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source: XIOS3/trunk/src/io/nc4_data_output.cpp @ 2385

Last change on this file since 2385 was 2385, checked in by jderouillat, 2 years ago
Move in a new method of CLocalView the management of a without redundancy full view connector (used in hash computation of elements)
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: 126.7 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	{
[2385]	80	int globalSize = domain->ni_glo.getValue()*domain->nj_glo.getValue();
	81	CArray<size_t,1> globalIndex; // No redundancy globalIndex will be computed with the connector
	82	shared_ptr<CGridTransformConnector> gridTransformConnector;
[2381]	83	// Compute a without redundancy element FULL view to enable a consistent hash computation
[2385]	84	domain->getLocalView(CElementView::FULL)->createWithoutRedundancyFullViewConnector( globalSize, comm_file, gridTransformConnector, globalIndex );
	85	int localSize = globalIndex.numElements();
	86
[2381]	87	CArray<double,1> lon_distributedValue, lat_distributedValue ;
	88	gridTransformConnector->transfer(domain->lonvalue, lon_distributedValue );
	89	gridTransformConnector->transfer(domain->latvalue, lat_distributedValue );
	90
	91	// Compute the distributed hash (v0) of the element
	92	// it will be associated to the default element name (= map key), and to the name really written
	93	int localHash = 0;
	94	for (int iloc=0; iloc<localSize ; iloc++ ) localHash+=globalIndex(iloc)lon_distributedValue(iloc)lat_distributedValue(iloc);
	95	int globalHash(0);
	96	MPI_Allreduce( &localHash, &globalHash, 1, MPI_INT, MPI_SUM, comm_file );
	97
	98	StdString defaultNameKey = domain->getDomainOutputName();
[2384]	99	if ( !relDomains_.count ( defaultNameKey ) )
[2381]	100	{
	101	// if defaultNameKey not in the map, write the element such as it is defined
[2384]	102	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) );
[2381]	103	}
	104	else // look if a hash associated this key is equal
	105	{
	106	bool elementIsInMap(false);
[2384]	107	auto defaultNameKeyElements = relDomains_.equal_range( defaultNameKey );
[2381]	108	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
	109	{
	110	if ( it->second.first == globalHash )
	111	{
	112	// if yes, associate the same ids to current element
[2384]	113	domain->name = it->second.second->getDomainOutputName();
	114	domain->lon_name = it->second.second->lon_name;
	115	domain->lat_name = it->second.second->lat_name;
[2381]	116	elementIsInMap = true;
	117	}
	118	}
	119	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
	120	if (!elementIsInMap) // ! in MAP
	121	{
	122	domain->name = domain->getId();
	123	domain->lon_name = "lon_"+domain->getId();
	124	domain->lat_name = "lat_"+domain->getId();
[2384]	125	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) ) ;
[2381]	126	}
	127	}
	128	}
	129
	130
[219]	131	std::vector<StdString> dim0, dim1;
[772]	132	StdString domid = domain->getDomainOutputName();
[318]	133	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
[706]	134	if (isWrittenDomain(domid)) return ;
[774]	135	else setWrittenDomain(domid);
[1132]	136
	137	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
[449]	138
[488]	139
[1158]	140	StdString dimXid, dimYid ;
	141
	142	nc_type typePrec ;
	143	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	144	else if (domain->prec==4) typePrec = NC_FLOAT ;
	145	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	146
[664]	147	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
[449]	148	switch (domain->type)
[433]	149	{
[449]	150	case CDomain::type_attr::curvilinear :
[1391]	151
	152	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
	153	else lonName = domain->lon_name;
	154
	155	if (domain->lat_name.isEmpty()) latName = "nav_lat";
	156	else latName = domain->lat_name;
	157
[1430]	158	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
	159	else dimXid=domain->dim_i_name.getValue() + appendDomid;
	160
	161	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
	162	else dimYid=domain->dim_j_name.getValue() + appendDomid;
	163
[449]	164	break ;
[1391]	165
[664]	166	case CDomain::type_attr::rectilinear :
[1391]	167
[1430]	168	if (domain->lon_name.isEmpty())
	169	{
	170	if (domain->dim_i_name.isEmpty())
	171	lonName = "lon";
	172	else
	173	lonName = domain->dim_i_name.getValue();
	174	}
[1391]	175	else lonName = domain->lon_name;
	176
[1430]	177	if (domain->lat_name.isEmpty())
	178	{
	179	if (domain->dim_j_name.isEmpty())
	180	latName = "lat";
	181	else
	182	latName = domain->dim_j_name.getValue();
	183	}
[1391]	184	else latName = domain->lat_name;
	185
[1430]	186	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
	187	else dimXid = domain->dim_i_name.getValue()+appendDomid;
	188
	189	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
	190	else dimYid = domain->dim_j_name.getValue()+appendDomid;
[449]	191	break;
[488]	192	}
	193
[617]	194	StdString dimVertId = StdString("nvertex").append(appendDomid);
	195
[449]	196	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	197	string areaId = "area" + appendDomid;
[219]	198
[498]	199	try
[219]	200	{
[498]	201	switch (SuperClass::type)
	202	{
	203	case (MULTI_FILE) :
	204	{
	205	switch (domain->type)
	206	{
	207	case CDomain::type_attr::curvilinear :
	208	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1415]	209	lonid = lonName+appendDomid;
	210	latid = latName+appendDomid;
[498]	211	break ;
[664]	212	case CDomain::type_attr::rectilinear :
[1415]	213	lonid = lonName+appendDomid;
	214	latid = latName+appendDomid;
[498]	215	dim0.push_back(dimYid);
	216	dim1.push_back(dimXid);
	217	break;
	218	}
[1430]	219	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	220	else bounds_lonid = "bounds_"+lonName+appendDomid;
	221	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	222	else bounds_latid = "bounds_"+latName+appendDomid;
[488]	223
[1553]	224	SuperClassWriter::addDimension(dimXid, domain->ni);
	225	SuperClassWriter::addDimension(dimYid, domain->nj);
[488]	226
[617]	227	if (domain->hasBounds)
	228	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	229
[1853]	230	if (context->intraCommSize_ > 1)
[498]	231	{
[1553]	232	this->writeLocalAttributes(domain->ibegin,
	233	domain->ni,
	234	domain->jbegin,
	235	domain->nj,
[616]	236	appendDomid);
[488]	237
[628]	238	if (singleDomain)
	239	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
[1553]	240	domain->ibegin,
	241	domain->ni,
	242	domain->jbegin,
	243	domain->nj,
[628]	244	domain->ni_glo,domain->nj_glo,
[1853]	245	context->intraCommRank_,context->intraCommSize_);
[449]	246	}
[488]	247
[665]	248	if (domain->hasLonLat)
[498]	249	{
[665]	250	switch (domain->type)
	251	{
	252	case CDomain::type_attr::curvilinear :
[1456]	253	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	254	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	255	break ;
	256	case CDomain::type_attr::rectilinear :
[1456]	257	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	258	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
[665]	259	break ;
	260	}
[488]	261
[665]	262	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	263	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
[219]	264
[665]	265	if (domain->hasBounds)
	266	{
	267	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	268	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
[617]	269
[665]	270	dim0.clear();
	271	dim0.push_back(dimYid);
	272	dim0.push_back(dimXid);
	273	dim0.push_back(dimVertId);
[1456]	274	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	275	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[665]	276	}
[617]	277	}
	278
[498]	279	dim0.clear();
[616]	280	dim0.push_back(dimYid);
[498]	281	dim0.push_back(dimXid);
[219]	282
[611]	283	if (domain->hasArea)
	284	{
[1456]	285	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	286	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	287	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	288	}
	289
[498]	290	SuperClassWriter::definition_end();
[449]	291
[665]	292	if (domain->hasLonLat)
[498]	293	{
[665]	294	switch (domain->type)
	295	{
[1129]	296	case CDomain::type_attr::curvilinear :
[1930]	297	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
	298	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
[665]	299	break;
	300	case CDomain::type_attr::rectilinear :
[1930]	301	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
[665]	302	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
[1930]	303	CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
[665]	304	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
	305	break;
	306	}
[611]	307
[665]	308	if (domain->hasBounds)
	309	{
[1930]	310	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
	311	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
[665]	312	}
[617]	313	}
	314
[611]	315	if (domain->hasArea)
[1129]	316	{
[1930]	317	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
[1129]	318	}
	319
[498]	320	SuperClassWriter::definition_start();
[219]	321
[498]	322	break;
	323	}
	324	case (ONE_FILE) :
	325	{
[1553]	326	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
	327	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
[286]	328
[617]	329	if (domain->hasBounds)
	330	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	331
[665]	332	if (domain->hasLonLat)
[498]	333	{
[665]	334	switch (domain->type)
	335	{
	336	case CDomain::type_attr::curvilinear :
	337	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1415]	338	lonid = lonName+appendDomid;
	339	latid = latName+appendDomid;
[1456]	340	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	341	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	342	break;
[449]	343
[665]	344	case CDomain::type_attr::rectilinear :
	345	dim0.push_back(dimYid);
	346	dim1.push_back(dimXid);
[1415]	347	lonid = lonName+appendDomid;
	348	latid = latName+appendDomid;
[1456]	349	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	350	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
[665]	351	break;
	352	}
[1430]	353	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	354	else bounds_lonid = "bounds_"+lonName+appendDomid;
	355	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	356	else bounds_latid = "bounds_"+latName+appendDomid;
[665]	357
	358	this->writeAxisAttributes
	359	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	360	this->writeAxisAttributes
	361	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
	362
	363	if (domain->hasBounds)
	364	{
	365	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	366	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
	367
	368	dim0.clear();
[498]	369	dim0.push_back(dimYid);
[665]	370	dim0.push_back(dimXid);
	371	dim0.push_back(dimVertId);
[1456]	372	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	373	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[665]	374	}
[498]	375	}
[611]	376
	377	if (domain->hasArea)
	378	{
	379	dim0.clear();
	380	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1456]	381	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	382	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	383	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	384	dim0.clear();
	385	}
	386
	387	SuperClassWriter::definition_end();
[286]	388
[498]	389	switch (domain->type)
[384]	390	{
[498]	391	case CDomain::type_attr::curvilinear :
[449]	392	{
[498]	393	std::vector<StdSize> start(2) ;
	394	std::vector<StdSize> count(2) ;
[1959]	395	start[1]=domain->ibegin;
	396	start[0]=domain->jbegin;
	397	count[1]=domain->ni ; count[0]=domain->nj ;
[488]	398
[665]	399	if (domain->hasLonLat)
	400	{
[1930]	401	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
	402	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
[665]	403	}
[498]	404	break;
	405	}
[664]	406	case CDomain::type_attr::rectilinear :
[449]	407	{
[665]	408	if (domain->hasLonLat)
[498]	409	{
[665]	410	std::vector<StdSize> start(1) ;
	411	std::vector<StdSize> count(1) ;
[1930]	412
	413	start[0]=domain->jbegin;
	414	count[0]=domain->nj;
	415	CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni));
	416	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
[665]	417
[1930]	418	start[0]=domain->ibegin;
	419	count[0]=domain->ni;
	420	CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1));
	421	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
[498]	422	}
	423	break;
[449]	424	}
[384]	425	}
[611]	426
[617]	427	if (domain->hasBounds)
	428	{
	429	std::vector<StdSize> start(3);
	430	std::vector<StdSize> count(3);
	431	if (domain->isEmpty())
	432	{
	433	start[2] = start[1] = start[0] = 0;
	434	count[2] = count[1] = count[0] = 0;
	435	}
	436	else
	437	{
	438	start[2] = 0;
[1553]	439	start[1] = domain->ibegin;
	440	start[0] = domain->jbegin;
[1099]	441	count[2] = domain->nvertex;
[1553]	442	count[1] = domain->ni;
	443	count[0] = domain->nj;
[617]	444	}
[1143]	445
[1930]	446	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
	447	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
[617]	448	}
	449
[611]	450	if (domain->hasArea)
	451	{
	452	std::vector<StdSize> start(2);
	453	std::vector<StdSize> count(2);
	454
[1930]	455	start[1] = domain->ibegin;
	456	start[0] = domain->jbegin;
	457	count[1] = domain->ni;
	458	count[0] = domain->nj;
[1143]	459
[1930]	460	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
[611]	461	}
	462
[498]	463	SuperClassWriter::definition_start();
	464	break;
	465	}
	466	default :
	467	ERROR("CNc4DataOutput::writeDomain(domain)",
	468	<< "[ type = " << SuperClass::type << "]"
	469	<< " not implemented yet !");
	470	}
[449]	471	}
[498]	472	catch (CNetCdfException& e)
	473	{
	474	StdString msg("On writing the domain : ");
	475	msg.append(domid); msg.append("\n");
	476	msg.append("In the context : ");
	477	msg.append(context->getId()); msg.append("\n");
	478	msg.append(e.what());
	479	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
	480	}
	481
[449]	482	domain->addRelFile(this->filename);
	483	}
[1622]	484	CATCH
[449]	485
[879]	486	//--------------------------------------------------------------
[878]	487
[879]	488	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
	489	{
	490	CContext* context = CContext::getCurrent() ;
[878]	491
[879]	492	if (domain->IsWritten(this->filename)) return;
[1494]	493
	494	StdString domid = domain->getDomainOutputName();
	495
	496	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
	497	// Thus the entire mesh connectivity will be generated at once.
	498	if (isWrittenDomain(domid)) return ;
	499	else setWrittenDomain(domid);
	500
[879]	501	domain->checkAttributes();
	502	if (domain->isEmpty())
	503	if (SuperClass::type==MULTI_FILE) return ;
[878]	504
[1158]	505	nc_type typePrec ;
	506	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	507	else if (domain->prec==4) typePrec = NC_FLOAT ;
	508	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	509
[879]	510	std::vector<StdString> dim0;
	511	StdString domainName = domain->name;
[924]	512	domain->assignMesh(domainName, domain->nvertex);
[1853]	513	domain->mesh->createMeshEpsilon(context->intraComm_, domain->lonvalue, domain->latvalue, domain->bounds_lonvalue, domain->bounds_latvalue);
[878]	514
[879]	515	StdString node_x = domainName + "_node_x";
	516	StdString node_y = domainName + "_node_y";
[878]	517
[879]	518	StdString edge_x = domainName + "_edge_x";
	519	StdString edge_y = domainName + "_edge_y";
	520	StdString edge_nodes = domainName + "_edge_nodes";
[878]	521
[879]	522	StdString face_x = domainName + "_face_x";
	523	StdString face_y = domainName + "_face_y";
	524	StdString face_nodes = domainName + "_face_nodes";
[902]	525	StdString face_edges = domainName + "_face_edges";
	526	StdString edge_faces = domainName + "_edge_face_links";
	527	StdString face_faces = domainName + "_face_links";
[878]	528
[879]	529	StdString dimNode = "n" + domainName + "_node";
	530	StdString dimEdge = "n" + domainName + "_edge";
	531	StdString dimFace = "n" + domainName + "_face";
	532	StdString dimVertex = "n" + domainName + "_vertex";
	533	StdString dimTwo = "Two";
[878]	534
[879]	535	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
[1494]	536	dim0.clear();
	537	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
	538	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
	539	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
	540	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
	541	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
[878]	542
[879]	543	try
	544	{
	545	switch (SuperClass::type)
	546	{
	547	case (ONE_FILE) :
	548	{
	549	// Adding nodes
	550	if (domain->nvertex == 1)
	551	{
	552	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	553	{
[902]	554	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
[879]	555	dim0.clear();
	556	dim0.push_back(dimNode);
[1456]	557	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	558	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	559	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	560	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	561	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	562	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	563	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	564	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	565	}
	566	} // domain->nvertex == 1
[878]	567
[879]	568	// Adding edges and nodes, if nodes have not been defined previously
	569	if (domain->nvertex == 2)
	570	{
	571	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	572	{
[924]	573	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	574	dim0.clear();
	575	dim0.push_back(dimNode);
[1456]	576	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	577	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	578	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	579	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	580	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	581	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	582	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	583	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	584	}
[924]	585	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
	586	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	587	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
	588	dim0.clear();
	589	dim0.push_back(dimEdge);
[1456]	590	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
[924]	591	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
	592	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
	593	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
[1456]	594	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
[924]	595	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
	596	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
	597	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	598	dim0.clear();
	599	dim0.push_back(dimEdge);
	600	dim0.push_back(dimTwo);
[1456]	601	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
[924]	602	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	603	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	604	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
[879]	605	} // domain->nvertex == 2
[878]	606
[879]	607	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
	608	if (domain->nvertex > 2)
	609	{
	610	// Nodes
	611	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	612	{
[924]	613	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	614	dim0.clear();
	615	dim0.push_back(dimNode);
[1456]	616	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	617	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	618	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	619	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	620	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	621	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	622	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	623	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	624	}
	625	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
	626	{
	627	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	628	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
[924]	629	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
[879]	630	dim0.clear();
	631	dim0.push_back(dimEdge);
[1456]	632	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
[879]	633	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
[924]	634	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
[879]	635	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
[1456]	636	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
[879]	637	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
[924]	638	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
[879]	639	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	640	dim0.clear();
	641	dim0.push_back(dimEdge);
	642	dim0.push_back(dimTwo);
[1456]	643	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
[879]	644	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	645	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	646	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
	647	}
[924]	648	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
	649	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
	650	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
	651	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
	652	dim0.clear();
	653	dim0.push_back(dimFace);
[1456]	654	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
[924]	655	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
	656	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
	657	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
[1456]	658	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
[924]	659	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
	660	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
	661	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
	662	dim0.clear();
	663	dim0.push_back(dimFace);
	664	dim0.push_back(dimVertex);
[1456]	665	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
[924]	666	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
	667	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
	668	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
	669	dim0.clear();
	670	dim0.push_back(dimFace);
	671	dim0.push_back(dimVertex);
[1456]	672	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
[924]	673	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
	674	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
	675	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
[929]	676	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
[924]	677	dim0.clear();
	678	dim0.push_back(dimEdge);
	679	dim0.push_back(dimTwo);
[1456]	680	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
[924]	681	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
	682	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
	683	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
	684	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
	685	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
	686	dim0.clear();
	687	dim0.push_back(dimFace);
	688	dim0.push_back(dimVertex);
[1456]	689	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
[924]	690	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
	691	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
	692	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
[929]	693	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
[924]	694	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
	695	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
[879]	696	} // domain->nvertex > 2
[878]	697
[879]	698	SuperClassWriter::definition_end();
[878]	699
[924]	700	std::vector<StdSize> startEdges(1) ;
	701	std::vector<StdSize> countEdges(1) ;
	702	std::vector<StdSize> startNodes(1) ;
	703	std::vector<StdSize> countNodes(1) ;
	704	std::vector<StdSize> startFaces(1) ;
	705	std::vector<StdSize> countFaces(1) ;
	706	std::vector<StdSize> startEdgeNodes(2) ;
	707	std::vector<StdSize> countEdgeNodes(2) ;
	708	std::vector<StdSize> startEdgeFaces(2) ;
	709	std::vector<StdSize> countEdgeFaces(2) ;
	710	std::vector<StdSize> startFaceConctv(2) ;
	711	std::vector<StdSize> countFaceConctv(2) ;
[902]	712
[1494]	713	if (domain->nvertex == 1)
[879]	714	{
[1494]	715	if (domain->isEmpty())
	716	{
	717	startNodes[0]=0 ;
	718	countNodes[0]=0 ;
	719	}
	720	else
	721	{
[1553]	722	startNodes[0] = domain->ibegin;
	723	countNodes[0] = domain->ni ;
[1494]	724	}
[924]	725
[1494]	726	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	727	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	728	}
	729	else if (domain->nvertex == 2)
	730	{
	731	if (domain->isEmpty())
	732	{
	733	startEdges[0]=0 ;
	734	countEdges[0]=0 ;
	735	startNodes[0]=0 ;
	736	countNodes[0]=0 ;
	737	startEdgeNodes[0]=0;
	738	startEdgeNodes[1]=0;
	739	countEdgeNodes[0]=0;
	740	countEdgeNodes[1]=0;
[924]	741
[1494]	742	}
	743	else
	744	{
[1553]	745	startEdges[0] = domain->ibegin;
	746	countEdges[0] = domain->ni;
[1494]	747	startNodes[0] = domain->mesh->node_start;
	748	countNodes[0] = domain->mesh->node_count;
[1553]	749	startEdgeNodes[0] = domain->ibegin;
[1494]	750	startEdgeNodes[1] = 0;
[1553]	751	countEdgeNodes[0] = domain->ni;
[1494]	752	countEdgeNodes[1] = 2;
	753	}
	754	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	755	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	756	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	757	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	758	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	759	}
[879]	760	else
	761	{
[1494]	762	if (domain->isEmpty())
	763	{
	764	startFaces[0] = 0 ;
	765	countFaces[0] = 0 ;
	766	startNodes[0] = 0;
	767	countNodes[0] = 0;
	768	startEdges[0] = 0;
	769	countEdges[0] = 0;
	770	startEdgeFaces[0] = 0;
	771	startEdgeFaces[1] = 0;
	772	countEdgeFaces[0] = 0;
	773	countEdgeFaces[1] = 0;
	774	startFaceConctv[0] = 0;
	775	startFaceConctv[1] = 0;
	776	countFaceConctv[0] = 0;
	777	countFaceConctv[1] = 0;
	778	}
	779	else
	780	{
[1553]	781	startFaces[0] = domain->ibegin;
	782	countFaces[0] = domain->ni ;
[1494]	783	startNodes[0] = domain->mesh->node_start;
	784	countNodes[0] = domain->mesh->node_count;
	785	startEdges[0] = domain->mesh->edge_start;
	786	countEdges[0] = domain->mesh->edge_count;
	787	startEdgeNodes[0] = domain->mesh->edge_start;
	788	startEdgeNodes[1] = 0;
	789	countEdgeNodes[0] = domain->mesh->edge_count;
	790	countEdgeNodes[1]= 2;
	791	startEdgeFaces[0] = domain->mesh->edge_start;
	792	startEdgeFaces[1]= 0;
	793	countEdgeFaces[0] = domain->mesh->edge_count;
	794	countEdgeFaces[1]= 2;
[1553]	795	startFaceConctv[0] = domain->ibegin;
[1494]	796	startFaceConctv[1] = 0;
[1553]	797	countFaceConctv[0] = domain->ni;
[1494]	798	countFaceConctv[1] = domain->nvertex;
	799	}
	800	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	801	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	802	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	803	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	804	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	805	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
	806	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
	807	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
	808	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
	809	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
	810	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
	811	}
[879]	812	SuperClassWriter::definition_start();
[878]	813
[879]	814	break;
	815	} // ONE_FILE
[878]	816
[879]	817	case (MULTI_FILE) :
	818	{
[1637]	819	ERROR("CNc4DataOutput::writeDomain(domain)",
	820	<< "[ type = multiple_file ]"
	821	<< " is not yet implemented for UGRID files !");
[879]	822	break;
	823	}
[878]	824
[879]	825	default :
	826	ERROR("CNc4DataOutput::writeDomain(domain)",
	827	<< "[ type = " << SuperClass::type << "]"
	828	<< " not implemented yet !");
	829	} // switch
	830	} // try
[878]	831
[879]	832	catch (CNetCdfException& e)
	833	{
	834	StdString msg("On writing the domain : ");
	835	msg.append(domid); msg.append("\n");
	836	msg.append("In the context : ");
	837	msg.append(context->getId()); msg.append("\n");
	838	msg.append(e.what());
[924]	839	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
[879]	840	}
[878]	841
[879]	842	domain->addRelFile(this->filename);
	843	}
[878]	844
[879]	845	//--------------------------------------------------------------
[878]	846
[879]	847	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
[449]	848	{
	849	CContext* context = CContext::getCurrent() ;
[488]	850
[449]	851	if (domain->IsWritten(this->filename)) return;
	852	domain->checkAttributes();
[488]	853
	854	if (domain->isEmpty())
[449]	855	if (SuperClass::type==MULTI_FILE) return ;
	856
	857	std::vector<StdString> dim0, dim1;
[772]	858	StdString domid = domain->getDomainOutputName();
[705]	859	if (isWrittenDomain(domid)) return ;
[774]	860	else setWrittenDomain(domid);
[705]	861
[449]	862	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
	863
[1430]	864	StdString lonName,latName, cellName ;
[1391]	865	if (domain->lon_name.isEmpty()) lonName = "lon";
	866	else lonName = domain->lon_name;
	867
	868	if (domain->lat_name.isEmpty()) latName = "lat";
	869	else latName = domain->lat_name;
	870
[1430]	871	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
	872	else cellName="cell";
	873	StdString dimXid = cellName+appendDomid;
[449]	874	StdString dimVertId = StdString("nvertex").append(appendDomid);
[488]	875
[449]	876	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	877	string areaId = "area" + appendDomid;
[449]	878
[1158]	879	nc_type typePrec ;
	880	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	881	else if (domain->prec==4) typePrec = NC_FLOAT ;
	882	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	883
[1132]	884	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
[1025]	885
[498]	886	try
[449]	887	{
[498]	888	switch (SuperClass::type)
	889	{
	890	case (MULTI_FILE) :
	891	{
	892	dim0.push_back(dimXid);
[1553]	893	SuperClassWriter::addDimension(dimXid, domain->ni);
[488]	894
[1415]	895	lonid = lonName+appendDomid;
	896	latid = latName+appendDomid;
[1430]	897	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	898	else bounds_lonid = "bounds_"+lonName+appendDomid;
	899	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	900	else bounds_latid = "bounds_"+latName+appendDomid;
	901
[665]	902	if (domain->hasLonLat)
	903	{
[1456]	904	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	905	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	906	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	907	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	908	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	909	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
	910	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	911	}
[498]	912	dim0.clear();
	913	if (domain->hasBounds)
	914	{
	915	dim0.push_back(dimXid);
	916	dim0.push_back(dimVertId);
[1456]	917	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	918	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[498]	919	}
	920
	921	dim0.clear();
[449]	922	dim0.push_back(dimXid);
[611]	923	if (domain->hasArea)
	924	{
[1456]	925	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	926	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	927	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	928	}
	929
[498]	930	SuperClassWriter::definition_end();
[449]	931
[665]	932	if (domain->hasLonLat)
[498]	933	{
[1930]	934	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
	935	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
[665]	936	if (domain->hasBounds)
	937	{
[1930]	938	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
	939	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
[665]	940	}
[498]	941	}
[611]	942
	943	if (domain->hasArea)
[1930]	944	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
[611]	945
[498]	946	SuperClassWriter::definition_start();
	947	break ;
	948	}
[488]	949
[498]	950	case (ONE_FILE) :
	951	{
[1415]	952	lonid = lonName+appendDomid;
	953	latid = latName+appendDomid;
[1430]	954	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	955	else bounds_lonid = "bounds_"+lonName+appendDomid;
	956	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	957	else bounds_latid = "bounds_"+latName+appendDomid;
[1391]	958
[498]	959	dim0.push_back(dimXid);
[1132]	960	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
[665]	961	if (domain->hasLonLat)
	962	{
[1456]	963	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	964	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	965
	966	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	967	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	968	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	969	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
[1025]	970	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
[665]	971	}
[498]	972	dim0.clear();
[449]	973
[498]	974	if (domain->hasBounds)
	975	{
	976	dim0.push_back(dimXid);
	977	dim0.push_back(dimVertId);
[1456]	978	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	979	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[498]	980	}
[488]	981
[611]	982	if (domain->hasArea)
	983	{
	984	dim0.clear();
	985	dim0.push_back(dimXid);
[1456]	986	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	987	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	988	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	989	}
	990
[498]	991	SuperClassWriter::definition_end();
[488]	992
[498]	993	std::vector<StdSize> start(1), startBounds(2) ;
	994	std::vector<StdSize> count(1), countBounds(2) ;
	995	if (domain->isEmpty())
	996	{
	997	start[0]=0 ;
	998	count[0]=0 ;
	999	startBounds[1]=0 ;
[1025]	1000	countBounds[1]=nvertex ;
[498]	1001	startBounds[0]=0 ;
	1002	countBounds[0]=0 ;
	1003	}
	1004	else
	1005	{
[1553]	1006	start[0]=domain->ibegin;
	1007	count[0]=domain->ni;
	1008	startBounds[0]=domain->ibegin;
[498]	1009	startBounds[1]=0 ;
[1553]	1010	countBounds[0]=domain->ni;
[1025]	1011	countBounds[1]=nvertex ;
[498]	1012	}
[665]	1013
	1014	if (domain->hasLonLat)
[498]	1015	{
[1930]	1016	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
	1017	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
[665]	1018	if (domain->hasBounds)
	1019	{
[1930]	1020	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
	1021	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
[665]	1022	}
[498]	1023	}
[488]	1024
[611]	1025	if (domain->hasArea)
[1930]	1026	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
[488]	1027
[498]	1028	SuperClassWriter::definition_start();
[488]	1029
[498]	1030	break;
	1031	}
	1032	default :
	1033	ERROR("CNc4DataOutput::writeDomain(domain)",
	1034	<< "[ type = " << SuperClass::type << "]"
	1035	<< " not implemented yet !");
	1036	}
[219]	1037	}
[498]	1038	catch (CNetCdfException& e)
	1039	{
	1040	StdString msg("On writing the domain : ");
	1041	msg.append(domid); msg.append("\n");
	1042	msg.append("In the context : ");
	1043	msg.append(context->getId()); msg.append("\n");
	1044	msg.append(e.what());
	1045	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
	1046	}
[219]	1047	domain->addRelFile(this->filename);
	1048	}
	1049	//--------------------------------------------------------------
	1050
[347]	1051	void CNc4DataOutput::writeAxis_(CAxis* axis)
[219]	1052	{
[1030]	1053	if (axis->IsWritten(this->filename)) return;
[2381]	1054
	1055	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
	1056	if (!axis->value.isEmpty() )
	1057	{
[2385]	1058	int globalSize = axis->n_glo.getValue();
	1059	CArray<size_t,1> globalIndex; // No redundancy globalIndex will be computed with the connector
	1060	shared_ptr<CGridTransformConnector> gridTransformConnector;
	1061	// Compute a without redundancy element FULL view to enable a consistent hash computation
	1062	axis->getLocalView(CElementView::FULL)->createWithoutRedundancyFullViewConnector( globalSize, comm_file, gridTransformConnector, globalIndex );
	1063	int localSize = globalIndex.numElements();
[2381]	1064
	1065	CArray<double,1> distributedValue ;
	1066	gridTransformConnector->transfer(axis->value, distributedValue );
	1067
	1068	// Compute the distributed hash (v0) of the element
	1069	// it will be associated to the default element name (= map key), and to the name really written
	1070	int localHash = 0;
	1071	for (int iloc=0; iloc<localSize ; iloc++ ) localHash+=globalIndex(iloc)*distributedValue(iloc);
	1072	int globalHash(0);
	1073	MPI_Allreduce( &localHash, &globalHash, 1, MPI_INT, MPI_SUM, comm_file );
	1074
	1075	StdString defaultNameKey = axis->getAxisOutputName();
	1076	if ( !relElements_.count ( defaultNameKey ) )
	1077	{
	1078	// if defaultNameKey not in the map, write the element such as it is defined
	1079	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, defaultNameKey) ) );
	1080	}
	1081	else // look if a hash associated this key is equal
	1082	{
	1083	bool elementIsInMap(false);
	1084	auto defaultNameKeyElements = relElements_.equal_range( defaultNameKey );
	1085	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
	1086	{
	1087	if ( it->second.first == globalHash )
	1088	{
	1089	// if yes, associate the same ids to current element
	1090	axis->name = it->second.second;
	1091	elementIsInMap = true;
	1092	}
	1093	}
	1094	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
	1095	if (!elementIsInMap) // ! in MAP
	1096	{
	1097	axis->name = axis->getId();
	1098	relElements_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis->getAxisOutputName()) ) ) ;// = axis->getId()
	1099	}
	1100	}
	1101	}
	1102
[1030]	1103	axis->checkAttributes();
[488]	1104
[1559]	1105	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
	1106	: axis->n_glo.getValue();
[1099]	1107
[1559]	1108	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
[1235]	1109
[1030]	1110	std::vector<StdString> dims;
	1111	StdString axisid = axis->getAxisOutputName();
[1435]	1112	StdString axisDim, axisBoundsId;
[1030]	1113	if (isWrittenAxis(axisid)) return ;
	1114	else setWrittenAxis(axisid);
[705]	1115
[1158]	1116	nc_type typePrec ;
	1117	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
[1235]	1118	else if (axis->prec==4) typePrec = NC_FLOAT ;
[1158]	1119	else if (axis->prec==8) typePrec = NC_DOUBLE ;
	1120
	1121	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
	1122	string strId="str_len" ;
[1030]	1123	try
	1124	{
[1433]	1125	if (axis->dim_name.isEmpty()) axisDim = axisid;
	1126	else axisDim=axis->dim_name.getValue();
[1559]	1127	SuperClassWriter::addDimension(axisDim, size);
[1433]	1128	dims.push_back(axisDim);
	1129
[1439]	1130	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
[1433]	1131
[1435]	1132	if (axis->hasValue \|\| !axis->label.isEmpty())
[816]	1133	{
[1158]	1134	if (!axis->label.isEmpty()) dims.push_back(strId);
[1430]	1135
[1456]	1136	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
[219]	1137
[1030]	1138	if (!axis->name.isEmpty())
	1139	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
[219]	1140
[1030]	1141	if (!axis->standard_name.isEmpty())
	1142	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
[540]	1143
[1030]	1144	if (!axis->long_name.isEmpty())
	1145	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
[219]	1146
[1030]	1147	if (!axis->unit.isEmpty())
	1148	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
[219]	1149
[1430]	1150	if (!axis->axis_type.isEmpty())
	1151	{
	1152	switch(axis->axis_type)
	1153	{
	1154	case CAxis::axis_type_attr::X :
	1155	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
	1156	break;
	1157	case CAxis::axis_type_attr::Y :
	1158	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
	1159	break;
	1160	case CAxis::axis_type_attr::Z :
	1161	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
	1162	break;
	1163	case CAxis::axis_type_attr::T :
	1164	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
	1165	break;
	1166	}
	1167	}
	1168
[1030]	1169	if (!axis->positive.isEmpty())
	1170	{
	1171	SuperClassWriter::addAttribute("positive",
	1172	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
	1173	&axisid);
	1174	}
[399]	1175
[1266]	1176	if (!axis->formula.isEmpty())
	1177	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
	1178
	1179	if (!axis->formula_term.isEmpty())
	1180	SuperClassWriter::addAttribute("formula_term", axis->formula_term.getValue(), &axisid);
	1181
[1435]	1182	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
[1249]	1183	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
[1030]	1184	{
	1185	dims.push_back("axis_nbounds");
[1456]	1186	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
[1030]	1187	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
[1288]	1188
	1189	if (!axis->standard_name.isEmpty())
	1190	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
	1191
	1192	if (!axis->unit.isEmpty())
	1193	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
	1194
[1266]	1195	if (!axis->formula_bounds.isEmpty())
[1288]	1196	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
[1266]	1197
	1198	if (!axis->formula_term_bounds.isEmpty())
[1288]	1199	SuperClassWriter::addAttribute("formula_term", axis->formula_term_bounds.getValue(), &axisBoundsId);
[1030]	1200	}
[1435]	1201	}
[816]	1202
[1435]	1203	SuperClassWriter::definition_end();
[1950]	1204
[1435]	1205	switch (SuperClass::type)
	1206	{
	1207	case MULTI_FILE:
[1030]	1208	{
[1435]	1209	if (axis->label.isEmpty())
[1437]	1210	{
	1211	if (!axis->value.isEmpty())
[1930]	1212	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
[633]	1213
[1437]	1214	if (!axis->bounds.isEmpty())
[1930]	1215	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
[1435]	1216	}
[1437]	1217	else
[1950]	1218	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
[1435]	1219
	1220	SuperClassWriter::definition_start();
	1221	break;
	1222	}
	1223	case ONE_FILE:
	1224	{
	1225	std::vector<StdSize> start(1), startBounds(2) ;
	1226	std::vector<StdSize> count(1), countBounds(2) ;
[1559]	1227	start[0] = startBounds[0] = axis->begin;
	1228	count[0] = countBounds[0] = axis->n;
[1435]	1229	startBounds[1] = 0;
	1230	countBounds[1] = 2;
	1231
	1232	if (axis->label.isEmpty())
[1437]	1233	{
	1234	if (!axis->value.isEmpty())
[1930]	1235	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
[1435]	1236
[1437]	1237	if (!axis->bounds.isEmpty())
[1930]	1238	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
[1435]	1239	}
[1437]	1240	else
[1435]	1241	{
	1242	std::vector<StdSize> startLabel(2), countLabel(2);
	1243	startLabel[0] = start[0]; startLabel[1] = 0;
	1244	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
[1950]	1245	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
[1435]	1246	}
[609]	1247
[1435]	1248	SuperClassWriter::definition_start();
	1249
	1250	break;
[609]	1251	}
[1435]	1252	default :
	1253	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
	1254	<< "[ type = " << SuperClass::type << "]"
	1255	<< " not implemented yet !");
[609]	1256	}
[1030]	1257	}
	1258	catch (CNetCdfException& e)
	1259	{
	1260	StdString msg("On writing the axis : ");
	1261	msg.append(axisid); msg.append("\n");
	1262	msg.append("In the context : ");
	1263	CContext* context = CContext::getCurrent() ;
	1264	msg.append(context->getId()); msg.append("\n");
	1265	msg.append(e.what());
	1266	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
	1267	}
[1158]	1268	axis->addRelFile(this->filename);
[391]	1269	}
[488]	1270
[887]	1271	void CNc4DataOutput::writeScalar_(CScalar* scalar)
	1272	{
	1273	if (scalar->IsWritten(this->filename)) return;
	1274	scalar->checkAttributes();
	1275	int scalarSize = 1;
	1276
	1277	StdString scalaId = scalar->getScalarOutputName();
[1430]	1278	StdString boundsId;
[887]	1279	if (isWrittenAxis(scalaId)) return ;
	1280	else setWrittenAxis(scalaId);
	1281
[1158]	1282	nc_type typePrec ;
	1283	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
	1284	else if (scalar->prec==4) typePrec = NC_FLOAT ;
	1285	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
	1286
[1435]	1287	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
	1288	string strId="str_len" ;
	1289
[887]	1290	try
	1291	{
[1439]	1292	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
[1435]	1293
	1294	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
[887]	1295	{
[1430]	1296	std::vector<StdString> dims;
	1297	StdString scalarDim = scalaId;
	1298
[1435]	1299	if (!scalar->label.isEmpty()) dims.push_back(strId);
	1300
[1158]	1301	SuperClassWriter::addVariable(scalaId, typePrec, dims);
[887]	1302
	1303	if (!scalar->name.isEmpty())
	1304	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
	1305
	1306	if (!scalar->standard_name.isEmpty())
	1307	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
	1308
	1309	if (!scalar->long_name.isEmpty())
	1310	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
	1311
	1312	if (!scalar->unit.isEmpty())
	1313	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
	1314
[1430]	1315	if (!scalar->axis_type.isEmpty())
	1316	{
	1317	switch(scalar->axis_type)
	1318	{
	1319	case CScalar::axis_type_attr::X :
	1320	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
	1321	break;
	1322	case CScalar::axis_type_attr::Y :
	1323	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
	1324	break;
	1325	case CScalar::axis_type_attr::Z :
	1326	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
	1327	break;
	1328	case CScalar::axis_type_attr::T :
	1329	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
	1330	break;
	1331	}
	1332	}
	1333
[1435]	1334	if (!scalar->positive.isEmpty())
[1430]	1335	{
[1435]	1336	SuperClassWriter::addAttribute("positive",
	1337	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
	1338	&scalaId);
	1339	}
	1340
	1341	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1342	{
[1436]	1343	dims.clear();
	1344	dims.push_back("axis_nbounds");
[1435]	1345	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
[1430]	1346	SuperClassWriter::addVariable(boundsId, typePrec, dims);
[1436]	1347	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
[1430]	1348	}
	1349
[887]	1350	SuperClassWriter::definition_end();
	1351
	1352	switch (SuperClass::type)
	1353	{
	1354	case MULTI_FILE:
	1355	{
	1356	CArray<double,1> scalarValue(scalarSize);
[1435]	1357	CArray<string,1> scalarLabel(scalarSize);
[1436]	1358	CArray<double,1> scalarBounds(scalarSize*2);
[1435]	1359
	1360	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
[1430]	1361	{
[1435]	1362	scalarValue(0) = scalar->value;
	1363	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
	1364	}
	1365
	1366	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1367	{
[1436]	1368	scalarBounds(0) = scalar->bounds(0);
	1369	scalarBounds(1) = scalar->bounds(1);
	1370	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
[1430]	1371	}
[1435]	1372
	1373	if (!scalar->label.isEmpty())
	1374	{
	1375	scalarLabel(0) = scalar->label;
	1376	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
	1377	}
	1378
[887]	1379	SuperClassWriter::definition_start();
	1380
	1381	break;
	1382	}
	1383	case ONE_FILE:
	1384	{
	1385	CArray<double,1> scalarValue(scalarSize);
[1435]	1386	CArray<string,1> scalarLabel(scalarSize);
[1436]	1387	CArray<double,1> scalarBounds(scalarSize*2);
[887]	1388
	1389	std::vector<StdSize> start(1);
	1390	std::vector<StdSize> count(1);
	1391	start[0] = 0;
	1392	count[0] = 1;
[1435]	1393	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
[1430]	1394	{
[1435]	1395	scalarValue(0) = scalar->value;
	1396	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
	1397	}
	1398	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1399	{
[1436]	1400	scalarBounds(0) = scalar->bounds(0);
	1401	scalarBounds(1) = scalar->bounds(1);
	1402	count[0] = 2;
	1403	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
[1430]	1404	}
[1435]	1405	if (!scalar->label.isEmpty())
	1406	{
	1407	scalarLabel(0) = scalar->label;
	1408	count[0] = stringArrayLen;
	1409	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
	1410	}
	1411
[887]	1412	SuperClassWriter::definition_start();
	1413
	1414	break;
	1415	}
	1416	default :
	1417	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
	1418	<< "[ type = " << SuperClass::type << "]"
	1419	<< " not implemented yet !");
	1420	}
	1421	}
	1422	}
	1423	catch (CNetCdfException& e)
	1424	{
	1425	StdString msg("On writing the scalar : ");
	1426	msg.append(scalaId); msg.append("\n");
	1427	msg.append("In the context : ");
	1428	CContext* context = CContext::getCurrent() ;
	1429	msg.append(context->getId()); msg.append("\n");
	1430	msg.append(e.what());
	1431	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
	1432	}
	1433	scalar->addRelFile(this->filename);
	1434	}
	1435
[676]	1436	//--------------------------------------------------------------
	1437
	1438	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
	1439	{
[1957]	1440	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
	1441
	1442	// NOTA : The cuurent algorithm to write compress elements of the grid
	1443	// will work pretting well when on server side you dont't get
	1444	// partial overlap on elements between differents participating process
	1445	// So the element must be totally distributed or non distributed
	1446	// If an element is partially overlaping betwwen process then the
	1447	// total compressed part will apear artificially greater than expected
	1448	// For the current implementation of writer which is decomposed only on
	1449	// one element, it will work as expected, but for future, it must be
	1450	// reconsidered again.
	1451	try
	1452	{
	1453	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1454	std::vector<StdString> domainList = grid->getDomainList();
	1455	std::vector<StdString> axisList = grid->getAxisList();
	1456	std::vector<StdString> scalarList = grid->getScalarList();
	1457	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
	1458	int commRank ;
	1459	MPI_Comm_rank(comm_file,&commRank) ;
[676]	1460
[1957]	1461	std::vector<StdString> dims;
[676]	1462
[1957]	1463	for (int i = 0; i < numElement; ++i)
	1464	{
	1465	StdString varId, compress;
	1466	CArray<size_t, 1> indexes;
	1467	bool isDistributed;
	1468	size_t nbIndexes, totalNbIndexes, offset;
	1469	size_t firstGlobalIndex;
	1470
	1471	if (2 == axisDomainOrder(i))
	1472	{
	1473	CDomain* domain = CDomain::get(domainList[idxDomain]);
	1474	StdString domId = domain->getDomainOutputName();
[676]	1475
[1957]	1476	if (!domain->isCompressible()
	1477	\|\| domain->type == CDomain::type_attr::unstructured
	1478	\|\| domain->isWrittenCompressed(this->filename)
	1479	\|\| isWrittenCompressedDomain(domId))
	1480	continue;
	1481
	1482	// unstructured grid seems not be taken into account why ?
[676]	1483
[1957]	1484	string lonName,latName ;
[676]	1485
[1957]	1486	if (domain->lon_name.isEmpty())
	1487	{
	1488	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
	1489	else lonName = "lon";
	1490	}
	1491	else lonName = domain->lon_name;
[676]	1492
[1957]	1493	if (domain->lat_name.isEmpty())
	1494	{
	1495	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
	1496	else latName = "lat";
	1497	}
	1498	else latName = domain->lat_name;
	1499
	1500	StdString appendDomId = singleDomain ? "" : "_" + domId;
[676]	1501
[1957]	1502	varId = domId + "_points";
	1503	compress = latName + appendDomId + " " + lonName + appendDomId;
	1504
[2267]	1505	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
[1957]	1506	workflowView->getGlobalIndexView(indexes) ;
	1507	nbIndexes = workflowView->getSize() ;
	1508	isDistributed = domain->isDistributed();
	1509	if (isDistributed)
	1510	{
	1511	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	1512	if (commRank==0) offset=0 ;
	1513	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
	1514	}
	1515	else
	1516	{
	1517	offset=0 ;
	1518	totalNbIndexes = nbIndexes ;
	1519	}
[676]	1520
[1957]	1521	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
[676]	1522
[1957]	1523	domain->addRelFileCompressed(this->filename);
	1524	setWrittenCompressedDomain(domId);
	1525	++idxDomain;
	1526	}
	1527	else if (1 == axisDomainOrder(i))
	1528	{
	1529	CAxis* axis = CAxis::get(axisList[idxAxis]);
	1530	StdString axisId = axis->getAxisOutputName();
[676]	1531
[1957]	1532	if (!axis->isCompressible()
	1533	\|\| axis->isWrittenCompressed(this->filename)
	1534	\|\| isWrittenCompressedAxis(axisId))
	1535	continue;
[676]	1536
[1957]	1537	varId = axisId + "_points";
	1538	compress = axisId;
[676]	1539
[2267]	1540	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
[1957]	1541	workflowView->getGlobalIndexView(indexes) ;
	1542	nbIndexes = workflowView->getSize() ;
	1543	isDistributed = axis->isDistributed();
	1544	if (isDistributed)
	1545	{
	1546	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	1547	if (commRank==0) offset=0 ;
	1548	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
	1549	}
	1550	else
	1551	{
	1552	offset=0 ;
	1553	totalNbIndexes = nbIndexes ;
	1554	}
	1555	firstGlobalIndex = axis->begin;
	1556
	1557	axis->addRelFileCompressed(this->filename);
	1558	setWrittenCompressedAxis(axisId);
	1559	++idxAxis;
	1560	}
	1561	else
	1562	{
	1563	//for scalar
	1564	}
[676]	1565
[1957]	1566	if (!varId.empty())
	1567	{
	1568	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
[774]	1569
[1957]	1570	dims.clear();
	1571	dims.push_back(varId);
	1572	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
[676]	1573
[1957]	1574	SuperClassWriter::addAttribute("compress", compress, &varId);
[676]	1575
[1957]	1576	switch (SuperClass::type)
	1577	{
	1578	case (MULTI_FILE):
	1579	{
	1580	indexes -= firstGlobalIndex;
	1581	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
	1582	break;
	1583	}
	1584	case (ONE_FILE):
	1585	{
	1586	std::vector<StdSize> start, count;
	1587	start.push_back(offset);
	1588	count.push_back(nbIndexes);
[676]	1589
[1957]	1590	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
	1591	break;
	1592	}
	1593	}
[1144]	1594	}
[1957]	1595	}
[676]	1596
[1957]	1597	grid->addRelFileCompressed(this->filename);
	1598	}
	1599	catch (CNetCdfException& e)
	1600	{
	1601	StdString msg("On writing compressed grid : ");
	1602	msg.append(grid->getId()); msg.append("\n");
	1603	msg.append("In the context : ");
	1604	CContext* context = CContext::getCurrent();
	1605	msg.append(context->getId()); msg.append("\n");
	1606	msg.append(e.what());
	1607	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
	1608	}
	1609	}
[676]	1610
	1611	//--------------------------------------------------------------
	1612
[391]	1613	void CNc4DataOutput::writeTimeDimension_(void)
	1614	{
[498]	1615	try
	1616	{
[802]	1617	SuperClassWriter::addDimension(getTimeCounterName());
[498]	1618	}
	1619	catch (CNetCdfException& e)
	1620	{
[614]	1621	StdString msg("On writing time dimension : time_couter\n");
[498]	1622	msg.append("In the context : ");
	1623	CContext* context = CContext::getCurrent() ;
	1624	msg.append(context->getId()); msg.append("\n");
	1625	msg.append(e.what());
	1626	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
	1627	}
[391]	1628	}
[676]	1629
[219]	1630	//--------------------------------------------------------------
	1631
[347]	1632	void CNc4DataOutput::writeField_(CField* field)
[219]	1633	{
[1158]	1634	CContext* context = CContext::getCurrent() ;
[300]	1635
[1158]	1636	std::vector<StdString> dims, coodinates;
[1869]	1637	CGrid* grid = field->getGrid();
[1158]	1638	if (!grid->doGridHaveDataToWrite())
[567]	1639	if (SuperClass::type==MULTI_FILE) return ;
[488]	1640
[1158]	1641	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1642	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
	1643	std::vector<StdString> domainList = grid->getDomainList();
	1644	std::vector<StdString> axisList = grid->getAxisList();
	1645	std::vector<StdString> scalarList = grid->getScalarList();
[219]	1646
[1158]	1647	StdString timeid = getTimeCounterName();
	1648	StdString dimXid,dimYid;
	1649	std::deque<StdString> dimIdList, dimCoordList;
	1650	bool hasArea = false;
	1651	StdString cellMeasures = "area:";
	1652	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
[488]	1653
[1158]	1654	for (int i = 0; i < numElement; ++i)
	1655	{
	1656	if (2 == axisDomainOrder(i))
	1657	{
	1658	CDomain* domain = CDomain::get(domainList[idxDomain]);
	1659	StdString domId = domain->getDomainOutputName();
	1660	StdString appendDomId = singleDomain ? "" : "_" + domId ;
[1391]	1661	StdString lonName,latName ;
[1430]	1662	StdString dimIname,dimJname ;
[676]	1663
[1415]	1664	if (domain->lon_name.isEmpty())
	1665	{
	1666	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
	1667	else lonName = "lon";
	1668	}
[1391]	1669	else lonName = domain->lon_name;
	1670
[1415]	1671	if (domain->lat_name.isEmpty())
	1672	{
	1673	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
	1674	else latName = "lat";
	1675	}
[1391]	1676	else latName = domain->lat_name;
[1430]	1677
	1678	if (domain->dim_i_name.isEmpty())
	1679	{
	1680	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
	1681	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
	1682	else dimIname = lonName;
	1683	}
	1684	else dimIname = domain->dim_i_name;
	1685
	1686	if (domain->dim_j_name.isEmpty())
	1687	{
	1688	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
	1689	else dimJname = latName;
	1690	}
	1691	else dimJname = domain->dim_j_name;
[1391]	1692
[1158]	1693	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
	1694	{
	1695	dimIdList.push_back(domId + "_points");
	1696	field->setUseCompressedOutput();
	1697	}
[676]	1698
[1158]	1699	switch (domain->type)
[879]	1700	{
[1158]	1701	case CDomain::type_attr::curvilinear:
	1702	if (!compressedOutput \|\| !domain->isCompressible())
	1703	{
[1430]	1704	dimXid=dimIname+appendDomId;
	1705	dimYid=dimJname+appendDomId;
[1158]	1706	dimIdList.push_back(dimXid);
	1707	dimIdList.push_back(dimYid);
	1708	}
[1415]	1709	dimCoordList.push_back(lonName+appendDomId);
	1710	dimCoordList.push_back(latName+appendDomId);
[1158]	1711	break ;
	1712	case CDomain::type_attr::rectilinear:
	1713	if (!compressedOutput \|\| !domain->isCompressible())
	1714	{
[1430]	1715	dimXid = dimIname+appendDomId;
	1716	dimYid = dimJname+appendDomId;
[1158]	1717	dimIdList.push_back(dimXid);
	1718	dimIdList.push_back(dimYid);
	1719	}
[1430]	1720	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
	1721	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
	1722
[1158]	1723	break ;
	1724	case CDomain::type_attr::unstructured:
	1725	{
	1726	if (SuperClassWriter::useCFConvention)
	1727	{
[1430]	1728	dimXid = dimIname + appendDomId;
[1158]	1729	dimIdList.push_back(dimXid);
[1415]	1730	dimCoordList.push_back(lonName+appendDomId);
	1731	dimCoordList.push_back(latName+appendDomId);
[1158]	1732	}
	1733	else
	1734	{
	1735	StdString domainName = domain->name;
	1736	if (domain->nvertex == 1)
	1737	{
	1738	dimXid = "n" + domainName + "_node";
	1739	dimIdList.push_back(dimXid);
	1740	dimCoordList.push_back(StdString(domainName + "_node_x"));
	1741	dimCoordList.push_back(StdString(domainName + "_node_y"));
	1742	}
	1743	else if (domain->nvertex == 2)
	1744	{
	1745	dimXid = "n" + domainName + "_edge";
	1746	dimIdList.push_back(dimXid);
	1747	dimCoordList.push_back(StdString(domainName + "_edge_x"));
	1748	dimCoordList.push_back(StdString(domainName + "_edge_y"));
	1749	}
	1750	else
	1751	{
	1752	dimXid = "n" + domainName + "_face";
	1753	dimIdList.push_back(dimXid);
	1754	dimCoordList.push_back(StdString(domainName + "_face_x"));
	1755	dimCoordList.push_back(StdString(domainName + "_face_y"));
	1756	}
	1757	} // ugrid convention
	1758	} // case unstructured domain
[879]	1759	}
[1158]	1760
	1761	if (domain->hasArea)
[879]	1762	{
[1158]	1763	hasArea = true;
	1764	cellMeasures += " area" + appendDomId;
[879]	1765	}
[1158]	1766	++idxDomain;
	1767	}
	1768	else if (1 == axisDomainOrder(i))
	1769	{
	1770	CAxis* axis = CAxis::get(axisList[idxAxis]);
	1771	StdString axisId = axis->getAxisOutputName();
[1430]	1772	StdString axisDim;
[1158]	1773
[1430]	1774	if (axis->dim_name.isEmpty()) axisDim = axisId;
	1775	else axisDim=axis->dim_name.getValue();
	1776
[1158]	1777	if (compressedOutput && axis->isCompressible())
[879]	1778	{
[1430]	1779	dimIdList.push_back(axisDim + "_points");
[1158]	1780	field->setUseCompressedOutput();
[879]	1781	}
[1158]	1782	else
[1430]	1783	dimIdList.push_back(axisDim);
[878]	1784
[1430]	1785	if (axisDim != axisId) dimCoordList.push_back(axisId);
[1158]	1786	++idxAxis;
	1787	}
[1430]	1788	else
[1158]	1789	{
[1430]	1790	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
	1791	StdString scalarId = scalar->getScalarOutputName();
[1446]	1792	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
	1793	dimCoordList.push_back(scalarId);
[1430]	1794	++idxScalar;
[1158]	1795	}
	1796	}
[488]	1797
[1158]	1798	StdString fieldid = field->getFieldOutputName();
[219]	1799
[1158]	1800	nc_type type ;
	1801	if (field->prec.isEmpty()) type = NC_FLOAT ;
	1802	else
	1803	{
	1804	if (field->prec==2) type = NC_SHORT ;
	1805	else if (field->prec==4) type = NC_FLOAT ;
	1806	else if (field->prec==8) type = NC_DOUBLE ;
	1807	}
[488]	1808
[1158]	1809	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
[488]	1810
[1158]	1811	if (wtime)
	1812	{
	1813	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
	1814	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
	1815	dims.push_back(timeid);
	1816	}
[488]	1817
[1961]	1818	while (!dimIdList.empty())
[1158]	1819	{
[1961]	1820	dims.push_back(dimIdList.back());
	1821	dimIdList.pop_back();
[1158]	1822	}
[219]	1823
[1158]	1824	while (!dimCoordList.empty())
	1825	{
	1826	coodinates.push_back(dimCoordList.back());
	1827	dimCoordList.pop_back();
	1828	}
[219]	1829
[1158]	1830	try
	1831	{
[498]	1832	SuperClassWriter::addVariable(fieldid, type, dims);
[488]	1833
[498]	1834	if (!field->standard_name.isEmpty())
	1835	SuperClassWriter::addAttribute
	1836	("standard_name", field->standard_name.getValue(), &fieldid);
[219]	1837
[498]	1838	if (!field->long_name.isEmpty())
	1839	SuperClassWriter::addAttribute
	1840	("long_name", field->long_name.getValue(), &fieldid);
[219]	1841
[498]	1842	if (!field->unit.isEmpty())
	1843	SuperClassWriter::addAttribute
	1844	("units", field->unit.getValue(), &fieldid);
[463]	1845
[1158]	1846	// Ugrid field attributes "mesh" and "location"
	1847	if (!SuperClassWriter::useCFConvention)
	1848	{
	1849	if (!domainList.empty())
	1850	{
	1851	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
	1852	StdString mesh = domain->name;
	1853	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
	1854	StdString location;
	1855	if (domain->nvertex == 1)
	1856	location = "node";
	1857	else if (domain->nvertex == 2)
	1858	location = "edge";
	1859	else if (domain->nvertex > 2)
	1860	location = "face";
	1861	SuperClassWriter::addAttribute("location", location, &fieldid);
	1862	}
	1863
	1864	}
	1865
	1866	if (!field->valid_min.isEmpty())
[498]	1867	SuperClassWriter::addAttribute
	1868	("valid_min", field->valid_min.getValue(), &fieldid);
[463]	1869
[498]	1870	if (!field->valid_max.isEmpty())
	1871	SuperClassWriter::addAttribute
	1872	("valid_max", field->valid_max.getValue(), &fieldid);
[464]	1873
[498]	1874	if (!field->scale_factor.isEmpty())
	1875	SuperClassWriter::addAttribute
	1876	("scale_factor", field->scale_factor.getValue(), &fieldid);
[464]	1877
[498]	1878	if (!field->add_offset.isEmpty())
	1879	SuperClassWriter::addAttribute
	1880	("add_offset", field->add_offset.getValue(), &fieldid);
[488]	1881
[498]	1882	SuperClassWriter::addAttribute
	1883	("online_operation", field->operation.getValue(), &fieldid);
[472]	1884
[498]	1885	// write child variables as attributes
[488]	1886
	1887
[1021]	1888	bool alreadyAddCellMethod = false;
	1889	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
	1890	if (!field->cell_methods.isEmpty())
	1891	{
[1158]	1892	StdString cellMethodString = field->cell_methods;
	1893	if (field->cell_methods_mode.isEmpty() \|\|
[1021]	1894	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
[1158]	1895	{
	1896	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
	1897	alreadyAddCellMethod = true;
	1898	}
	1899	else
	1900	{
	1901	switch (field->cell_methods_mode)
	1902	{
	1903	case (CField::cell_methods_mode_attr::prefix):
	1904	cellMethodsPrefix = cellMethodString;
	1905	cellMethodsPrefix += " ";
	1906	break;
	1907	case (CField::cell_methods_mode_attr::suffix):
	1908	cellMethodsSuffix = " ";
	1909	cellMethodsSuffix += cellMethodString;
	1910	break;
	1911	case (CField::cell_methods_mode_attr::none):
	1912	break;
	1913	default:
	1914	break;
	1915	}
	1916	}
[1021]	1917	}
[488]	1918
[1021]	1919
[498]	1920	if (wtime)
	1921	{
[614]	1922	CDuration freqOp = field->freq_op.getValue();
	1923	freqOp.solveTimeStep(*context->calendar);
	1924	StdString freqOpStr = freqOp.toStringUDUnits();
[612]	1925	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
[437]	1926
[614]	1927	CDuration freqOut = field->getRelFile()->output_freq.getValue();
	1928	freqOut.solveTimeStep(*context->calendar);
	1929	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
[612]	1930
[1021]	1931	StdString cellMethods(cellMethodsPrefix + "time: ");
[612]	1932	if (field->operation.getValue() == "instant") cellMethods += "point";
	1933	else if (field->operation.getValue() == "average") cellMethods += "mean";
	1934	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
	1935	else cellMethods += field->operation;
[614]	1936	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
	1937	cellMethods += " (interval: " + freqOpStr + ")";
[1021]	1938	cellMethods += cellMethodsSuffix;
	1939	if (!alreadyAddCellMethod)
	1940	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
[498]	1941	}
[488]	1942
[611]	1943	if (hasArea)
	1944	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
	1945
[498]	1946	if (!field->default_value.isEmpty())
	1947	{
[1424]	1948	double default_value = field->default_value.getValue();
	1949	if (type == NC_DOUBLE)
	1950	{
	1951	SuperClassWriter::setDefaultValue(fieldid, &default_value);
	1952	}
	1953	else if (type == NC_SHORT)
	1954	{
	1955	short sdefault_value = (short)default_value;
	1956	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
	1957	}
	1958	else
	1959	{
	1960	float fdefault_value = (float)default_value;
	1961	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
	1962	}
[498]	1963	}
	1964	else
[517]	1965	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
[219]	1966
[606]	1967	if (field->compression_level.isEmpty())
[1872]	1968	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
[606]	1969	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
	1970
[878]	1971	{ // Ecriture des coordonnes
[488]	1972
[498]	1973	StdString coordstr; //boost::algorithm::join(coodinates, " ")
	1974	std::vector<StdString>::iterator
	1975	itc = coodinates.begin(), endc = coodinates.end();
[488]	1976
[498]	1977	for (; itc!= endc; itc++)
	1978	{
	1979	StdString & coord = *itc;
	1980	if (itc+1 != endc)
	1981	coordstr.append(coord).append(" ");
	1982	else coordstr.append(coord);
	1983	}
[219]	1984
[498]	1985	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
[219]	1986
[498]	1987	}
[1222]	1988
	1989	vector<CVariable*> listVars = field->getAllVariables() ;
	1990	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
	1991
[219]	1992	}
[498]	1993	catch (CNetCdfException& e)
	1994	{
	1995	StdString msg("On writing field : ");
	1996	msg.append(fieldid); msg.append("\n");
	1997	msg.append("In the context : ");
	1998	msg.append(context->getId()); msg.append("\n");
	1999	msg.append(e.what());
	2000	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
	2001	}
[879]	2002	} // writeField_()
[219]	2003
	2004	//--------------------------------------------------------------
	2005
[347]	2006	void CNc4DataOutput::writeFile_ (CFile* file)
[219]	2007	{
[773]	2008	StdString filename = file->getFileOutputName();
[219]	2009	StdString description = (!file->description.isEmpty())
	2010	? file->description.getValue()
[335]	2011	: StdString("Created by xios");
[609]	2012
	2013	singleDomain = (file->nbDomains == 1);
	2014
[1158]	2015	StdString conv_str ;
	2016	if (file->convention_str.isEmpty())
	2017	{
	2018	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
	2019	else conv_str="UGRID" ;
	2020	}
	2021	else conv_str=file->convention_str ;
	2022
[498]	2023	try
	2024	{
[1309]	2025	if (!appendMode) this->writeFileAttributes(filename, description,
	2026	conv_str,
	2027	StdString("An IPSL model"),
	2028	this->getTimeStamp());
[609]	2029
[701]	2030	if (!appendMode)
	2031	SuperClassWriter::addDimension("axis_nbounds", 2);
[498]	2032	}
	2033	catch (CNetCdfException& e)
	2034	{
	2035	StdString msg("On writing file : ");
	2036	msg.append(filename); msg.append("\n");
	2037	msg.append("In the context : ");
	2038	CContext* context = CContext::getCurrent() ;
	2039	msg.append(context->getId()); msg.append("\n");
	2040	msg.append(e.what());
	2041	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
	2042	}
[219]	2043	}
[488]	2044
[472]	2045	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
	2046	{
[773]	2047	StdString name = var->getVariableOutputName();
[488]	2048
[498]	2049	try
	2050	{
[527]	2051	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	2052	addAttribute(name, var->getData<int>(), &fieldId);
	2053	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	2054	addAttribute(name, var->getData<short int>(), &fieldId);
	2055	else if (var->type.getValue() == CVariable::type_attr::t_float)
	2056	addAttribute(name, var->getData<float>(), &fieldId);
	2057	else if (var->type.getValue() == CVariable::type_attr::t_double)
	2058	addAttribute(name, var->getData<double>(), &fieldId);
	2059	else if (var->type.getValue() == CVariable::type_attr::t_string)
	2060	addAttribute(name, var->getData<string>(), &fieldId);
	2061	else
	2062	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
	2063	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	2064	}
	2065	catch (CNetCdfException& e)
	2066	{
	2067	StdString msg("On writing attributes of variable with name : ");
	2068	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
	2069	msg.append("In the context : ");
	2070	CContext* context = CContext::getCurrent() ;
	2071	msg.append(context->getId()); msg.append("\n");
	2072	msg.append(e.what());
	2073	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
	2074	}
[472]	2075	}
[488]	2076
[472]	2077	void CNc4DataOutput::writeAttribute_ (CVariable* var)
	2078	{
[773]	2079	StdString name = var->getVariableOutputName();
	2080
[498]	2081	try
	2082	{
[527]	2083	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	2084	addAttribute(name, var->getData<int>());
	2085	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	2086	addAttribute(name, var->getData<short int>());
	2087	else if (var->type.getValue() == CVariable::type_attr::t_float)
	2088	addAttribute(name, var->getData<float>());
	2089	else if (var->type.getValue() == CVariable::type_attr::t_double)
	2090	addAttribute(name, var->getData<double>());
	2091	else if (var->type.getValue() == CVariable::type_attr::t_string)
	2092	addAttribute(name, var->getData<string>());
	2093	else
	2094	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
	2095	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	2096	}
	2097	catch (CNetCdfException& e)
	2098	{
	2099	StdString msg("On writing attributes of variable with name : ");
	2100	msg.append(name); msg.append("\n");
	2101	msg.append("In the context : ");
	2102	CContext* context = CContext::getCurrent() ;
	2103	msg.append(context->getId()); msg.append("\n");
	2104	msg.append(e.what());
	2105	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
	2106	}
[488]	2107	}
	2108
[321]	2109	void CNc4DataOutput::syncFile_ (void)
	2110	{
[498]	2111	try
	2112	{
	2113	SuperClassWriter::sync() ;
	2114	}
	2115	catch (CNetCdfException& e)
	2116	{
	2117	StdString msg("On synchronizing the write among processes");
	2118	msg.append("In the context : ");
	2119	CContext* context = CContext::getCurrent() ;
	2120	msg.append(context->getId()); msg.append("\n");
	2121	msg.append(e.what());
	2122	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	2123	}
[321]	2124	}
[219]	2125
[286]	2126	void CNc4DataOutput::closeFile_ (void)
	2127	{
[498]	2128	try
	2129	{
	2130	SuperClassWriter::close() ;
	2131	}
	2132	catch (CNetCdfException& e)
	2133	{
	2134	StdString msg("On closing file");
	2135	msg.append("In the context : ");
	2136	CContext* context = CContext::getCurrent() ;
	2137	msg.append(context->getId()); msg.append("\n");
	2138	msg.append(e.what());
	2139	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	2140	}
	2141
[286]	2142	}
	2143
[219]	2144	//---------------------------------------------------------------
	2145
	2146	StdString CNc4DataOutput::getTimeStamp(void) const
	2147	{
	2148	const int buffer_size = 100;
	2149	time_t rawtime;
	2150	struct tm * timeinfo = NULL;
	2151	char buffer [buffer_size];
[1158]	2152	StdString formatStr;
	2153	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
	2154	else formatStr=file->time_stamp_format;
[219]	2155
[1158]	2156	// time ( &rawtime );
	2157	// timeinfo = localtime ( &rawtime );
[219]	2158	time ( &rawtime );
[1158]	2159	timeinfo = gmtime ( &rawtime );
	2160	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
[219]	2161
	2162	return (StdString(buffer));
	2163	}
[488]	2164
[219]	2165	//---------------------------------------------------------------
[488]	2166
[1961]	2167	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
	2168	const CDate& currentWrite, int nstep)
[219]	2169	{
[707]	2170	CContext* context = CContext::getCurrent();
[1869]	2171	CGrid* grid = field->getGrid();
[1961]	2172
	2173	if (nstep<1)
[1158]	2174	{
[1961]	2175	return nstep;
[1158]	2176	}
[952]	2177
[707]	2178	if (!grid->doGridHaveDataToWrite())
[1158]	2179	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
	2180	{
[1961]	2181	return nstep;
[1158]	2182	}
[488]	2183
[770]	2184	StdString fieldid = field->getFieldOutputName();
[286]	2185
[707]	2186	StdOStringStream oss;
	2187	string timeAxisId;
[1158]	2188	if (field->hasTimeInstant) timeAxisId = "time_instant";
	2189	else if (field->hasTimeCentered) timeAxisId = "time_centered";
[488]	2190
[802]	2191	StdString timeBoundId = getTimeCounterName() + "_bounds";
[449]	2192
[707]	2193	StdString timeAxisBoundId;
[1158]	2194	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
	2195	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
[488]	2196
[707]	2197	if (!field->wasWritten())
	2198	{
[1872]	2199	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
[1158]	2200	field->getOperationTimeType() != func::CFunctor::once)
[707]	2201	{
[1158]	2202	double factorUnit;
[1872]	2203	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
[1158]	2204	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
	2205	else factorUnit=1 ;
[1962]	2206	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
[707]	2207	}
[488]	2208
[707]	2209	field->setWritten();
	2210	}
[488]	2211
	2212
[707]	2213	CArray<double,1> time_data(1);
	2214	CArray<double,1> time_data_bound(2);
	2215	CArray<double,1> time_counter(1);
	2216	CArray<double,1> time_counter_bound(2);
	2217
	2218	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
[1158]	2219	bool wtimeCounter =false ;
	2220	bool wtimeData =false ;
	2221
[707]	2222
[444]	2223	if (wtime)
	2224	{
[1158]	2225
	2226	if (field->hasTimeInstant)
	2227	{
[1961]	2228	time_data(0) = time_data_bound(1) = (Time) lastWrite;
	2229	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
[1158]	2230	if (timeCounterType==instant)
	2231	{
	2232	time_counter(0) = time_data(0);
	2233	time_counter_bound(0) = time_data_bound(0);
	2234	time_counter_bound(1) = time_data_bound(1);
	2235	wtimeCounter=true ;
	2236	}
	2237	if (hasTimeInstant) wtimeData=true ;
	2238	}
	2239	else if (field->hasTimeCentered)
[488]	2240	{
[1961]	2241	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
	2242	time_data_bound(0) = (Time)lastWrite;
	2243	time_data_bound(1) = (Time)currentWrite;
[1158]	2244	if (timeCounterType==centered)
	2245	{
	2246	time_counter(0) = time_data(0) ;
	2247	time_counter_bound(0) = time_data_bound(0) ;
	2248	time_counter_bound(1) = time_data_bound(1) ;
	2249	wtimeCounter=true ;
	2250	}
	2251	if (hasTimeCentered) wtimeData=true ;
[488]	2252	}
	2253
[1158]	2254	if (timeCounterType==record)
	2255	{
[1961]	2256	time_counter(0) = nstep - 1;
	2257	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
[1158]	2258	wtimeCounter=true ;
	2259	}
[692]	2260
[1872]	2261	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
[692]	2262	{
[1158]	2263	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
	2264	time_data/=secByDay;
	2265	time_data_bound/=secByDay;
	2266	time_counter/=secByDay;
	2267	time_counter_bound/=secByDay;
[692]	2268	}
	2269	}
	2270
[1853]	2271	bool isRoot = (context->intraCommRank_ == 0);
[488]	2272
[498]	2273	try
[219]	2274	{
[567]	2275	switch (SuperClass::type)
[498]	2276	{
[567]	2277	case (MULTI_FILE) :
	2278	{
[1158]	2279	CTimer::get("Files : writing data").resume();
[1961]	2280	SuperClassWriter::writeData(data, fieldid, isCollective, nstep - 1);
[1158]	2281	CTimer::get("Files : writing data").suspend();
[567]	2282	if (wtime)
	2283	{
[1158]	2284	CTimer::get("Files : writing time axis").resume();
	2285	if ( wtimeData)
[692]	2286	{
[1961]	2287	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
	2288	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
[1158]	2289	}
	2290	if (wtimeCounter)
	2291	{
[1961]	2292	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
	2293	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
[692]	2294	}
[1158]	2295	CTimer::get("Files : writing time axis").suspend();
[567]	2296	}
[707]	2297	break;
[567]	2298	}
	2299	case (ONE_FILE) :
	2300	{
[464]	2301
[676]	2302	std::vector<StdSize> start, count;
[464]	2303
[676]	2304	if (field->getUseCompressedOutput())
	2305	{
[1957]	2306	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	2307	std::vector<StdString> domainList = grid->getDomainList();
	2308	std::vector<StdString> axisList = grid->getAxisList();
	2309	int numElement = axisDomainOrder.numElements();
	2310	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
	2311	int idx = domainList.size() * 2 + axisList.size() - 1;
	2312	int commRank ;
[464]	2313
[1957]	2314	MPI_Comm_rank(comm_file,&commRank) ;
[676]	2315
[1957]	2316	start.reserve(idx+1);
	2317	count.reserve(idx+1);
	2318
	2319	for (int i = numElement - 1; i >= 0; --i)
	2320	{
	2321	if (2 == axisDomainOrder(i))
[676]	2322	{
[1957]	2323	CDomain* domain = CDomain::get(domainList[idxDomain]);
	2324
	2325	if (domain->isCompressible())
[676]	2326	{
[1957]	2327	size_t offset ;
	2328	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
	2329	if (domain->isDistributed())
[676]	2330	{
[1957]	2331	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	2332	if (commRank==0) offset=0 ;
[676]	2333	}
[1957]	2334	else offset=0 ;
	2335
	2336	start.push_back(offset);
	2337	count.push_back(nbIndexes);
	2338	idx -= 2;
	2339	}
	2340	else
	2341	{
	2342	if ((domain->type) != CDomain::type_attr::unstructured)
[676]	2343	{
[1957]	2344	start.push_back(domain->jbegin);
	2345	count.push_back(domain->nj);
[676]	2346	}
[1957]	2347	--idx;
	2348	start.push_back(domain->ibegin);
	2349	count.push_back(domain->ni);
	2350	--idx;
[676]	2351	}
[1957]	2352	--idxDomain;
	2353	}
	2354	else if (1 == axisDomainOrder(i))
	2355	{
	2356	CAxis* axis = CAxis::get(axisList[idxAxis]);
	2357
	2358	if (axis->isCompressible())
[676]	2359	{
[1957]	2360	size_t offset ;
	2361	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
	2362	if (axis->isDistributed())
[676]	2363	{
[1957]	2364	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	2365	if (commRank==0) offset=0 ;
[676]	2366	}
[1957]	2367	else offset=0 ;
	2368
	2369	start.push_back(offset);
	2370	count.push_back(nbIndexes);
[676]	2371	}
[1957]	2372	else
	2373	{
	2374	start.push_back(axis->begin);
	2375	count.push_back(axis->n);
	2376	}
	2377	--idxAxis;
	2378	--idx;
[676]	2379	}
[1158]	2380	}
[1961]	2381	}
[676]	2382	else
[498]	2383	{
[887]	2384	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
[705]	2385	std::vector<StdString> domainList = grid->getDomainList();
	2386	std::vector<StdString> axisList = grid->getAxisList();
[2264]	2387	std::vector<StdString> scalarList = grid->getScalarList() ;
[705]	2388	int numElement = axisDomainOrder.numElements();
	2389	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
[1553]	2390	int idx = domainList.size() * 2 + axisList.size() - 1;
[705]	2391
[1553]	2392	start.reserve(idx+1);
	2393	count.reserve(idx+1);
[705]	2394
	2395	for (int i = numElement - 1; i >= 0; --i)
	2396	{
[887]	2397	if (2 == axisDomainOrder(i))
[705]	2398	{
	2399	CDomain* domain = CDomain::get(domainList[idxDomain]);
[710]	2400	if ((domain->type) != CDomain::type_attr::unstructured)
[705]	2401	{
[1553]	2402	start.push_back(domain->jbegin);
	2403	count.push_back(domain->nj);
[705]	2404	}
	2405	--idx ;
[1143]	2406
[1553]	2407	start.push_back(domain->ibegin);
	2408	count.push_back(domain->ni);
[705]	2409	--idx ;
	2410	--idxDomain;
	2411	}
[887]	2412	else if (1 == axisDomainOrder(i))
[705]	2413	{
[1143]	2414	CAxis* axis = CAxis::get(axisList[idxAxis]);
[1559]	2415	start.push_back(axis->begin);
	2416	count.push_back(axis->n);
[705]	2417	--idx;
[1025]	2418	--idxAxis;
[887]	2419	}
	2420	else
	2421	{
	2422	if (1 == axisDomainOrder.numElements())
	2423	{
[2264]	2424	CScalar* scalar = CScalar::get(scalarList[scalarList.size()-1]);
[887]	2425	start.push_back(0);
[2264]	2426	count.push_back(scalar->n);
[887]	2427	}
	2428	--idx;
	2429	}
[705]	2430	}
[498]	2431	}
[488]	2432
[1158]	2433
	2434	CTimer::get("Files : writing data").resume();
[1961]	2435	SuperClassWriter::writeData(data, fieldid, isCollective, nstep - 1, &start, &count);
[1158]	2436	CTimer::get("Files : writing data").suspend();
	2437
	2438	if (wtime)
	2439	{
	2440	CTimer::get("Files : writing time axis").resume();
	2441	if ( wtimeData)
[692]	2442	{
[1961]	2443	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
	2444	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
[692]	2445	}
[1158]	2446	if (wtimeCounter)
	2447	{
[1961]	2448	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
	2449	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
[586]	2450
[1158]	2451	}
	2452	CTimer::get("Files : writing time axis").suspend();
	2453	}
	2454
[586]	2455	break;
[286]	2456	}
[567]	2457	}
[1961]	2458	return nstep ;
[219]	2459	}
[498]	2460	catch (CNetCdfException& e)
	2461	{
	2462	StdString msg("On writing field data: ");
	2463	msg.append(fieldid); msg.append("\n");
	2464	msg.append("In the context : ");
	2465	msg.append(context->getId()); msg.append("\n");
	2466	msg.append(e.what());
[1130]	2467	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
[498]	2468	}
[219]	2469	}
	2470
	2471	//---------------------------------------------------------------
	2472
	2473	void CNc4DataOutput::writeTimeAxis_
[347]	2474	(CField* field,
[1542]	2475	const std::shared_ptr<CCalendar> cal)
[219]	2476	{
	2477	StdOStringStream oss;
[1158]	2478	bool createInstantAxis=false ;
	2479	bool createCenteredAxis=false ;
	2480	bool createTimeCounterAxis=false ;
	2481
[645]	2482	if (field->getOperationTimeType() == func::CFunctor::once) return ;
[488]	2483
	2484
[1158]	2485	StdString axisId ;
	2486	StdString axisBoundId;
[802]	2487	StdString timeid(getTimeCounterName());
[614]	2488	StdString timeBoundId("axis_nbounds");
[488]	2489
[1158]	2490	StdString strTimeUnits ;
[1872]	2491	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
[1158]	2492	else strTimeUnits="seconds since " ;
	2493
	2494	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
	2495	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
	2496
	2497
[1872]	2498	if (field->getRelFile()->time_counter.isEmpty())
[488]	2499	{
[1158]	2500	if (timeCounterType==none) createTimeCounterAxis=true ;
	2501	if (field->hasTimeCentered)
	2502	{
	2503	timeCounterType=centered ;
	2504	if (!hasTimeCentered) createCenteredAxis=true ;
	2505	}
	2506	if (field->hasTimeInstant)
	2507	{
	2508	if (timeCounterType==none) timeCounterType=instant ;
	2509	if (!hasTimeInstant) createInstantAxis=true ;
	2510	}
[488]	2511	}
[1872]	2512	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
[1158]	2513	{
	2514	if (field->hasTimeCentered)
	2515	{
	2516	if (!hasTimeCentered) createCenteredAxis=true ;
	2517	}
	2518	if (field->hasTimeInstant)
	2519	{
	2520	if (timeCounterType==none) createTimeCounterAxis=true ;
	2521	timeCounterType=instant ;
	2522	if (!hasTimeInstant) createInstantAxis=true ;
	2523	}
	2524	}
[1872]	2525	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
[1158]	2526	{
	2527	if (field->hasTimeCentered)
	2528	{
	2529	if (timeCounterType==none) createTimeCounterAxis=true ;
	2530	timeCounterType=centered ;
	2531	if (!hasTimeCentered) createCenteredAxis=true ;
	2532	}
	2533	if (field->hasTimeInstant)
	2534	{
	2535	if (!hasTimeInstant) createInstantAxis=true ;
	2536	}
	2537	}
[1872]	2538	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
[1158]	2539	{
	2540	if (field->hasTimeCentered)
	2541	{
	2542	if (!hasTimeCentered) createCenteredAxis=true ;
	2543	}
	2544	if (field->hasTimeInstant)
	2545	{
	2546	if (timeCounterType==none) createTimeCounterAxis=true ;
	2547	timeCounterType=instant ;
	2548	}
	2549	}
[1872]	2550	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
[1158]	2551	{
	2552	if (field->hasTimeCentered)
	2553	{
	2554	if (timeCounterType==none) createTimeCounterAxis=true ;
	2555	timeCounterType=centered ;
	2556	}
	2557	if (field->hasTimeInstant)
	2558	{
	2559	if (!hasTimeInstant) createInstantAxis=true ;
	2560	}
	2561	}
[1872]	2562	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
[1158]	2563	{
	2564	if (field->hasTimeCentered)
	2565	{
	2566	if (timeCounterType==none) createTimeCounterAxis=true ;
	2567	if (timeCounterType==instant) createInstantAxis=true ;
	2568	timeCounterType=centered ;
	2569	}
	2570	if (field->hasTimeInstant)
	2571	{
	2572	if (timeCounterType==none)
	2573	{
	2574	createTimeCounterAxis=true ;
	2575	timeCounterType=instant ;
	2576	}
	2577	if (timeCounterType==centered)
	2578	{
	2579	if (!hasTimeInstant) createInstantAxis=true ;
	2580	}
	2581	}
	2582	}
[1872]	2583	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
[1158]	2584	{
	2585	if (field->hasTimeCentered)
	2586	{
	2587	if (!hasTimeCentered) createCenteredAxis=true ;
	2588	}
	2589	if (field->hasTimeInstant)
	2590	{
	2591	if (!hasTimeInstant) createInstantAxis=true ;
	2592	}
	2593	}
[1872]	2594	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
[1158]	2595	{
	2596	if (timeCounterType==none) createTimeCounterAxis=true ;
	2597	timeCounterType=record ;
	2598	if (field->hasTimeCentered)
	2599	{
	2600	if (!hasTimeCentered) createCenteredAxis=true ;
	2601	}
	2602	if (field->hasTimeInstant)
	2603	{
	2604	if (!hasTimeInstant) createInstantAxis=true ;
	2605	}
	2606	}
	2607
	2608	if (createInstantAxis)
	2609	{
	2610	axisId="time_instant" ;
	2611	axisBoundId="time_instant_bounds";
	2612	hasTimeInstant=true ;
	2613	}
[488]	2614
[1158]	2615	if (createCenteredAxis)
	2616	{
	2617	axisId="time_centered" ;
	2618	axisBoundId="time_centered_bounds";
	2619	hasTimeCentered=true ;
	2620	}
	2621
	2622
[498]	2623	try
[219]	2624	{
[1158]	2625	std::vector<StdString> dims;
	2626
	2627	if (createInstantAxis \|\| createCenteredAxis)
	2628	{
	2629	// Adding time_instant or time_centered
	2630	dims.push_back(timeid);
	2631	if (!SuperClassWriter::varExist(axisId))
	2632	{
	2633	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
[488]	2634
[1158]	2635	CDate timeOrigin=cal->getTimeOrigin() ;
	2636	StdOStringStream oss2;
	2637	StdString strInitdate=oss2.str() ;
	2638	StdString strTimeOrigin=timeOrigin.toString() ;
	2639	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
	2640	strTimeOrigin, axisBoundId);
	2641	}
[219]	2642
[1158]	2643	// Adding time_instant_bounds or time_centered_bounds variables
	2644	if (!SuperClassWriter::varExist(axisBoundId))
	2645	{
	2646	dims.clear() ;
	2647	dims.push_back(timeid);
	2648	dims.push_back(timeBoundId);
	2649	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2650	}
[498]	2651	}
[488]	2652
[1158]	2653	if (createTimeCounterAxis)
[498]	2654	{
[692]	2655	// Adding time_counter
[1158]	2656	axisId = getTimeCounterName();
[802]	2657	axisBoundId = getTimeCounterName() + "_bounds";
[692]	2658	dims.clear();
	2659	dims.push_back(timeid);
[1158]	2660	if (!SuperClassWriter::varExist(axisId))
[692]	2661	{
[1158]	2662	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
	2663	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
[488]	2664
[1872]	2665	if (field->getRelFile()->time_counter.isEmpty() \|\|
	2666	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
[692]	2667	{
	2668	CDate timeOrigin = cal->getTimeOrigin();
	2669	StdString strTimeOrigin = timeOrigin.toString();
[498]	2670
[1158]	2671	this->writeTimeAxisAttributes(axisId, cal->getType(),
	2672	strTimeUnits+strTimeOrigin,
[692]	2673	strTimeOrigin, axisBoundId);
	2674	}
	2675	}
	2676
	2677	// Adding time_counter_bound dimension
[1872]	2678	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
[692]	2679	{
	2680	if (!SuperClassWriter::varExist(axisBoundId))
	2681	{
	2682	dims.clear();
	2683	dims.push_back(timeid);
	2684	dims.push_back(timeBoundId);
	2685	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2686	}
	2687	}
[498]	2688	}
[488]	2689	}
[498]	2690	catch (CNetCdfException& e)
[488]	2691	{
[498]	2692	StdString msg("On writing time axis data: ");
	2693	msg.append("In the context : ");
	2694	CContext* context = CContext::getCurrent() ;
	2695	msg.append(context->getId()); msg.append("\n");
	2696	msg.append(e.what());
	2697	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
[1542]	2698	const std::shared_ptr<CCalendar> cal)", << msg);
[488]	2699	}
[219]	2700	}
	2701
	2702	//---------------------------------------------------------------
[488]	2703
[219]	2704	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
	2705	const StdString & calendar,
	2706	const StdString & units,
	2707	const StdString & time_origin,
[488]	2708	const StdString & time_bounds,
[219]	2709	const StdString & standard_name,
[613]	2710	const StdString & long_name)
[219]	2711	{
[498]	2712	try
	2713	{
	2714	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2715	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
	2716	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
	2717	SuperClassWriter::addAttribute("units", units , &axis_name);
	2718	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
	2719	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
	2720	}
	2721	catch (CNetCdfException& e)
	2722	{
	2723	StdString msg("On writing time axis Attribute: ");
	2724	msg.append("In the context : ");
	2725	CContext* context = CContext::getCurrent() ;
	2726	msg.append(context->getId()); msg.append("\n");
	2727	msg.append(e.what());
	2728	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
[613]	2729	const StdString & calendar,\
	2730	const StdString & units, \
	2731	const StdString & time_origin, \
	2732	const StdString & time_bounds, \
	2733	const StdString & standard_name, \
	2734	const StdString & long_name)", << msg);
[498]	2735	}
[219]	2736	}
[488]	2737
[219]	2738	//---------------------------------------------------------------
	2739
	2740	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
	2741	const StdString & axis,
	2742	const StdString & standard_name,
	2743	const StdString & long_name,
	2744	const StdString & units,
	2745	const StdString & nav_model)
	2746	{
[498]	2747	try
	2748	{
[613]	2749	if (!axis.empty())
	2750	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
	2751
[498]	2752	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2753	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
	2754	SuperClassWriter::addAttribute("units" , units , &axis_name);
[973]	2755	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
[498]	2756	}
	2757	catch (CNetCdfException& e)
	2758	{
	2759	StdString msg("On writing Axis Attribute: ");
	2760	msg.append("In the context : ");
	2761	CContext* context = CContext::getCurrent() ;
	2762	msg.append(context->getId()); msg.append("\n");
	2763	msg.append(e.what());
	2764	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
[613]	2765	const StdString & axis, \
	2766	const StdString & standard_name, \
	2767	const StdString & long_name, \
	2768	const StdString & units, \
	2769	const StdString & nav_model)", << msg);
[498]	2770	}
[219]	2771	}
	2772
	2773	//---------------------------------------------------------------
[488]	2774
[219]	2775	void CNc4DataOutput::writeLocalAttributes
	2776	(int ibegin, int ni, int jbegin, int nj, StdString domid)
	2777	{
[498]	2778	try
	2779	{
[318]	2780	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
	2781	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
	2782	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
	2783	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
[498]	2784	}
	2785	catch (CNetCdfException& e)
	2786	{
	2787	StdString msg("On writing Local Attributes: ");
	2788	msg.append("In the context : ");
	2789	CContext* context = CContext::getCurrent() ;
	2790	msg.append(context->getId()); msg.append("\n");
	2791	msg.append(e.what());
	2792	ERROR("CNc4DataOutput::writeLocalAttributes \
	2793	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
	2794	}
	2795
[219]	2796	}
	2797
[628]	2798	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
	2799	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
[391]	2800	{
	2801	CArray<int,1> array(2) ;
	2802
[498]	2803	try
	2804	{
	2805	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
	2806	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
[629]	2807	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
[498]	2808	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
	2809	array=ni_glo,nj_glo ;
	2810	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
	2811	array=ni,nj ;
	2812	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
[819]	2813	array=ibegin+1,jbegin+1 ;
[498]	2814	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
[819]	2815	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
[498]	2816	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
	2817	array=0,0 ;
	2818	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
	2819	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
	2820	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
	2821	/*
	2822	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
	2823	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
	2824	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
	2825	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
	2826	*/
	2827	}
	2828	catch (CNetCdfException& e)
	2829	{
[628]	2830	StdString msg("On writing Local Attributes IOIPSL \n");
[498]	2831	msg.append("In the context : ");
	2832	CContext* context = CContext::getCurrent() ;
	2833	msg.append(context->getId()); msg.append("\n");
	2834	msg.append(e.what());
	2835	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
	2836	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
	2837	}
[391]	2838	}
[219]	2839	//---------------------------------------------------------------
	2840
	2841	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
	2842	const StdString & description,
	2843	const StdString & conventions,
	2844	const StdString & production,
	2845	const StdString & timeStamp)
	2846	{
[498]	2847	try
	2848	{
	2849	SuperClassWriter::addAttribute("name" , name);
	2850	SuperClassWriter::addAttribute("description", description);
[613]	2851	SuperClassWriter::addAttribute("title" , description);
	2852	SuperClassWriter::addAttribute("Conventions", conventions);
[1158]	2853	// SuperClassWriter::addAttribute("production" , production);
	2854
	2855	StdString timeStampStr ;
	2856	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
	2857	else timeStampStr=file->time_stamp_name ;
	2858	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
	2859
	2860	StdString uuidName ;
	2861	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
	2862	else uuidName=file->uuid_name ;
	2863
	2864	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
	2865	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
	2866
[498]	2867	}
	2868	catch (CNetCdfException& e)
	2869	{
	2870	StdString msg("On writing File Attributes \n ");
	2871	msg.append("In the context : ");
	2872	CContext* context = CContext::getCurrent() ;
	2873	msg.append(context->getId()); msg.append("\n");
	2874	msg.append(e.what());
	2875	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
	2876	const StdString & description, \
	2877	const StdString & conventions, \
	2878	const StdString & production, \
	2879	const StdString & timeStamp)", << msg);
	2880	}
[219]	2881	}
	2882
	2883	//---------------------------------------------------------------
	2884
	2885	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
	2886	int data_dim,
	2887	int data_ni,
	2888	int data_nj,
	2889	int data_ibegin,
	2890	int data_jbegin)
	2891	{
[498]	2892	try
	2893	{
	2894	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
	2895	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
	2896	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
	2897	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
	2898	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
	2899	}
	2900	catch (CNetCdfException& e)
	2901	{
	2902	StdString msg("On writing Mask Attributes \n ");
	2903	msg.append("In the context : ");
	2904	CContext* context = CContext::getCurrent() ;
	2905	msg.append(context->getId()); msg.append("\n");
	2906	msg.append(e.what());
	2907	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
	2908	int data_dim, \
	2909	int data_ni, \
	2910	int data_nj, \
	2911	int data_ibegin, \
	2912	int data_jbegin)", << msg);
	2913	}
[219]	2914	}
	2915
	2916	///--------------------------------------------------------------
	2917
[1158]	2918	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
[707]	2919	{
	2920	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
	2921	if (it == timeToRecordCache.end())
	2922	{
[802]	2923	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
[1158]	2924	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
	2925	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
[707]	2926
	2927	CArray<double,2> timeAxisBounds;
[1158]	2928	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
	2929
[707]	2930	StdSize record = 0;
	2931	double dtime(time);
[1158]	2932	for (int n = dimSize[0] - 1; n >= 0; n--)
[707]	2933	{
[1158]	2934	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
	2935	timeAxisBounds*=factorUnit ;
	2936	if (timeAxisBounds(1, 0) < dtime)
[707]	2937	{
	2938	record = n + 1;
	2939	break;
	2940	}
	2941	}
	2942	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
	2943	}
	2944	return it->second;
	2945	}
[774]	2946
	2947	///--------------------------------------------------------------
	2948
	2949	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
	2950	{
	2951	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
	2952	}
	2953
	2954	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
	2955	{
	2956	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
	2957	}
	2958
	2959	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
	2960	{
	2961	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
	2962	}
	2963
	2964	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
	2965	{
	2966	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
	2967	}
	2968
[887]	2969	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
	2970	{
	2971	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
	2972	}
	2973
[774]	2974	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
	2975	{
	2976	this->writtenDomains.insert(domainName);
	2977	}
	2978
	2979	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
	2980	{
	2981	this->writtenCompressedDomains.insert(domainName);
	2982	}
	2983
	2984	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
	2985	{
	2986	this->writtenAxis.insert(axisName);
	2987	}
	2988
	2989	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
	2990	{
	2991	this->writtenCompressedAxis.insert(axisName);
	2992	}
[887]	2993
	2994	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
	2995	{
	2996	this->writtenScalar.insert(scalarName);
	2997	}
[335]	2998	} // namespace xios

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