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source: XIOS3/trunk/src/io/nc4_data_output.cpp @ 2628

Last change on this file since 2628 was 2628, checked in by jderouillat, 2 months ago
New timers integration/reporting
Property copyright set to Software name : XIOS (Xml I/O Server) http://forge.ipsl.jussieu.fr/ioserver Creation date : January 2009 Licence : CeCCIL version2 see license file in root directory : Licence_CeCILL_V2-en.txt or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement) CNRS/IPSL (Institut Pierre Simon Laplace) Project Manager : Yann Meurdesoif yann.meurdesoif@cea.fr Property svn:executable set to ``*
File size: 129.6 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"
[2600]	14
	15	#include <limits.h>
	16	#define X_FLOAT_MAX FLT_MAX
	17	#define X_FLOAT_MIN FLT_MIN
	18	#define X_SHORT_MAX SHRT_MAX
	19	#define X_SHORT_MIN SHRT_MIN
	20
[335]	21	namespace xios
[219]	22	{
[2628]	23	extern CLogType logProfile ;
[878]	24	/// ////////////////////// Dfinitions ////////////////////// ///
[219]	25	CNc4DataOutput::CNc4DataOutput
[1158]	26	(CFile* file, const StdString & filename, bool exist)
[219]	27	: SuperClass()
	28	, SuperClassWriter(filename, exist)
	29	, filename(filename)
[2389]	30	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
[219]	31	{
[1158]	32	SuperClass::type = MULTI_FILE;
[1456]	33	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
[219]	34	}
	35
	36	CNc4DataOutput::CNc4DataOutput
[1158]	37	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
[1639]	38	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
[219]	39	: SuperClass()
[878]	40	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
[379]	41	, comm_file(comm_file)
[219]	42	, filename(filename)
[335]	43	, isCollective(isCollective)
[2389]	44	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
[219]	45	{
[1158]	46	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
[1459]	47	if (file==NULL) compressionLevel = 0 ;
	48	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
[219]	49	}
	50
	51	CNc4DataOutput::~CNc4DataOutput(void)
[879]	52	{ /* Ne rien faire de plus */ }
[219]	53
	54	///--------------------------------------------------------------
	55
	56	const StdString & CNc4DataOutput::getFileName(void) const
	57	{
	58	return (this->filename);
	59	}
	60
	61	//---------------------------------------------------------------
	62
[347]	63	void CNc4DataOutput::writeDomain_(CDomain* domain)
[1622]	64	TRY
[219]	65	{
[1391]	66	StdString lonName,latName ;
[1249]	67
[2387]	68	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
	69	if (!domain->lonvalue.isEmpty() )
	70	{
	71	// The hash of the element will be associated to the default element name (= map key), and to the name really written
	72	int globalHash = domain->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
	73
	74	StdString defaultNameKey = domain->getDomainOutputName();
	75	if ( !relDomains_.count ( defaultNameKey ) )
	76	{
	77	// if defaultNameKey not in the map, write the element such as it is defined
	78	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) );
	79	}
	80	else // look if a hash associated this key is equal
	81	{
	82	bool elementIsInMap(false);
	83	auto defaultNameKeyElements = relDomains_.equal_range( defaultNameKey );
	84	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
	85	{
	86	if ( it->second.first == globalHash )
	87	{
	88	// if yes, associate the same ids to current element
[2389]	89	domain->renameAttributesBeforeWriting( it->second.second );
[2387]	90	elementIsInMap = true;
	91	}
	92	}
	93	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
	94	if (!elementIsInMap) // ! in MAP
	95	{
[2389]	96	domain->renameAttributesBeforeWriting();
[2387]	97	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) ) ;
	98	}
	99	}
	100	}
	101
[881]	102	if (domain->type == CDomain::type_attr::unstructured)
	103	{
	104	if (SuperClassWriter::useCFConvention)
	105	writeUnstructuredDomain(domain) ;
	106	else
	107	writeUnstructuredDomainUgrid(domain) ;
	108	return ;
	109	}
[488]	110
[347]	111	CContext* context = CContext::getCurrent() ;
[219]	112	if (domain->IsWritten(this->filename)) return;
	113	domain->checkAttributes();
[488]	114
	115	if (domain->isEmpty())
[881]	116	if (SuperClass::type==MULTI_FILE) return;
[219]	117
[2381]	118
[219]	119	std::vector<StdString> dim0, dim1;
[772]	120	StdString domid = domain->getDomainOutputName();
[318]	121	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
[706]	122	if (isWrittenDomain(domid)) return ;
[774]	123	else setWrittenDomain(domid);
[1132]	124
	125	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
[449]	126
[488]	127
[1158]	128	StdString dimXid, dimYid ;
	129
	130	nc_type typePrec ;
	131	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	132	else if (domain->prec==4) typePrec = NC_FLOAT ;
	133	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	134
[664]	135	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
[449]	136	switch (domain->type)
[433]	137	{
[449]	138	case CDomain::type_attr::curvilinear :
[1391]	139
	140	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
	141	else lonName = domain->lon_name;
	142
	143	if (domain->lat_name.isEmpty()) latName = "nav_lat";
	144	else latName = domain->lat_name;
	145
[1430]	146	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
	147	else dimXid=domain->dim_i_name.getValue() + appendDomid;
	148
	149	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
	150	else dimYid=domain->dim_j_name.getValue() + appendDomid;
	151
[449]	152	break ;
[1391]	153
[664]	154	case CDomain::type_attr::rectilinear :
[1391]	155
[1430]	156	if (domain->lon_name.isEmpty())
	157	{
	158	if (domain->dim_i_name.isEmpty())
	159	lonName = "lon";
	160	else
	161	lonName = domain->dim_i_name.getValue();
	162	}
[1391]	163	else lonName = domain->lon_name;
	164
[1430]	165	if (domain->lat_name.isEmpty())
	166	{
	167	if (domain->dim_j_name.isEmpty())
	168	latName = "lat";
	169	else
	170	latName = domain->dim_j_name.getValue();
	171	}
[1391]	172	else latName = domain->lat_name;
	173
[1430]	174	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
	175	else dimXid = domain->dim_i_name.getValue()+appendDomid;
	176
	177	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
	178	else dimYid = domain->dim_j_name.getValue()+appendDomid;
[449]	179	break;
[488]	180	}
	181
[617]	182	StdString dimVertId = StdString("nvertex").append(appendDomid);
	183
[449]	184	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	185	string areaId = "area" + appendDomid;
[219]	186
[498]	187	try
[219]	188	{
[498]	189	switch (SuperClass::type)
	190	{
	191	case (MULTI_FILE) :
	192	{
	193	switch (domain->type)
	194	{
	195	case CDomain::type_attr::curvilinear :
	196	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1415]	197	lonid = lonName+appendDomid;
	198	latid = latName+appendDomid;
[498]	199	break ;
[664]	200	case CDomain::type_attr::rectilinear :
[1415]	201	lonid = lonName+appendDomid;
	202	latid = latName+appendDomid;
[498]	203	dim0.push_back(dimYid);
	204	dim1.push_back(dimXid);
	205	break;
	206	}
[1430]	207	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	208	else bounds_lonid = "bounds_"+lonName+appendDomid;
	209	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	210	else bounds_latid = "bounds_"+latName+appendDomid;
[488]	211
[2507]	212	SuperClassWriter::addDimension(dimXid, domain->niValue_);
	213	SuperClassWriter::addDimension(dimYid, domain->njValue_);
[488]	214
[617]	215	if (domain->hasBounds)
	216	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	217
[1853]	218	if (context->intraCommSize_ > 1)
[498]	219	{
[2507]	220	this->writeLocalAttributes(domain->ibeginValue_,
	221	domain->niValue_,
	222	domain->jbeginValue_,
	223	domain->njValue_,
[616]	224	appendDomid);
[488]	225
[628]	226	if (singleDomain)
	227	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
[2507]	228	domain->ibeginValue_,
	229	domain->niValue_,
	230	domain->jbeginValue_,
	231	domain->njValue_,
[628]	232	domain->ni_glo,domain->nj_glo,
[1853]	233	context->intraCommRank_,context->intraCommSize_);
[449]	234	}
[488]	235
[665]	236	if (domain->hasLonLat)
[498]	237	{
[665]	238	switch (domain->type)
	239	{
	240	case CDomain::type_attr::curvilinear :
[1456]	241	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	242	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	243	break ;
	244	case CDomain::type_attr::rectilinear :
[1456]	245	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	246	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
[665]	247	break ;
	248	}
[488]	249
[665]	250	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	251	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
[219]	252
[665]	253	if (domain->hasBounds)
	254	{
	255	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	256	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
[617]	257
[665]	258	dim0.clear();
	259	dim0.push_back(dimYid);
	260	dim0.push_back(dimXid);
	261	dim0.push_back(dimVertId);
[1456]	262	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	263	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[665]	264	}
[617]	265	}
	266
[498]	267	dim0.clear();
[616]	268	dim0.push_back(dimYid);
[498]	269	dim0.push_back(dimXid);
[219]	270
[611]	271	if (domain->hasArea)
	272	{
[1456]	273	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	274	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	275	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	276	}
	277
[498]	278	SuperClassWriter::definition_end();
[449]	279
[665]	280	if (domain->hasLonLat)
[498]	281	{
[665]	282	switch (domain->type)
	283	{
[1129]	284	case CDomain::type_attr::curvilinear :
[1930]	285	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
	286	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
[665]	287	break;
	288	case CDomain::type_attr::rectilinear :
[2550]	289	//CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
	290	CArray<double,1> lat;
	291	lat.resize( domain->njValue_);
	292	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
[665]	293	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
[2550]	294	//CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
	295	CArray<double,1> lon = domain->lonvalue(Range(0,domain->niValue_-1));
[665]	296	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
	297	break;
	298	}
[611]	299
[665]	300	if (domain->hasBounds)
	301	{
[1930]	302	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
	303	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
[665]	304	}
[617]	305	}
	306
[611]	307	if (domain->hasArea)
[1129]	308	{
[1930]	309	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
[1129]	310	}
	311
[498]	312	SuperClassWriter::definition_start();
[219]	313
[498]	314	break;
	315	}
	316	case (ONE_FILE) :
	317	{
[1553]	318	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
	319	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
[286]	320
[617]	321	if (domain->hasBounds)
	322	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	323
[665]	324	if (domain->hasLonLat)
[498]	325	{
[665]	326	switch (domain->type)
	327	{
	328	case CDomain::type_attr::curvilinear :
	329	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1415]	330	lonid = lonName+appendDomid;
	331	latid = latName+appendDomid;
[1456]	332	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	333	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	334	break;
[449]	335
[665]	336	case CDomain::type_attr::rectilinear :
	337	dim0.push_back(dimYid);
	338	dim1.push_back(dimXid);
[1415]	339	lonid = lonName+appendDomid;
	340	latid = latName+appendDomid;
[1456]	341	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	342	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
[665]	343	break;
	344	}
[1430]	345	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	346	else bounds_lonid = "bounds_"+lonName+appendDomid;
	347	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	348	else bounds_latid = "bounds_"+latName+appendDomid;
[665]	349
	350	this->writeAxisAttributes
	351	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	352	this->writeAxisAttributes
	353	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
	354
	355	if (domain->hasBounds)
	356	{
	357	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	358	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
	359
	360	dim0.clear();
[498]	361	dim0.push_back(dimYid);
[665]	362	dim0.push_back(dimXid);
	363	dim0.push_back(dimVertId);
[1456]	364	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	365	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[665]	366	}
[498]	367	}
[611]	368
	369	if (domain->hasArea)
	370	{
	371	dim0.clear();
	372	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1456]	373	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	374	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	375	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	376	dim0.clear();
	377	}
	378
	379	SuperClassWriter::definition_end();
[286]	380
[498]	381	switch (domain->type)
[384]	382	{
[498]	383	case CDomain::type_attr::curvilinear :
[449]	384	{
[498]	385	std::vector<StdSize> start(2) ;
	386	std::vector<StdSize> count(2) ;
[2507]	387	start[1]=domain->ibeginValue_;
	388	start[0]=domain->jbeginValue_;
	389	count[1]=domain->niValue_ ; count[0]=domain->njValue_ ;
[488]	390
[665]	391	if (domain->hasLonLat)
	392	{
[1930]	393	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
	394	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
[665]	395	}
[498]	396	break;
	397	}
[664]	398	case CDomain::type_attr::rectilinear :
[449]	399	{
[665]	400	if (domain->hasLonLat)
[498]	401	{
[665]	402	std::vector<StdSize> start(1) ;
	403	std::vector<StdSize> count(1) ;
[1930]	404
[2507]	405	start[0]=domain->jbeginValue_;
	406	count[0]=domain->njValue_;
[2394]	407	CArray<double,1> lat;
[2507]	408	lat.resize( domain->njValue_);
	409	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
[1930]	410	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
[665]	411
[2507]	412	start[0]=domain->ibeginValue_;
	413	count[0]=domain->niValue_;
[2613]	414	CArray<double,1> lon;
	415	lon.resize( domain->niValue_);
	416	for (int i=0;i<domain->niValue_;i++) lon(i) = domain->lonvalue(i);
[1930]	417	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
[498]	418	}
	419	break;
[449]	420	}
[384]	421	}
[611]	422
[617]	423	if (domain->hasBounds)
	424	{
	425	std::vector<StdSize> start(3);
	426	std::vector<StdSize> count(3);
	427	if (domain->isEmpty())
	428	{
	429	start[2] = start[1] = start[0] = 0;
	430	count[2] = count[1] = count[0] = 0;
	431	}
	432	else
	433	{
	434	start[2] = 0;
[2507]	435	start[1] = domain->ibeginValue_;
	436	start[0] = domain->jbeginValue_;
[1099]	437	count[2] = domain->nvertex;
[2507]	438	count[1] = domain->niValue_;
	439	count[0] = domain->njValue_;
[617]	440	}
[1143]	441
[1930]	442	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
	443	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
[617]	444	}
	445
[611]	446	if (domain->hasArea)
	447	{
	448	std::vector<StdSize> start(2);
	449	std::vector<StdSize> count(2);
	450
[2507]	451	start[1] = domain->ibeginValue_;
	452	start[0] = domain->jbeginValue_;
	453	count[1] = domain->niValue_;
	454	count[0] = domain->njValue_;
[1143]	455
[1930]	456	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
[611]	457	}
	458
[498]	459	SuperClassWriter::definition_start();
	460	break;
	461	}
	462	default :
	463	ERROR("CNc4DataOutput::writeDomain(domain)",
	464	<< "[ type = " << SuperClass::type << "]"
	465	<< " not implemented yet !");
	466	}
[449]	467	}
[498]	468	catch (CNetCdfException& e)
	469	{
	470	StdString msg("On writing the domain : ");
	471	msg.append(domid); msg.append("\n");
	472	msg.append("In the context : ");
	473	msg.append(context->getId()); msg.append("\n");
	474	msg.append(e.what());
	475	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
	476	}
	477
[449]	478	domain->addRelFile(this->filename);
	479	}
[1622]	480	CATCH
[449]	481
[879]	482	//--------------------------------------------------------------
[878]	483
[879]	484	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
	485	{
	486	CContext* context = CContext::getCurrent() ;
[878]	487
[879]	488	if (domain->IsWritten(this->filename)) return;
[1494]	489
	490	StdString domid = domain->getDomainOutputName();
	491
	492	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
	493	// Thus the entire mesh connectivity will be generated at once.
	494	if (isWrittenDomain(domid)) return ;
	495	else setWrittenDomain(domid);
	496
[879]	497	domain->checkAttributes();
	498	if (domain->isEmpty())
	499	if (SuperClass::type==MULTI_FILE) return ;
[878]	500
[1158]	501	nc_type typePrec ;
	502	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	503	else if (domain->prec==4) typePrec = NC_FLOAT ;
	504	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	505
[879]	506	std::vector<StdString> dim0;
	507	StdString domainName = domain->name;
[878]	508
[879]	509	StdString node_x = domainName + "_node_x";
	510	StdString node_y = domainName + "_node_y";
[878]	511
[879]	512	StdString edge_x = domainName + "_edge_x";
	513	StdString edge_y = domainName + "_edge_y";
	514	StdString edge_nodes = domainName + "_edge_nodes";
[878]	515
[879]	516	StdString face_x = domainName + "_face_x";
	517	StdString face_y = domainName + "_face_y";
	518	StdString face_nodes = domainName + "_face_nodes";
[902]	519	StdString face_edges = domainName + "_face_edges";
	520	StdString edge_faces = domainName + "_edge_face_links";
	521	StdString face_faces = domainName + "_face_links";
[878]	522
[879]	523	StdString dimNode = "n" + domainName + "_node";
	524	StdString dimEdge = "n" + domainName + "_edge";
	525	StdString dimFace = "n" + domainName + "_face";
	526	StdString dimVertex = "n" + domainName + "_vertex";
	527	StdString dimTwo = "Two";
[878]	528
[879]	529	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
[1494]	530	dim0.clear();
	531	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
	532	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
	533	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
	534	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
	535	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
[878]	536
[879]	537	try
	538	{
	539	switch (SuperClass::type)
	540	{
	541	case (ONE_FILE) :
	542	{
	543	// Adding nodes
	544	if (domain->nvertex == 1)
	545	{
	546	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	547	{
[902]	548	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
[879]	549	dim0.clear();
	550	dim0.push_back(dimNode);
[1456]	551	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	552	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	553	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	554	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	555	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	556	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	557	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	558	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	559	}
	560	} // domain->nvertex == 1
[878]	561
[879]	562	// Adding edges and nodes, if nodes have not been defined previously
	563	if (domain->nvertex == 2)
	564	{
	565	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	566	{
[924]	567	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	568	dim0.clear();
	569	dim0.push_back(dimNode);
[1456]	570	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	571	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	572	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	573	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	574	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	575	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	576	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	577	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	578	}
[924]	579	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
	580	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	581	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
	582	dim0.clear();
	583	dim0.push_back(dimEdge);
[1456]	584	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
[924]	585	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
	586	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
	587	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
[1456]	588	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
[924]	589	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
	590	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
	591	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	592	dim0.clear();
	593	dim0.push_back(dimEdge);
	594	dim0.push_back(dimTwo);
[1456]	595	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
[924]	596	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	597	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	598	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
[879]	599	} // domain->nvertex == 2
[878]	600
[879]	601	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
	602	if (domain->nvertex > 2)
	603	{
	604	// Nodes
	605	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	606	{
[924]	607	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	608	dim0.clear();
	609	dim0.push_back(dimNode);
[1456]	610	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	611	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	612	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	613	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	614	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	615	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	616	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	617	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	618	}
	619	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
	620	{
	621	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	622	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
[2409]	623	SuperClassWriter::addAttribute("face_edge_connectivity", face_edges, &domainName);
	624	SuperClassWriter::addAttribute("edge_face_connectivity", edge_faces, &domainName);
[924]	625	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
[879]	626	dim0.clear();
	627	dim0.push_back(dimEdge);
[1456]	628	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
[879]	629	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
[924]	630	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
[879]	631	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
[1456]	632	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
[879]	633	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
[924]	634	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
[879]	635	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	636	dim0.clear();
	637	dim0.push_back(dimEdge);
	638	dim0.push_back(dimTwo);
[1456]	639	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
[879]	640	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	641	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	642	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
	643	}
[2409]	644	SuperClassWriter::addAttribute("face_face_connectivity", face_faces, &domainName);
[924]	645	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
	646	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
	647	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
	648	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
	649	dim0.clear();
	650	dim0.push_back(dimFace);
[1456]	651	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
[924]	652	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
	653	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
	654	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
[1456]	655	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
[924]	656	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
	657	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
	658	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
	659	dim0.clear();
	660	dim0.push_back(dimFace);
	661	dim0.push_back(dimVertex);
[1456]	662	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
[924]	663	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
	664	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
	665	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
	666	dim0.clear();
	667	dim0.push_back(dimFace);
	668	dim0.push_back(dimVertex);
[1456]	669	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
[924]	670	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
	671	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
	672	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
[929]	673	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
[924]	674	dim0.clear();
	675	dim0.push_back(dimEdge);
	676	dim0.push_back(dimTwo);
[1456]	677	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
[2413]	678	SuperClassWriter::addAttribute("cf_role", StdString("edge_face_connectivity"), &edge_faces);
[924]	679	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
	680	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
	681	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
	682	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
	683	dim0.clear();
	684	dim0.push_back(dimFace);
	685	dim0.push_back(dimVertex);
[1456]	686	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
[2413]	687	SuperClassWriter::addAttribute("cf_role", StdString("face_face_connectivity"), &face_faces);
[924]	688	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
	689	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
[929]	690	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
[924]	691	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
	692	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
[879]	693	} // domain->nvertex > 2
[878]	694
[879]	695	SuperClassWriter::definition_end();
[878]	696
[924]	697	std::vector<StdSize> startEdges(1) ;
	698	std::vector<StdSize> countEdges(1) ;
	699	std::vector<StdSize> startNodes(1) ;
	700	std::vector<StdSize> countNodes(1) ;
	701	std::vector<StdSize> startFaces(1) ;
	702	std::vector<StdSize> countFaces(1) ;
	703	std::vector<StdSize> startEdgeNodes(2) ;
	704	std::vector<StdSize> countEdgeNodes(2) ;
	705	std::vector<StdSize> startEdgeFaces(2) ;
	706	std::vector<StdSize> countEdgeFaces(2) ;
	707	std::vector<StdSize> startFaceConctv(2) ;
	708	std::vector<StdSize> countFaceConctv(2) ;
[902]	709
[1494]	710	if (domain->nvertex == 1)
[879]	711	{
[1494]	712	if (domain->isEmpty())
	713	{
	714	startNodes[0]=0 ;
	715	countNodes[0]=0 ;
	716	}
	717	else
	718	{
[2507]	719	startNodes[0] = domain->ibeginValue_;
	720	countNodes[0] = domain->niValue_ ;
[1494]	721	}
[924]	722
[1494]	723	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	724	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	725	}
	726	else if (domain->nvertex == 2)
	727	{
	728	if (domain->isEmpty())
	729	{
	730	startEdges[0]=0 ;
	731	countEdges[0]=0 ;
	732	startNodes[0]=0 ;
	733	countNodes[0]=0 ;
	734	startEdgeNodes[0]=0;
	735	startEdgeNodes[1]=0;
	736	countEdgeNodes[0]=0;
	737	countEdgeNodes[1]=0;
[924]	738
[1494]	739	}
	740	else
	741	{
[2507]	742	startEdges[0] = domain->ibeginValue_;
	743	countEdges[0] = domain->niValue_;
[1494]	744	startNodes[0] = domain->mesh->node_start;
	745	countNodes[0] = domain->mesh->node_count;
[2409]	746	if (countNodes[0]==0) startNodes[0]=0 ; // for netcdf error
[2507]	747	startEdgeNodes[0] = domain->ibeginValue_;
[1494]	748	startEdgeNodes[1] = 0;
[2507]	749	countEdgeNodes[0] = domain->niValue_;
[1494]	750	countEdgeNodes[1] = 2;
	751	}
	752	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	753	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	754	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	755	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	756	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	757	}
[879]	758	else
	759	{
[1494]	760	if (domain->isEmpty())
	761	{
	762	startFaces[0] = 0 ;
	763	countFaces[0] = 0 ;
	764	startNodes[0] = 0;
	765	countNodes[0] = 0;
	766	startEdges[0] = 0;
	767	countEdges[0] = 0;
	768	startEdgeFaces[0] = 0;
	769	startEdgeFaces[1] = 0;
	770	countEdgeFaces[0] = 0;
	771	countEdgeFaces[1] = 0;
	772	startFaceConctv[0] = 0;
	773	startFaceConctv[1] = 0;
	774	countFaceConctv[0] = 0;
	775	countFaceConctv[1] = 0;
	776	}
	777	else
	778	{
[2507]	779	startFaces[0] = domain->ibeginValue_;
	780	countFaces[0] = domain->niValue_ ;
[1494]	781	startNodes[0] = domain->mesh->node_start;
	782	countNodes[0] = domain->mesh->node_count;
[2409]	783	if (countNodes[0]==0) startNodes[0]=0;
	784
[1494]	785	startEdges[0] = domain->mesh->edge_start;
	786	countEdges[0] = domain->mesh->edge_count;
[2409]	787	if (countEdges[0]==0) startEdges[0]=0 ; // for netcdf error
	788
[1494]	789	startEdgeNodes[0] = domain->mesh->edge_start;
[2409]	790	countEdgeNodes[0] = domain->mesh->edge_count;
	791	if (countEdgeNodes[0]==0) startEdgeNodes[0]=0; // for netcdf error
[1494]	792	startEdgeNodes[1] = 0;
	793	countEdgeNodes[1]= 2;
[2409]	794
[1494]	795	startEdgeFaces[0] = domain->mesh->edge_start;
[2409]	796	countEdgeFaces[0] = domain->mesh->edge_count;
	797	if (countEdgeFaces[0]==0) startEdgeFaces[0]=0 ; // for netcdf error
[1494]	798	startEdgeFaces[1]= 0;
	799	countEdgeFaces[1]= 2;
[2409]	800
[2507]	801	startFaceConctv[0] = domain->ibeginValue_;
	802	countFaceConctv[0] = domain->niValue_;
[1494]	803	startFaceConctv[1] = 0;
	804	countFaceConctv[1] = domain->nvertex;
	805	}
	806	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	807	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	808	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	809	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	810	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	811	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
	812	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
	813	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
	814	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
	815	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
	816	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
	817	}
[879]	818	SuperClassWriter::definition_start();
[878]	819
[879]	820	break;
	821	} // ONE_FILE
[878]	822
[879]	823	case (MULTI_FILE) :
	824	{
[1637]	825	ERROR("CNc4DataOutput::writeDomain(domain)",
	826	<< "[ type = multiple_file ]"
	827	<< " is not yet implemented for UGRID files !");
[879]	828	break;
	829	}
[878]	830
[879]	831	default :
	832	ERROR("CNc4DataOutput::writeDomain(domain)",
	833	<< "[ type = " << SuperClass::type << "]"
	834	<< " not implemented yet !");
	835	} // switch
	836	} // try
[878]	837
[879]	838	catch (CNetCdfException& e)
	839	{
	840	StdString msg("On writing the domain : ");
	841	msg.append(domid); msg.append("\n");
	842	msg.append("In the context : ");
	843	msg.append(context->getId()); msg.append("\n");
	844	msg.append(e.what());
[924]	845	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
[879]	846	}
[878]	847
[879]	848	domain->addRelFile(this->filename);
	849	}
[878]	850
[879]	851	//--------------------------------------------------------------
[878]	852
[879]	853	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
[449]	854	{
	855	CContext* context = CContext::getCurrent() ;
[488]	856
[449]	857	if (domain->IsWritten(this->filename)) return;
	858	domain->checkAttributes();
[488]	859
	860	if (domain->isEmpty())
[449]	861	if (SuperClass::type==MULTI_FILE) return ;
	862
	863	std::vector<StdString> dim0, dim1;
[772]	864	StdString domid = domain->getDomainOutputName();
[705]	865	if (isWrittenDomain(domid)) return ;
[774]	866	else setWrittenDomain(domid);
[705]	867
[449]	868	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
	869
[1430]	870	StdString lonName,latName, cellName ;
[1391]	871	if (domain->lon_name.isEmpty()) lonName = "lon";
	872	else lonName = domain->lon_name;
	873
	874	if (domain->lat_name.isEmpty()) latName = "lat";
	875	else latName = domain->lat_name;
	876
[1430]	877	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
	878	else cellName="cell";
	879	StdString dimXid = cellName+appendDomid;
[2387]	880	StdString dimVertId;
[2535]	881	if (domain->nvertex_name.isEmpty()) dimVertId = "nvertex"+appendDomid;
[2395]	882	else dimVertId = domain->nvertex_name;
[488]	883
[449]	884	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	885	string areaId = "area" + appendDomid;
[449]	886
[1158]	887	nc_type typePrec ;
	888	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	889	else if (domain->prec==4) typePrec = NC_FLOAT ;
	890	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	891
[1132]	892	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
[1025]	893
[498]	894	try
[449]	895	{
[498]	896	switch (SuperClass::type)
	897	{
	898	case (MULTI_FILE) :
	899	{
	900	dim0.push_back(dimXid);
[1553]	901	SuperClassWriter::addDimension(dimXid, domain->ni);
[488]	902
[1415]	903	lonid = lonName+appendDomid;
	904	latid = latName+appendDomid;
[1430]	905	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	906	else bounds_lonid = "bounds_"+lonName+appendDomid;
	907	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	908	else bounds_latid = "bounds_"+latName+appendDomid;
	909
[665]	910	if (domain->hasLonLat)
	911	{
[1456]	912	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	913	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	914	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	915	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	916	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	917	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
	918	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	919	}
[498]	920	dim0.clear();
	921	if (domain->hasBounds)
	922	{
	923	dim0.push_back(dimXid);
	924	dim0.push_back(dimVertId);
[1456]	925	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	926	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[498]	927	}
	928
	929	dim0.clear();
[449]	930	dim0.push_back(dimXid);
[611]	931	if (domain->hasArea)
	932	{
[1456]	933	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	934	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	935	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	936	}
	937
[498]	938	SuperClassWriter::definition_end();
[449]	939
[665]	940	if (domain->hasLonLat)
[498]	941	{
[1930]	942	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
	943	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
[665]	944	if (domain->hasBounds)
	945	{
[1930]	946	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
	947	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
[665]	948	}
[498]	949	}
[611]	950
	951	if (domain->hasArea)
[1930]	952	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
[611]	953
[498]	954	SuperClassWriter::definition_start();
	955	break ;
	956	}
[488]	957
[498]	958	case (ONE_FILE) :
	959	{
[1415]	960	lonid = lonName+appendDomid;
	961	latid = latName+appendDomid;
[1430]	962	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	963	else bounds_lonid = "bounds_"+lonName+appendDomid;
	964	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	965	else bounds_latid = "bounds_"+latName+appendDomid;
[1391]	966
[498]	967	dim0.push_back(dimXid);
[1132]	968	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
[665]	969	if (domain->hasLonLat)
	970	{
[1456]	971	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	972	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	973
	974	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	975	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	976	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	977	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
[1025]	978	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
[665]	979	}
[498]	980	dim0.clear();
[449]	981
[498]	982	if (domain->hasBounds)
	983	{
	984	dim0.push_back(dimXid);
	985	dim0.push_back(dimVertId);
[1456]	986	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	987	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[498]	988	}
[488]	989
[611]	990	if (domain->hasArea)
	991	{
	992	dim0.clear();
	993	dim0.push_back(dimXid);
[1456]	994	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	995	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	996	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	997	}
	998
[498]	999	SuperClassWriter::definition_end();
[488]	1000
[498]	1001	std::vector<StdSize> start(1), startBounds(2) ;
	1002	std::vector<StdSize> count(1), countBounds(2) ;
	1003	if (domain->isEmpty())
	1004	{
	1005	start[0]=0 ;
	1006	count[0]=0 ;
	1007	startBounds[1]=0 ;
[1025]	1008	countBounds[1]=nvertex ;
[498]	1009	startBounds[0]=0 ;
	1010	countBounds[0]=0 ;
	1011	}
	1012	else
	1013	{
[2507]	1014	start[0]=domain->ibeginValue_;
	1015	count[0]=domain->niValue_;
	1016	startBounds[0]=domain->ibeginValue_;
[498]	1017	startBounds[1]=0 ;
[2507]	1018	countBounds[0]=domain->niValue_;
[1025]	1019	countBounds[1]=nvertex ;
[498]	1020	}
[665]	1021
	1022	if (domain->hasLonLat)
[498]	1023	{
[1930]	1024	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
	1025	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
[665]	1026	if (domain->hasBounds)
	1027	{
[1930]	1028	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
	1029	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
[665]	1030	}
[498]	1031	}
[488]	1032
[611]	1033	if (domain->hasArea)
[1930]	1034	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
[488]	1035
[498]	1036	SuperClassWriter::definition_start();
[488]	1037
[498]	1038	break;
	1039	}
	1040	default :
	1041	ERROR("CNc4DataOutput::writeDomain(domain)",
	1042	<< "[ type = " << SuperClass::type << "]"
	1043	<< " not implemented yet !");
	1044	}
[219]	1045	}
[498]	1046	catch (CNetCdfException& e)
	1047	{
	1048	StdString msg("On writing the domain : ");
	1049	msg.append(domid); msg.append("\n");
	1050	msg.append("In the context : ");
	1051	msg.append(context->getId()); msg.append("\n");
	1052	msg.append(e.what());
	1053	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
	1054	}
[219]	1055	domain->addRelFile(this->filename);
	1056	}
	1057	//--------------------------------------------------------------
	1058
[347]	1059	void CNc4DataOutput::writeAxis_(CAxis* axis)
[219]	1060	{
[1030]	1061	if (axis->IsWritten(this->filename)) return;
[2381]	1062
	1063	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
	1064	if (!axis->value.isEmpty() )
	1065	{
[2386]	1066	// The hash of the element will be associated to the default element name (= map key), and to the name really written
	1067	int globalHash = axis->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
[2381]	1068
	1069	StdString defaultNameKey = axis->getAxisOutputName();
[2389]	1070	if ( !relAxis_.count ( defaultNameKey ) )
[2381]	1071	{
	1072	// if defaultNameKey not in the map, write the element such as it is defined
[2389]	1073	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) );
[2381]	1074	}
	1075	else // look if a hash associated this key is equal
	1076	{
	1077	bool elementIsInMap(false);
[2389]	1078	auto defaultNameKeyElements = relAxis_.equal_range( defaultNameKey );
[2381]	1079	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
	1080	{
	1081	if ( it->second.first == globalHash )
	1082	{
	1083	// if yes, associate the same ids to current element
[2389]	1084	axis->renameAttributesBeforeWriting( it->second.second );
[2381]	1085	elementIsInMap = true;
	1086	}
	1087	}
	1088	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
	1089	if (!elementIsInMap) // ! in MAP
	1090	{
[2389]	1091	axis->renameAttributesBeforeWriting();
	1092	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) ) ;// = axis->getId()
[2381]	1093	}
	1094	}
	1095	}
	1096
[1030]	1097	axis->checkAttributes();
[488]	1098
[1559]	1099	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
	1100	: axis->n_glo.getValue();
[1099]	1101
[1559]	1102	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
[1235]	1103
[1030]	1104	std::vector<StdString> dims;
	1105	StdString axisid = axis->getAxisOutputName();
[1435]	1106	StdString axisDim, axisBoundsId;
[1030]	1107	if (isWrittenAxis(axisid)) return ;
	1108	else setWrittenAxis(axisid);
[705]	1109
[1158]	1110	nc_type typePrec ;
	1111	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
[1235]	1112	else if (axis->prec==4) typePrec = NC_FLOAT ;
[1158]	1113	else if (axis->prec==8) typePrec = NC_DOUBLE ;
	1114
	1115	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
	1116	string strId="str_len" ;
[1030]	1117	try
	1118	{
[1433]	1119	if (axis->dim_name.isEmpty()) axisDim = axisid;
	1120	else axisDim=axis->dim_name.getValue();
[1559]	1121	SuperClassWriter::addDimension(axisDim, size);
[1433]	1122	dims.push_back(axisDim);
	1123
[1439]	1124	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
[1433]	1125
[2507]	1126	if (axis->hasValue() \|\| !axis->label.isEmpty())
[816]	1127	{
[1158]	1128	if (!axis->label.isEmpty()) dims.push_back(strId);
[1430]	1129
[1456]	1130	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
[219]	1131
[1030]	1132	if (!axis->name.isEmpty())
	1133	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
[219]	1134
[1030]	1135	if (!axis->standard_name.isEmpty())
	1136	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
[540]	1137
[1030]	1138	if (!axis->long_name.isEmpty())
	1139	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
[219]	1140
[1030]	1141	if (!axis->unit.isEmpty())
	1142	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
[219]	1143
[1430]	1144	if (!axis->axis_type.isEmpty())
	1145	{
	1146	switch(axis->axis_type)
	1147	{
	1148	case CAxis::axis_type_attr::X :
	1149	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
	1150	break;
	1151	case CAxis::axis_type_attr::Y :
	1152	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
	1153	break;
	1154	case CAxis::axis_type_attr::Z :
	1155	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
	1156	break;
	1157	case CAxis::axis_type_attr::T :
	1158	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
	1159	break;
	1160	}
	1161	}
	1162
[1030]	1163	if (!axis->positive.isEmpty())
	1164	{
	1165	SuperClassWriter::addAttribute("positive",
	1166	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
	1167	&axisid);
	1168	}
[399]	1169
[1266]	1170	if (!axis->formula.isEmpty())
	1171	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
	1172
	1173	if (!axis->formula_term.isEmpty())
[2436]	1174	SuperClassWriter::addAttribute("formula_terms", axis->formula_term.getValue(), &axisid);
[1266]	1175
[1435]	1176	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
[1249]	1177	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
[1030]	1178	{
	1179	dims.push_back("axis_nbounds");
[1456]	1180	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
[1030]	1181	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
[1288]	1182
	1183	if (!axis->standard_name.isEmpty())
	1184	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
	1185
	1186	if (!axis->unit.isEmpty())
	1187	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
	1188
[1266]	1189	if (!axis->formula_bounds.isEmpty())
[1288]	1190	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
[1266]	1191
	1192	if (!axis->formula_term_bounds.isEmpty())
[2436]	1193	SuperClassWriter::addAttribute("formula_terms", axis->formula_term_bounds.getValue(), &axisBoundsId);
[1030]	1194	}
[1435]	1195	}
[816]	1196
[1435]	1197	SuperClassWriter::definition_end();
[1950]	1198
[1435]	1199	switch (SuperClass::type)
	1200	{
	1201	case MULTI_FILE:
[1030]	1202	{
[1435]	1203	if (axis->label.isEmpty())
[1437]	1204	{
	1205	if (!axis->value.isEmpty())
[1930]	1206	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
[633]	1207
[1437]	1208	if (!axis->bounds.isEmpty())
[1930]	1209	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
[1435]	1210	}
[1437]	1211	else
[1950]	1212	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
[1435]	1213
	1214	SuperClassWriter::definition_start();
	1215	break;
	1216	}
	1217	case ONE_FILE:
	1218	{
	1219	std::vector<StdSize> start(1), startBounds(2) ;
	1220	std::vector<StdSize> count(1), countBounds(2) ;
[1559]	1221	start[0] = startBounds[0] = axis->begin;
	1222	count[0] = countBounds[0] = axis->n;
[1435]	1223	startBounds[1] = 0;
	1224	countBounds[1] = 2;
	1225
	1226	if (axis->label.isEmpty())
[1437]	1227	{
	1228	if (!axis->value.isEmpty())
[1930]	1229	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
[1435]	1230
[1437]	1231	if (!axis->bounds.isEmpty())
[1930]	1232	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
[1435]	1233	}
[1437]	1234	else
[1435]	1235	{
	1236	std::vector<StdSize> startLabel(2), countLabel(2);
	1237	startLabel[0] = start[0]; startLabel[1] = 0;
	1238	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
[1950]	1239	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
[1435]	1240	}
[609]	1241
[1435]	1242	SuperClassWriter::definition_start();
	1243
	1244	break;
[609]	1245	}
[1435]	1246	default :
	1247	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
	1248	<< "[ type = " << SuperClass::type << "]"
	1249	<< " not implemented yet !");
[609]	1250	}
[1030]	1251	}
	1252	catch (CNetCdfException& e)
	1253	{
	1254	StdString msg("On writing the axis : ");
	1255	msg.append(axisid); msg.append("\n");
	1256	msg.append("In the context : ");
	1257	CContext* context = CContext::getCurrent() ;
	1258	msg.append(context->getId()); msg.append("\n");
	1259	msg.append(e.what());
	1260	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
	1261	}
[1158]	1262	axis->addRelFile(this->filename);
[391]	1263	}
[488]	1264
[887]	1265	void CNc4DataOutput::writeScalar_(CScalar* scalar)
	1266	{
	1267	if (scalar->IsWritten(this->filename)) return;
	1268	scalar->checkAttributes();
	1269	int scalarSize = 1;
	1270
	1271	StdString scalaId = scalar->getScalarOutputName();
[1430]	1272	StdString boundsId;
[887]	1273	if (isWrittenAxis(scalaId)) return ;
	1274	else setWrittenAxis(scalaId);
	1275
[1158]	1276	nc_type typePrec ;
	1277	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
	1278	else if (scalar->prec==4) typePrec = NC_FLOAT ;
	1279	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
	1280
[1435]	1281	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
	1282	string strId="str_len" ;
	1283
[887]	1284	try
	1285	{
[1439]	1286	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
[1435]	1287
	1288	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
[887]	1289	{
[1430]	1290	std::vector<StdString> dims;
	1291	StdString scalarDim = scalaId;
	1292
[1435]	1293	if (!scalar->label.isEmpty()) dims.push_back(strId);
	1294
[1158]	1295	SuperClassWriter::addVariable(scalaId, typePrec, dims);
[887]	1296
	1297	if (!scalar->name.isEmpty())
	1298	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
	1299
	1300	if (!scalar->standard_name.isEmpty())
	1301	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
	1302
	1303	if (!scalar->long_name.isEmpty())
	1304	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
	1305
	1306	if (!scalar->unit.isEmpty())
	1307	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
	1308
[1430]	1309	if (!scalar->axis_type.isEmpty())
	1310	{
	1311	switch(scalar->axis_type)
	1312	{
	1313	case CScalar::axis_type_attr::X :
	1314	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
	1315	break;
	1316	case CScalar::axis_type_attr::Y :
	1317	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
	1318	break;
	1319	case CScalar::axis_type_attr::Z :
	1320	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
	1321	break;
	1322	case CScalar::axis_type_attr::T :
	1323	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
	1324	break;
	1325	}
	1326	}
	1327
[1435]	1328	if (!scalar->positive.isEmpty())
[1430]	1329	{
[1435]	1330	SuperClassWriter::addAttribute("positive",
	1331	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
	1332	&scalaId);
	1333	}
	1334
	1335	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1336	{
[1436]	1337	dims.clear();
	1338	dims.push_back("axis_nbounds");
[1435]	1339	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
[1430]	1340	SuperClassWriter::addVariable(boundsId, typePrec, dims);
[1436]	1341	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
[1430]	1342	}
	1343
[887]	1344	SuperClassWriter::definition_end();
	1345
	1346	switch (SuperClass::type)
	1347	{
	1348	case MULTI_FILE:
	1349	{
	1350	CArray<double,1> scalarValue(scalarSize);
[1435]	1351	CArray<string,1> scalarLabel(scalarSize);
[1436]	1352	CArray<double,1> scalarBounds(scalarSize*2);
[1435]	1353
	1354	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
[1430]	1355	{
[1435]	1356	scalarValue(0) = scalar->value;
	1357	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
	1358	}
	1359
	1360	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1361	{
[1436]	1362	scalarBounds(0) = scalar->bounds(0);
	1363	scalarBounds(1) = scalar->bounds(1);
	1364	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
[1430]	1365	}
[1435]	1366
	1367	if (!scalar->label.isEmpty())
	1368	{
	1369	scalarLabel(0) = scalar->label;
	1370	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
	1371	}
	1372
[887]	1373	SuperClassWriter::definition_start();
	1374
	1375	break;
	1376	}
	1377	case ONE_FILE:
	1378	{
	1379	CArray<double,1> scalarValue(scalarSize);
[1435]	1380	CArray<string,1> scalarLabel(scalarSize);
[1436]	1381	CArray<double,1> scalarBounds(scalarSize*2);
[887]	1382
	1383	std::vector<StdSize> start(1);
	1384	std::vector<StdSize> count(1);
	1385	start[0] = 0;
	1386	count[0] = 1;
[1435]	1387	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
[1430]	1388	{
[1435]	1389	scalarValue(0) = scalar->value;
	1390	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
	1391	}
	1392	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1393	{
[1436]	1394	scalarBounds(0) = scalar->bounds(0);
	1395	scalarBounds(1) = scalar->bounds(1);
	1396	count[0] = 2;
	1397	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
[1430]	1398	}
[1435]	1399	if (!scalar->label.isEmpty())
	1400	{
	1401	scalarLabel(0) = scalar->label;
	1402	count[0] = stringArrayLen;
	1403	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
	1404	}
	1405
[887]	1406	SuperClassWriter::definition_start();
	1407
	1408	break;
	1409	}
	1410	default :
	1411	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
	1412	<< "[ type = " << SuperClass::type << "]"
	1413	<< " not implemented yet !");
	1414	}
	1415	}
	1416	}
	1417	catch (CNetCdfException& e)
	1418	{
	1419	StdString msg("On writing the scalar : ");
	1420	msg.append(scalaId); msg.append("\n");
	1421	msg.append("In the context : ");
	1422	CContext* context = CContext::getCurrent() ;
	1423	msg.append(context->getId()); msg.append("\n");
	1424	msg.append(e.what());
	1425	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
	1426	}
	1427	scalar->addRelFile(this->filename);
	1428	}
	1429
[676]	1430	//--------------------------------------------------------------
	1431
	1432	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
	1433	{
[1957]	1434	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
	1435
	1436	// NOTA : The cuurent algorithm to write compress elements of the grid
	1437	// will work pretting well when on server side you dont't get
	1438	// partial overlap on elements between differents participating process
	1439	// So the element must be totally distributed or non distributed
	1440	// If an element is partially overlaping betwwen process then the
	1441	// total compressed part will apear artificially greater than expected
	1442	// For the current implementation of writer which is decomposed only on
	1443	// one element, it will work as expected, but for future, it must be
	1444	// reconsidered again.
	1445	try
	1446	{
	1447	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1448	std::vector<StdString> domainList = grid->getDomainList();
	1449	std::vector<StdString> axisList = grid->getAxisList();
	1450	std::vector<StdString> scalarList = grid->getScalarList();
	1451	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
	1452	int commRank ;
	1453	MPI_Comm_rank(comm_file,&commRank) ;
[676]	1454
[1957]	1455	std::vector<StdString> dims;
[676]	1456
[1957]	1457	for (int i = 0; i < numElement; ++i)
	1458	{
	1459	StdString varId, compress;
	1460	CArray<size_t, 1> indexes;
	1461	bool isDistributed;
	1462	size_t nbIndexes, totalNbIndexes, offset;
	1463	size_t firstGlobalIndex;
	1464
	1465	if (2 == axisDomainOrder(i))
	1466	{
	1467	CDomain* domain = CDomain::get(domainList[idxDomain]);
	1468	StdString domId = domain->getDomainOutputName();
[676]	1469
[1957]	1470	if (!domain->isCompressible()
	1471	\|\| domain->type == CDomain::type_attr::unstructured
	1472	\|\| domain->isWrittenCompressed(this->filename)
	1473	\|\| isWrittenCompressedDomain(domId))
	1474	continue;
	1475
	1476	// unstructured grid seems not be taken into account why ?
[676]	1477
[1957]	1478	string lonName,latName ;
[676]	1479
[1957]	1480	if (domain->lon_name.isEmpty())
	1481	{
	1482	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
	1483	else lonName = "lon";
	1484	}
	1485	else lonName = domain->lon_name;
[676]	1486
[1957]	1487	if (domain->lat_name.isEmpty())
	1488	{
	1489	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
	1490	else latName = "lat";
	1491	}
	1492	else latName = domain->lat_name;
	1493
	1494	StdString appendDomId = singleDomain ? "" : "_" + domId;
[676]	1495
[1957]	1496	varId = domId + "_points";
	1497	compress = latName + appendDomId + " " + lonName + appendDomId;
	1498
[2267]	1499	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
[1957]	1500	workflowView->getGlobalIndexView(indexes) ;
	1501	nbIndexes = workflowView->getSize() ;
	1502	isDistributed = domain->isDistributed();
	1503	if (isDistributed)
	1504	{
	1505	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	1506	if (commRank==0) offset=0 ;
	1507	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
	1508	}
	1509	else
	1510	{
	1511	offset=0 ;
	1512	totalNbIndexes = nbIndexes ;
	1513	}
[676]	1514
[2507]	1515	firstGlobalIndex = domain->ibeginValue_ + domain->jbeginValue_ * domain->ni_glo;
[676]	1516
[1957]	1517	domain->addRelFileCompressed(this->filename);
	1518	setWrittenCompressedDomain(domId);
	1519	++idxDomain;
	1520	}
	1521	else if (1 == axisDomainOrder(i))
	1522	{
	1523	CAxis* axis = CAxis::get(axisList[idxAxis]);
	1524	StdString axisId = axis->getAxisOutputName();
[676]	1525
[1957]	1526	if (!axis->isCompressible()
	1527	\|\| axis->isWrittenCompressed(this->filename)
	1528	\|\| isWrittenCompressedAxis(axisId))
	1529	continue;
[676]	1530
[1957]	1531	varId = axisId + "_points";
	1532	compress = axisId;
[676]	1533
[2267]	1534	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
[1957]	1535	workflowView->getGlobalIndexView(indexes) ;
	1536	nbIndexes = workflowView->getSize() ;
	1537	isDistributed = axis->isDistributed();
	1538	if (isDistributed)
	1539	{
	1540	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	1541	if (commRank==0) offset=0 ;
	1542	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
	1543	}
	1544	else
	1545	{
	1546	offset=0 ;
	1547	totalNbIndexes = nbIndexes ;
	1548	}
	1549	firstGlobalIndex = axis->begin;
	1550
	1551	axis->addRelFileCompressed(this->filename);
	1552	setWrittenCompressedAxis(axisId);
	1553	++idxAxis;
	1554	}
	1555	else
	1556	{
	1557	//for scalar
	1558	}
[676]	1559
[1957]	1560	if (!varId.empty())
	1561	{
	1562	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
[774]	1563
[1957]	1564	dims.clear();
	1565	dims.push_back(varId);
	1566	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
[676]	1567
[1957]	1568	SuperClassWriter::addAttribute("compress", compress, &varId);
[676]	1569
[1957]	1570	switch (SuperClass::type)
	1571	{
	1572	case (MULTI_FILE):
	1573	{
	1574	indexes -= firstGlobalIndex;
	1575	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
	1576	break;
	1577	}
	1578	case (ONE_FILE):
	1579	{
	1580	std::vector<StdSize> start, count;
	1581	start.push_back(offset);
	1582	count.push_back(nbIndexes);
[676]	1583
[1957]	1584	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
	1585	break;
	1586	}
	1587	}
[1144]	1588	}
[1957]	1589	}
[676]	1590
[1957]	1591	grid->addRelFileCompressed(this->filename);
	1592	}
	1593	catch (CNetCdfException& e)
	1594	{
	1595	StdString msg("On writing compressed grid : ");
	1596	msg.append(grid->getId()); msg.append("\n");
	1597	msg.append("In the context : ");
	1598	CContext* context = CContext::getCurrent();
	1599	msg.append(context->getId()); msg.append("\n");
	1600	msg.append(e.what());
	1601	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
	1602	}
	1603	}
[676]	1604
	1605	//--------------------------------------------------------------
	1606
[391]	1607	void CNc4DataOutput::writeTimeDimension_(void)
	1608	{
[498]	1609	try
	1610	{
[802]	1611	SuperClassWriter::addDimension(getTimeCounterName());
[498]	1612	}
	1613	catch (CNetCdfException& e)
	1614	{
[614]	1615	StdString msg("On writing time dimension : time_couter\n");
[498]	1616	msg.append("In the context : ");
	1617	CContext* context = CContext::getCurrent() ;
	1618	msg.append(context->getId()); msg.append("\n");
	1619	msg.append(e.what());
	1620	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
	1621	}
[391]	1622	}
[676]	1623
[219]	1624	//--------------------------------------------------------------
	1625
[347]	1626	void CNc4DataOutput::writeField_(CField* field)
[219]	1627	{
[1158]	1628	CContext* context = CContext::getCurrent() ;
[300]	1629
[1158]	1630	std::vector<StdString> dims, coodinates;
[1869]	1631	CGrid* grid = field->getGrid();
[1158]	1632	if (!grid->doGridHaveDataToWrite())
[567]	1633	if (SuperClass::type==MULTI_FILE) return ;
[488]	1634
[1158]	1635	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1636	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
	1637	std::vector<StdString> domainList = grid->getDomainList();
	1638	std::vector<StdString> axisList = grid->getAxisList();
	1639	std::vector<StdString> scalarList = grid->getScalarList();
[219]	1640
[1158]	1641	StdString timeid = getTimeCounterName();
	1642	StdString dimXid,dimYid;
	1643	std::deque<StdString> dimIdList, dimCoordList;
	1644	bool hasArea = false;
	1645	StdString cellMeasures = "area:";
	1646	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
[488]	1647
[1158]	1648	for (int i = 0; i < numElement; ++i)
	1649	{
	1650	if (2 == axisDomainOrder(i))
	1651	{
	1652	CDomain* domain = CDomain::get(domainList[idxDomain]);
	1653	StdString domId = domain->getDomainOutputName();
	1654	StdString appendDomId = singleDomain ? "" : "_" + domId ;
[1391]	1655	StdString lonName,latName ;
[1430]	1656	StdString dimIname,dimJname ;
[676]	1657
[1415]	1658	if (domain->lon_name.isEmpty())
	1659	{
	1660	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
	1661	else lonName = "lon";
	1662	}
[1391]	1663	else lonName = domain->lon_name;
	1664
[1415]	1665	if (domain->lat_name.isEmpty())
	1666	{
	1667	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
	1668	else latName = "lat";
	1669	}
[1391]	1670	else latName = domain->lat_name;
[1430]	1671
	1672	if (domain->dim_i_name.isEmpty())
	1673	{
	1674	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
	1675	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
	1676	else dimIname = lonName;
	1677	}
	1678	else dimIname = domain->dim_i_name;
	1679
	1680	if (domain->dim_j_name.isEmpty())
	1681	{
	1682	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
	1683	else dimJname = latName;
	1684	}
	1685	else dimJname = domain->dim_j_name;
[1391]	1686
[1158]	1687	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
	1688	{
	1689	dimIdList.push_back(domId + "_points");
	1690	field->setUseCompressedOutput();
	1691	}
[676]	1692
[1158]	1693	switch (domain->type)
[879]	1694	{
[1158]	1695	case CDomain::type_attr::curvilinear:
	1696	if (!compressedOutput \|\| !domain->isCompressible())
	1697	{
[1430]	1698	dimXid=dimIname+appendDomId;
	1699	dimYid=dimJname+appendDomId;
[1158]	1700	dimIdList.push_back(dimXid);
	1701	dimIdList.push_back(dimYid);
	1702	}
[1415]	1703	dimCoordList.push_back(lonName+appendDomId);
	1704	dimCoordList.push_back(latName+appendDomId);
[1158]	1705	break ;
	1706	case CDomain::type_attr::rectilinear:
	1707	if (!compressedOutput \|\| !domain->isCompressible())
	1708	{
[1430]	1709	dimXid = dimIname+appendDomId;
	1710	dimYid = dimJname+appendDomId;
[1158]	1711	dimIdList.push_back(dimXid);
	1712	dimIdList.push_back(dimYid);
	1713	}
[1430]	1714	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
	1715	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
	1716
[1158]	1717	break ;
	1718	case CDomain::type_attr::unstructured:
	1719	{
	1720	if (SuperClassWriter::useCFConvention)
	1721	{
[1430]	1722	dimXid = dimIname + appendDomId;
[1158]	1723	dimIdList.push_back(dimXid);
[1415]	1724	dimCoordList.push_back(lonName+appendDomId);
	1725	dimCoordList.push_back(latName+appendDomId);
[1158]	1726	}
	1727	else
	1728	{
	1729	StdString domainName = domain->name;
	1730	if (domain->nvertex == 1)
	1731	{
	1732	dimXid = "n" + domainName + "_node";
	1733	dimIdList.push_back(dimXid);
	1734	dimCoordList.push_back(StdString(domainName + "_node_x"));
	1735	dimCoordList.push_back(StdString(domainName + "_node_y"));
	1736	}
	1737	else if (domain->nvertex == 2)
	1738	{
	1739	dimXid = "n" + domainName + "_edge";
	1740	dimIdList.push_back(dimXid);
	1741	dimCoordList.push_back(StdString(domainName + "_edge_x"));
	1742	dimCoordList.push_back(StdString(domainName + "_edge_y"));
	1743	}
	1744	else
	1745	{
	1746	dimXid = "n" + domainName + "_face";
	1747	dimIdList.push_back(dimXid);
	1748	dimCoordList.push_back(StdString(domainName + "_face_x"));
	1749	dimCoordList.push_back(StdString(domainName + "_face_y"));
	1750	}
	1751	} // ugrid convention
	1752	} // case unstructured domain
[879]	1753	}
[1158]	1754
	1755	if (domain->hasArea)
[879]	1756	{
[1158]	1757	hasArea = true;
	1758	cellMeasures += " area" + appendDomId;
[879]	1759	}
[1158]	1760	++idxDomain;
	1761	}
	1762	else if (1 == axisDomainOrder(i))
	1763	{
	1764	CAxis* axis = CAxis::get(axisList[idxAxis]);
	1765	StdString axisId = axis->getAxisOutputName();
[1430]	1766	StdString axisDim;
[1158]	1767
[1430]	1768	if (axis->dim_name.isEmpty()) axisDim = axisId;
	1769	else axisDim=axis->dim_name.getValue();
	1770
[1158]	1771	if (compressedOutput && axis->isCompressible())
[879]	1772	{
[1430]	1773	dimIdList.push_back(axisDim + "_points");
[1158]	1774	field->setUseCompressedOutput();
[879]	1775	}
[1158]	1776	else
[1430]	1777	dimIdList.push_back(axisDim);
[878]	1778
[1430]	1779	if (axisDim != axisId) dimCoordList.push_back(axisId);
[1158]	1780	++idxAxis;
	1781	}
[1430]	1782	else
[1158]	1783	{
[1430]	1784	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
	1785	StdString scalarId = scalar->getScalarOutputName();
[1446]	1786	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
	1787	dimCoordList.push_back(scalarId);
[1430]	1788	++idxScalar;
[1158]	1789	}
	1790	}
[488]	1791
[1158]	1792	StdString fieldid = field->getFieldOutputName();
[219]	1793
[1158]	1794	nc_type type ;
	1795	if (field->prec.isEmpty()) type = NC_FLOAT ;
	1796	else
	1797	{
	1798	if (field->prec==2) type = NC_SHORT ;
	1799	else if (field->prec==4) type = NC_FLOAT ;
	1800	else if (field->prec==8) type = NC_DOUBLE ;
	1801	}
[488]	1802
[1158]	1803	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
[488]	1804
[1158]	1805	if (wtime)
	1806	{
	1807	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
	1808	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
	1809	dims.push_back(timeid);
	1810	}
[488]	1811
[1961]	1812	while (!dimIdList.empty())
[1158]	1813	{
[1961]	1814	dims.push_back(dimIdList.back());
	1815	dimIdList.pop_back();
[1158]	1816	}
[219]	1817
[1158]	1818	while (!dimCoordList.empty())
	1819	{
	1820	coodinates.push_back(dimCoordList.back());
	1821	dimCoordList.pop_back();
	1822	}
[219]	1823
[1158]	1824	try
	1825	{
[2481]	1826	SuperClassWriter::addVariable(fieldid, type, dims, false);
[2479]	1827	SuperClassWriter::addChunk(field, type, dims);
[488]	1828
[498]	1829	if (!field->standard_name.isEmpty())
	1830	SuperClassWriter::addAttribute
	1831	("standard_name", field->standard_name.getValue(), &fieldid);
[219]	1832
[498]	1833	if (!field->long_name.isEmpty())
	1834	SuperClassWriter::addAttribute
	1835	("long_name", field->long_name.getValue(), &fieldid);
[219]	1836
[498]	1837	if (!field->unit.isEmpty())
	1838	SuperClassWriter::addAttribute
	1839	("units", field->unit.getValue(), &fieldid);
[463]	1840
[1158]	1841	// Ugrid field attributes "mesh" and "location"
	1842	if (!SuperClassWriter::useCFConvention)
	1843	{
	1844	if (!domainList.empty())
	1845	{
	1846	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
	1847	StdString mesh = domain->name;
	1848	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
	1849	StdString location;
	1850	if (domain->nvertex == 1)
	1851	location = "node";
	1852	else if (domain->nvertex == 2)
	1853	location = "edge";
	1854	else if (domain->nvertex > 2)
	1855	location = "face";
	1856	SuperClassWriter::addAttribute("location", location, &fieldid);
	1857	}
	1858
	1859	}
	1860
	1861	if (!field->valid_min.isEmpty())
[498]	1862	SuperClassWriter::addAttribute
	1863	("valid_min", field->valid_min.getValue(), &fieldid);
[463]	1864
[498]	1865	if (!field->valid_max.isEmpty())
	1866	SuperClassWriter::addAttribute
	1867	("valid_max", field->valid_max.getValue(), &fieldid);
[464]	1868
[498]	1869	if (!field->scale_factor.isEmpty())
	1870	SuperClassWriter::addAttribute
	1871	("scale_factor", field->scale_factor.getValue(), &fieldid);
[464]	1872
[498]	1873	if (!field->add_offset.isEmpty())
	1874	SuperClassWriter::addAttribute
	1875	("add_offset", field->add_offset.getValue(), &fieldid);
[488]	1876
[498]	1877	SuperClassWriter::addAttribute
	1878	("online_operation", field->operation.getValue(), &fieldid);
[472]	1879
[498]	1880	// write child variables as attributes
[488]	1881
	1882
[1021]	1883	bool alreadyAddCellMethod = false;
	1884	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
	1885	if (!field->cell_methods.isEmpty())
	1886	{
[1158]	1887	StdString cellMethodString = field->cell_methods;
	1888	if (field->cell_methods_mode.isEmpty() \|\|
[1021]	1889	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
[1158]	1890	{
	1891	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
	1892	alreadyAddCellMethod = true;
	1893	}
	1894	else
	1895	{
	1896	switch (field->cell_methods_mode)
	1897	{
	1898	case (CField::cell_methods_mode_attr::prefix):
	1899	cellMethodsPrefix = cellMethodString;
	1900	cellMethodsPrefix += " ";
	1901	break;
	1902	case (CField::cell_methods_mode_attr::suffix):
	1903	cellMethodsSuffix = " ";
	1904	cellMethodsSuffix += cellMethodString;
	1905	break;
	1906	case (CField::cell_methods_mode_attr::none):
	1907	break;
	1908	default:
	1909	break;
	1910	}
	1911	}
[1021]	1912	}
[488]	1913
[1021]	1914
[498]	1915	if (wtime)
	1916	{
[614]	1917	CDuration freqOp = field->freq_op.getValue();
	1918	freqOp.solveTimeStep(*context->calendar);
	1919	StdString freqOpStr = freqOp.toStringUDUnits();
[612]	1920	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
[437]	1921
[614]	1922	CDuration freqOut = field->getRelFile()->output_freq.getValue();
	1923	freqOut.solveTimeStep(*context->calendar);
	1924	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
[612]	1925
[1021]	1926	StdString cellMethods(cellMethodsPrefix + "time: ");
[612]	1927	if (field->operation.getValue() == "instant") cellMethods += "point";
	1928	else if (field->operation.getValue() == "average") cellMethods += "mean";
	1929	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
	1930	else cellMethods += field->operation;
[614]	1931	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
	1932	cellMethods += " (interval: " + freqOpStr + ")";
[1021]	1933	cellMethods += cellMethodsSuffix;
	1934	if (!alreadyAddCellMethod)
	1935	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
[498]	1936	}
[488]	1937
[611]	1938	if (hasArea)
	1939	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
	1940
[498]	1941	if (!field->default_value.isEmpty())
	1942	{
[1424]	1943	double default_value = field->default_value.getValue();
	1944	if (type == NC_DOUBLE)
	1945	{
	1946	SuperClassWriter::setDefaultValue(fieldid, &default_value);
	1947	}
	1948	else if (type == NC_SHORT)
	1949	{
	1950	short sdefault_value = (short)default_value;
	1951	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
	1952	}
	1953	else
	1954	{
	1955	float fdefault_value = (float)default_value;
	1956	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
	1957	}
[498]	1958	}
	1959	else
[517]	1960	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
[219]	1961
[606]	1962	if (field->compression_level.isEmpty())
[1872]	1963	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
[2577]	1964	if ( (field->compression_level.getValue()>0)&&(field->compression_type.isEmpty()) )
[2529]	1965	field->compression_type.setValue( "gzip" );
	1966	if (field->compression_type.isEmpty())
	1967	field->compression_type = "None";
	1968	if (field->compression_params.isEmpty())
	1969	field->compression_params.resize( 0 );
	1970	SuperClassWriter::setCompressionLevel(fieldid, field->compression_type, field->compression_level, field->compression_params);
[606]	1971
[878]	1972	{ // Ecriture des coordonnes
[488]	1973
[498]	1974	StdString coordstr; //boost::algorithm::join(coodinates, " ")
	1975	std::vector<StdString>::iterator
	1976	itc = coodinates.begin(), endc = coodinates.end();
[488]	1977
[498]	1978	for (; itc!= endc; itc++)
	1979	{
	1980	StdString & coord = *itc;
	1981	if (itc+1 != endc)
	1982	coordstr.append(coord).append(" ");
	1983	else coordstr.append(coord);
	1984	}
[219]	1985
[498]	1986	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
[219]	1987
[498]	1988	}
[1222]	1989
	1990	vector<CVariable*> listVars = field->getAllVariables() ;
	1991	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
	1992
[219]	1993	}
[498]	1994	catch (CNetCdfException& e)
	1995	{
	1996	StdString msg("On writing field : ");
	1997	msg.append(fieldid); msg.append("\n");
	1998	msg.append("In the context : ");
	1999	msg.append(context->getId()); msg.append("\n");
	2000	msg.append(e.what());
	2001	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
	2002	}
[879]	2003	} // writeField_()
[219]	2004
	2005	//--------------------------------------------------------------
	2006
[347]	2007	void CNc4DataOutput::writeFile_ (CFile* file)
[219]	2008	{
[773]	2009	StdString filename = file->getFileOutputName();
[219]	2010	StdString description = (!file->description.isEmpty())
	2011	? file->description.getValue()
[335]	2012	: StdString("Created by xios");
[609]	2013
	2014	singleDomain = (file->nbDomains == 1);
	2015
[1158]	2016	StdString conv_str ;
	2017	if (file->convention_str.isEmpty())
	2018	{
	2019	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
	2020	else conv_str="UGRID" ;
	2021	}
	2022	else conv_str=file->convention_str ;
	2023
[498]	2024	try
	2025	{
[1309]	2026	if (!appendMode) this->writeFileAttributes(filename, description,
	2027	conv_str,
	2028	StdString("An IPSL model"),
	2029	this->getTimeStamp());
[609]	2030
[701]	2031	if (!appendMode)
	2032	SuperClassWriter::addDimension("axis_nbounds", 2);
[498]	2033	}
	2034	catch (CNetCdfException& e)
	2035	{
	2036	StdString msg("On writing file : ");
	2037	msg.append(filename); msg.append("\n");
	2038	msg.append("In the context : ");
	2039	CContext* context = CContext::getCurrent() ;
	2040	msg.append(context->getId()); msg.append("\n");
	2041	msg.append(e.what());
	2042	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
	2043	}
[219]	2044	}
[488]	2045
[472]	2046	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
	2047	{
[773]	2048	StdString name = var->getVariableOutputName();
[488]	2049
[498]	2050	try
	2051	{
[527]	2052	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	2053	addAttribute(name, var->getData<int>(), &fieldId);
	2054	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	2055	addAttribute(name, var->getData<short int>(), &fieldId);
	2056	else if (var->type.getValue() == CVariable::type_attr::t_float)
	2057	addAttribute(name, var->getData<float>(), &fieldId);
	2058	else if (var->type.getValue() == CVariable::type_attr::t_double)
	2059	addAttribute(name, var->getData<double>(), &fieldId);
	2060	else if (var->type.getValue() == CVariable::type_attr::t_string)
	2061	addAttribute(name, var->getData<string>(), &fieldId);
	2062	else
	2063	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
	2064	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	2065	}
	2066	catch (CNetCdfException& e)
	2067	{
	2068	StdString msg("On writing attributes of variable with name : ");
	2069	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
	2070	msg.append("In the context : ");
	2071	CContext* context = CContext::getCurrent() ;
	2072	msg.append(context->getId()); msg.append("\n");
	2073	msg.append(e.what());
	2074	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
	2075	}
[472]	2076	}
[488]	2077
[472]	2078	void CNc4DataOutput::writeAttribute_ (CVariable* var)
	2079	{
[773]	2080	StdString name = var->getVariableOutputName();
	2081
[498]	2082	try
	2083	{
[527]	2084	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	2085	addAttribute(name, var->getData<int>());
	2086	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	2087	addAttribute(name, var->getData<short int>());
	2088	else if (var->type.getValue() == CVariable::type_attr::t_float)
	2089	addAttribute(name, var->getData<float>());
	2090	else if (var->type.getValue() == CVariable::type_attr::t_double)
	2091	addAttribute(name, var->getData<double>());
	2092	else if (var->type.getValue() == CVariable::type_attr::t_string)
	2093	addAttribute(name, var->getData<string>());
	2094	else
	2095	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
	2096	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	2097	}
	2098	catch (CNetCdfException& e)
	2099	{
	2100	StdString msg("On writing attributes of variable with name : ");
	2101	msg.append(name); msg.append("\n");
	2102	msg.append("In the context : ");
	2103	CContext* context = CContext::getCurrent() ;
	2104	msg.append(context->getId()); msg.append("\n");
	2105	msg.append(e.what());
	2106	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
	2107	}
[488]	2108	}
	2109
[321]	2110	void CNc4DataOutput::syncFile_ (void)
	2111	{
[498]	2112	try
	2113	{
	2114	SuperClassWriter::sync() ;
	2115	}
	2116	catch (CNetCdfException& e)
	2117	{
	2118	StdString msg("On synchronizing the write among processes");
	2119	msg.append("In the context : ");
	2120	CContext* context = CContext::getCurrent() ;
	2121	msg.append(context->getId()); msg.append("\n");
	2122	msg.append(e.what());
	2123	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	2124	}
[321]	2125	}
[219]	2126
[286]	2127	void CNc4DataOutput::closeFile_ (void)
	2128	{
[498]	2129	try
	2130	{
	2131	SuperClassWriter::close() ;
	2132	}
	2133	catch (CNetCdfException& e)
	2134	{
	2135	StdString msg("On closing file");
	2136	msg.append("In the context : ");
	2137	CContext* context = CContext::getCurrent() ;
	2138	msg.append(context->getId()); msg.append("\n");
	2139	msg.append(e.what());
	2140	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	2141	}
	2142
[286]	2143	}
	2144
[219]	2145	//---------------------------------------------------------------
	2146
	2147	StdString CNc4DataOutput::getTimeStamp(void) const
	2148	{
	2149	const int buffer_size = 100;
	2150	time_t rawtime;
	2151	struct tm * timeinfo = NULL;
	2152	char buffer [buffer_size];
[1158]	2153	StdString formatStr;
	2154	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
	2155	else formatStr=file->time_stamp_format;
[219]	2156
[1158]	2157	// time ( &rawtime );
	2158	// timeinfo = localtime ( &rawtime );
[219]	2159	time ( &rawtime );
[1158]	2160	timeinfo = gmtime ( &rawtime );
	2161	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
[219]	2162
	2163	return (StdString(buffer));
	2164	}
[488]	2165
[219]	2166	//---------------------------------------------------------------
[488]	2167
[1961]	2168	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
	2169	const CDate& currentWrite, int nstep)
[219]	2170	{
[707]	2171	CContext* context = CContext::getCurrent();
[1869]	2172	CGrid* grid = field->getGrid();
[1961]	2173
	2174	if (nstep<1)
[1158]	2175	{
[1961]	2176	return nstep;
[1158]	2177	}
[952]	2178
[707]	2179	if (!grid->doGridHaveDataToWrite())
[1158]	2180	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
	2181	{
[1961]	2182	return nstep;
[1158]	2183	}
[488]	2184
[770]	2185	StdString fieldid = field->getFieldOutputName();
[286]	2186
[707]	2187	StdOStringStream oss;
	2188	string timeAxisId;
[1158]	2189	if (field->hasTimeInstant) timeAxisId = "time_instant";
	2190	else if (field->hasTimeCentered) timeAxisId = "time_centered";
[488]	2191
[802]	2192	StdString timeBoundId = getTimeCounterName() + "_bounds";
[449]	2193
[707]	2194	StdString timeAxisBoundId;
[1158]	2195	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
	2196	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
[488]	2197
[707]	2198	if (!field->wasWritten())
	2199	{
[1872]	2200	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
[1158]	2201	field->getOperationTimeType() != func::CFunctor::once)
[707]	2202	{
[1158]	2203	double factorUnit;
[1872]	2204	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
[1158]	2205	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
	2206	else factorUnit=1 ;
[1962]	2207	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
[707]	2208	}
[488]	2209
[707]	2210	field->setWritten();
	2211	}
[488]	2212
	2213
[707]	2214	CArray<double,1> time_data(1);
	2215	CArray<double,1> time_data_bound(2);
	2216	CArray<double,1> time_counter(1);
	2217	CArray<double,1> time_counter_bound(2);
	2218
	2219	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
[1158]	2220	bool wtimeCounter =false ;
	2221	bool wtimeData =false ;
	2222
[707]	2223
[444]	2224	if (wtime)
	2225	{
[1158]	2226
	2227	if (field->hasTimeInstant)
	2228	{
[2542]	2229	time_data(0) = time_data_bound(1) = (Time) currentWrite;
[1961]	2230	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
[1158]	2231	if (timeCounterType==instant)
	2232	{
	2233	time_counter(0) = time_data(0);
	2234	time_counter_bound(0) = time_data_bound(0);
	2235	time_counter_bound(1) = time_data_bound(1);
	2236	wtimeCounter=true ;
	2237	}
	2238	if (hasTimeInstant) wtimeData=true ;
	2239	}
	2240	else if (field->hasTimeCentered)
[488]	2241	{
[1961]	2242	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
	2243	time_data_bound(0) = (Time)lastWrite;
	2244	time_data_bound(1) = (Time)currentWrite;
[1158]	2245	if (timeCounterType==centered)
	2246	{
	2247	time_counter(0) = time_data(0) ;
	2248	time_counter_bound(0) = time_data_bound(0) ;
	2249	time_counter_bound(1) = time_data_bound(1) ;
	2250	wtimeCounter=true ;
	2251	}
	2252	if (hasTimeCentered) wtimeData=true ;
[488]	2253	}
	2254
[1158]	2255	if (timeCounterType==record)
	2256	{
[1961]	2257	time_counter(0) = nstep - 1;
	2258	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
[1158]	2259	wtimeCounter=true ;
	2260	}
[692]	2261
[1872]	2262	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
[692]	2263	{
[1158]	2264	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
	2265	time_data/=secByDay;
	2266	time_data_bound/=secByDay;
	2267	time_counter/=secByDay;
	2268	time_counter_bound/=secByDay;
[692]	2269	}
	2270	}
	2271
[1853]	2272	bool isRoot = (context->intraCommRank_ == 0);
[488]	2273
[498]	2274	try
[219]	2275	{
[567]	2276	switch (SuperClass::type)
[498]	2277	{
[567]	2278	case (MULTI_FILE) :
	2279	{
[2628]	2280	if (info.isActive(logProfile)) CTimer::get("Files : writing data").resume();
[2600]	2281	writeAndConvertData(field, data, nstep - 1);
[2628]	2282	if (info.isActive(logProfile)) CTimer::get("Files : writing data").suspend();
[567]	2283	if (wtime)
	2284	{
[2628]	2285	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").resume();
[1158]	2286	if ( wtimeData)
[692]	2287	{
[1961]	2288	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
	2289	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
[1158]	2290	}
	2291	if (wtimeCounter)
	2292	{
[1961]	2293	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
	2294	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
[692]	2295	}
[2628]	2296	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").suspend();
[567]	2297	}
[707]	2298	break;
[567]	2299	}
	2300	case (ONE_FILE) :
	2301	{
[464]	2302
[676]	2303	std::vector<StdSize> start, count;
[464]	2304
[676]	2305	if (field->getUseCompressedOutput())
	2306	{
[1957]	2307	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	2308	std::vector<StdString> domainList = grid->getDomainList();
	2309	std::vector<StdString> axisList = grid->getAxisList();
	2310	int numElement = axisDomainOrder.numElements();
	2311	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
	2312	int idx = domainList.size() * 2 + axisList.size() - 1;
	2313	int commRank ;
[464]	2314
[1957]	2315	MPI_Comm_rank(comm_file,&commRank) ;
[676]	2316
[1957]	2317	start.reserve(idx+1);
	2318	count.reserve(idx+1);
	2319
	2320	for (int i = numElement - 1; i >= 0; --i)
	2321	{
	2322	if (2 == axisDomainOrder(i))
[676]	2323	{
[1957]	2324	CDomain* domain = CDomain::get(domainList[idxDomain]);
	2325
	2326	if (domain->isCompressible())
[676]	2327	{
[1957]	2328	size_t offset ;
	2329	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
	2330	if (domain->isDistributed())
[676]	2331	{
[1957]	2332	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	2333	if (commRank==0) offset=0 ;
[676]	2334	}
[1957]	2335	else offset=0 ;
	2336
	2337	start.push_back(offset);
	2338	count.push_back(nbIndexes);
	2339	idx -= 2;
	2340	}
	2341	else
	2342	{
	2343	if ((domain->type) != CDomain::type_attr::unstructured)
[676]	2344	{
[2507]	2345	start.push_back(domain->jbeginValue_);
	2346	count.push_back(domain->njValue_);
[676]	2347	}
[1957]	2348	--idx;
[2507]	2349	start.push_back(domain->ibeginValue_);
	2350	count.push_back(domain->niValue_);
[1957]	2351	--idx;
[676]	2352	}
[1957]	2353	--idxDomain;
	2354	}
	2355	else if (1 == axisDomainOrder(i))
	2356	{
	2357	CAxis* axis = CAxis::get(axisList[idxAxis]);
	2358
	2359	if (axis->isCompressible())
[676]	2360	{
[1957]	2361	size_t offset ;
	2362	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
	2363	if (axis->isDistributed())
[676]	2364	{
[1957]	2365	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	2366	if (commRank==0) offset=0 ;
[676]	2367	}
[1957]	2368	else offset=0 ;
	2369
	2370	start.push_back(offset);
	2371	count.push_back(nbIndexes);
[676]	2372	}
[1957]	2373	else
	2374	{
	2375	start.push_back(axis->begin);
	2376	count.push_back(axis->n);
	2377	}
	2378	--idxAxis;
	2379	--idx;
[676]	2380	}
[1158]	2381	}
[1961]	2382	}
[676]	2383	else
[498]	2384	{
[887]	2385	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
[705]	2386	std::vector<StdString> domainList = grid->getDomainList();
	2387	std::vector<StdString> axisList = grid->getAxisList();
[2264]	2388	std::vector<StdString> scalarList = grid->getScalarList() ;
[705]	2389	int numElement = axisDomainOrder.numElements();
[2391]	2390	int idxDomain = domainList.size() - 1 ;
	2391	int idxAxis = axisList.size() - 1 ;
	2392	int idxScalar = scalarList.size() - 1 ;
[1553]	2393	int idx = domainList.size() * 2 + axisList.size() - 1;
[705]	2394
[1553]	2395	start.reserve(idx+1);
	2396	count.reserve(idx+1);
[705]	2397
	2398	for (int i = numElement - 1; i >= 0; --i)
	2399	{
[887]	2400	if (2 == axisDomainOrder(i))
[705]	2401	{
	2402	CDomain* domain = CDomain::get(domainList[idxDomain]);
[710]	2403	if ((domain->type) != CDomain::type_attr::unstructured)
[705]	2404	{
[2507]	2405	start.push_back(domain->jbeginValue_);
	2406	count.push_back(domain->njValue_);
[705]	2407	}
	2408	--idx ;
[1143]	2409
[2507]	2410	start.push_back(domain->ibeginValue_);
	2411	count.push_back(domain->niValue_);
[705]	2412	--idx ;
	2413	--idxDomain;
	2414	}
[887]	2415	else if (1 == axisDomainOrder(i))
[705]	2416	{
[1143]	2417	CAxis* axis = CAxis::get(axisList[idxAxis]);
[1559]	2418	start.push_back(axis->begin);
	2419	count.push_back(axis->n);
[705]	2420	--idx;
[1025]	2421	--idxAxis;
[887]	2422	}
	2423	else
	2424	{
[2391]	2425	if (idx ==-1)
[887]	2426	{
[2391]	2427	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
[887]	2428	start.push_back(0);
[2264]	2429	count.push_back(scalar->n);
[2391]	2430	idx-- ;
[887]	2431	}
[2391]	2432	else if (idx<-1)
	2433	{
	2434	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
	2435	count.back()*=scalar->n;
	2436	idx-- ;
	2437	}
	2438	--idxScalar;
[887]	2439	}
[705]	2440	}
[498]	2441	}
[488]	2442
[1158]	2443
[2628]	2444	if (info.isActive(logProfile)) CTimer::get("Files : writing data").resume();
[2600]	2445	writeAndConvertData(field, data, nstep - 1, &start, &count);
[2628]	2446	if (info.isActive(logProfile)) CTimer::get("Files : writing data").suspend();
[1158]	2447
	2448	if (wtime)
	2449	{
[2628]	2450	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").resume();
[1158]	2451	if ( wtimeData)
[692]	2452	{
[1961]	2453	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
	2454	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
[692]	2455	}
[1158]	2456	if (wtimeCounter)
	2457	{
[1961]	2458	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
	2459	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
[586]	2460
[1158]	2461	}
[2628]	2462	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").suspend();
[1158]	2463	}
	2464
[586]	2465	break;
[286]	2466	}
[567]	2467	}
[1961]	2468	return nstep ;
[219]	2469	}
[498]	2470	catch (CNetCdfException& e)
	2471	{
	2472	StdString msg("On writing field data: ");
	2473	msg.append(fieldid); msg.append("\n");
	2474	msg.append("In the context : ");
	2475	msg.append(context->getId()); msg.append("\n");
	2476	msg.append(e.what());
[1130]	2477	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
[498]	2478	}
[219]	2479	}
	2480
[2600]	2481	void CNc4DataOutput::writeAndConvertData(CField* field, const CArray<double,1>& data, StdSize record, const std::vector<StdSize> start, const std::vector<StdSize> count)
	2482	{
	2483	StdString fieldid = field->getFieldOutputName();
	2484	nc_type type ;
	2485	if (field->prec.isEmpty()) type = NC_FLOAT ;
	2486	else
	2487	{
	2488	if (field->prec==2) type = NC_SHORT ;
	2489	else if (field->prec==4) type = NC_FLOAT ;
	2490	else if (field->prec==8) type = NC_DOUBLE ;
	2491	}
	2492
	2493	bool conversionByNetCDF = true; // default : conversion operated by NetCDF for now (legacy behaviour)
[2617]	2494	if (!field->conversion_by_netcdf.isEmpty())
[2600]	2495	{
[2617]	2496	// use conversion_by_netcdf = ".false." to bypass NetCDF conversion
[2600]	2497	// poor performances from NC_DOUBLE to NC_FLOAT with isgreater/isless in recent NetCDF available at TGCC
[2617]	2498	conversionByNetCDF = field->conversion_by_netcdf;
[2600]	2499	}
	2500	if ( ( type == NC_DOUBLE ) \|\| ( conversionByNetCDF ) )
	2501	{
	2502	SuperClassWriter::writeData(data, fieldid, isCollective, record, start, count);
	2503	}
	2504	else if ( type == NC_FLOAT )
	2505	{
	2506	CArray<float,1> f_data;
	2507	f_data.resize( data.numElements() );
	2508	for (int i = 0; i < data.numElements(); i++)
	2509	{
	2510	if (data(i) <= X_FLOAT_MAX \|\| data(i) >= X_FLOAT_MIN)
	2511	f_data(i) = data(i);
	2512	else if (data(i) > X_FLOAT_MAX)
	2513	f_data(i) = X_FLOAT_MAX;
	2514	else if (data(i) < X_FLOAT_MIN)
	2515	f_data(i) = X_FLOAT_MIN;
	2516	}
	2517	SuperClassWriter::writeData(f_data, fieldid, isCollective, record, start, count);
	2518	}
	2519	else if ( type == NC_SHORT )
	2520	{
	2521	CArray<short,1> s_data;
	2522	s_data.resize( data.numElements() );
	2523	for (int i = 0; i < data.numElements(); i++)
	2524	{
	2525	if (data(i) <= X_SHORT_MAX \|\| data(i) >= X_SHORT_MIN)
	2526	s_data(i) = data(i);
	2527	else if (data(i) > X_SHORT_MAX)
	2528	s_data(i) = X_SHORT_MAX;
	2529	else if (data(i) < X_SHORT_MIN)
	2530	s_data(i) = X_SHORT_MIN;
	2531	}
	2532	SuperClassWriter::writeData(s_data, fieldid, isCollective, record, start, count);
	2533	}
	2534	else
	2535	{
	2536	ERROR("CNc4DataOutput::writeAndConvertData(...)", << "Type conversion not managed for " << fieldid );
	2537	}
	2538
	2539	}
	2540
[219]	2541	//---------------------------------------------------------------
	2542
	2543	void CNc4DataOutput::writeTimeAxis_
[347]	2544	(CField* field,
[1542]	2545	const std::shared_ptr<CCalendar> cal)
[219]	2546	{
	2547	StdOStringStream oss;
[1158]	2548	bool createInstantAxis=false ;
	2549	bool createCenteredAxis=false ;
	2550	bool createTimeCounterAxis=false ;
	2551
[645]	2552	if (field->getOperationTimeType() == func::CFunctor::once) return ;
[488]	2553
	2554
[1158]	2555	StdString axisId ;
	2556	StdString axisBoundId;
[802]	2557	StdString timeid(getTimeCounterName());
[614]	2558	StdString timeBoundId("axis_nbounds");
[488]	2559
[1158]	2560	StdString strTimeUnits ;
[1872]	2561	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
[1158]	2562	else strTimeUnits="seconds since " ;
	2563
	2564	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
	2565	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
	2566
	2567
[1872]	2568	if (field->getRelFile()->time_counter.isEmpty())
[488]	2569	{
[1158]	2570	if (timeCounterType==none) createTimeCounterAxis=true ;
	2571	if (field->hasTimeCentered)
	2572	{
	2573	timeCounterType=centered ;
	2574	if (!hasTimeCentered) createCenteredAxis=true ;
	2575	}
	2576	if (field->hasTimeInstant)
	2577	{
	2578	if (timeCounterType==none) timeCounterType=instant ;
	2579	if (!hasTimeInstant) createInstantAxis=true ;
	2580	}
[488]	2581	}
[1872]	2582	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
[1158]	2583	{
	2584	if (field->hasTimeCentered)
	2585	{
	2586	if (!hasTimeCentered) createCenteredAxis=true ;
	2587	}
	2588	if (field->hasTimeInstant)
	2589	{
	2590	if (timeCounterType==none) createTimeCounterAxis=true ;
	2591	timeCounterType=instant ;
	2592	if (!hasTimeInstant) createInstantAxis=true ;
	2593	}
	2594	}
[1872]	2595	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
[1158]	2596	{
	2597	if (field->hasTimeCentered)
	2598	{
	2599	if (timeCounterType==none) createTimeCounterAxis=true ;
	2600	timeCounterType=centered ;
	2601	if (!hasTimeCentered) createCenteredAxis=true ;
	2602	}
	2603	if (field->hasTimeInstant)
	2604	{
	2605	if (!hasTimeInstant) createInstantAxis=true ;
	2606	}
	2607	}
[1872]	2608	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
[1158]	2609	{
	2610	if (field->hasTimeCentered)
	2611	{
	2612	if (!hasTimeCentered) createCenteredAxis=true ;
	2613	}
	2614	if (field->hasTimeInstant)
	2615	{
	2616	if (timeCounterType==none) createTimeCounterAxis=true ;
	2617	timeCounterType=instant ;
	2618	}
	2619	}
[1872]	2620	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
[1158]	2621	{
	2622	if (field->hasTimeCentered)
	2623	{
	2624	if (timeCounterType==none) createTimeCounterAxis=true ;
	2625	timeCounterType=centered ;
	2626	}
	2627	if (field->hasTimeInstant)
	2628	{
	2629	if (!hasTimeInstant) createInstantAxis=true ;
	2630	}
	2631	}
[1872]	2632	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
[1158]	2633	{
	2634	if (field->hasTimeCentered)
	2635	{
	2636	if (timeCounterType==none) createTimeCounterAxis=true ;
	2637	if (timeCounterType==instant) createInstantAxis=true ;
	2638	timeCounterType=centered ;
	2639	}
	2640	if (field->hasTimeInstant)
	2641	{
	2642	if (timeCounterType==none)
	2643	{
	2644	createTimeCounterAxis=true ;
	2645	timeCounterType=instant ;
	2646	}
	2647	if (timeCounterType==centered)
	2648	{
	2649	if (!hasTimeInstant) createInstantAxis=true ;
	2650	}
	2651	}
	2652	}
[1872]	2653	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
[1158]	2654	{
	2655	if (field->hasTimeCentered)
	2656	{
	2657	if (!hasTimeCentered) createCenteredAxis=true ;
	2658	}
	2659	if (field->hasTimeInstant)
	2660	{
	2661	if (!hasTimeInstant) createInstantAxis=true ;
	2662	}
	2663	}
[1872]	2664	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
[1158]	2665	{
	2666	if (timeCounterType==none) createTimeCounterAxis=true ;
	2667	timeCounterType=record ;
	2668	if (field->hasTimeCentered)
	2669	{
	2670	if (!hasTimeCentered) createCenteredAxis=true ;
	2671	}
	2672	if (field->hasTimeInstant)
	2673	{
	2674	if (!hasTimeInstant) createInstantAxis=true ;
	2675	}
	2676	}
	2677
	2678	if (createInstantAxis)
	2679	{
	2680	axisId="time_instant" ;
	2681	axisBoundId="time_instant_bounds";
	2682	hasTimeInstant=true ;
	2683	}
[488]	2684
[1158]	2685	if (createCenteredAxis)
	2686	{
	2687	axisId="time_centered" ;
	2688	axisBoundId="time_centered_bounds";
	2689	hasTimeCentered=true ;
	2690	}
	2691
	2692
[498]	2693	try
[219]	2694	{
[1158]	2695	std::vector<StdString> dims;
	2696
	2697	if (createInstantAxis \|\| createCenteredAxis)
	2698	{
	2699	// Adding time_instant or time_centered
	2700	dims.push_back(timeid);
	2701	if (!SuperClassWriter::varExist(axisId))
	2702	{
	2703	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
[488]	2704
[1158]	2705	CDate timeOrigin=cal->getTimeOrigin() ;
	2706	StdOStringStream oss2;
	2707	StdString strInitdate=oss2.str() ;
	2708	StdString strTimeOrigin=timeOrigin.toString() ;
	2709	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
	2710	strTimeOrigin, axisBoundId);
	2711	}
[219]	2712
[1158]	2713	// Adding time_instant_bounds or time_centered_bounds variables
	2714	if (!SuperClassWriter::varExist(axisBoundId))
	2715	{
	2716	dims.clear() ;
	2717	dims.push_back(timeid);
	2718	dims.push_back(timeBoundId);
	2719	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2720	}
[498]	2721	}
[488]	2722
[1158]	2723	if (createTimeCounterAxis)
[498]	2724	{
[692]	2725	// Adding time_counter
[1158]	2726	axisId = getTimeCounterName();
[802]	2727	axisBoundId = getTimeCounterName() + "_bounds";
[692]	2728	dims.clear();
	2729	dims.push_back(timeid);
[1158]	2730	if (!SuperClassWriter::varExist(axisId))
[692]	2731	{
[1158]	2732	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
	2733	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
[488]	2734
[1872]	2735	if (field->getRelFile()->time_counter.isEmpty() \|\|
	2736	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
[692]	2737	{
	2738	CDate timeOrigin = cal->getTimeOrigin();
	2739	StdString strTimeOrigin = timeOrigin.toString();
[498]	2740
[1158]	2741	this->writeTimeAxisAttributes(axisId, cal->getType(),
	2742	strTimeUnits+strTimeOrigin,
[692]	2743	strTimeOrigin, axisBoundId);
	2744	}
	2745	}
	2746
	2747	// Adding time_counter_bound dimension
[1872]	2748	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
[692]	2749	{
	2750	if (!SuperClassWriter::varExist(axisBoundId))
	2751	{
	2752	dims.clear();
	2753	dims.push_back(timeid);
	2754	dims.push_back(timeBoundId);
	2755	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2756	}
	2757	}
[498]	2758	}
[488]	2759	}
[498]	2760	catch (CNetCdfException& e)
[488]	2761	{
[498]	2762	StdString msg("On writing time axis data: ");
	2763	msg.append("In the context : ");
	2764	CContext* context = CContext::getCurrent() ;
	2765	msg.append(context->getId()); msg.append("\n");
	2766	msg.append(e.what());
	2767	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
[1542]	2768	const std::shared_ptr<CCalendar> cal)", << msg);
[488]	2769	}
[219]	2770	}
	2771
	2772	//---------------------------------------------------------------
[488]	2773
[219]	2774	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
	2775	const StdString & calendar,
	2776	const StdString & units,
	2777	const StdString & time_origin,
[488]	2778	const StdString & time_bounds,
[219]	2779	const StdString & standard_name,
[613]	2780	const StdString & long_name)
[219]	2781	{
[498]	2782	try
	2783	{
	2784	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2785	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
	2786	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
	2787	SuperClassWriter::addAttribute("units", units , &axis_name);
	2788	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
	2789	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
	2790	}
	2791	catch (CNetCdfException& e)
	2792	{
	2793	StdString msg("On writing time axis Attribute: ");
	2794	msg.append("In the context : ");
	2795	CContext* context = CContext::getCurrent() ;
	2796	msg.append(context->getId()); msg.append("\n");
	2797	msg.append(e.what());
	2798	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
[613]	2799	const StdString & calendar,\
	2800	const StdString & units, \
	2801	const StdString & time_origin, \
	2802	const StdString & time_bounds, \
	2803	const StdString & standard_name, \
	2804	const StdString & long_name)", << msg);
[498]	2805	}
[219]	2806	}
[488]	2807
[219]	2808	//---------------------------------------------------------------
	2809
	2810	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
	2811	const StdString & axis,
	2812	const StdString & standard_name,
	2813	const StdString & long_name,
	2814	const StdString & units,
	2815	const StdString & nav_model)
	2816	{
[498]	2817	try
	2818	{
[613]	2819	if (!axis.empty())
	2820	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
	2821
[498]	2822	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2823	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
	2824	SuperClassWriter::addAttribute("units" , units , &axis_name);
[973]	2825	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
[498]	2826	}
	2827	catch (CNetCdfException& e)
	2828	{
	2829	StdString msg("On writing Axis Attribute: ");
	2830	msg.append("In the context : ");
	2831	CContext* context = CContext::getCurrent() ;
	2832	msg.append(context->getId()); msg.append("\n");
	2833	msg.append(e.what());
	2834	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
[613]	2835	const StdString & axis, \
	2836	const StdString & standard_name, \
	2837	const StdString & long_name, \
	2838	const StdString & units, \
	2839	const StdString & nav_model)", << msg);
[498]	2840	}
[219]	2841	}
	2842
	2843	//---------------------------------------------------------------
[488]	2844
[219]	2845	void CNc4DataOutput::writeLocalAttributes
	2846	(int ibegin, int ni, int jbegin, int nj, StdString domid)
	2847	{
[498]	2848	try
	2849	{
[318]	2850	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
	2851	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
	2852	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
	2853	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
[498]	2854	}
	2855	catch (CNetCdfException& e)
	2856	{
	2857	StdString msg("On writing Local Attributes: ");
	2858	msg.append("In the context : ");
	2859	CContext* context = CContext::getCurrent() ;
	2860	msg.append(context->getId()); msg.append("\n");
	2861	msg.append(e.what());
	2862	ERROR("CNc4DataOutput::writeLocalAttributes \
	2863	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
	2864	}
	2865
[219]	2866	}
	2867
[628]	2868	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
	2869	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
[391]	2870	{
	2871	CArray<int,1> array(2) ;
	2872
[498]	2873	try
	2874	{
	2875	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
	2876	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
[629]	2877	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
[498]	2878	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
	2879	array=ni_glo,nj_glo ;
	2880	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
	2881	array=ni,nj ;
	2882	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
[819]	2883	array=ibegin+1,jbegin+1 ;
[498]	2884	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
[819]	2885	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
[498]	2886	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
	2887	array=0,0 ;
	2888	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
	2889	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
	2890	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
	2891	/*
	2892	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
	2893	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
	2894	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
	2895	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
	2896	*/
	2897	}
	2898	catch (CNetCdfException& e)
	2899	{
[628]	2900	StdString msg("On writing Local Attributes IOIPSL \n");
[498]	2901	msg.append("In the context : ");
	2902	CContext* context = CContext::getCurrent() ;
	2903	msg.append(context->getId()); msg.append("\n");
	2904	msg.append(e.what());
	2905	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
	2906	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
	2907	}
[391]	2908	}
[219]	2909	//---------------------------------------------------------------
	2910
	2911	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
	2912	const StdString & description,
	2913	const StdString & conventions,
	2914	const StdString & production,
	2915	const StdString & timeStamp)
	2916	{
[498]	2917	try
	2918	{
	2919	SuperClassWriter::addAttribute("name" , name);
	2920	SuperClassWriter::addAttribute("description", description);
[613]	2921	SuperClassWriter::addAttribute("title" , description);
	2922	SuperClassWriter::addAttribute("Conventions", conventions);
[1158]	2923	// SuperClassWriter::addAttribute("production" , production);
	2924
	2925	StdString timeStampStr ;
	2926	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
	2927	else timeStampStr=file->time_stamp_name ;
	2928	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
	2929
	2930	StdString uuidName ;
	2931	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
	2932	else uuidName=file->uuid_name ;
	2933
	2934	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
	2935	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
	2936
[498]	2937	}
	2938	catch (CNetCdfException& e)
	2939	{
	2940	StdString msg("On writing File Attributes \n ");
	2941	msg.append("In the context : ");
	2942	CContext* context = CContext::getCurrent() ;
	2943	msg.append(context->getId()); msg.append("\n");
	2944	msg.append(e.what());
	2945	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
	2946	const StdString & description, \
	2947	const StdString & conventions, \
	2948	const StdString & production, \
	2949	const StdString & timeStamp)", << msg);
	2950	}
[219]	2951	}
	2952
	2953	//---------------------------------------------------------------
	2954
	2955	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
	2956	int data_dim,
	2957	int data_ni,
	2958	int data_nj,
	2959	int data_ibegin,
	2960	int data_jbegin)
	2961	{
[498]	2962	try
	2963	{
	2964	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
	2965	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
	2966	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
	2967	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
	2968	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
	2969	}
	2970	catch (CNetCdfException& e)
	2971	{
	2972	StdString msg("On writing Mask Attributes \n ");
	2973	msg.append("In the context : ");
	2974	CContext* context = CContext::getCurrent() ;
	2975	msg.append(context->getId()); msg.append("\n");
	2976	msg.append(e.what());
	2977	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
	2978	int data_dim, \
	2979	int data_ni, \
	2980	int data_nj, \
	2981	int data_ibegin, \
	2982	int data_jbegin)", << msg);
	2983	}
[219]	2984	}
	2985
	2986	///--------------------------------------------------------------
	2987
[1158]	2988	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
[707]	2989	{
	2990	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
	2991	if (it == timeToRecordCache.end())
	2992	{
[802]	2993	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
[1158]	2994	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
	2995	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
[707]	2996
	2997	CArray<double,2> timeAxisBounds;
[1158]	2998	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
	2999
[707]	3000	StdSize record = 0;
	3001	double dtime(time);
[1158]	3002	for (int n = dimSize[0] - 1; n >= 0; n--)
[707]	3003	{
[1158]	3004	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
	3005	timeAxisBounds*=factorUnit ;
	3006	if (timeAxisBounds(1, 0) < dtime)
[707]	3007	{
	3008	record = n + 1;
	3009	break;
	3010	}
	3011	}
	3012	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
	3013	}
	3014	return it->second;
	3015	}
[774]	3016
	3017	///--------------------------------------------------------------
	3018
	3019	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
	3020	{
	3021	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
	3022	}
	3023
	3024	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
	3025	{
	3026	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
	3027	}
	3028
	3029	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
	3030	{
	3031	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
	3032	}
	3033
	3034	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
	3035	{
	3036	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
	3037	}
	3038
[887]	3039	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
	3040	{
	3041	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
	3042	}
	3043
[774]	3044	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
	3045	{
	3046	this->writtenDomains.insert(domainName);
	3047	}
	3048
	3049	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
	3050	{
	3051	this->writtenCompressedDomains.insert(domainName);
	3052	}
	3053
	3054	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
	3055	{
	3056	this->writtenAxis.insert(axisName);
	3057	}
	3058
	3059	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
	3060	{
	3061	this->writtenCompressedAxis.insert(axisName);
	3062	}
[887]	3063
	3064	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
	3065	{
	3066	this->writtenScalar.insert(scalarName);
	3067	}
[335]	3068	} // namespace xios

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