
2560	this->writtenCompressedAxis.insert(axisName);
2561	}
2562
2563	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2564	{
2565	this->writtenScalar.insert(scalarName);
2566	}
2567	} // namespace xios

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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 929

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