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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 1045

Last change on this file since 1045 was 1045, checked in by ymipsl, 7 years ago

New attributs prec for axis, domain and scalar to control the output precision of the coordinates.
Correct values are 4 or 8 to output in single or double precision. Default is single precision.

YM

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

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