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source: XIOS3/trunk/src/io/nc4_data_output.cpp @ 2384

Last change on this file since 2384 was 2384, checked in by jderouillat, 2 years ago
Replace OutputDomainName? by a CDomain pointer in the hash table which manage element names. Replace unordered_multimap by multimap
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: 129.4 KB

Rev	Line
[219]	1	#include "nc4_data_output.hpp"
	2
[352]	3	#include "attribute_template.hpp"
	4	#include "group_template.hpp"
[219]	5
	6	#include "file.hpp"
	7	#include "calendar.hpp"
[278]	8	#include "context.hpp"
[300]	9	#include "context_server.hpp"
[498]	10	#include "netCdfException.hpp"
	11	#include "exception.hpp"
[1158]	12	#include "timer.hpp"
	13	#include "uuid.hpp"
[335]	14	namespace xios
[219]	15	{
[878]	16	/// ////////////////////// Dfinitions ////////////////////// ///
[219]	17	CNc4DataOutput::CNc4DataOutput
[1158]	18	(CFile* file, const StdString & filename, bool exist)
[219]	19	: SuperClass()
	20	, SuperClassWriter(filename, exist)
	21	, filename(filename)
[2381]	22	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relElements_()
[219]	23	{
[1158]	24	SuperClass::type = MULTI_FILE;
[1456]	25	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
[219]	26	}
	27
	28	CNc4DataOutput::CNc4DataOutput
[1158]	29	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
[1639]	30	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
[219]	31	: SuperClass()
[878]	32	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
[379]	33	, comm_file(comm_file)
[219]	34	, filename(filename)
[335]	35	, isCollective(isCollective)
[2381]	36	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relElements_()
[219]	37	{
[1158]	38	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
[1459]	39	if (file==NULL) compressionLevel = 0 ;
	40	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
[219]	41	}
	42
	43	CNc4DataOutput::~CNc4DataOutput(void)
[879]	44	{ /* Ne rien faire de plus */ }
[219]	45
	46	///--------------------------------------------------------------
	47
	48	const StdString & CNc4DataOutput::getFileName(void) const
	49	{
	50	return (this->filename);
	51	}
	52
	53	//---------------------------------------------------------------
	54
[347]	55	void CNc4DataOutput::writeDomain_(CDomain* domain)
[1622]	56	TRY
[219]	57	{
[1391]	58	StdString lonName,latName ;
[1249]	59
[881]	60	if (domain->type == CDomain::type_attr::unstructured)
	61	{
	62	if (SuperClassWriter::useCFConvention)
	63	writeUnstructuredDomain(domain) ;
	64	else
	65	writeUnstructuredDomainUgrid(domain) ;
	66	return ;
	67	}
[488]	68
[347]	69	CContext* context = CContext::getCurrent() ;
[219]	70	if (domain->IsWritten(this->filename)) return;
	71	domain->checkAttributes();
[488]	72
	73	if (domain->isEmpty())
[881]	74	if (SuperClass::type==MULTI_FILE) return;
[219]	75
[2381]	76
	77	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
	78	if (!domain->lonvalue.isEmpty() )
	79	{
	80	int comm_file_rank(0);
	81	MPI_Comm_rank( comm_file, &comm_file_rank );
	82	int comm_file_size(1);
	83	MPI_Comm_size( comm_file, &comm_file_size );
	84
	85	// Get element current FULL view
	86	shared_ptr<CLocalView> srcView = domain->getLocalView(CElementView::FULL) ;
	87	vector<shared_ptr<CLocalView>> srcViews;
	88	srcViews.push_back( srcView );
	89
	90	// Compute a without redundancy element FULL view to enable a consistent hash computation
	91	vector<shared_ptr<CLocalView>> remoteViews;
	92	shared_ptr<CLocalView> remoteView;
	93	// define the remote view without redundancy (naive distribution of the remote view)
	94	int globalSize = domain->ni_glo.getValue()*domain->nj_glo.getValue();
	95	int localSize = globalSize/comm_file_size;
	96	if ( (comm_file_rank==comm_file_size-1) && (localSize*comm_file_size != globalSize ) )
	97	localSize += globalSize-localSize*comm_file_size;
	98	CArray<size_t,1> globalIndex( localSize );
	99	CArray<int,1> index( localSize );
	100	for (int iloc=0; iloc<localSize ; iloc++ )
	101	{
	102	globalIndex(iloc) = comm_file_rank*(globalSize/comm_file_size) + iloc;
	103	index(iloc) = iloc;
	104	}
	105	shared_ptr<CLocalElement> localElement = make_shared<CLocalElement>(comm_file_rank, globalSize, globalIndex) ;
	106	localElement->addView(CElementView::FULL, index) ;
	107	remoteView = localElement->getView(CElementView::FULL) ;
	108	remoteViews.push_back( remoteView );
	109
	110	// Compute the connector between current and without redundancy FULL views
	111	shared_ptr<CGridTransformConnector> gridTransformConnector = make_shared<CGridTransformConnector>(srcViews, remoteViews, comm_file ) ;
	112	gridTransformConnector->computeConnector(true) ; // eliminateRedondant = true
	113	CArray<double,1> lon_distributedValue, lat_distributedValue ;
	114	gridTransformConnector->transfer(domain->lonvalue, lon_distributedValue );
	115	gridTransformConnector->transfer(domain->latvalue, lat_distributedValue );
	116
	117	// Compute the distributed hash (v0) of the element
	118	// it will be associated to the default element name (= map key), and to the name really written
	119	int localHash = 0;
	120	for (int iloc=0; iloc<localSize ; iloc++ ) localHash+=globalIndex(iloc)lon_distributedValue(iloc)lat_distributedValue(iloc);
	121	int globalHash(0);
	122	globalHash = localHash;
	123	MPI_Allreduce( &localHash, &globalHash, 1, MPI_INT, MPI_SUM, comm_file );
	124
	125	StdString defaultNameKey = domain->getDomainOutputName();
[2384]	126	if ( !relDomains_.count ( defaultNameKey ) )
[2381]	127	{
	128	// if defaultNameKey not in the map, write the element such as it is defined
[2384]	129	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) );
[2381]	130	}
	131	else // look if a hash associated this key is equal
	132	{
	133	bool elementIsInMap(false);
[2384]	134	auto defaultNameKeyElements = relDomains_.equal_range( defaultNameKey );
[2381]	135	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
	136	{
	137	if ( it->second.first == globalHash )
	138	{
	139	// if yes, associate the same ids to current element
[2384]	140	domain->name = it->second.second->getDomainOutputName();
	141	domain->lon_name = it->second.second->lon_name;
	142	domain->lat_name = it->second.second->lat_name;
[2381]	143	elementIsInMap = true;
	144	}
	145	}
	146	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
	147	if (!elementIsInMap) // ! in MAP
	148	{
	149	domain->name = domain->getId();
	150	domain->lon_name = "lon_"+domain->getId();
	151	domain->lat_name = "lat_"+domain->getId();
[2384]	152	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) ) ;
[2381]	153	}
	154	}
	155	}
	156
	157
[219]	158	std::vector<StdString> dim0, dim1;
[772]	159	StdString domid = domain->getDomainOutputName();
[318]	160	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
[706]	161	if (isWrittenDomain(domid)) return ;
[774]	162	else setWrittenDomain(domid);
[1132]	163
	164	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
[449]	165
[488]	166
[1158]	167	StdString dimXid, dimYid ;
	168
	169	nc_type typePrec ;
	170	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	171	else if (domain->prec==4) typePrec = NC_FLOAT ;
	172	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	173
[664]	174	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
[449]	175	switch (domain->type)
[433]	176	{
[449]	177	case CDomain::type_attr::curvilinear :
[1391]	178
	179	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
	180	else lonName = domain->lon_name;
	181
	182	if (domain->lat_name.isEmpty()) latName = "nav_lat";
	183	else latName = domain->lat_name;
	184
[1430]	185	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
	186	else dimXid=domain->dim_i_name.getValue() + appendDomid;
	187
	188	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
	189	else dimYid=domain->dim_j_name.getValue() + appendDomid;
	190
[449]	191	break ;
[1391]	192
[664]	193	case CDomain::type_attr::rectilinear :
[1391]	194
[1430]	195	if (domain->lon_name.isEmpty())
	196	{
	197	if (domain->dim_i_name.isEmpty())
	198	lonName = "lon";
	199	else
	200	lonName = domain->dim_i_name.getValue();
	201	}
[1391]	202	else lonName = domain->lon_name;
	203
[1430]	204	if (domain->lat_name.isEmpty())
	205	{
	206	if (domain->dim_j_name.isEmpty())
	207	latName = "lat";
	208	else
	209	latName = domain->dim_j_name.getValue();
	210	}
[1391]	211	else latName = domain->lat_name;
	212
[1430]	213	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
	214	else dimXid = domain->dim_i_name.getValue()+appendDomid;
	215
	216	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
	217	else dimYid = domain->dim_j_name.getValue()+appendDomid;
[449]	218	break;
[488]	219	}
	220
[617]	221	StdString dimVertId = StdString("nvertex").append(appendDomid);
	222
[449]	223	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	224	string areaId = "area" + appendDomid;
[219]	225
[498]	226	try
[219]	227	{
[498]	228	switch (SuperClass::type)
	229	{
	230	case (MULTI_FILE) :
	231	{
	232	switch (domain->type)
	233	{
	234	case CDomain::type_attr::curvilinear :
	235	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1415]	236	lonid = lonName+appendDomid;
	237	latid = latName+appendDomid;
[498]	238	break ;
[664]	239	case CDomain::type_attr::rectilinear :
[1415]	240	lonid = lonName+appendDomid;
	241	latid = latName+appendDomid;
[498]	242	dim0.push_back(dimYid);
	243	dim1.push_back(dimXid);
	244	break;
	245	}
[1430]	246	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	247	else bounds_lonid = "bounds_"+lonName+appendDomid;
	248	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	249	else bounds_latid = "bounds_"+latName+appendDomid;
[488]	250
[1553]	251	SuperClassWriter::addDimension(dimXid, domain->ni);
	252	SuperClassWriter::addDimension(dimYid, domain->nj);
[488]	253
[617]	254	if (domain->hasBounds)
	255	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	256
[1853]	257	if (context->intraCommSize_ > 1)
[498]	258	{
[1553]	259	this->writeLocalAttributes(domain->ibegin,
	260	domain->ni,
	261	domain->jbegin,
	262	domain->nj,
[616]	263	appendDomid);
[488]	264
[628]	265	if (singleDomain)
	266	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
[1553]	267	domain->ibegin,
	268	domain->ni,
	269	domain->jbegin,
	270	domain->nj,
[628]	271	domain->ni_glo,domain->nj_glo,
[1853]	272	context->intraCommRank_,context->intraCommSize_);
[449]	273	}
[488]	274
[665]	275	if (domain->hasLonLat)
[498]	276	{
[665]	277	switch (domain->type)
	278	{
	279	case CDomain::type_attr::curvilinear :
[1456]	280	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	281	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	282	break ;
	283	case CDomain::type_attr::rectilinear :
[1456]	284	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	285	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
[665]	286	break ;
	287	}
[488]	288
[665]	289	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	290	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
[219]	291
[665]	292	if (domain->hasBounds)
	293	{
	294	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	295	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
[617]	296
[665]	297	dim0.clear();
	298	dim0.push_back(dimYid);
	299	dim0.push_back(dimXid);
	300	dim0.push_back(dimVertId);
[1456]	301	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	302	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[665]	303	}
[617]	304	}
	305
[498]	306	dim0.clear();
[616]	307	dim0.push_back(dimYid);
[498]	308	dim0.push_back(dimXid);
[219]	309
[611]	310	if (domain->hasArea)
	311	{
[1456]	312	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	313	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	314	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	315	}
	316
[498]	317	SuperClassWriter::definition_end();
[449]	318
[665]	319	if (domain->hasLonLat)
[498]	320	{
[665]	321	switch (domain->type)
	322	{
[1129]	323	case CDomain::type_attr::curvilinear :
[1930]	324	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
	325	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
[665]	326	break;
	327	case CDomain::type_attr::rectilinear :
[1930]	328	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
[665]	329	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
[1930]	330	CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
[665]	331	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
	332	break;
	333	}
[611]	334
[665]	335	if (domain->hasBounds)
	336	{
[1930]	337	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
	338	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
[665]	339	}
[617]	340	}
	341
[611]	342	if (domain->hasArea)
[1129]	343	{
[1930]	344	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
[1129]	345	}
	346
[498]	347	SuperClassWriter::definition_start();
[219]	348
[498]	349	break;
	350	}
	351	case (ONE_FILE) :
	352	{
[1553]	353	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
	354	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
[286]	355
[617]	356	if (domain->hasBounds)
	357	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	358
[665]	359	if (domain->hasLonLat)
[498]	360	{
[665]	361	switch (domain->type)
	362	{
	363	case CDomain::type_attr::curvilinear :
	364	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1415]	365	lonid = lonName+appendDomid;
	366	latid = latName+appendDomid;
[1456]	367	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	368	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	369	break;
[449]	370
[665]	371	case CDomain::type_attr::rectilinear :
	372	dim0.push_back(dimYid);
	373	dim1.push_back(dimXid);
[1415]	374	lonid = lonName+appendDomid;
	375	latid = latName+appendDomid;
[1456]	376	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	377	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
[665]	378	break;
	379	}
[1430]	380	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	381	else bounds_lonid = "bounds_"+lonName+appendDomid;
	382	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	383	else bounds_latid = "bounds_"+latName+appendDomid;
[665]	384
	385	this->writeAxisAttributes
	386	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	387	this->writeAxisAttributes
	388	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
	389
	390	if (domain->hasBounds)
	391	{
	392	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	393	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
	394
	395	dim0.clear();
[498]	396	dim0.push_back(dimYid);
[665]	397	dim0.push_back(dimXid);
	398	dim0.push_back(dimVertId);
[1456]	399	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	400	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[665]	401	}
[498]	402	}
[611]	403
	404	if (domain->hasArea)
	405	{
	406	dim0.clear();
	407	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1456]	408	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	409	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	410	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	411	dim0.clear();
	412	}
	413
	414	SuperClassWriter::definition_end();
[286]	415
[498]	416	switch (domain->type)
[384]	417	{
[498]	418	case CDomain::type_attr::curvilinear :
[449]	419	{
[498]	420	std::vector<StdSize> start(2) ;
	421	std::vector<StdSize> count(2) ;
[1959]	422	start[1]=domain->ibegin;
	423	start[0]=domain->jbegin;
	424	count[1]=domain->ni ; count[0]=domain->nj ;
[488]	425
[665]	426	if (domain->hasLonLat)
	427	{
[1930]	428	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
	429	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
[665]	430	}
[498]	431	break;
	432	}
[664]	433	case CDomain::type_attr::rectilinear :
[449]	434	{
[665]	435	if (domain->hasLonLat)
[498]	436	{
[665]	437	std::vector<StdSize> start(1) ;
	438	std::vector<StdSize> count(1) ;
[1930]	439
	440	start[0]=domain->jbegin;
	441	count[0]=domain->nj;
	442	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni));
	443	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
[665]	444
[1930]	445	start[0]=domain->ibegin;
	446	count[0]=domain->ni;
	447	CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1));
	448	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
[498]	449	}
	450	break;
[449]	451	}
[384]	452	}
[611]	453
[617]	454	if (domain->hasBounds)
	455	{
	456	std::vector<StdSize> start(3);
	457	std::vector<StdSize> count(3);
	458	if (domain->isEmpty())
	459	{
	460	start[2] = start[1] = start[0] = 0;
	461	count[2] = count[1] = count[0] = 0;
	462	}
	463	else
	464	{
	465	start[2] = 0;
[1553]	466	start[1] = domain->ibegin;
	467	start[0] = domain->jbegin;
[1099]	468	count[2] = domain->nvertex;
[1553]	469	count[1] = domain->ni;
	470	count[0] = domain->nj;
[617]	471	}
[1143]	472
[1930]	473	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
	474	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
[617]	475	}
	476
[611]	477	if (domain->hasArea)
	478	{
	479	std::vector<StdSize> start(2);
	480	std::vector<StdSize> count(2);
	481
[1930]	482	start[1] = domain->ibegin;
	483	start[0] = domain->jbegin;
	484	count[1] = domain->ni;
	485	count[0] = domain->nj;
[1143]	486
[1930]	487	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
[611]	488	}
	489
[498]	490	SuperClassWriter::definition_start();
	491	break;
	492	}
	493	default :
	494	ERROR("CNc4DataOutput::writeDomain(domain)",
	495	<< "[ type = " << SuperClass::type << "]"
	496	<< " not implemented yet !");
	497	}
[449]	498	}
[498]	499	catch (CNetCdfException& e)
	500	{
	501	StdString msg("On writing the domain : ");
	502	msg.append(domid); msg.append("\n");
	503	msg.append("In the context : ");
	504	msg.append(context->getId()); msg.append("\n");
	505	msg.append(e.what());
	506	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
	507	}
	508
[449]	509	domain->addRelFile(this->filename);
	510	}
[1622]	511	CATCH
[449]	512
[879]	513	//--------------------------------------------------------------
[878]	514
[879]	515	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
	516	{
	517	CContext* context = CContext::getCurrent() ;
[878]	518
[879]	519	if (domain->IsWritten(this->filename)) return;
[1494]	520
	521	StdString domid = domain->getDomainOutputName();
	522
	523	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
	524	// Thus the entire mesh connectivity will be generated at once.
	525	if (isWrittenDomain(domid)) return ;
	526	else setWrittenDomain(domid);
	527
[879]	528	domain->checkAttributes();
	529	if (domain->isEmpty())
	530	if (SuperClass::type==MULTI_FILE) return ;
[878]	531
[1158]	532	nc_type typePrec ;
	533	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	534	else if (domain->prec==4) typePrec = NC_FLOAT ;
	535	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	536
[879]	537	std::vector<StdString> dim0;
	538	StdString domainName = domain->name;
[924]	539	domain->assignMesh(domainName, domain->nvertex);
[1853]	540	domain->mesh->createMeshEpsilon(context->intraComm_, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
[878]	541
[879]	542	StdString node_x = domainName + "_node_x";
	543	StdString node_y = domainName + "_node_y";
[878]	544
[879]	545	StdString edge_x = domainName + "_edge_x";
	546	StdString edge_y = domainName + "_edge_y";
	547	StdString edge_nodes = domainName + "_edge_nodes";
[878]	548
[879]	549	StdString face_x = domainName + "_face_x";
	550	StdString face_y = domainName + "_face_y";
	551	StdString face_nodes = domainName + "_face_nodes";
[902]	552	StdString face_edges = domainName + "_face_edges";
	553	StdString edge_faces = domainName + "_edge_face_links";
	554	StdString face_faces = domainName + "_face_links";
[878]	555
[879]	556	StdString dimNode = "n" + domainName + "_node";
	557	StdString dimEdge = "n" + domainName + "_edge";
	558	StdString dimFace = "n" + domainName + "_face";
	559	StdString dimVertex = "n" + domainName + "_vertex";
	560	StdString dimTwo = "Two";
[878]	561
[879]	562	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
[1494]	563	dim0.clear();
	564	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
	565	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
	566	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
	567	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
	568	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
[878]	569
[879]	570	try
	571	{
	572	switch (SuperClass::type)
	573	{
	574	case (ONE_FILE) :
	575	{
	576	// Adding nodes
	577	if (domain->nvertex == 1)
	578	{
	579	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	580	{
[902]	581	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
[879]	582	dim0.clear();
	583	dim0.push_back(dimNode);
[1456]	584	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	585	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	586	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	587	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	588	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	589	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	590	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	591	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	592	}
	593	} // domain->nvertex == 1
[878]	594
[879]	595	// Adding edges and nodes, if nodes have not been defined previously
	596	if (domain->nvertex == 2)
	597	{
	598	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	599	{
[924]	600	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	601	dim0.clear();
	602	dim0.push_back(dimNode);
[1456]	603	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	604	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	605	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	606	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	607	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	608	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	609	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	610	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	611	}
[924]	612	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
	613	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	614	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
	615	dim0.clear();
	616	dim0.push_back(dimEdge);
[1456]	617	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
[924]	618	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
	619	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
	620	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
[1456]	621	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
[924]	622	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
	623	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
	624	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	625	dim0.clear();
	626	dim0.push_back(dimEdge);
	627	dim0.push_back(dimTwo);
[1456]	628	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
[924]	629	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	630	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	631	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
[879]	632	} // domain->nvertex == 2
[878]	633
[879]	634	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
	635	if (domain->nvertex > 2)
	636	{
	637	// Nodes
	638	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	639	{
[924]	640	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	641	dim0.clear();
	642	dim0.push_back(dimNode);
[1456]	643	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	644	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	645	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	646	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	647	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	648	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	649	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	650	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	651	}
	652	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
	653	{
	654	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	655	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
[924]	656	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
[879]	657	dim0.clear();
	658	dim0.push_back(dimEdge);
[1456]	659	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
[879]	660	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
[924]	661	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
[879]	662	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
[1456]	663	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
[879]	664	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
[924]	665	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
[879]	666	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	667	dim0.clear();
	668	dim0.push_back(dimEdge);
	669	dim0.push_back(dimTwo);
[1456]	670	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
[879]	671	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	672	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	673	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
	674	}
[924]	675	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
	676	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
	677	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
	678	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
	679	dim0.clear();
	680	dim0.push_back(dimFace);
[1456]	681	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
[924]	682	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
	683	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
	684	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
[1456]	685	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
[924]	686	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
	687	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
	688	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
	689	dim0.clear();
	690	dim0.push_back(dimFace);
	691	dim0.push_back(dimVertex);
[1456]	692	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
[924]	693	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
	694	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
	695	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
	696	dim0.clear();
	697	dim0.push_back(dimFace);
	698	dim0.push_back(dimVertex);
[1456]	699	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
[924]	700	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
	701	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
	702	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
[929]	703	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
[924]	704	dim0.clear();
	705	dim0.push_back(dimEdge);
	706	dim0.push_back(dimTwo);
[1456]	707	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
[924]	708	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
	709	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
	710	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
	711	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
	712	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
	713	dim0.clear();
	714	dim0.push_back(dimFace);
	715	dim0.push_back(dimVertex);
[1456]	716	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
[924]	717	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
	718	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
	719	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
[929]	720	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
[924]	721	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
	722	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
[879]	723	} // domain->nvertex > 2
[878]	724
[879]	725	SuperClassWriter::definition_end();
[878]	726
[924]	727	std::vector<StdSize> startEdges(1) ;
	728	std::vector<StdSize> countEdges(1) ;
	729	std::vector<StdSize> startNodes(1) ;
	730	std::vector<StdSize> countNodes(1) ;
	731	std::vector<StdSize> startFaces(1) ;
	732	std::vector<StdSize> countFaces(1) ;
	733	std::vector<StdSize> startEdgeNodes(2) ;
	734	std::vector<StdSize> countEdgeNodes(2) ;
	735	std::vector<StdSize> startEdgeFaces(2) ;
	736	std::vector<StdSize> countEdgeFaces(2) ;
	737	std::vector<StdSize> startFaceConctv(2) ;
	738	std::vector<StdSize> countFaceConctv(2) ;
[902]	739
[1494]	740	if (domain->nvertex == 1)
[879]	741	{
[1494]	742	if (domain->isEmpty())
	743	{
	744	startNodes[0]=0 ;
	745	countNodes[0]=0 ;
	746	}
	747	else
	748	{
[1553]	749	startNodes[0] = domain->ibegin;
	750	countNodes[0] = domain->ni ;
[1494]	751	}
[924]	752
[1494]	753	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	754	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	755	}
	756	else if (domain->nvertex == 2)
	757	{
	758	if (domain->isEmpty())
	759	{
	760	startEdges[0]=0 ;
	761	countEdges[0]=0 ;
	762	startNodes[0]=0 ;
	763	countNodes[0]=0 ;
	764	startEdgeNodes[0]=0;
	765	startEdgeNodes[1]=0;
	766	countEdgeNodes[0]=0;
	767	countEdgeNodes[1]=0;
[924]	768
[1494]	769	}
	770	else
	771	{
[1553]	772	startEdges[0] = domain->ibegin;
	773	countEdges[0] = domain->ni;
[1494]	774	startNodes[0] = domain->mesh->node_start;
	775	countNodes[0] = domain->mesh->node_count;
[1553]	776	startEdgeNodes[0] = domain->ibegin;
[1494]	777	startEdgeNodes[1] = 0;
[1553]	778	countEdgeNodes[0] = domain->ni;
[1494]	779	countEdgeNodes[1] = 2;
	780	}
	781	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	782	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	783	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	784	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	785	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	786	}
[879]	787	else
	788	{
[1494]	789	if (domain->isEmpty())
	790	{
	791	startFaces[0] = 0 ;
	792	countFaces[0] = 0 ;
	793	startNodes[0] = 0;
	794	countNodes[0] = 0;
	795	startEdges[0] = 0;
	796	countEdges[0] = 0;
	797	startEdgeFaces[0] = 0;
	798	startEdgeFaces[1] = 0;
	799	countEdgeFaces[0] = 0;
	800	countEdgeFaces[1] = 0;
	801	startFaceConctv[0] = 0;
	802	startFaceConctv[1] = 0;
	803	countFaceConctv[0] = 0;
	804	countFaceConctv[1] = 0;
	805	}
	806	else
	807	{
[1553]	808	startFaces[0] = domain->ibegin;
	809	countFaces[0] = domain->ni ;
[1494]	810	startNodes[0] = domain->mesh->node_start;
	811	countNodes[0] = domain->mesh->node_count;
	812	startEdges[0] = domain->mesh->edge_start;
	813	countEdges[0] = domain->mesh->edge_count;
	814	startEdgeNodes[0] = domain->mesh->edge_start;
	815	startEdgeNodes[1] = 0;
	816	countEdgeNodes[0] = domain->mesh->edge_count;
	817	countEdgeNodes[1]= 2;
	818	startEdgeFaces[0] = domain->mesh->edge_start;
	819	startEdgeFaces[1]= 0;
	820	countEdgeFaces[0] = domain->mesh->edge_count;
	821	countEdgeFaces[1]= 2;
[1553]	822	startFaceConctv[0] = domain->ibegin;
[1494]	823	startFaceConctv[1] = 0;
[1553]	824	countFaceConctv[0] = domain->ni;
[1494]	825	countFaceConctv[1] = domain->nvertex;
	826	}
	827	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	828	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	829	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	830	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	831	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	832	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
	833	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
	834	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
	835	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
	836	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
	837	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
	838	}
[879]	839	SuperClassWriter::definition_start();
[878]	840
[879]	841	break;
	842	} // ONE_FILE
[878]	843
[879]	844	case (MULTI_FILE) :
	845	{
[1637]	846	ERROR("CNc4DataOutput::writeDomain(domain)",
	847	<< "[ type = multiple_file ]"
	848	<< " is not yet implemented for UGRID files !");
[879]	849	break;
	850	}
[878]	851
[879]	852	default :
	853	ERROR("CNc4DataOutput::writeDomain(domain)",
	854	<< "[ type = " << SuperClass::type << "]"
	855	<< " not implemented yet !");
	856	} // switch
	857	} // try
[878]	858
[879]	859	catch (CNetCdfException& e)
	860	{
	861	StdString msg("On writing the domain : ");
	862	msg.append(domid); msg.append("\n");
	863	msg.append("In the context : ");
	864	msg.append(context->getId()); msg.append("\n");
	865	msg.append(e.what());
[924]	866	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
[879]	867	}
[878]	868
[879]	869	domain->addRelFile(this->filename);
	870	}
[878]	871
[879]	872	//--------------------------------------------------------------
[878]	873
[879]	874	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
[449]	875	{
	876	CContext* context = CContext::getCurrent() ;
[488]	877
[449]	878	if (domain->IsWritten(this->filename)) return;
	879	domain->checkAttributes();
[488]	880
	881	if (domain->isEmpty())
[449]	882	if (SuperClass::type==MULTI_FILE) return ;
	883
	884	std::vector<StdString> dim0, dim1;
[772]	885	StdString domid = domain->getDomainOutputName();
[705]	886	if (isWrittenDomain(domid)) return ;
[774]	887	else setWrittenDomain(domid);
[705]	888
[449]	889	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
	890
[1430]	891	StdString lonName,latName, cellName ;
[1391]	892	if (domain->lon_name.isEmpty()) lonName = "lon";
	893	else lonName = domain->lon_name;
	894
	895	if (domain->lat_name.isEmpty()) latName = "lat";
	896	else latName = domain->lat_name;
	897
[1430]	898	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
	899	else cellName="cell";
	900	StdString dimXid = cellName+appendDomid;
[449]	901	StdString dimVertId = StdString("nvertex").append(appendDomid);
[488]	902
[449]	903	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	904	string areaId = "area" + appendDomid;
[449]	905
[1158]	906	nc_type typePrec ;
	907	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	908	else if (domain->prec==4) typePrec = NC_FLOAT ;
	909	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	910
[1132]	911	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
[1025]	912
[498]	913	try
[449]	914	{
[498]	915	switch (SuperClass::type)
	916	{
	917	case (MULTI_FILE) :
	918	{
	919	dim0.push_back(dimXid);
[1553]	920	SuperClassWriter::addDimension(dimXid, domain->ni);
[488]	921
[1415]	922	lonid = lonName+appendDomid;
	923	latid = latName+appendDomid;
[1430]	924	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	925	else bounds_lonid = "bounds_"+lonName+appendDomid;
	926	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	927	else bounds_latid = "bounds_"+latName+appendDomid;
	928
[665]	929	if (domain->hasLonLat)
	930	{
[1456]	931	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	932	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	933	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	934	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	935	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	936	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
	937	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	938	}
[498]	939	dim0.clear();
	940	if (domain->hasBounds)
	941	{
	942	dim0.push_back(dimXid);
	943	dim0.push_back(dimVertId);
[1456]	944	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	945	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[498]	946	}
	947
	948	dim0.clear();
[449]	949	dim0.push_back(dimXid);
[611]	950	if (domain->hasArea)
	951	{
[1456]	952	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	953	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	954	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	955	}
	956
[498]	957	SuperClassWriter::definition_end();
[449]	958
[665]	959	if (domain->hasLonLat)
[498]	960	{
[1930]	961	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
	962	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
[665]	963	if (domain->hasBounds)
	964	{
[1930]	965	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
	966	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
[665]	967	}
[498]	968	}
[611]	969
	970	if (domain->hasArea)
[1930]	971	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
[611]	972
[498]	973	SuperClassWriter::definition_start();
	974	break ;
	975	}
[488]	976
[498]	977	case (ONE_FILE) :
	978	{
[1415]	979	lonid = lonName+appendDomid;
	980	latid = latName+appendDomid;
[1430]	981	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	982	else bounds_lonid = "bounds_"+lonName+appendDomid;
	983	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	984	else bounds_latid = "bounds_"+latName+appendDomid;
[1391]	985
[498]	986	dim0.push_back(dimXid);
[1132]	987	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
[665]	988	if (domain->hasLonLat)
	989	{
[1456]	990	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	991	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	992
	993	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	994	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	995	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	996	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
[1025]	997	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
[665]	998	}
[498]	999	dim0.clear();
[449]	1000
[498]	1001	if (domain->hasBounds)
	1002	{
	1003	dim0.push_back(dimXid);
	1004	dim0.push_back(dimVertId);
[1456]	1005	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	1006	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[498]	1007	}
[488]	1008
[611]	1009	if (domain->hasArea)
	1010	{
	1011	dim0.clear();
	1012	dim0.push_back(dimXid);
[1456]	1013	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	1014	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	1015	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	1016	}
	1017
[498]	1018	SuperClassWriter::definition_end();
[488]	1019
[498]	1020	std::vector<StdSize> start(1), startBounds(2) ;
	1021	std::vector<StdSize> count(1), countBounds(2) ;
	1022	if (domain->isEmpty())
	1023	{
	1024	start[0]=0 ;
	1025	count[0]=0 ;
	1026	startBounds[1]=0 ;
[1025]	1027	countBounds[1]=nvertex ;
[498]	1028	startBounds[0]=0 ;
	1029	countBounds[0]=0 ;
	1030	}
	1031	else
	1032	{
[1553]	1033	start[0]=domain->ibegin;
	1034	count[0]=domain->ni;
	1035	startBounds[0]=domain->ibegin;
[498]	1036	startBounds[1]=0 ;
[1553]	1037	countBounds[0]=domain->ni;
[1025]	1038	countBounds[1]=nvertex ;
[498]	1039	}
[665]	1040
	1041	if (domain->hasLonLat)
[498]	1042	{
[1930]	1043	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
	1044	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
[665]	1045	if (domain->hasBounds)
	1046	{
[1930]	1047	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
	1048	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
[665]	1049	}
[498]	1050	}
[488]	1051
[611]	1052	if (domain->hasArea)
[1930]	1053	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
[488]	1054
[498]	1055	SuperClassWriter::definition_start();
[488]	1056
[498]	1057	break;
	1058	}
	1059	default :
	1060	ERROR("CNc4DataOutput::writeDomain(domain)",
	1061	<< "[ type = " << SuperClass::type << "]"
	1062	<< " not implemented yet !");
	1063	}
[219]	1064	}
[498]	1065	catch (CNetCdfException& e)
	1066	{
	1067	StdString msg("On writing the domain : ");
	1068	msg.append(domid); msg.append("\n");
	1069	msg.append("In the context : ");
	1070	msg.append(context->getId()); msg.append("\n");
	1071	msg.append(e.what());
	1072	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
	1073	}
[219]	1074	domain->addRelFile(this->filename);
	1075	}
	1076	//--------------------------------------------------------------
	1077
[347]	1078	void CNc4DataOutput::writeAxis_(CAxis* axis)
[219]	1079	{
[1030]	1080	if (axis->IsWritten(this->filename)) return;
[2381]	1081
	1082	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
	1083	if (!axis->value.isEmpty() )
	1084	{
	1085	int comm_file_rank(0);
	1086	MPI_Comm_rank( comm_file, &comm_file_rank );
	1087	int comm_file_size(1);
	1088	MPI_Comm_size( comm_file, &comm_file_size );
	1089
	1090	// Get element current FULL view
	1091	shared_ptr<CLocalView> srcView = axis->getLocalView(CElementView::FULL) ;
	1092	vector<shared_ptr<CLocalView>> srcViews;
	1093	srcViews.push_back( srcView );
	1094
	1095	// Compute a without redundancy element FULL view to enable a consistent hash computation
	1096	vector<shared_ptr<CLocalView>> remoteViews;
	1097	shared_ptr<CLocalView> remoteView;
	1098	// define the remote view without redundancy (naive distribution of the remote view)
	1099	int globalSize = axis->n_glo.getValue();
	1100	int localSize = globalSize/comm_file_size;
	1101	if ( (comm_file_rank==comm_file_size-1) && (localSize*comm_file_size != globalSize ) )
	1102	localSize += globalSize-localSize*comm_file_size;
	1103	CArray<size_t,1> globalIndex( localSize );
	1104	CArray<int,1> index( localSize );
	1105	for (int iloc=0; iloc<localSize ; iloc++ )
	1106	{
	1107	globalIndex(iloc) = comm_file_rank*(globalSize/comm_file_size) + iloc;
	1108	index(iloc) = iloc;
	1109	}
	1110	shared_ptr<CLocalElement> localElement = make_shared<CLocalElement>(comm_file_rank, globalSize, globalIndex) ;
	1111	localElement->addView(CElementView::FULL, index) ;
	1112	remoteView = localElement->getView(CElementView::FULL) ;
	1113	remoteViews.push_back( remoteView );
	1114
	1115	// Compute the connector between current and without redundancy FULL views
	1116	shared_ptr<CGridTransformConnector> gridTransformConnector = make_shared<CGridTransformConnector>(srcViews, remoteViews, comm_file ) ;
	1117	gridTransformConnector->computeConnector(true) ; // eliminateRedondant = true
	1118	CArray<double,1> distributedValue ;
	1119	gridTransformConnector->transfer(axis->value, distributedValue );
	1120
	1121	// Compute the distributed hash (v0) of the element
	1122	// it will be associated to the default element name (= map key), and to the name really written
	1123	int localHash = 0;
	1124	for (int iloc=0; iloc<localSize ; iloc++ ) localHash+=globalIndex(iloc)*distributedValue(iloc);
	1125	int globalHash(0);
	1126	globalHash = localHash;
	1127	MPI_Allreduce( &localHash, &globalHash, 1, MPI_INT, MPI_SUM, comm_file );
	1128
	1129	StdString defaultNameKey = axis->getAxisOutputName();
	1130	if ( !relElements_.count ( defaultNameKey ) )
	1131	{
	1132	// if defaultNameKey not in the map, write the element such as it is defined
	1133	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, defaultNameKey) ) );
	1134	}
	1135	else // look if a hash associated this key is equal
	1136	{
	1137	bool elementIsInMap(false);
	1138	auto defaultNameKeyElements = relElements_.equal_range( defaultNameKey );
	1139	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
	1140	{
	1141	if ( it->second.first == globalHash )
	1142	{
	1143	// if yes, associate the same ids to current element
	1144	axis->name = it->second.second;
	1145	elementIsInMap = true;
	1146	}
	1147	}
	1148	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
	1149	if (!elementIsInMap) // ! in MAP
	1150	{
	1151	axis->name = axis->getId();
	1152	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis->getAxisOutputName()) ) ) ;// = axis->getId()
	1153	}
	1154	}
	1155	}
	1156
[1030]	1157	axis->checkAttributes();
[488]	1158
[1559]	1159	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
	1160	: axis->n_glo.getValue();
[1099]	1161
[1559]	1162	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
[1235]	1163
[1030]	1164	std::vector<StdString> dims;
	1165	StdString axisid = axis->getAxisOutputName();
[1435]	1166	StdString axisDim, axisBoundsId;
[1030]	1167	if (isWrittenAxis(axisid)) return ;
	1168	else setWrittenAxis(axisid);
[705]	1169
[1158]	1170	nc_type typePrec ;
	1171	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
[1235]	1172	else if (axis->prec==4) typePrec = NC_FLOAT ;
[1158]	1173	else if (axis->prec==8) typePrec = NC_DOUBLE ;
	1174
	1175	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
	1176	string strId="str_len" ;
[1030]	1177	try
	1178	{
[1433]	1179	if (axis->dim_name.isEmpty()) axisDim = axisid;
	1180	else axisDim=axis->dim_name.getValue();
[1559]	1181	SuperClassWriter::addDimension(axisDim, size);
[1433]	1182	dims.push_back(axisDim);
	1183
[1439]	1184	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
[1433]	1185
[1435]	1186	if (axis->hasValue \|\| !axis->label.isEmpty())
[816]	1187	{
[1158]	1188	if (!axis->label.isEmpty()) dims.push_back(strId);
[1430]	1189
[1456]	1190	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
[219]	1191
[1030]	1192	if (!axis->name.isEmpty())
	1193	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
[219]	1194
[1030]	1195	if (!axis->standard_name.isEmpty())
	1196	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
[540]	1197
[1030]	1198	if (!axis->long_name.isEmpty())
	1199	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
[219]	1200
[1030]	1201	if (!axis->unit.isEmpty())
	1202	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
[219]	1203
[1430]	1204	if (!axis->axis_type.isEmpty())
	1205	{
	1206	switch(axis->axis_type)
	1207	{
	1208	case CAxis::axis_type_attr::X :
	1209	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
	1210	break;
	1211	case CAxis::axis_type_attr::Y :
	1212	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
	1213	break;
	1214	case CAxis::axis_type_attr::Z :
	1215	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
	1216	break;
	1217	case CAxis::axis_type_attr::T :
	1218	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
	1219	break;
	1220	}
	1221	}
	1222
[1030]	1223	if (!axis->positive.isEmpty())
	1224	{
	1225	SuperClassWriter::addAttribute("positive",
	1226	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
	1227	&axisid);
	1228	}
[399]	1229
[1266]	1230	if (!axis->formula.isEmpty())
	1231	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
	1232
	1233	if (!axis->formula_term.isEmpty())
	1234	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
	1235
[1435]	1236	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
[1249]	1237	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
[1030]	1238	{
	1239	dims.push_back("axis_nbounds");
[1456]	1240	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
[1030]	1241	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
[1288]	1242
	1243	if (!axis->standard_name.isEmpty())
	1244	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
	1245
	1246	if (!axis->unit.isEmpty())
	1247	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
	1248
[1266]	1249	if (!axis->formula_bounds.isEmpty())
[1288]	1250	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
[1266]	1251
	1252	if (!axis->formula_term_bounds.isEmpty())
[1288]	1253	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
[1030]	1254	}
[1435]	1255	}
[816]	1256
[1435]	1257	SuperClassWriter::definition_end();
[1950]	1258
[1435]	1259	switch (SuperClass::type)
	1260	{
	1261	case MULTI_FILE:
[1030]	1262	{
[1435]	1263	if (axis->label.isEmpty())
[1437]	1264	{
	1265	if (!axis->value.isEmpty())
[1930]	1266	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
[633]	1267
[1437]	1268	if (!axis->bounds.isEmpty())
[1930]	1269	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
[1435]	1270	}
[1437]	1271	else
[1950]	1272	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
[1435]	1273
	1274	SuperClassWriter::definition_start();
	1275	break;
	1276	}
	1277	case ONE_FILE:
	1278	{
	1279	std::vector<StdSize> start(1), startBounds(2) ;
	1280	std::vector<StdSize> count(1), countBounds(2) ;
[1559]	1281	start[0] = startBounds[0] = axis->begin;
	1282	count[0] = countBounds[0] = axis->n;
[1435]	1283	startBounds[1] = 0;
	1284	countBounds[1] = 2;
	1285
	1286	if (axis->label.isEmpty())
[1437]	1287	{
	1288	if (!axis->value.isEmpty())
[1930]	1289	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
[1435]	1290
[1437]	1291	if (!axis->bounds.isEmpty())
[1930]	1292	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
[1435]	1293	}
[1437]	1294	else
[1435]	1295	{
	1296	std::vector<StdSize> startLabel(2), countLabel(2);
	1297	startLabel[0] = start[0]; startLabel[1] = 0;
	1298	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
[1950]	1299	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
[1435]	1300	}
[609]	1301
[1435]	1302	SuperClassWriter::definition_start();
	1303
	1304	break;
[609]	1305	}
[1435]	1306	default :
	1307	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
	1308	<< "[ type = " << SuperClass::type << "]"
	1309	<< " not implemented yet !");
[609]	1310	}
[1030]	1311	}
	1312	catch (CNetCdfException& e)
	1313	{
	1314	StdString msg("On writing the axis : ");
	1315	msg.append(axisid); msg.append("\n");
	1316	msg.append("In the context : ");
	1317	CContext* context = CContext::getCurrent() ;
	1318	msg.append(context->getId()); msg.append("\n");
	1319	msg.append(e.what());
	1320	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
	1321	}
[1158]	1322	axis->addRelFile(this->filename);
[391]	1323	}
[488]	1324
[887]	1325	void CNc4DataOutput::writeScalar_(CScalar* scalar)
	1326	{
	1327	if (scalar->IsWritten(this->filename)) return;
	1328	scalar->checkAttributes();
	1329	int scalarSize = 1;
	1330
	1331	StdString scalaId = scalar->getScalarOutputName();
[1430]	1332	StdString boundsId;
[887]	1333	if (isWrittenAxis(scalaId)) return ;
	1334	else setWrittenAxis(scalaId);
	1335
[1158]	1336	nc_type typePrec ;
	1337	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
	1338	else if (scalar->prec==4) typePrec = NC_FLOAT ;
	1339	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
	1340
[1435]	1341	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
	1342	string strId="str_len" ;
	1343
[887]	1344	try
	1345	{
[1439]	1346	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
[1435]	1347
	1348	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
[887]	1349	{
[1430]	1350	std::vector<StdString> dims;
	1351	StdString scalarDim = scalaId;
	1352
[1435]	1353	if (!scalar->label.isEmpty()) dims.push_back(strId);
	1354
[1158]	1355	SuperClassWriter::addVariable(scalaId, typePrec, dims);
[887]	1356
	1357	if (!scalar->name.isEmpty())
	1358	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
	1359
	1360	if (!scalar->standard_name.isEmpty())
	1361	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
	1362
	1363	if (!scalar->long_name.isEmpty())
	1364	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
	1365
	1366	if (!scalar->unit.isEmpty())
	1367	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
	1368
[1430]	1369	if (!scalar->axis_type.isEmpty())
	1370	{
	1371	switch(scalar->axis_type)
	1372	{
	1373	case CScalar::axis_type_attr::X :
	1374	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
	1375	break;
	1376	case CScalar::axis_type_attr::Y :
	1377	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
	1378	break;
	1379	case CScalar::axis_type_attr::Z :
	1380	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
	1381	break;
	1382	case CScalar::axis_type_attr::T :
	1383	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
	1384	break;
	1385	}
	1386	}
	1387
[1435]	1388	if (!scalar->positive.isEmpty())
[1430]	1389	{
[1435]	1390	SuperClassWriter::addAttribute("positive",
	1391	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
	1392	&scalaId);
	1393	}
	1394
	1395	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1396	{
[1436]	1397	dims.clear();
	1398	dims.push_back("axis_nbounds");
[1435]	1399	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
[1430]	1400	SuperClassWriter::addVariable(boundsId, typePrec, dims);
[1436]	1401	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
[1430]	1402	}
	1403
[887]	1404	SuperClassWriter::definition_end();
	1405
	1406	switch (SuperClass::type)
	1407	{
	1408	case MULTI_FILE:
	1409	{
	1410	CArray<double,1> scalarValue(scalarSize);
[1435]	1411	CArray<string,1> scalarLabel(scalarSize);
[1436]	1412	CArray<double,1> scalarBounds(scalarSize*2);
[1435]	1413
	1414	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
[1430]	1415	{
[1435]	1416	scalarValue(0) = scalar->value;
	1417	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
	1418	}
	1419
	1420	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1421	{
[1436]	1422	scalarBounds(0) = scalar->bounds(0);
	1423	scalarBounds(1) = scalar->bounds(1);
	1424	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
[1430]	1425	}
[1435]	1426
	1427	if (!scalar->label.isEmpty())
	1428	{
	1429	scalarLabel(0) = scalar->label;
	1430	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
	1431	}
	1432
[887]	1433	SuperClassWriter::definition_start();
	1434
	1435	break;
	1436	}
	1437	case ONE_FILE:
	1438	{
	1439	CArray<double,1> scalarValue(scalarSize);
[1435]	1440	CArray<string,1> scalarLabel(scalarSize);
[1436]	1441	CArray<double,1> scalarBounds(scalarSize*2);
[887]	1442
	1443	std::vector<StdSize> start(1);
	1444	std::vector<StdSize> count(1);
	1445	start[0] = 0;
	1446	count[0] = 1;
[1435]	1447	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
[1430]	1448	{
[1435]	1449	scalarValue(0) = scalar->value;
	1450	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
	1451	}
	1452	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1453	{
[1436]	1454	scalarBounds(0) = scalar->bounds(0);
	1455	scalarBounds(1) = scalar->bounds(1);
	1456	count[0] = 2;
	1457	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
[1430]	1458	}
[1435]	1459	if (!scalar->label.isEmpty())
	1460	{
	1461	scalarLabel(0) = scalar->label;
	1462	count[0] = stringArrayLen;
	1463	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
	1464	}
	1465
[887]	1466	SuperClassWriter::definition_start();
	1467
	1468	break;
	1469	}
	1470	default :
	1471	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
	1472	<< "[ type = " << SuperClass::type << "]"
	1473	<< " not implemented yet !");
	1474	}
	1475	}
	1476	}
	1477	catch (CNetCdfException& e)
	1478	{
	1479	StdString msg("On writing the scalar : ");
	1480	msg.append(scalaId); msg.append("\n");
	1481	msg.append("In the context : ");
	1482	CContext* context = CContext::getCurrent() ;
	1483	msg.append(context->getId()); msg.append("\n");
	1484	msg.append(e.what());
	1485	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
	1486	}
	1487	scalar->addRelFile(this->filename);
	1488	}
	1489
[676]	1490	//--------------------------------------------------------------
	1491
	1492	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
	1493	{
[1957]	1494	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
	1495
	1496	// NOTA : The cuurent algorithm to write compress elements of the grid
	1497	// will work pretting well when on server side you dont't get
	1498	// partial overlap on elements between differents participating process
	1499	// So the element must be totally distributed or non distributed
	1500	// If an element is partially overlaping betwwen process then the
	1501	// total compressed part will apear artificially greater than expected
	1502	// For the current implementation of writer which is decomposed only on
	1503	// one element, it will work as expected, but for future, it must be
	1504	// reconsidered again.
	1505	try
	1506	{
	1507	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1508	std::vector<StdString> domainList = grid->getDomainList();
	1509	std::vector<StdString> axisList = grid->getAxisList();
	1510	std::vector<StdString> scalarList = grid->getScalarList();
	1511	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
	1512	int commRank ;
	1513	MPI_Comm_rank(comm_file,&commRank) ;
[676]	1514
[1957]	1515	std::vector<StdString> dims;
[676]	1516
[1957]	1517	for (int i = 0; i < numElement; ++i)
	1518	{
	1519	StdString varId, compress;
	1520	CArray<size_t, 1> indexes;
	1521	bool isDistributed;
	1522	size_t nbIndexes, totalNbIndexes, offset;
	1523	size_t firstGlobalIndex;
	1524
	1525	if (2 == axisDomainOrder(i))
	1526	{
	1527	CDomain* domain = CDomain::get(domainList[idxDomain]);
	1528	StdString domId = domain->getDomainOutputName();
[676]	1529
[1957]	1530	if (!domain->isCompressible()
	1531	\|\| domain->type == CDomain::type_attr::unstructured
	1532	\|\| domain->isWrittenCompressed(this->filename)
	1533	\|\| isWrittenCompressedDomain(domId))
	1534	continue;
	1535
	1536	// unstructured grid seems not be taken into account why ?
[676]	1537
[1957]	1538	string lonName,latName ;
[676]	1539
[1957]	1540	if (domain->lon_name.isEmpty())
	1541	{
	1542	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
	1543	else lonName = "lon";
	1544	}
	1545	else lonName = domain->lon_name;
[676]	1546
[1957]	1547	if (domain->lat_name.isEmpty())
	1548	{
	1549	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
	1550	else latName = "lat";
	1551	}
	1552	else latName = domain->lat_name;
	1553
	1554	StdString appendDomId = singleDomain ? "" : "_" + domId;
[676]	1555
[1957]	1556	varId = domId + "_points";
	1557	compress = latName + appendDomId + " " + lonName + appendDomId;
	1558
[2267]	1559	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
[1957]	1560	workflowView->getGlobalIndexView(indexes) ;
	1561	nbIndexes = workflowView->getSize() ;
	1562	isDistributed = domain->isDistributed();
	1563	if (isDistributed)
	1564	{
	1565	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	1566	if (commRank==0) offset=0 ;
	1567	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
	1568	}
	1569	else
	1570	{
	1571	offset=0 ;
	1572	totalNbIndexes = nbIndexes ;
	1573	}
[676]	1574
[1957]	1575	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
[676]	1576
[1957]	1577	domain->addRelFileCompressed(this->filename);
	1578	setWrittenCompressedDomain(domId);
	1579	++idxDomain;
	1580	}
	1581	else if (1 == axisDomainOrder(i))
	1582	{
	1583	CAxis* axis = CAxis::get(axisList[idxAxis]);
	1584	StdString axisId = axis->getAxisOutputName();
[676]	1585
[1957]	1586	if (!axis->isCompressible()
	1587	\|\| axis->isWrittenCompressed(this->filename)
	1588	\|\| isWrittenCompressedAxis(axisId))
	1589	continue;
[676]	1590
[1957]	1591	varId = axisId + "_points";
	1592	compress = axisId;
[676]	1593
[2267]	1594	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
[1957]	1595	workflowView->getGlobalIndexView(indexes) ;
	1596	nbIndexes = workflowView->getSize() ;
	1597	isDistributed = axis->isDistributed();
	1598	if (isDistributed)
	1599	{
	1600	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	1601	if (commRank==0) offset=0 ;
	1602	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
	1603	}
	1604	else
	1605	{
	1606	offset=0 ;
	1607	totalNbIndexes = nbIndexes ;
	1608	}
	1609	firstGlobalIndex = axis->begin;
	1610
	1611	axis->addRelFileCompressed(this->filename);
	1612	setWrittenCompressedAxis(axisId);
	1613	++idxAxis;
	1614	}
	1615	else
	1616	{
	1617	//for scalar
	1618	}
[676]	1619
[1957]	1620	if (!varId.empty())
	1621	{
	1622	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
[774]	1623
[1957]	1624	dims.clear();
	1625	dims.push_back(varId);
	1626	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
[676]	1627
[1957]	1628	SuperClassWriter::addAttribute("compress", compress, &varId);
[676]	1629
[1957]	1630	switch (SuperClass::type)
	1631	{
	1632	case (MULTI_FILE):
	1633	{
	1634	indexes -= firstGlobalIndex;
	1635	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
	1636	break;
	1637	}
	1638	case (ONE_FILE):
	1639	{
	1640	std::vector<StdSize> start, count;
	1641	start.push_back(offset);
	1642	count.push_back(nbIndexes);
[676]	1643
[1957]	1644	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
	1645	break;
	1646	}
	1647	}
[1144]	1648	}
[1957]	1649	}
[676]	1650
[1957]	1651	grid->addRelFileCompressed(this->filename);
	1652	}
	1653	catch (CNetCdfException& e)
	1654	{
	1655	StdString msg("On writing compressed grid : ");
	1656	msg.append(grid->getId()); msg.append("\n");
	1657	msg.append("In the context : ");
	1658	CContext* context = CContext::getCurrent();
	1659	msg.append(context->getId()); msg.append("\n");
	1660	msg.append(e.what());
	1661	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
	1662	}
	1663	}
[676]	1664
	1665	//--------------------------------------------------------------
	1666
[391]	1667	void CNc4DataOutput::writeTimeDimension_(void)
	1668	{
[498]	1669	try
	1670	{
[802]	1671	SuperClassWriter::addDimension(getTimeCounterName());
[498]	1672	}
	1673	catch (CNetCdfException& e)
	1674	{
[614]	1675	StdString msg("On writing time dimension : time_couter\n");
[498]	1676	msg.append("In the context : ");
	1677	CContext* context = CContext::getCurrent() ;
	1678	msg.append(context->getId()); msg.append("\n");
	1679	msg.append(e.what());
	1680	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
	1681	}
[391]	1682	}
[676]	1683
[219]	1684	//--------------------------------------------------------------
	1685
[347]	1686	void CNc4DataOutput::writeField_(CField* field)
[219]	1687	{
[1158]	1688	CContext* context = CContext::getCurrent() ;
[300]	1689
[1158]	1690	std::vector<StdString> dims, coodinates;
[1869]	1691	CGrid* grid = field->getGrid();
[1158]	1692	if (!grid->doGridHaveDataToWrite())
[567]	1693	if (SuperClass::type==MULTI_FILE) return ;
[488]	1694
[1158]	1695	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1696	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
	1697	std::vector<StdString> domainList = grid->getDomainList();
	1698	std::vector<StdString> axisList = grid->getAxisList();
	1699	std::vector<StdString> scalarList = grid->getScalarList();
[219]	1700
[1158]	1701	StdString timeid = getTimeCounterName();
	1702	StdString dimXid,dimYid;
	1703	std::deque<StdString> dimIdList, dimCoordList;
	1704	bool hasArea = false;
	1705	StdString cellMeasures = "area:";
	1706	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
[488]	1707
[1158]	1708	for (int i = 0; i < numElement; ++i)
	1709	{
	1710	if (2 == axisDomainOrder(i))
	1711	{
	1712	CDomain* domain = CDomain::get(domainList[idxDomain]);
	1713	StdString domId = domain->getDomainOutputName();
	1714	StdString appendDomId = singleDomain ? "" : "_" + domId ;
[1391]	1715	StdString lonName,latName ;
[1430]	1716	StdString dimIname,dimJname ;
[676]	1717
[1415]	1718	if (domain->lon_name.isEmpty())
	1719	{
	1720	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
	1721	else lonName = "lon";
	1722	}
[1391]	1723	else lonName = domain->lon_name;
	1724
[1415]	1725	if (domain->lat_name.isEmpty())
	1726	{
	1727	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
	1728	else latName = "lat";
	1729	}
[1391]	1730	else latName = domain->lat_name;
[1430]	1731
	1732	if (domain->dim_i_name.isEmpty())
	1733	{
	1734	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
	1735	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
	1736	else dimIname = lonName;
	1737	}
	1738	else dimIname = domain->dim_i_name;
	1739
	1740	if (domain->dim_j_name.isEmpty())
	1741	{
	1742	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
	1743	else dimJname = latName;
	1744	}
	1745	else dimJname = domain->dim_j_name;
[1391]	1746
[1158]	1747	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
	1748	{
	1749	dimIdList.push_back(domId + "_points");
	1750	field->setUseCompressedOutput();
	1751	}
[676]	1752
[1158]	1753	switch (domain->type)
[879]	1754	{
[1158]	1755	case CDomain::type_attr::curvilinear:
	1756	if (!compressedOutput \|\| !domain->isCompressible())
	1757	{
[1430]	1758	dimXid=dimIname+appendDomId;
	1759	dimYid=dimJname+appendDomId;
[1158]	1760	dimIdList.push_back(dimXid);
	1761	dimIdList.push_back(dimYid);
	1762	}
[1415]	1763	dimCoordList.push_back(lonName+appendDomId);
	1764	dimCoordList.push_back(latName+appendDomId);
[1158]	1765	break ;
	1766	case CDomain::type_attr::rectilinear:
	1767	if (!compressedOutput \|\| !domain->isCompressible())
	1768	{
[1430]	1769	dimXid = dimIname+appendDomId;
	1770	dimYid = dimJname+appendDomId;
[1158]	1771	dimIdList.push_back(dimXid);
	1772	dimIdList.push_back(dimYid);
	1773	}
[1430]	1774	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
	1775	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
	1776
[1158]	1777	break ;
	1778	case CDomain::type_attr::unstructured:
	1779	{
	1780	if (SuperClassWriter::useCFConvention)
	1781	{
[1430]	1782	dimXid = dimIname + appendDomId;
[1158]	1783	dimIdList.push_back(dimXid);
[1415]	1784	dimCoordList.push_back(lonName+appendDomId);
	1785	dimCoordList.push_back(latName+appendDomId);
[1158]	1786	}
	1787	else
	1788	{
	1789	StdString domainName = domain->name;
	1790	if (domain->nvertex == 1)
	1791	{
	1792	dimXid = "n" + domainName + "_node";
	1793	dimIdList.push_back(dimXid);
	1794	dimCoordList.push_back(StdString(domainName + "_node_x"));
	1795	dimCoordList.push_back(StdString(domainName + "_node_y"));
	1796	}
	1797	else if (domain->nvertex == 2)
	1798	{
	1799	dimXid = "n" + domainName + "_edge";
	1800	dimIdList.push_back(dimXid);
	1801	dimCoordList.push_back(StdString(domainName + "_edge_x"));
	1802	dimCoordList.push_back(StdString(domainName + "_edge_y"));
	1803	}
	1804	else
	1805	{
	1806	dimXid = "n" + domainName + "_face";
	1807	dimIdList.push_back(dimXid);
	1808	dimCoordList.push_back(StdString(domainName + "_face_x"));
	1809	dimCoordList.push_back(StdString(domainName + "_face_y"));
	1810	}
	1811	} // ugrid convention
	1812	} // case unstructured domain
[879]	1813	}
[1158]	1814
	1815	if (domain->hasArea)
[879]	1816	{
[1158]	1817	hasArea = true;
	1818	cellMeasures += " area" + appendDomId;
[879]	1819	}
[1158]	1820	++idxDomain;
	1821	}
	1822	else if (1 == axisDomainOrder(i))
	1823	{
	1824	CAxis* axis = CAxis::get(axisList[idxAxis]);
	1825	StdString axisId = axis->getAxisOutputName();
[1430]	1826	StdString axisDim;
[1158]	1827
[1430]	1828	if (axis->dim_name.isEmpty()) axisDim = axisId;
	1829	else axisDim=axis->dim_name.getValue();
	1830
[1158]	1831	if (compressedOutput && axis->isCompressible())
[879]	1832	{
[1430]	1833	dimIdList.push_back(axisDim + "_points");
[1158]	1834	field->setUseCompressedOutput();
[879]	1835	}
[1158]	1836	else
[1430]	1837	dimIdList.push_back(axisDim);
[878]	1838
[1430]	1839	if (axisDim != axisId) dimCoordList.push_back(axisId);
[1158]	1840	++idxAxis;
	1841	}
[1430]	1842	else
[1158]	1843	{
[1430]	1844	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
	1845	StdString scalarId = scalar->getScalarOutputName();
[1446]	1846	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
	1847	dimCoordList.push_back(scalarId);
[1430]	1848	++idxScalar;
[1158]	1849	}
	1850	}
[488]	1851
[1158]	1852	StdString fieldid = field->getFieldOutputName();
[219]	1853
[1158]	1854	nc_type type ;
	1855	if (field->prec.isEmpty()) type = NC_FLOAT ;
	1856	else
	1857	{
	1858	if (field->prec==2) type = NC_SHORT ;
	1859	else if (field->prec==4) type = NC_FLOAT ;
	1860	else if (field->prec==8) type = NC_DOUBLE ;
	1861	}
[488]	1862
[1158]	1863	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
[488]	1864
[1158]	1865	if (wtime)
	1866	{
	1867	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
	1868	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
	1869	dims.push_back(timeid);
	1870	}
[488]	1871
[1961]	1872	while (!dimIdList.empty())
[1158]	1873	{
[1961]	1874	dims.push_back(dimIdList.back());
	1875	dimIdList.pop_back();
[1158]	1876	}
[219]	1877
[1158]	1878	while (!dimCoordList.empty())
	1879	{
	1880	coodinates.push_back(dimCoordList.back());
	1881	dimCoordList.pop_back();
	1882	}
[219]	1883
[1158]	1884	try
	1885	{
[498]	1886	SuperClassWriter::addVariable(fieldid, type, dims);
[488]	1887
[498]	1888	if (!field->standard_name.isEmpty())
	1889	SuperClassWriter::addAttribute
	1890	("standard_name", field->standard_name.getValue(), &fieldid);
[219]	1891
[498]	1892	if (!field->long_name.isEmpty())
	1893	SuperClassWriter::addAttribute
	1894	("long_name", field->long_name.getValue(), &fieldid);
[219]	1895
[498]	1896	if (!field->unit.isEmpty())
	1897	SuperClassWriter::addAttribute
	1898	("units", field->unit.getValue(), &fieldid);
[463]	1899
[1158]	1900	// Ugrid field attributes "mesh" and "location"
	1901	if (!SuperClassWriter::useCFConvention)
	1902	{
	1903	if (!domainList.empty())
	1904	{
	1905	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
	1906	StdString mesh = domain->name;
	1907	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
	1908	StdString location;
	1909	if (domain->nvertex == 1)
	1910	location = "node";
	1911	else if (domain->nvertex == 2)
	1912	location = "edge";
	1913	else if (domain->nvertex > 2)
	1914	location = "face";
	1915	SuperClassWriter::addAttribute("location", location, &fieldid);
	1916	}
	1917
	1918	}
	1919
	1920	if (!field->valid_min.isEmpty())
[498]	1921	SuperClassWriter::addAttribute
	1922	("valid_min", field->valid_min.getValue(), &fieldid);
[463]	1923
[498]	1924	if (!field->valid_max.isEmpty())
	1925	SuperClassWriter::addAttribute
	1926	("valid_max", field->valid_max.getValue(), &fieldid);
[464]	1927
[498]	1928	if (!field->scale_factor.isEmpty())
	1929	SuperClassWriter::addAttribute
	1930	("scale_factor", field->scale_factor.getValue(), &fieldid);
[464]	1931
[498]	1932	if (!field->add_offset.isEmpty())
	1933	SuperClassWriter::addAttribute
	1934	("add_offset", field->add_offset.getValue(), &fieldid);
[488]	1935
[498]	1936	SuperClassWriter::addAttribute
	1937	("online_operation", field->operation.getValue(), &fieldid);
[472]	1938
[498]	1939	// write child variables as attributes
[488]	1940
	1941
[1021]	1942	bool alreadyAddCellMethod = false;
	1943	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
	1944	if (!field->cell_methods.isEmpty())
	1945	{
[1158]	1946	StdString cellMethodString = field->cell_methods;
	1947	if (field->cell_methods_mode.isEmpty() \|\|
[1021]	1948	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
[1158]	1949	{
	1950	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
	1951	alreadyAddCellMethod = true;
	1952	}
	1953	else
	1954	{
	1955	switch (field->cell_methods_mode)
	1956	{
	1957	case (CField::cell_methods_mode_attr::prefix):
	1958	cellMethodsPrefix = cellMethodString;
	1959	cellMethodsPrefix += " ";
	1960	break;
	1961	case (CField::cell_methods_mode_attr::suffix):
	1962	cellMethodsSuffix = " ";
	1963	cellMethodsSuffix += cellMethodString;
	1964	break;
	1965	case (CField::cell_methods_mode_attr::none):
	1966	break;
	1967	default:
	1968	break;
	1969	}
	1970	}
[1021]	1971	}
[488]	1972
[1021]	1973
[498]	1974	if (wtime)
	1975	{
[614]	1976	CDuration freqOp = field->freq_op.getValue();
	1977	freqOp.solveTimeStep(*context->calendar);
	1978	StdString freqOpStr = freqOp.toStringUDUnits();
[612]	1979	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
[437]	1980
[614]	1981	CDuration freqOut = field->getRelFile()->output_freq.getValue();
	1982	freqOut.solveTimeStep(*context->calendar);
	1983	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
[612]	1984
[1021]	1985	StdString cellMethods(cellMethodsPrefix + "time: ");
[612]	1986	if (field->operation.getValue() == "instant") cellMethods += "point";
	1987	else if (field->operation.getValue() == "average") cellMethods += "mean";
	1988	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
	1989	else cellMethods += field->operation;
[614]	1990	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
	1991	cellMethods += " (interval: " + freqOpStr + ")";
[1021]	1992	cellMethods += cellMethodsSuffix;
	1993	if (!alreadyAddCellMethod)
	1994	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
[498]	1995	}
[488]	1996
[611]	1997	if (hasArea)
	1998	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
	1999
[498]	2000	if (!field->default_value.isEmpty())
	2001	{
[1424]	2002	double default_value = field->default_value.getValue();
	2003	if (type == NC_DOUBLE)
	2004	{
	2005	SuperClassWriter::setDefaultValue(fieldid, &default_value);
	2006	}
	2007	else if (type == NC_SHORT)
	2008	{
	2009	short sdefault_value = (short)default_value;
	2010	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
	2011	}
	2012	else
	2013	{
	2014	float fdefault_value = (float)default_value;
	2015	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
	2016	}
[498]	2017	}
	2018	else
[517]	2019	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
[219]	2020
[606]	2021	if (field->compression_level.isEmpty())
[1872]	2022	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
[606]	2023	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
	2024
[878]	2025	{ // Ecriture des coordonnes
[488]	2026
[498]	2027	StdString coordstr; //boost::algorithm::join(coodinates, " ")
	2028	std::vector<StdString>::iterator
	2029	itc = coodinates.begin(), endc = coodinates.end();
[488]	2030
[498]	2031	for (; itc!= endc; itc++)
	2032	{
	2033	StdString & coord = *itc;
	2034	if (itc+1 != endc)
	2035	coordstr.append(coord).append(" ");
	2036	else coordstr.append(coord);
	2037	}
[219]	2038
[498]	2039	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
[219]	2040
[498]	2041	}
[1222]	2042
	2043	vector<CVariable*> listVars = field->getAllVariables() ;
	2044	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
	2045
[219]	2046	}
[498]	2047	catch (CNetCdfException& e)
	2048	{
	2049	StdString msg("On writing field : ");
	2050	msg.append(fieldid); msg.append("\n");
	2051	msg.append("In the context : ");
	2052	msg.append(context->getId()); msg.append("\n");
	2053	msg.append(e.what());
	2054	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
	2055	}
[879]	2056	} // writeField_()
[219]	2057
	2058	//--------------------------------------------------------------
	2059
[347]	2060	void CNc4DataOutput::writeFile_ (CFile* file)
[219]	2061	{
[773]	2062	StdString filename = file->getFileOutputName();
[219]	2063	StdString description = (!file->description.isEmpty())
	2064	? file->description.getValue()
[335]	2065	: StdString("Created by xios");
[609]	2066
	2067	singleDomain = (file->nbDomains == 1);
	2068
[1158]	2069	StdString conv_str ;
	2070	if (file->convention_str.isEmpty())
	2071	{
	2072	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
	2073	else conv_str="UGRID" ;
	2074	}
	2075	else conv_str=file->convention_str ;
	2076
[498]	2077	try
	2078	{
[1309]	2079	if (!appendMode) this->writeFileAttributes(filename, description,
	2080	conv_str,
	2081	StdString("An IPSL model"),
	2082	this->getTimeStamp());
[609]	2083
[701]	2084	if (!appendMode)
	2085	SuperClassWriter::addDimension("axis_nbounds", 2);
[498]	2086	}
	2087	catch (CNetCdfException& e)
	2088	{
	2089	StdString msg("On writing file : ");
	2090	msg.append(filename); msg.append("\n");
	2091	msg.append("In the context : ");
	2092	CContext* context = CContext::getCurrent() ;
	2093	msg.append(context->getId()); msg.append("\n");
	2094	msg.append(e.what());
	2095	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
	2096	}
[219]	2097	}
[488]	2098
[472]	2099	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
	2100	{
[773]	2101	StdString name = var->getVariableOutputName();
[488]	2102
[498]	2103	try
	2104	{
[527]	2105	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	2106	addAttribute(name, var->getData<int>(), &fieldId);
	2107	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	2108	addAttribute(name, var->getData<short int>(), &fieldId);
	2109	else if (var->type.getValue() == CVariable::type_attr::t_float)
	2110	addAttribute(name, var->getData<float>(), &fieldId);
	2111	else if (var->type.getValue() == CVariable::type_attr::t_double)
	2112	addAttribute(name, var->getData<double>(), &fieldId);
	2113	else if (var->type.getValue() == CVariable::type_attr::t_string)
	2114	addAttribute(name, var->getData<string>(), &fieldId);
	2115	else
	2116	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
	2117	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	2118	}
	2119	catch (CNetCdfException& e)
	2120	{
	2121	StdString msg("On writing attributes of variable with name : ");
	2122	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
	2123	msg.append("In the context : ");
	2124	CContext* context = CContext::getCurrent() ;
	2125	msg.append(context->getId()); msg.append("\n");
	2126	msg.append(e.what());
	2127	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
	2128	}
[472]	2129	}
[488]	2130
[472]	2131	void CNc4DataOutput::writeAttribute_ (CVariable* var)
	2132	{
[773]	2133	StdString name = var->getVariableOutputName();
	2134
[498]	2135	try
	2136	{
[527]	2137	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	2138	addAttribute(name, var->getData<int>());
	2139	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	2140	addAttribute(name, var->getData<short int>());
	2141	else if (var->type.getValue() == CVariable::type_attr::t_float)
	2142	addAttribute(name, var->getData<float>());
	2143	else if (var->type.getValue() == CVariable::type_attr::t_double)
	2144	addAttribute(name, var->getData<double>());
	2145	else if (var->type.getValue() == CVariable::type_attr::t_string)
	2146	addAttribute(name, var->getData<string>());
	2147	else
	2148	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
	2149	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	2150	}
	2151	catch (CNetCdfException& e)
	2152	{
	2153	StdString msg("On writing attributes of variable with name : ");
	2154	msg.append(name); msg.append("\n");
	2155	msg.append("In the context : ");
	2156	CContext* context = CContext::getCurrent() ;
	2157	msg.append(context->getId()); msg.append("\n");
	2158	msg.append(e.what());
	2159	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
	2160	}
[488]	2161	}
	2162
[321]	2163	void CNc4DataOutput::syncFile_ (void)
	2164	{
[498]	2165	try
	2166	{
	2167	SuperClassWriter::sync() ;
	2168	}
	2169	catch (CNetCdfException& e)
	2170	{
	2171	StdString msg("On synchronizing the write among processes");
	2172	msg.append("In the context : ");
	2173	CContext* context = CContext::getCurrent() ;
	2174	msg.append(context->getId()); msg.append("\n");
	2175	msg.append(e.what());
	2176	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	2177	}
[321]	2178	}
[219]	2179
[286]	2180	void CNc4DataOutput::closeFile_ (void)
	2181	{
[498]	2182	try
	2183	{
	2184	SuperClassWriter::close() ;
	2185	}
	2186	catch (CNetCdfException& e)
	2187	{
	2188	StdString msg("On closing file");
	2189	msg.append("In the context : ");
	2190	CContext* context = CContext::getCurrent() ;
	2191	msg.append(context->getId()); msg.append("\n");
	2192	msg.append(e.what());
	2193	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	2194	}
	2195
[286]	2196	}
	2197
[219]	2198	//---------------------------------------------------------------
	2199
	2200	StdString CNc4DataOutput::getTimeStamp(void) const
	2201	{
	2202	const int buffer_size = 100;
	2203	time_t rawtime;
	2204	struct tm * timeinfo = NULL;
	2205	char buffer [buffer_size];
[1158]	2206	StdString formatStr;
	2207	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
	2208	else formatStr=file->time_stamp_format;
[219]	2209
[1158]	2210	// time ( &rawtime );
	2211	// timeinfo = localtime ( &rawtime );
[219]	2212	time ( &rawtime );
[1158]	2213	timeinfo = gmtime ( &rawtime );
	2214	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
[219]	2215
	2216	return (StdString(buffer));
	2217	}
[488]	2218
[219]	2219	//---------------------------------------------------------------
[488]	2220
[1961]	2221	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
	2222	const CDate& currentWrite, int nstep)
[219]	2223	{
[707]	2224	CContext* context = CContext::getCurrent();
[1869]	2225	CGrid* grid = field->getGrid();
[1961]	2226
	2227	if (nstep<1)
[1158]	2228	{
[1961]	2229	return nstep;
[1158]	2230	}
[952]	2231
[707]	2232	if (!grid->doGridHaveDataToWrite())
[1158]	2233	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
	2234	{
[1961]	2235	return nstep;
[1158]	2236	}
[488]	2237
[770]	2238	StdString fieldid = field->getFieldOutputName();
[286]	2239
[707]	2240	StdOStringStream oss;
	2241	string timeAxisId;
[1158]	2242	if (field->hasTimeInstant) timeAxisId = "time_instant";
	2243	else if (field->hasTimeCentered) timeAxisId = "time_centered";
[488]	2244
[802]	2245	StdString timeBoundId = getTimeCounterName() + "_bounds";
[449]	2246
[707]	2247	StdString timeAxisBoundId;
[1158]	2248	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
	2249	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
[488]	2250
[707]	2251	if (!field->wasWritten())
	2252	{
[1872]	2253	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
[1158]	2254	field->getOperationTimeType() != func::CFunctor::once)
[707]	2255	{
[1158]	2256	double factorUnit;
[1872]	2257	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
[1158]	2258	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
	2259	else factorUnit=1 ;
[1962]	2260	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
[707]	2261	}
[488]	2262
[707]	2263	field->setWritten();
	2264	}
[488]	2265
	2266
[707]	2267	CArray<double,1> time_data(1);
	2268	CArray<double,1> time_data_bound(2);
	2269	CArray<double,1> time_counter(1);
	2270	CArray<double,1> time_counter_bound(2);
	2271
	2272	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
[1158]	2273	bool wtimeCounter =false ;
	2274	bool wtimeData =false ;
	2275
[707]	2276
[444]	2277	if (wtime)
	2278	{
[1158]	2279
	2280	if (field->hasTimeInstant)
	2281	{
[1961]	2282	time_data(0) = time_data_bound(1) = (Time) lastWrite;
	2283	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
[1158]	2284	if (timeCounterType==instant)
	2285	{
	2286	time_counter(0) = time_data(0);
	2287	time_counter_bound(0) = time_data_bound(0);
	2288	time_counter_bound(1) = time_data_bound(1);
	2289	wtimeCounter=true ;
	2290	}
	2291	if (hasTimeInstant) wtimeData=true ;
	2292	}
	2293	else if (field->hasTimeCentered)
[488]	2294	{
[1961]	2295	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
	2296	time_data_bound(0) = (Time)lastWrite;
	2297	time_data_bound(1) = (Time)currentWrite;
[1158]	2298	if (timeCounterType==centered)
	2299	{
	2300	time_counter(0) = time_data(0) ;
	2301	time_counter_bound(0) = time_data_bound(0) ;
	2302	time_counter_bound(1) = time_data_bound(1) ;
	2303	wtimeCounter=true ;
	2304	}
	2305	if (hasTimeCentered) wtimeData=true ;
[488]	2306	}
	2307
[1158]	2308	if (timeCounterType==record)
	2309	{
[1961]	2310	time_counter(0) = nstep - 1;
	2311	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
[1158]	2312	wtimeCounter=true ;
	2313	}
[692]	2314
[1872]	2315	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
[692]	2316	{
[1158]	2317	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
	2318	time_data/=secByDay;
	2319	time_data_bound/=secByDay;
	2320	time_counter/=secByDay;
	2321	time_counter_bound/=secByDay;
[692]	2322	}
	2323	}
	2324
[1853]	2325	bool isRoot = (context->intraCommRank_ == 0);
[488]	2326
[498]	2327	try
[219]	2328	{
[567]	2329	switch (SuperClass::type)
[498]	2330	{
[567]	2331	case (MULTI_FILE) :
	2332	{
[1158]	2333	CTimer::get("Files : writing data").resume();
[1961]	2334	SuperClassWriter::writeData(data, fieldid, isCollective, nstep - 1);
[1158]	2335	CTimer::get("Files : writing data").suspend();
[567]	2336	if (wtime)
	2337	{
[1158]	2338	CTimer::get("Files : writing time axis").resume();
	2339	if ( wtimeData)
[692]	2340	{
[1961]	2341	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
	2342	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
[1158]	2343	}
	2344	if (wtimeCounter)
	2345	{
[1961]	2346	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
	2347	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
[692]	2348	}
[1158]	2349	CTimer::get("Files : writing time axis").suspend();
[567]	2350	}
[707]	2351	break;
[567]	2352	}
	2353	case (ONE_FILE) :
	2354	{
[464]	2355
[676]	2356	std::vector<StdSize> start, count;
[464]	2357
[676]	2358	if (field->getUseCompressedOutput())
	2359	{
[1957]	2360	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	2361	std::vector<StdString> domainList = grid->getDomainList();
	2362	std::vector<StdString> axisList = grid->getAxisList();
	2363	int numElement = axisDomainOrder.numElements();
	2364	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
	2365	int idx = domainList.size() * 2 + axisList.size() - 1;
	2366	int commRank ;
[464]	2367
[1957]	2368	MPI_Comm_rank(comm_file,&commRank) ;
[676]	2369
[1957]	2370	start.reserve(idx+1);
	2371	count.reserve(idx+1);
	2372
	2373	for (int i = numElement - 1; i >= 0; --i)
	2374	{
	2375	if (2 == axisDomainOrder(i))
[676]	2376	{
[1957]	2377	CDomain* domain = CDomain::get(domainList[idxDomain]);
	2378
	2379	if (domain->isCompressible())
[676]	2380	{
[1957]	2381	size_t offset ;
	2382	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
	2383	if (domain->isDistributed())
[676]	2384	{
[1957]	2385	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	2386	if (commRank==0) offset=0 ;
[676]	2387	}
[1957]	2388	else offset=0 ;
	2389
	2390	start.push_back(offset);
	2391	count.push_back(nbIndexes);
	2392	idx -= 2;
	2393	}
	2394	else
	2395	{
	2396	if ((domain->type) != CDomain::type_attr::unstructured)
[676]	2397	{
[1957]	2398	start.push_back(domain->jbegin);
	2399	count.push_back(domain->nj);
[676]	2400	}
[1957]	2401	--idx;
	2402	start.push_back(domain->ibegin);
	2403	count.push_back(domain->ni);
	2404	--idx;
[676]	2405	}
[1957]	2406	--idxDomain;
	2407	}
	2408	else if (1 == axisDomainOrder(i))
	2409	{
	2410	CAxis* axis = CAxis::get(axisList[idxAxis]);
	2411
	2412	if (axis->isCompressible())
[676]	2413	{
[1957]	2414	size_t offset ;
	2415	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
	2416	if (axis->isDistributed())
[676]	2417	{
[1957]	2418	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	2419	if (commRank==0) offset=0 ;
[676]	2420	}
[1957]	2421	else offset=0 ;
	2422
	2423	start.push_back(offset);
	2424	count.push_back(nbIndexes);
[676]	2425	}
[1957]	2426	else
	2427	{
	2428	start.push_back(axis->begin);
	2429	count.push_back(axis->n);
	2430	}
	2431	--idxAxis;
	2432	--idx;
[676]	2433	}
[1158]	2434	}
[1961]	2435	}
[676]	2436	else
[498]	2437	{
[887]	2438	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
[705]	2439	std::vector<StdString> domainList = grid->getDomainList();
	2440	std::vector<StdString> axisList = grid->getAxisList();
[2264]	2441	std::vector<StdString> scalarList = grid->getScalarList() ;
[705]	2442	int numElement = axisDomainOrder.numElements();
	2443	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
[1553]	2444	int idx = domainList.size() * 2 + axisList.size() - 1;
[705]	2445
[1553]	2446	start.reserve(idx+1);
	2447	count.reserve(idx+1);
[705]	2448
	2449	for (int i = numElement - 1; i >= 0; --i)
	2450	{
[887]	2451	if (2 == axisDomainOrder(i))
[705]	2452	{
	2453	CDomain* domain = CDomain::get(domainList[idxDomain]);
[710]	2454	if ((domain->type) != CDomain::type_attr::unstructured)
[705]	2455	{
[1553]	2456	start.push_back(domain->jbegin);
	2457	count.push_back(domain->nj);
[705]	2458	}
	2459	--idx ;
[1143]	2460
[1553]	2461	start.push_back(domain->ibegin);
	2462	count.push_back(domain->ni);
[705]	2463	--idx ;
	2464	--idxDomain;
	2465	}
[887]	2466	else if (1 == axisDomainOrder(i))
[705]	2467	{
[1143]	2468	CAxis* axis = CAxis::get(axisList[idxAxis]);
[1559]	2469	start.push_back(axis->begin);
	2470	count.push_back(axis->n);
[705]	2471	--idx;
[1025]	2472	--idxAxis;
[887]	2473	}
	2474	else
	2475	{
	2476	if (1 == axisDomainOrder.numElements())
	2477	{
[2264]	2478	CScalar* scalar = CScalar::get(scalarList[scalarList.size()-1]);
[887]	2479	start.push_back(0);
[2264]	2480	count.push_back(scalar->n);
[887]	2481	}
	2482	--idx;
	2483	}
[705]	2484	}
[498]	2485	}
[488]	2486
[1158]	2487
	2488	CTimer::get("Files : writing data").resume();
[1961]	2489	SuperClassWriter::writeData(data, fieldid, isCollective, nstep - 1, &start, &count);
[1158]	2490	CTimer::get("Files : writing data").suspend();
	2491
	2492	if (wtime)
	2493	{
	2494	CTimer::get("Files : writing time axis").resume();
	2495	if ( wtimeData)
[692]	2496	{
[1961]	2497	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
	2498	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
[692]	2499	}
[1158]	2500	if (wtimeCounter)
	2501	{
[1961]	2502	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
	2503	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
[586]	2504
[1158]	2505	}
	2506	CTimer::get("Files : writing time axis").suspend();
	2507	}
	2508
[586]	2509	break;
[286]	2510	}
[567]	2511	}
[1961]	2512	return nstep ;
[219]	2513	}
[498]	2514	catch (CNetCdfException& e)
	2515	{
	2516	StdString msg("On writing field data: ");
	2517	msg.append(fieldid); msg.append("\n");
	2518	msg.append("In the context : ");
	2519	msg.append(context->getId()); msg.append("\n");
	2520	msg.append(e.what());
[1130]	2521	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
[498]	2522	}
[219]	2523	}
	2524
	2525	//---------------------------------------------------------------
	2526
	2527	void CNc4DataOutput::writeTimeAxis_
[347]	2528	(CField* field,
[1542]	2529	const std::shared_ptr<CCalendar> cal)
[219]	2530	{
	2531	StdOStringStream oss;
[1158]	2532	bool createInstantAxis=false ;
	2533	bool createCenteredAxis=false ;
	2534	bool createTimeCounterAxis=false ;
	2535
[645]	2536	if (field->getOperationTimeType() == func::CFunctor::once) return ;
[488]	2537
	2538
[1158]	2539	StdString axisId ;
	2540	StdString axisBoundId;
[802]	2541	StdString timeid(getTimeCounterName());
[614]	2542	StdString timeBoundId("axis_nbounds");
[488]	2543
[1158]	2544	StdString strTimeUnits ;
[1872]	2545	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
[1158]	2546	else strTimeUnits="seconds since " ;
	2547
	2548	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
	2549	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
	2550
	2551
[1872]	2552	if (field->getRelFile()->time_counter.isEmpty())
[488]	2553	{
[1158]	2554	if (timeCounterType==none) createTimeCounterAxis=true ;
	2555	if (field->hasTimeCentered)
	2556	{
	2557	timeCounterType=centered ;
	2558	if (!hasTimeCentered) createCenteredAxis=true ;
	2559	}
	2560	if (field->hasTimeInstant)
	2561	{
	2562	if (timeCounterType==none) timeCounterType=instant ;
	2563	if (!hasTimeInstant) createInstantAxis=true ;
	2564	}
[488]	2565	}
[1872]	2566	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
[1158]	2567	{
	2568	if (field->hasTimeCentered)
	2569	{
	2570	if (!hasTimeCentered) createCenteredAxis=true ;
	2571	}
	2572	if (field->hasTimeInstant)
	2573	{
	2574	if (timeCounterType==none) createTimeCounterAxis=true ;
	2575	timeCounterType=instant ;
	2576	if (!hasTimeInstant) createInstantAxis=true ;
	2577	}
	2578	}
[1872]	2579	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
[1158]	2580	{
	2581	if (field->hasTimeCentered)
	2582	{
	2583	if (timeCounterType==none) createTimeCounterAxis=true ;
	2584	timeCounterType=centered ;
	2585	if (!hasTimeCentered) createCenteredAxis=true ;
	2586	}
	2587	if (field->hasTimeInstant)
	2588	{
	2589	if (!hasTimeInstant) createInstantAxis=true ;
	2590	}
	2591	}
[1872]	2592	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
[1158]	2593	{
	2594	if (field->hasTimeCentered)
	2595	{
	2596	if (!hasTimeCentered) createCenteredAxis=true ;
	2597	}
	2598	if (field->hasTimeInstant)
	2599	{
	2600	if (timeCounterType==none) createTimeCounterAxis=true ;
	2601	timeCounterType=instant ;
	2602	}
	2603	}
[1872]	2604	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
[1158]	2605	{
	2606	if (field->hasTimeCentered)
	2607	{
	2608	if (timeCounterType==none) createTimeCounterAxis=true ;
	2609	timeCounterType=centered ;
	2610	}
	2611	if (field->hasTimeInstant)
	2612	{
	2613	if (!hasTimeInstant) createInstantAxis=true ;
	2614	}
	2615	}
[1872]	2616	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
[1158]	2617	{
	2618	if (field->hasTimeCentered)
	2619	{
	2620	if (timeCounterType==none) createTimeCounterAxis=true ;
	2621	if (timeCounterType==instant) createInstantAxis=true ;
	2622	timeCounterType=centered ;
	2623	}
	2624	if (field->hasTimeInstant)
	2625	{
	2626	if (timeCounterType==none)
	2627	{
	2628	createTimeCounterAxis=true ;
	2629	timeCounterType=instant ;
	2630	}
	2631	if (timeCounterType==centered)
	2632	{
	2633	if (!hasTimeInstant) createInstantAxis=true ;
	2634	}
	2635	}
	2636	}
[1872]	2637	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
[1158]	2638	{
	2639	if (field->hasTimeCentered)
	2640	{
	2641	if (!hasTimeCentered) createCenteredAxis=true ;
	2642	}
	2643	if (field->hasTimeInstant)
	2644	{
	2645	if (!hasTimeInstant) createInstantAxis=true ;
	2646	}
	2647	}
[1872]	2648	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
[1158]	2649	{
	2650	if (timeCounterType==none) createTimeCounterAxis=true ;
	2651	timeCounterType=record ;
	2652	if (field->hasTimeCentered)
	2653	{
	2654	if (!hasTimeCentered) createCenteredAxis=true ;
	2655	}
	2656	if (field->hasTimeInstant)
	2657	{
	2658	if (!hasTimeInstant) createInstantAxis=true ;
	2659	}
	2660	}
	2661
	2662	if (createInstantAxis)
	2663	{
	2664	axisId="time_instant" ;
	2665	axisBoundId="time_instant_bounds";
	2666	hasTimeInstant=true ;
	2667	}
[488]	2668
[1158]	2669	if (createCenteredAxis)
	2670	{
	2671	axisId="time_centered" ;
	2672	axisBoundId="time_centered_bounds";
	2673	hasTimeCentered=true ;
	2674	}
	2675
	2676
[498]	2677	try
[219]	2678	{
[1158]	2679	std::vector<StdString> dims;
	2680
	2681	if (createInstantAxis \|\| createCenteredAxis)
	2682	{
	2683	// Adding time_instant or time_centered
	2684	dims.push_back(timeid);
	2685	if (!SuperClassWriter::varExist(axisId))
	2686	{
	2687	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
[488]	2688
[1158]	2689	CDate timeOrigin=cal->getTimeOrigin() ;
	2690	StdOStringStream oss2;
	2691	StdString strInitdate=oss2.str() ;
	2692	StdString strTimeOrigin=timeOrigin.toString() ;
	2693	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
	2694	strTimeOrigin, axisBoundId);
	2695	}
[219]	2696
[1158]	2697	// Adding time_instant_bounds or time_centered_bounds variables
	2698	if (!SuperClassWriter::varExist(axisBoundId))
	2699	{
	2700	dims.clear() ;
	2701	dims.push_back(timeid);
	2702	dims.push_back(timeBoundId);
	2703	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2704	}
[498]	2705	}
[488]	2706
[1158]	2707	if (createTimeCounterAxis)
[498]	2708	{
[692]	2709	// Adding time_counter
[1158]	2710	axisId = getTimeCounterName();
[802]	2711	axisBoundId = getTimeCounterName() + "_bounds";
[692]	2712	dims.clear();
	2713	dims.push_back(timeid);
[1158]	2714	if (!SuperClassWriter::varExist(axisId))
[692]	2715	{
[1158]	2716	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
	2717	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
[488]	2718
[1872]	2719	if (field->getRelFile()->time_counter.isEmpty() \|\|
	2720	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
[692]	2721	{
	2722	CDate timeOrigin = cal->getTimeOrigin();
	2723	StdString strTimeOrigin = timeOrigin.toString();
[498]	2724
[1158]	2725	this->writeTimeAxisAttributes(axisId, cal->getType(),
	2726	strTimeUnits+strTimeOrigin,
[692]	2727	strTimeOrigin, axisBoundId);
	2728	}
	2729	}
	2730
	2731	// Adding time_counter_bound dimension
[1872]	2732	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
[692]	2733	{
	2734	if (!SuperClassWriter::varExist(axisBoundId))
	2735	{
	2736	dims.clear();
	2737	dims.push_back(timeid);
	2738	dims.push_back(timeBoundId);
	2739	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2740	}
	2741	}
[498]	2742	}
[488]	2743	}
[498]	2744	catch (CNetCdfException& e)
[488]	2745	{
[498]	2746	StdString msg("On writing time axis data: ");
	2747	msg.append("In the context : ");
	2748	CContext* context = CContext::getCurrent() ;
	2749	msg.append(context->getId()); msg.append("\n");
	2750	msg.append(e.what());
	2751	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
[1542]	2752	const std::shared_ptr<CCalendar> cal)", << msg);
[488]	2753	}
[219]	2754	}
	2755
	2756	//---------------------------------------------------------------
[488]	2757
[219]	2758	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
	2759	const StdString & calendar,
	2760	const StdString & units,
	2761	const StdString & time_origin,
[488]	2762	const StdString & time_bounds,
[219]	2763	const StdString & standard_name,
[613]	2764	const StdString & long_name)
[219]	2765	{
[498]	2766	try
	2767	{
	2768	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2769	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
	2770	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
	2771	SuperClassWriter::addAttribute("units", units , &axis_name);
	2772	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
	2773	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
	2774	}
	2775	catch (CNetCdfException& e)
	2776	{
	2777	StdString msg("On writing time axis Attribute: ");
	2778	msg.append("In the context : ");
	2779	CContext* context = CContext::getCurrent() ;
	2780	msg.append(context->getId()); msg.append("\n");
	2781	msg.append(e.what());
	2782	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
[613]	2783	const StdString & calendar,\
	2784	const StdString & units, \
	2785	const StdString & time_origin, \
	2786	const StdString & time_bounds, \
	2787	const StdString & standard_name, \
	2788	const StdString & long_name)", << msg);
[498]	2789	}
[219]	2790	}
[488]	2791
[219]	2792	//---------------------------------------------------------------
	2793
	2794	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
	2795	const StdString & axis,
	2796	const StdString & standard_name,
	2797	const StdString & long_name,
	2798	const StdString & units,
	2799	const StdString & nav_model)
	2800	{
[498]	2801	try
	2802	{
[613]	2803	if (!axis.empty())
	2804	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
	2805
[498]	2806	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2807	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
	2808	SuperClassWriter::addAttribute("units" , units , &axis_name);
[973]	2809	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
[498]	2810	}
	2811	catch (CNetCdfException& e)
	2812	{
	2813	StdString msg("On writing Axis Attribute: ");
	2814	msg.append("In the context : ");
	2815	CContext* context = CContext::getCurrent() ;
	2816	msg.append(context->getId()); msg.append("\n");
	2817	msg.append(e.what());
	2818	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
[613]	2819	const StdString & axis, \
	2820	const StdString & standard_name, \
	2821	const StdString & long_name, \
	2822	const StdString & units, \
	2823	const StdString & nav_model)", << msg);
[498]	2824	}
[219]	2825	}
	2826
	2827	//---------------------------------------------------------------
[488]	2828
[219]	2829	void CNc4DataOutput::writeLocalAttributes
	2830	(int ibegin, int ni, int jbegin, int nj, StdString domid)
	2831	{
[498]	2832	try
	2833	{
[318]	2834	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
	2835	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
	2836	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
	2837	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
[498]	2838	}
	2839	catch (CNetCdfException& e)
	2840	{
	2841	StdString msg("On writing Local Attributes: ");
	2842	msg.append("In the context : ");
	2843	CContext* context = CContext::getCurrent() ;
	2844	msg.append(context->getId()); msg.append("\n");
	2845	msg.append(e.what());
	2846	ERROR("CNc4DataOutput::writeLocalAttributes \
	2847	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
	2848	}
	2849
[219]	2850	}
	2851
[628]	2852	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
	2853	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
[391]	2854	{
	2855	CArray<int,1> array(2) ;
	2856
[498]	2857	try
	2858	{
	2859	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
	2860	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
[629]	2861	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
[498]	2862	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
	2863	array=ni_glo,nj_glo ;
	2864	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
	2865	array=ni,nj ;
	2866	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
[819]	2867	array=ibegin+1,jbegin+1 ;
[498]	2868	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
[819]	2869	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
[498]	2870	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
	2871	array=0,0 ;
	2872	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
	2873	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
	2874	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
	2875	/*
	2876	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
	2877	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
	2878	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
	2879	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
	2880	*/
	2881	}
	2882	catch (CNetCdfException& e)
	2883	{
[628]	2884	StdString msg("On writing Local Attributes IOIPSL \n");
[498]	2885	msg.append("In the context : ");
	2886	CContext* context = CContext::getCurrent() ;
	2887	msg.append(context->getId()); msg.append("\n");
	2888	msg.append(e.what());
	2889	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
	2890	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
	2891	}
[391]	2892	}
[219]	2893	//---------------------------------------------------------------
	2894
	2895	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
	2896	const StdString & description,
	2897	const StdString & conventions,
	2898	const StdString & production,
	2899	const StdString & timeStamp)
	2900	{
[498]	2901	try
	2902	{
	2903	SuperClassWriter::addAttribute("name" , name);
	2904	SuperClassWriter::addAttribute("description", description);
[613]	2905	SuperClassWriter::addAttribute("title" , description);
	2906	SuperClassWriter::addAttribute("Conventions", conventions);
[1158]	2907	// SuperClassWriter::addAttribute("production" , production);
	2908
	2909	StdString timeStampStr ;
	2910	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
	2911	else timeStampStr=file->time_stamp_name ;
	2912	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
	2913
	2914	StdString uuidName ;
	2915	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
	2916	else uuidName=file->uuid_name ;
	2917
	2918	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
	2919	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
	2920
[498]	2921	}
	2922	catch (CNetCdfException& e)
	2923	{
	2924	StdString msg("On writing File Attributes \n ");
	2925	msg.append("In the context : ");
	2926	CContext* context = CContext::getCurrent() ;
	2927	msg.append(context->getId()); msg.append("\n");
	2928	msg.append(e.what());
	2929	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
	2930	const StdString & description, \
	2931	const StdString & conventions, \
	2932	const StdString & production, \
	2933	const StdString & timeStamp)", << msg);
	2934	}
[219]	2935	}
	2936
	2937	//---------------------------------------------------------------
	2938
	2939	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
	2940	int data_dim,
	2941	int data_ni,
	2942	int data_nj,
	2943	int data_ibegin,
	2944	int data_jbegin)
	2945	{
[498]	2946	try
	2947	{
	2948	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
	2949	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
	2950	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
	2951	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
	2952	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
	2953	}
	2954	catch (CNetCdfException& e)
	2955	{
	2956	StdString msg("On writing Mask Attributes \n ");
	2957	msg.append("In the context : ");
	2958	CContext* context = CContext::getCurrent() ;
	2959	msg.append(context->getId()); msg.append("\n");
	2960	msg.append(e.what());
	2961	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
	2962	int data_dim, \
	2963	int data_ni, \
	2964	int data_nj, \
	2965	int data_ibegin, \
	2966	int data_jbegin)", << msg);
	2967	}
[219]	2968	}
	2969
	2970	///--------------------------------------------------------------
	2971
[1158]	2972	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
[707]	2973	{
	2974	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
	2975	if (it == timeToRecordCache.end())
	2976	{
[802]	2977	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
[1158]	2978	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
	2979	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
[707]	2980
	2981	CArray<double,2> timeAxisBounds;
[1158]	2982	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
	2983
[707]	2984	StdSize record = 0;
	2985	double dtime(time);
[1158]	2986	for (int n = dimSize[0] - 1; n >= 0; n--)
[707]	2987	{
[1158]	2988	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
	2989	timeAxisBounds*=factorUnit ;
	2990	if (timeAxisBounds(1, 0) < dtime)
[707]	2991	{
	2992	record = n + 1;
	2993	break;
	2994	}
	2995	}
	2996	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
	2997	}
	2998	return it->second;
	2999	}
[774]	3000
	3001	///--------------------------------------------------------------
	3002
	3003	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
	3004	{
	3005	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
	3006	}
	3007
	3008	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
	3009	{
	3010	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
	3011	}
	3012
	3013	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
	3014	{
	3015	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
	3016	}
	3017
	3018	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
	3019	{
	3020	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
	3021	}
	3022
[887]	3023	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
	3024	{
	3025	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
	3026	}
	3027
[774]	3028	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
	3029	{
	3030	this->writtenDomains.insert(domainName);
	3031	}
	3032
	3033	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
	3034	{
	3035	this->writtenCompressedDomains.insert(domainName);
	3036	}
	3037
	3038	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
	3039	{
	3040	this->writtenAxis.insert(axisName);
	3041	}
	3042
	3043	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
	3044	{
	3045	this->writtenCompressedAxis.insert(axisName);
	3046	}
[887]	3047
	3048	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
	3049	{
	3050	this->writtenScalar.insert(scalarName);
	3051	}
[335]	3052	} // namespace xios

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