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nc4_data_output.cpp

Last change on this file was 2629, checked in by jderouillat, 2 months ago
Delete boost dependencies, the few features used are replaced by functions stored in extern/boost_extraction
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>
[2629]	16	#include <cfloat>
[2600]	17	#define X_FLOAT_MAX FLT_MAX
	18	#define X_FLOAT_MIN FLT_MIN
	19	#define X_SHORT_MAX SHRT_MAX
	20	#define X_SHORT_MIN SHRT_MIN
	21
[335]	22	namespace xios
[219]	23	{
[2628]	24	extern CLogType logProfile ;
[878]	25	/// ////////////////////// Dfinitions ////////////////////// ///
[219]	26	CNc4DataOutput::CNc4DataOutput
[1158]	27	(CFile* file, const StdString & filename, bool exist)
[219]	28	: SuperClass()
	29	, SuperClassWriter(filename, exist)
	30	, filename(filename)
[2389]	31	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
[219]	32	{
[1158]	33	SuperClass::type = MULTI_FILE;
[1456]	34	compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
[219]	35	}
	36
	37	CNc4DataOutput::CNc4DataOutput
[1158]	38	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
[1639]	39	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
[219]	40	: SuperClass()
[878]	41	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
[379]	42	, comm_file(comm_file)
[219]	43	, filename(filename)
[335]	44	, isCollective(isCollective)
[2389]	45	, file(file),hasTimeInstant(false),hasTimeCentered(false), timeCounterType(none), relAxis_(), relDomains_()
[219]	46	{
[1158]	47	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
[1459]	48	if (file==NULL) compressionLevel = 0 ;
	49	else compressionLevel= file->compression_level.isEmpty() ? 0 :file->compression_level ;
[219]	50	}
	51
	52	CNc4DataOutput::~CNc4DataOutput(void)
[879]	53	{ /* Ne rien faire de plus */ }
[219]	54
	55	///--------------------------------------------------------------
	56
	57	const StdString & CNc4DataOutput::getFileName(void) const
	58	{
	59	return (this->filename);
	60	}
	61
	62	//---------------------------------------------------------------
	63
[347]	64	void CNc4DataOutput::writeDomain_(CDomain* domain)
[1622]	65	TRY
[219]	66	{
[1391]	67	StdString lonName,latName ;
[1249]	68
[2387]	69	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
	70	if (!domain->lonvalue.isEmpty() )
	71	{
	72	// The hash of the element will be associated to the default element name (= map key), and to the name really written
	73	int globalHash = domain->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
	74
	75	StdString defaultNameKey = domain->getDomainOutputName();
	76	if ( !relDomains_.count ( defaultNameKey ) )
	77	{
	78	// if defaultNameKey not in the map, write the element such as it is defined
	79	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) );
	80	}
	81	else // look if a hash associated this key is equal
	82	{
	83	bool elementIsInMap(false);
	84	auto defaultNameKeyElements = relDomains_.equal_range( defaultNameKey );
	85	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
	86	{
	87	if ( it->second.first == globalHash )
	88	{
	89	// if yes, associate the same ids to current element
[2389]	90	domain->renameAttributesBeforeWriting( it->second.second );
[2387]	91	elementIsInMap = true;
	92	}
	93	}
	94	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
	95	if (!elementIsInMap) // ! in MAP
	96	{
[2389]	97	domain->renameAttributesBeforeWriting();
[2387]	98	relDomains_.insert( make_pair( defaultNameKey, make_pair(globalHash, domain) ) ) ;
	99	}
	100	}
	101	}
	102
[881]	103	if (domain->type == CDomain::type_attr::unstructured)
	104	{
	105	if (SuperClassWriter::useCFConvention)
	106	writeUnstructuredDomain(domain) ;
	107	else
	108	writeUnstructuredDomainUgrid(domain) ;
	109	return ;
	110	}
[488]	111
[347]	112	CContext* context = CContext::getCurrent() ;
[219]	113	if (domain->IsWritten(this->filename)) return;
	114	domain->checkAttributes();
[488]	115
	116	if (domain->isEmpty())
[881]	117	if (SuperClass::type==MULTI_FILE) return;
[219]	118
[2381]	119
[219]	120	std::vector<StdString> dim0, dim1;
[772]	121	StdString domid = domain->getDomainOutputName();
[318]	122	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
[706]	123	if (isWrittenDomain(domid)) return ;
[774]	124	else setWrittenDomain(domid);
[1132]	125
	126	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
[449]	127
[488]	128
[1158]	129	StdString dimXid, dimYid ;
	130
	131	nc_type typePrec ;
	132	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	133	else if (domain->prec==4) typePrec = NC_FLOAT ;
	134	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	135
[664]	136	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
[449]	137	switch (domain->type)
[433]	138	{
[449]	139	case CDomain::type_attr::curvilinear :
[1391]	140
	141	if (domain->lon_name.isEmpty()) lonName = "nav_lon";
	142	else lonName = domain->lon_name;
	143
	144	if (domain->lat_name.isEmpty()) latName = "nav_lat";
	145	else latName = domain->lat_name;
	146
[1430]	147	if (domain->dim_i_name.isEmpty()) dimXid=StdString("x").append(appendDomid);
	148	else dimXid=domain->dim_i_name.getValue() + appendDomid;
	149
	150	if (domain->dim_j_name.isEmpty()) dimYid=StdString("y").append(appendDomid);
	151	else dimYid=domain->dim_j_name.getValue() + appendDomid;
	152
[449]	153	break ;
[1391]	154
[664]	155	case CDomain::type_attr::rectilinear :
[1391]	156
[1430]	157	if (domain->lon_name.isEmpty())
	158	{
	159	if (domain->dim_i_name.isEmpty())
	160	lonName = "lon";
	161	else
	162	lonName = domain->dim_i_name.getValue();
	163	}
[1391]	164	else lonName = domain->lon_name;
	165
[1430]	166	if (domain->lat_name.isEmpty())
	167	{
	168	if (domain->dim_j_name.isEmpty())
	169	latName = "lat";
	170	else
	171	latName = domain->dim_j_name.getValue();
	172	}
[1391]	173	else latName = domain->lat_name;
	174
[1430]	175	if (domain->dim_i_name.isEmpty()) dimXid = lonName+appendDomid;
	176	else dimXid = domain->dim_i_name.getValue()+appendDomid;
	177
	178	if (domain->dim_j_name.isEmpty()) dimYid = latName+appendDomid;
	179	else dimYid = domain->dim_j_name.getValue()+appendDomid;
[449]	180	break;
[488]	181	}
	182
[617]	183	StdString dimVertId = StdString("nvertex").append(appendDomid);
	184
[449]	185	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	186	string areaId = "area" + appendDomid;
[219]	187
[498]	188	try
[219]	189	{
[498]	190	switch (SuperClass::type)
	191	{
	192	case (MULTI_FILE) :
	193	{
	194	switch (domain->type)
	195	{
	196	case CDomain::type_attr::curvilinear :
	197	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1415]	198	lonid = lonName+appendDomid;
	199	latid = latName+appendDomid;
[498]	200	break ;
[664]	201	case CDomain::type_attr::rectilinear :
[1415]	202	lonid = lonName+appendDomid;
	203	latid = latName+appendDomid;
[498]	204	dim0.push_back(dimYid);
	205	dim1.push_back(dimXid);
	206	break;
	207	}
[1430]	208	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	209	else bounds_lonid = "bounds_"+lonName+appendDomid;
	210	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	211	else bounds_latid = "bounds_"+latName+appendDomid;
[488]	212
[2507]	213	SuperClassWriter::addDimension(dimXid, domain->niValue_);
	214	SuperClassWriter::addDimension(dimYid, domain->njValue_);
[488]	215
[617]	216	if (domain->hasBounds)
	217	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	218
[1853]	219	if (context->intraCommSize_ > 1)
[498]	220	{
[2507]	221	this->writeLocalAttributes(domain->ibeginValue_,
	222	domain->niValue_,
	223	domain->jbeginValue_,
	224	domain->njValue_,
[616]	225	appendDomid);
[488]	226
[628]	227	if (singleDomain)
	228	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
[2507]	229	domain->ibeginValue_,
	230	domain->niValue_,
	231	domain->jbeginValue_,
	232	domain->njValue_,
[628]	233	domain->ni_glo,domain->nj_glo,
[1853]	234	context->intraCommRank_,context->intraCommSize_);
[449]	235	}
[488]	236
[665]	237	if (domain->hasLonLat)
[498]	238	{
[665]	239	switch (domain->type)
	240	{
	241	case CDomain::type_attr::curvilinear :
[1456]	242	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	243	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	244	break ;
	245	case CDomain::type_attr::rectilinear :
[1456]	246	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	247	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
[665]	248	break ;
	249	}
[488]	250
[665]	251	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	252	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
[219]	253
[665]	254	if (domain->hasBounds)
	255	{
	256	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	257	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
[617]	258
[665]	259	dim0.clear();
	260	dim0.push_back(dimYid);
	261	dim0.push_back(dimXid);
	262	dim0.push_back(dimVertId);
[1456]	263	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	264	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[665]	265	}
[617]	266	}
	267
[498]	268	dim0.clear();
[616]	269	dim0.push_back(dimYid);
[498]	270	dim0.push_back(dimXid);
[219]	271
[611]	272	if (domain->hasArea)
	273	{
[1456]	274	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	275	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	276	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	277	}
	278
[498]	279	SuperClassWriter::definition_end();
[449]	280
[665]	281	if (domain->hasLonLat)
[498]	282	{
[665]	283	switch (domain->type)
	284	{
[1129]	285	case CDomain::type_attr::curvilinear :
[1930]	286	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
	287	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
[665]	288	break;
	289	case CDomain::type_attr::rectilinear :
[2550]	290	//CArray<double,1> lat = domain->latvalue(Range(fromStart,toEnd,domain->ni)) ;
	291	CArray<double,1> lat;
	292	lat.resize( domain->njValue_);
	293	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
[665]	294	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
[2550]	295	//CArray<double,1> lon = domain->lonvalue(Range(0,domain->ni-1)) ;
	296	CArray<double,1> lon = domain->lonvalue(Range(0,domain->niValue_-1));
[665]	297	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
	298	break;
	299	}
[611]	300
[665]	301	if (domain->hasBounds)
	302	{
[1930]	303	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
	304	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
[665]	305	}
[617]	306	}
	307
[611]	308	if (domain->hasArea)
[1129]	309	{
[1930]	310	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
[1129]	311	}
	312
[498]	313	SuperClassWriter::definition_start();
[219]	314
[498]	315	break;
	316	}
	317	case (ONE_FILE) :
	318	{
[1553]	319	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
	320	SuperClassWriter::addDimension(dimYid, domain->nj_glo);
[286]	321
[617]	322	if (domain->hasBounds)
	323	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	324
[665]	325	if (domain->hasLonLat)
[498]	326	{
[665]	327	switch (domain->type)
	328	{
	329	case CDomain::type_attr::curvilinear :
	330	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1415]	331	lonid = lonName+appendDomid;
	332	latid = latName+appendDomid;
[1456]	333	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	334	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	335	break;
[449]	336
[665]	337	case CDomain::type_attr::rectilinear :
	338	dim0.push_back(dimYid);
	339	dim1.push_back(dimXid);
[1415]	340	lonid = lonName+appendDomid;
	341	latid = latName+appendDomid;
[1456]	342	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	343	SuperClassWriter::addVariable(lonid, typePrec, dim1, compressionLevel);
[665]	344	break;
	345	}
[1430]	346	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	347	else bounds_lonid = "bounds_"+lonName+appendDomid;
	348	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	349	else bounds_latid = "bounds_"+latName+appendDomid;
[665]	350
	351	this->writeAxisAttributes
	352	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	353	this->writeAxisAttributes
	354	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
	355
	356	if (domain->hasBounds)
	357	{
	358	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	359	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
	360
	361	dim0.clear();
[498]	362	dim0.push_back(dimYid);
[665]	363	dim0.push_back(dimXid);
	364	dim0.push_back(dimVertId);
[1456]	365	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	366	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[665]	367	}
[498]	368	}
[611]	369
	370	if (domain->hasArea)
	371	{
	372	dim0.clear();
	373	dim0.push_back(dimYid); dim0.push_back(dimXid);
[1456]	374	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	375	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	376	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	377	dim0.clear();
	378	}
	379
	380	SuperClassWriter::definition_end();
[286]	381
[498]	382	switch (domain->type)
[384]	383	{
[498]	384	case CDomain::type_attr::curvilinear :
[449]	385	{
[498]	386	std::vector<StdSize> start(2) ;
	387	std::vector<StdSize> count(2) ;
[2507]	388	start[1]=domain->ibeginValue_;
	389	start[0]=domain->jbeginValue_;
	390	count[1]=domain->niValue_ ; count[0]=domain->njValue_ ;
[488]	391
[665]	392	if (domain->hasLonLat)
	393	{
[1930]	394	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
	395	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
[665]	396	}
[498]	397	break;
	398	}
[664]	399	case CDomain::type_attr::rectilinear :
[449]	400	{
[665]	401	if (domain->hasLonLat)
[498]	402	{
[665]	403	std::vector<StdSize> start(1) ;
	404	std::vector<StdSize> count(1) ;
[1930]	405
[2507]	406	start[0]=domain->jbeginValue_;
	407	count[0]=domain->njValue_;
[2394]	408	CArray<double,1> lat;
[2507]	409	lat.resize( domain->njValue_);
	410	for (int j=0;j<domain->njValue_;j++) lat(j) = domain->latvalue(j*domain->niValue_);
[1930]	411	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
[665]	412
[2507]	413	start[0]=domain->ibeginValue_;
	414	count[0]=domain->niValue_;
[2613]	415	CArray<double,1> lon;
	416	lon.resize( domain->niValue_);
	417	for (int i=0;i<domain->niValue_;i++) lon(i) = domain->lonvalue(i);
[1930]	418	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
[498]	419	}
	420	break;
[449]	421	}
[384]	422	}
[611]	423
[617]	424	if (domain->hasBounds)
	425	{
	426	std::vector<StdSize> start(3);
	427	std::vector<StdSize> count(3);
	428	if (domain->isEmpty())
	429	{
	430	start[2] = start[1] = start[0] = 0;
	431	count[2] = count[1] = count[0] = 0;
	432	}
	433	else
	434	{
	435	start[2] = 0;
[2507]	436	start[1] = domain->ibeginValue_;
	437	start[0] = domain->jbeginValue_;
[1099]	438	count[2] = domain->nvertex;
[2507]	439	count[1] = domain->niValue_;
	440	count[0] = domain->njValue_;
[617]	441	}
[1143]	442
[1930]	443	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0, &start, &count); // will probably not working for rectilinear
	444	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0, &start, &count);
[617]	445	}
	446
[611]	447	if (domain->hasArea)
	448	{
	449	std::vector<StdSize> start(2);
	450	std::vector<StdSize> count(2);
	451
[2507]	452	start[1] = domain->ibeginValue_;
	453	start[0] = domain->jbeginValue_;
	454	count[1] = domain->niValue_;
	455	count[0] = domain->njValue_;
[1143]	456
[1930]	457	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
[611]	458	}
	459
[498]	460	SuperClassWriter::definition_start();
	461	break;
	462	}
	463	default :
	464	ERROR("CNc4DataOutput::writeDomain(domain)",
	465	<< "[ type = " << SuperClass::type << "]"
	466	<< " not implemented yet !");
	467	}
[449]	468	}
[498]	469	catch (CNetCdfException& e)
	470	{
	471	StdString msg("On writing the domain : ");
	472	msg.append(domid); msg.append("\n");
	473	msg.append("In the context : ");
	474	msg.append(context->getId()); msg.append("\n");
	475	msg.append(e.what());
	476	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
	477	}
	478
[449]	479	domain->addRelFile(this->filename);
	480	}
[1622]	481	CATCH
[449]	482
[879]	483	//--------------------------------------------------------------
[878]	484
[879]	485	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
	486	{
	487	CContext* context = CContext::getCurrent() ;
[878]	488
[879]	489	if (domain->IsWritten(this->filename)) return;
[1494]	490
	491	StdString domid = domain->getDomainOutputName();
	492
	493	// The first domain for the same mesh that will be written is that with the highest value of nvertex.
	494	// Thus the entire mesh connectivity will be generated at once.
	495	if (isWrittenDomain(domid)) return ;
	496	else setWrittenDomain(domid);
	497
[879]	498	domain->checkAttributes();
	499	if (domain->isEmpty())
	500	if (SuperClass::type==MULTI_FILE) return ;
[878]	501
[1158]	502	nc_type typePrec ;
	503	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	504	else if (domain->prec==4) typePrec = NC_FLOAT ;
	505	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	506
[879]	507	std::vector<StdString> dim0;
	508	StdString domainName = domain->name;
[878]	509
[879]	510	StdString node_x = domainName + "_node_x";
	511	StdString node_y = domainName + "_node_y";
[878]	512
[879]	513	StdString edge_x = domainName + "_edge_x";
	514	StdString edge_y = domainName + "_edge_y";
	515	StdString edge_nodes = domainName + "_edge_nodes";
[878]	516
[879]	517	StdString face_x = domainName + "_face_x";
	518	StdString face_y = domainName + "_face_y";
	519	StdString face_nodes = domainName + "_face_nodes";
[902]	520	StdString face_edges = domainName + "_face_edges";
	521	StdString edge_faces = domainName + "_edge_face_links";
	522	StdString face_faces = domainName + "_face_links";
[878]	523
[879]	524	StdString dimNode = "n" + domainName + "_node";
	525	StdString dimEdge = "n" + domainName + "_edge";
	526	StdString dimFace = "n" + domainName + "_face";
	527	StdString dimVertex = "n" + domainName + "_vertex";
	528	StdString dimTwo = "Two";
[878]	529
[879]	530	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
[1494]	531	dim0.clear();
	532	SuperClassWriter::addVariable(domainName, NC_INT, dim0, compressionLevel);
	533	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
	534	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
	535	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
	536	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
[878]	537
[879]	538	try
	539	{
	540	switch (SuperClass::type)
	541	{
	542	case (ONE_FILE) :
	543	{
	544	// Adding nodes
	545	if (domain->nvertex == 1)
	546	{
	547	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	548	{
[902]	549	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
[879]	550	dim0.clear();
	551	dim0.push_back(dimNode);
[1456]	552	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	553	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	554	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	555	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	556	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	557	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	558	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	559	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	560	}
	561	} // domain->nvertex == 1
[878]	562
[879]	563	// Adding edges and nodes, if nodes have not been defined previously
	564	if (domain->nvertex == 2)
	565	{
	566	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	567	{
[924]	568	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	569	dim0.clear();
	570	dim0.push_back(dimNode);
[1456]	571	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	572	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	573	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	574	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	575	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	576	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	577	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	578	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	579	}
[924]	580	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
	581	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	582	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
	583	dim0.clear();
	584	dim0.push_back(dimEdge);
[1456]	585	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
[924]	586	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
	587	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
	588	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
[1456]	589	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
[924]	590	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
	591	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
	592	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	593	dim0.clear();
	594	dim0.push_back(dimEdge);
	595	dim0.push_back(dimTwo);
[1456]	596	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
[924]	597	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	598	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	599	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
[879]	600	} // domain->nvertex == 2
[878]	601
[879]	602	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
	603	if (domain->nvertex > 2)
	604	{
	605	// Nodes
	606	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	607	{
[924]	608	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	609	dim0.clear();
	610	dim0.push_back(dimNode);
[1456]	611	SuperClassWriter::addVariable(node_x, typePrec, dim0, compressionLevel);
[879]	612	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	613	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	614	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
[1456]	615	SuperClassWriter::addVariable(node_y, typePrec, dim0, compressionLevel);
[879]	616	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	617	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	618	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	619	}
	620	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
	621	{
	622	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	623	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
[2409]	624	SuperClassWriter::addAttribute("face_edge_connectivity", face_edges, &domainName);
	625	SuperClassWriter::addAttribute("edge_face_connectivity", edge_faces, &domainName);
[924]	626	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
[879]	627	dim0.clear();
	628	dim0.push_back(dimEdge);
[1456]	629	SuperClassWriter::addVariable(edge_x, typePrec, dim0, compressionLevel);
[879]	630	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
[924]	631	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
[879]	632	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
[1456]	633	SuperClassWriter::addVariable(edge_y, typePrec, dim0, compressionLevel);
[879]	634	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
[924]	635	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
[879]	636	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	637	dim0.clear();
	638	dim0.push_back(dimEdge);
	639	dim0.push_back(dimTwo);
[1456]	640	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0, compressionLevel);
[879]	641	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	642	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	643	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
	644	}
[2409]	645	SuperClassWriter::addAttribute("face_face_connectivity", face_faces, &domainName);
[924]	646	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
	647	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
	648	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
	649	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
	650	dim0.clear();
	651	dim0.push_back(dimFace);
[1456]	652	SuperClassWriter::addVariable(face_x, typePrec, dim0, compressionLevel);
[924]	653	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
	654	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
	655	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
[1456]	656	SuperClassWriter::addVariable(face_y, typePrec, dim0, compressionLevel);
[924]	657	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
	658	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
	659	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
	660	dim0.clear();
	661	dim0.push_back(dimFace);
	662	dim0.push_back(dimVertex);
[1456]	663	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0, compressionLevel);
[924]	664	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
	665	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
	666	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
	667	dim0.clear();
	668	dim0.push_back(dimFace);
	669	dim0.push_back(dimVertex);
[1456]	670	SuperClassWriter::addVariable(face_edges, NC_INT, dim0, compressionLevel);
[924]	671	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
	672	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
	673	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
[929]	674	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
[924]	675	dim0.clear();
	676	dim0.push_back(dimEdge);
	677	dim0.push_back(dimTwo);
[1456]	678	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0, compressionLevel);
[2413]	679	SuperClassWriter::addAttribute("cf_role", StdString("edge_face_connectivity"), &edge_faces);
[924]	680	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
	681	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
	682	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
	683	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
	684	dim0.clear();
	685	dim0.push_back(dimFace);
	686	dim0.push_back(dimVertex);
[1456]	687	SuperClassWriter::addVariable(face_faces, NC_INT, dim0, compressionLevel);
[2413]	688	SuperClassWriter::addAttribute("cf_role", StdString("face_face_connectivity"), &face_faces);
[924]	689	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
	690	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
[929]	691	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
[924]	692	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
	693	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
[879]	694	} // domain->nvertex > 2
[878]	695
[879]	696	SuperClassWriter::definition_end();
[878]	697
[924]	698	std::vector<StdSize> startEdges(1) ;
	699	std::vector<StdSize> countEdges(1) ;
	700	std::vector<StdSize> startNodes(1) ;
	701	std::vector<StdSize> countNodes(1) ;
	702	std::vector<StdSize> startFaces(1) ;
	703	std::vector<StdSize> countFaces(1) ;
	704	std::vector<StdSize> startEdgeNodes(2) ;
	705	std::vector<StdSize> countEdgeNodes(2) ;
	706	std::vector<StdSize> startEdgeFaces(2) ;
	707	std::vector<StdSize> countEdgeFaces(2) ;
	708	std::vector<StdSize> startFaceConctv(2) ;
	709	std::vector<StdSize> countFaceConctv(2) ;
[902]	710
[1494]	711	if (domain->nvertex == 1)
[879]	712	{
[1494]	713	if (domain->isEmpty())
	714	{
	715	startNodes[0]=0 ;
	716	countNodes[0]=0 ;
	717	}
	718	else
	719	{
[2507]	720	startNodes[0] = domain->ibeginValue_;
	721	countNodes[0] = domain->niValue_ ;
[1494]	722	}
[924]	723
[1494]	724	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	725	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	726	}
	727	else if (domain->nvertex == 2)
	728	{
	729	if (domain->isEmpty())
	730	{
	731	startEdges[0]=0 ;
	732	countEdges[0]=0 ;
	733	startNodes[0]=0 ;
	734	countNodes[0]=0 ;
	735	startEdgeNodes[0]=0;
	736	startEdgeNodes[1]=0;
	737	countEdgeNodes[0]=0;
	738	countEdgeNodes[1]=0;
[924]	739
[1494]	740	}
	741	else
	742	{
[2507]	743	startEdges[0] = domain->ibeginValue_;
	744	countEdges[0] = domain->niValue_;
[1494]	745	startNodes[0] = domain->mesh->node_start;
	746	countNodes[0] = domain->mesh->node_count;
[2409]	747	if (countNodes[0]==0) startNodes[0]=0 ; // for netcdf error
[2507]	748	startEdgeNodes[0] = domain->ibeginValue_;
[1494]	749	startEdgeNodes[1] = 0;
[2507]	750	countEdgeNodes[0] = domain->niValue_;
[1494]	751	countEdgeNodes[1] = 2;
	752	}
	753	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	754	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	755	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	756	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	757	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	758	}
[879]	759	else
	760	{
[1494]	761	if (domain->isEmpty())
	762	{
	763	startFaces[0] = 0 ;
	764	countFaces[0] = 0 ;
	765	startNodes[0] = 0;
	766	countNodes[0] = 0;
	767	startEdges[0] = 0;
	768	countEdges[0] = 0;
	769	startEdgeFaces[0] = 0;
	770	startEdgeFaces[1] = 0;
	771	countEdgeFaces[0] = 0;
	772	countEdgeFaces[1] = 0;
	773	startFaceConctv[0] = 0;
	774	startFaceConctv[1] = 0;
	775	countFaceConctv[0] = 0;
	776	countFaceConctv[1] = 0;
	777	}
	778	else
	779	{
[2507]	780	startFaces[0] = domain->ibeginValue_;
	781	countFaces[0] = domain->niValue_ ;
[1494]	782	startNodes[0] = domain->mesh->node_start;
	783	countNodes[0] = domain->mesh->node_count;
[2409]	784	if (countNodes[0]==0) startNodes[0]=0;
	785
[1494]	786	startEdges[0] = domain->mesh->edge_start;
	787	countEdges[0] = domain->mesh->edge_count;
[2409]	788	if (countEdges[0]==0) startEdges[0]=0 ; // for netcdf error
	789
[1494]	790	startEdgeNodes[0] = domain->mesh->edge_start;
[2409]	791	countEdgeNodes[0] = domain->mesh->edge_count;
	792	if (countEdgeNodes[0]==0) startEdgeNodes[0]=0; // for netcdf error
[1494]	793	startEdgeNodes[1] = 0;
	794	countEdgeNodes[1]= 2;
[2409]	795
[1494]	796	startEdgeFaces[0] = domain->mesh->edge_start;
[2409]	797	countEdgeFaces[0] = domain->mesh->edge_count;
	798	if (countEdgeFaces[0]==0) startEdgeFaces[0]=0 ; // for netcdf error
[1494]	799	startEdgeFaces[1]= 0;
	800	countEdgeFaces[1]= 2;
[2409]	801
[2507]	802	startFaceConctv[0] = domain->ibeginValue_;
	803	countFaceConctv[0] = domain->niValue_;
[1494]	804	startFaceConctv[1] = 0;
	805	countFaceConctv[1] = domain->nvertex;
	806	}
	807	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	808	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	809	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	810	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	811	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	812	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
	813	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
	814	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
	815	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
	816	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
	817	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
	818	}
[879]	819	SuperClassWriter::definition_start();
[878]	820
[879]	821	break;
	822	} // ONE_FILE
[878]	823
[879]	824	case (MULTI_FILE) :
	825	{
[1637]	826	ERROR("CNc4DataOutput::writeDomain(domain)",
	827	<< "[ type = multiple_file ]"
	828	<< " is not yet implemented for UGRID files !");
[879]	829	break;
	830	}
[878]	831
[879]	832	default :
	833	ERROR("CNc4DataOutput::writeDomain(domain)",
	834	<< "[ type = " << SuperClass::type << "]"
	835	<< " not implemented yet !");
	836	} // switch
	837	} // try
[878]	838
[879]	839	catch (CNetCdfException& e)
	840	{
	841	StdString msg("On writing the domain : ");
	842	msg.append(domid); msg.append("\n");
	843	msg.append("In the context : ");
	844	msg.append(context->getId()); msg.append("\n");
	845	msg.append(e.what());
[924]	846	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
[879]	847	}
[878]	848
[879]	849	domain->addRelFile(this->filename);
	850	}
[878]	851
[879]	852	//--------------------------------------------------------------
[878]	853
[879]	854	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
[449]	855	{
	856	CContext* context = CContext::getCurrent() ;
[488]	857
[449]	858	if (domain->IsWritten(this->filename)) return;
	859	domain->checkAttributes();
[488]	860
	861	if (domain->isEmpty())
[449]	862	if (SuperClass::type==MULTI_FILE) return ;
	863
	864	std::vector<StdString> dim0, dim1;
[772]	865	StdString domid = domain->getDomainOutputName();
[705]	866	if (isWrittenDomain(domid)) return ;
[774]	867	else setWrittenDomain(domid);
[705]	868
[449]	869	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
	870
[1430]	871	StdString lonName,latName, cellName ;
[1391]	872	if (domain->lon_name.isEmpty()) lonName = "lon";
	873	else lonName = domain->lon_name;
	874
	875	if (domain->lat_name.isEmpty()) latName = "lat";
	876	else latName = domain->lat_name;
	877
[1430]	878	if (!domain->dim_i_name.isEmpty()) cellName=domain->dim_i_name;
	879	else cellName="cell";
	880	StdString dimXid = cellName+appendDomid;
[2387]	881	StdString dimVertId;
[2535]	882	if (domain->nvertex_name.isEmpty()) dimVertId = "nvertex"+appendDomid;
[2395]	883	else dimVertId = domain->nvertex_name;
[488]	884
[449]	885	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	886	string areaId = "area" + appendDomid;
[449]	887
[1158]	888	nc_type typePrec ;
	889	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
	890	else if (domain->prec==4) typePrec = NC_FLOAT ;
	891	else if (domain->prec==8) typePrec = NC_DOUBLE ;
	892
[1132]	893	int nvertex = (domain->nvertex.isEmpty()) ? 0 : domain->nvertex;
[1025]	894
[498]	895	try
[449]	896	{
[498]	897	switch (SuperClass::type)
	898	{
	899	case (MULTI_FILE) :
	900	{
	901	dim0.push_back(dimXid);
[1553]	902	SuperClassWriter::addDimension(dimXid, domain->ni);
[488]	903
[1415]	904	lonid = lonName+appendDomid;
	905	latid = latName+appendDomid;
[1430]	906	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	907	else bounds_lonid = "bounds_"+lonName+appendDomid;
	908	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	909	else bounds_latid = "bounds_"+latName+appendDomid;
	910
[665]	911	if (domain->hasLonLat)
	912	{
[1456]	913	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	914	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	915	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	916	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	917	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	918	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
	919	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	920	}
[498]	921	dim0.clear();
	922	if (domain->hasBounds)
	923	{
	924	dim0.push_back(dimXid);
	925	dim0.push_back(dimVertId);
[1456]	926	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	927	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[498]	928	}
	929
	930	dim0.clear();
[449]	931	dim0.push_back(dimXid);
[611]	932	if (domain->hasArea)
	933	{
[1456]	934	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	935	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	936	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	937	}
	938
[498]	939	SuperClassWriter::definition_end();
[449]	940
[665]	941	if (domain->hasLonLat)
[498]	942	{
[1930]	943	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0);
	944	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0);
[665]	945	if (domain->hasBounds)
	946	{
[1930]	947	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0);
	948	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0);
[665]	949	}
[498]	950	}
[611]	951
	952	if (domain->hasArea)
[1930]	953	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0);
[611]	954
[498]	955	SuperClassWriter::definition_start();
	956	break ;
	957	}
[488]	958
[498]	959	case (ONE_FILE) :
	960	{
[1415]	961	lonid = lonName+appendDomid;
	962	latid = latName+appendDomid;
[1430]	963	if (!domain->bounds_lon_name.isEmpty()) bounds_lonid = domain->bounds_lon_name;
	964	else bounds_lonid = "bounds_"+lonName+appendDomid;
	965	if (!domain->bounds_lat_name.isEmpty()) bounds_latid = domain->bounds_lat_name;
	966	else bounds_latid = "bounds_"+latName+appendDomid;
[1391]	967
[498]	968	dim0.push_back(dimXid);
[1132]	969	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
[665]	970	if (domain->hasLonLat)
	971	{
[1456]	972	SuperClassWriter::addVariable(latid, typePrec, dim0, compressionLevel);
	973	SuperClassWriter::addVariable(lonid, typePrec, dim0, compressionLevel);
[665]	974
	975	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	976	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	977	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	978	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
[1025]	979	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, nvertex);
[665]	980	}
[498]	981	dim0.clear();
[449]	982
[498]	983	if (domain->hasBounds)
	984	{
	985	dim0.push_back(dimXid);
	986	dim0.push_back(dimVertId);
[1456]	987	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0, compressionLevel);
	988	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0, compressionLevel);
[498]	989	}
[488]	990
[611]	991	if (domain->hasArea)
	992	{
	993	dim0.clear();
	994	dim0.push_back(dimXid);
[1456]	995	SuperClassWriter::addVariable(areaId, typePrec, dim0, compressionLevel);
[614]	996	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	997	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	998	}
	999
[498]	1000	SuperClassWriter::definition_end();
[488]	1001
[498]	1002	std::vector<StdSize> start(1), startBounds(2) ;
	1003	std::vector<StdSize> count(1), countBounds(2) ;
	1004	if (domain->isEmpty())
	1005	{
	1006	start[0]=0 ;
	1007	count[0]=0 ;
	1008	startBounds[1]=0 ;
[1025]	1009	countBounds[1]=nvertex ;
[498]	1010	startBounds[0]=0 ;
	1011	countBounds[0]=0 ;
	1012	}
	1013	else
	1014	{
[2507]	1015	start[0]=domain->ibeginValue_;
	1016	count[0]=domain->niValue_;
	1017	startBounds[0]=domain->ibeginValue_;
[498]	1018	startBounds[1]=0 ;
[2507]	1019	countBounds[0]=domain->niValue_;
[1025]	1020	countBounds[1]=nvertex ;
[498]	1021	}
[665]	1022
	1023	if (domain->hasLonLat)
[498]	1024	{
[1930]	1025	SuperClassWriter::writeData(domain->latvalue, latid, isCollective, 0,&start,&count);
	1026	SuperClassWriter::writeData(domain->lonvalue, lonid, isCollective, 0,&start,&count);
[665]	1027	if (domain->hasBounds)
	1028	{
[1930]	1029	SuperClassWriter::writeData(domain->bounds_lonvalue, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
	1030	SuperClassWriter::writeData(domain->bounds_latvalue, bounds_latid, isCollective, 0,&startBounds,&countBounds);
[665]	1031	}
[498]	1032	}
[488]	1033
[611]	1034	if (domain->hasArea)
[1930]	1035	SuperClassWriter::writeData(domain->areavalue, areaId, isCollective, 0, &start, &count);
[488]	1036
[498]	1037	SuperClassWriter::definition_start();
[488]	1038
[498]	1039	break;
	1040	}
	1041	default :
	1042	ERROR("CNc4DataOutput::writeDomain(domain)",
	1043	<< "[ type = " << SuperClass::type << "]"
	1044	<< " not implemented yet !");
	1045	}
[219]	1046	}
[498]	1047	catch (CNetCdfException& e)
	1048	{
	1049	StdString msg("On writing the domain : ");
	1050	msg.append(domid); msg.append("\n");
	1051	msg.append("In the context : ");
	1052	msg.append(context->getId()); msg.append("\n");
	1053	msg.append(e.what());
	1054	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
	1055	}
[219]	1056	domain->addRelFile(this->filename);
	1057	}
	1058	//--------------------------------------------------------------
	1059
[347]	1060	void CNc4DataOutput::writeAxis_(CAxis* axis)
[219]	1061	{
[1030]	1062	if (axis->IsWritten(this->filename)) return;
[2381]	1063
	1064	// Check that the name associated to the current element is not in conflict with an existing element (due to CGrid::duplicateSentGrid)
	1065	if (!axis->value.isEmpty() )
	1066	{
[2386]	1067	// The hash of the element will be associated to the default element name (= map key), and to the name really written
	1068	int globalHash = axis->computeAttributesHash( comm_file ); // Need a MPI_Comm to distribute without redundancy some attributs (value)
[2381]	1069
	1070	StdString defaultNameKey = axis->getAxisOutputName();
[2389]	1071	if ( !relAxis_.count ( defaultNameKey ) )
[2381]	1072	{
	1073	// if defaultNameKey not in the map, write the element such as it is defined
[2389]	1074	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) );
[2381]	1075	}
	1076	else // look if a hash associated this key is equal
	1077	{
	1078	bool elementIsInMap(false);
[2389]	1079	auto defaultNameKeyElements = relAxis_.equal_range( defaultNameKey );
[2381]	1080	for (auto it = defaultNameKeyElements.first; it != defaultNameKeyElements.second; it++)
	1081	{
	1082	if ( it->second.first == globalHash )
	1083	{
	1084	// if yes, associate the same ids to current element
[2389]	1085	axis->renameAttributesBeforeWriting( it->second.second );
[2381]	1086	elementIsInMap = true;
	1087	}
	1088	}
	1089	// if no : inheritance has been excessive, define new names and store it (could be used by another grid)
	1090	if (!elementIsInMap) // ! in MAP
	1091	{
[2389]	1092	axis->renameAttributesBeforeWriting();
	1093	relAxis_.insert( make_pair( defaultNameKey, make_pair(globalHash, axis) ) ) ;// = axis->getId()
[2381]	1094	}
	1095	}
	1096	}
	1097
[1030]	1098	axis->checkAttributes();
[488]	1099
[1559]	1100	int size = (MULTI_FILE == SuperClass::type) ? axis->n.getValue()
	1101	: axis->n_glo.getValue();
[1099]	1102
[1559]	1103	if ((0 == axis->n) && (MULTI_FILE == SuperClass::type)) return;
[1235]	1104
[1030]	1105	std::vector<StdString> dims;
	1106	StdString axisid = axis->getAxisOutputName();
[1435]	1107	StdString axisDim, axisBoundsId;
[1030]	1108	if (isWrittenAxis(axisid)) return ;
	1109	else setWrittenAxis(axisid);
[705]	1110
[1158]	1111	nc_type typePrec ;
	1112	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
[1235]	1113	else if (axis->prec==4) typePrec = NC_FLOAT ;
[1158]	1114	else if (axis->prec==8) typePrec = NC_DOUBLE ;
	1115
	1116	if (!axis->label.isEmpty()) typePrec = NC_CHAR ;
	1117	string strId="str_len" ;
[1030]	1118	try
	1119	{
[1433]	1120	if (axis->dim_name.isEmpty()) axisDim = axisid;
	1121	else axisDim=axis->dim_name.getValue();
[1559]	1122	SuperClassWriter::addDimension(axisDim, size);
[1433]	1123	dims.push_back(axisDim);
	1124
[1439]	1125	if (!axis->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
[1433]	1126
[2507]	1127	if (axis->hasValue() \|\| !axis->label.isEmpty())
[816]	1128	{
[1158]	1129	if (!axis->label.isEmpty()) dims.push_back(strId);
[1430]	1130
[1456]	1131	SuperClassWriter::addVariable(axisid, typePrec, dims, compressionLevel);
[219]	1132
[1030]	1133	if (!axis->name.isEmpty())
	1134	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
[219]	1135
[1030]	1136	if (!axis->standard_name.isEmpty())
	1137	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
[540]	1138
[1030]	1139	if (!axis->long_name.isEmpty())
	1140	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
[219]	1141
[1030]	1142	if (!axis->unit.isEmpty())
	1143	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
[219]	1144
[1430]	1145	if (!axis->axis_type.isEmpty())
	1146	{
	1147	switch(axis->axis_type)
	1148	{
	1149	case CAxis::axis_type_attr::X :
	1150	SuperClassWriter::addAttribute("axis", string("X"), &axisid);
	1151	break;
	1152	case CAxis::axis_type_attr::Y :
	1153	SuperClassWriter::addAttribute("axis", string("Y"), &axisid);
	1154	break;
	1155	case CAxis::axis_type_attr::Z :
	1156	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
	1157	break;
	1158	case CAxis::axis_type_attr::T :
	1159	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
	1160	break;
	1161	}
	1162	}
	1163
[1030]	1164	if (!axis->positive.isEmpty())
	1165	{
	1166	SuperClassWriter::addAttribute("positive",
	1167	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
	1168	&axisid);
	1169	}
[399]	1170
[1266]	1171	if (!axis->formula.isEmpty())
	1172	SuperClassWriter::addAttribute("formula", axis->formula.getValue(), &axisid);
	1173
	1174	if (!axis->formula_term.isEmpty())
[2436]	1175	SuperClassWriter::addAttribute("formula_terms", axis->formula_term.getValue(), &axisid);
[1266]	1176
[1435]	1177	axisBoundsId = (axis->bounds_name.isEmpty()) ? axisid + "_bounds" : axis->bounds_name;
[1249]	1178	if (!axis->bounds.isEmpty() && axis->label.isEmpty())
[1030]	1179	{
	1180	dims.push_back("axis_nbounds");
[1456]	1181	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims, compressionLevel);
[1030]	1182	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
[1288]	1183
	1184	if (!axis->standard_name.isEmpty())
	1185	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisBoundsId);
	1186
	1187	if (!axis->unit.isEmpty())
	1188	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisBoundsId);
	1189
[1266]	1190	if (!axis->formula_bounds.isEmpty())
[1288]	1191	SuperClassWriter::addAttribute("formula", axis->formula_bounds.getValue(), &axisBoundsId);
[1266]	1192
	1193	if (!axis->formula_term_bounds.isEmpty())
[2436]	1194	SuperClassWriter::addAttribute("formula_terms", axis->formula_term_bounds.getValue(), &axisBoundsId);
[1030]	1195	}
[1435]	1196	}
[816]	1197
[1435]	1198	SuperClassWriter::definition_end();
[1950]	1199
[1435]	1200	switch (SuperClass::type)
	1201	{
	1202	case MULTI_FILE:
[1030]	1203	{
[1435]	1204	if (axis->label.isEmpty())
[1437]	1205	{
	1206	if (!axis->value.isEmpty())
[1930]	1207	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0);
[633]	1208
[1437]	1209	if (!axis->bounds.isEmpty())
[1930]	1210	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0);
[1435]	1211	}
[1437]	1212	else
[1950]	1213	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0);
[1435]	1214
	1215	SuperClassWriter::definition_start();
	1216	break;
	1217	}
	1218	case ONE_FILE:
	1219	{
	1220	std::vector<StdSize> start(1), startBounds(2) ;
	1221	std::vector<StdSize> count(1), countBounds(2) ;
[1559]	1222	start[0] = startBounds[0] = axis->begin;
	1223	count[0] = countBounds[0] = axis->n;
[1435]	1224	startBounds[1] = 0;
	1225	countBounds[1] = 2;
	1226
	1227	if (axis->label.isEmpty())
[1437]	1228	{
	1229	if (!axis->value.isEmpty())
[1930]	1230	SuperClassWriter::writeData(axis->value, axisid, isCollective, 0, &start, &count);
[1435]	1231
[1437]	1232	if (!axis->bounds.isEmpty())
[1930]	1233	SuperClassWriter::writeData(axis->bounds, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
[1435]	1234	}
[1437]	1235	else
[1435]	1236	{
	1237	std::vector<StdSize> startLabel(2), countLabel(2);
	1238	startLabel[0] = start[0]; startLabel[1] = 0;
	1239	countLabel[0] = count[0]; countLabel[1] = stringArrayLen;
[1950]	1240	SuperClassWriter::writeData(axis->label, axisid, isCollective, 0, &startLabel, &countLabel);
[1435]	1241	}
[609]	1242
[1435]	1243	SuperClassWriter::definition_start();
	1244
	1245	break;
[609]	1246	}
[1435]	1247	default :
	1248	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
	1249	<< "[ type = " << SuperClass::type << "]"
	1250	<< " not implemented yet !");
[609]	1251	}
[1030]	1252	}
	1253	catch (CNetCdfException& e)
	1254	{
	1255	StdString msg("On writing the axis : ");
	1256	msg.append(axisid); msg.append("\n");
	1257	msg.append("In the context : ");
	1258	CContext* context = CContext::getCurrent() ;
	1259	msg.append(context->getId()); msg.append("\n");
	1260	msg.append(e.what());
	1261	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
	1262	}
[1158]	1263	axis->addRelFile(this->filename);
[391]	1264	}
[488]	1265
[887]	1266	void CNc4DataOutput::writeScalar_(CScalar* scalar)
	1267	{
	1268	if (scalar->IsWritten(this->filename)) return;
	1269	scalar->checkAttributes();
	1270	int scalarSize = 1;
	1271
	1272	StdString scalaId = scalar->getScalarOutputName();
[1430]	1273	StdString boundsId;
[887]	1274	if (isWrittenAxis(scalaId)) return ;
	1275	else setWrittenAxis(scalaId);
	1276
[1158]	1277	nc_type typePrec ;
	1278	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
	1279	else if (scalar->prec==4) typePrec = NC_FLOAT ;
	1280	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
	1281
[1435]	1282	if (!scalar->label.isEmpty()) typePrec = NC_CHAR ;
	1283	string strId="str_len" ;
	1284
[887]	1285	try
	1286	{
[1439]	1287	if (!scalar->label.isEmpty() && !SuperClassWriter::dimExist(strId)) SuperClassWriter::addDimension(strId, stringArrayLen);
[1435]	1288
	1289	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
[887]	1290	{
[1430]	1291	std::vector<StdString> dims;
	1292	StdString scalarDim = scalaId;
	1293
[1435]	1294	if (!scalar->label.isEmpty()) dims.push_back(strId);
	1295
[1158]	1296	SuperClassWriter::addVariable(scalaId, typePrec, dims);
[887]	1297
	1298	if (!scalar->name.isEmpty())
	1299	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
	1300
	1301	if (!scalar->standard_name.isEmpty())
	1302	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
	1303
	1304	if (!scalar->long_name.isEmpty())
	1305	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
	1306
	1307	if (!scalar->unit.isEmpty())
	1308	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
	1309
[1430]	1310	if (!scalar->axis_type.isEmpty())
	1311	{
	1312	switch(scalar->axis_type)
	1313	{
	1314	case CScalar::axis_type_attr::X :
	1315	SuperClassWriter::addAttribute("axis", string("X"), &scalaId);
	1316	break;
	1317	case CScalar::axis_type_attr::Y :
	1318	SuperClassWriter::addAttribute("axis", string("Y"), &scalaId);
	1319	break;
	1320	case CScalar::axis_type_attr::Z :
	1321	SuperClassWriter::addAttribute("axis", string("Z"), &scalaId);
	1322	break;
	1323	case CScalar::axis_type_attr::T :
	1324	SuperClassWriter::addAttribute("axis", string("T"), &scalaId);
	1325	break;
	1326	}
	1327	}
	1328
[1435]	1329	if (!scalar->positive.isEmpty())
[1430]	1330	{
[1435]	1331	SuperClassWriter::addAttribute("positive",
	1332	(scalar->positive == CScalar::positive_attr::up) ? string("up") : string("down"),
	1333	&scalaId);
	1334	}
	1335
	1336	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1337	{
[1436]	1338	dims.clear();
	1339	dims.push_back("axis_nbounds");
[1435]	1340	boundsId = (scalar->bounds_name.isEmpty()) ? (scalaId + "_bounds") : scalar->bounds_name.getValue();
[1430]	1341	SuperClassWriter::addVariable(boundsId, typePrec, dims);
[1436]	1342	SuperClassWriter::addAttribute("bounds", boundsId, &scalaId);
[1430]	1343	}
	1344
[887]	1345	SuperClassWriter::definition_end();
	1346
	1347	switch (SuperClass::type)
	1348	{
	1349	case MULTI_FILE:
	1350	{
	1351	CArray<double,1> scalarValue(scalarSize);
[1435]	1352	CArray<string,1> scalarLabel(scalarSize);
[1436]	1353	CArray<double,1> scalarBounds(scalarSize*2);
[1435]	1354
	1355	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
[1430]	1356	{
[1435]	1357	scalarValue(0) = scalar->value;
	1358	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
	1359	}
	1360
	1361	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1362	{
[1436]	1363	scalarBounds(0) = scalar->bounds(0);
	1364	scalarBounds(1) = scalar->bounds(1);
	1365	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0);
[1430]	1366	}
[1435]	1367
	1368	if (!scalar->label.isEmpty())
	1369	{
	1370	scalarLabel(0) = scalar->label;
	1371	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0);
	1372	}
	1373
[887]	1374	SuperClassWriter::definition_start();
	1375
	1376	break;
	1377	}
	1378	case ONE_FILE:
	1379	{
	1380	CArray<double,1> scalarValue(scalarSize);
[1435]	1381	CArray<string,1> scalarLabel(scalarSize);
[1436]	1382	CArray<double,1> scalarBounds(scalarSize*2);
[887]	1383
	1384	std::vector<StdSize> start(1);
	1385	std::vector<StdSize> count(1);
	1386	start[0] = 0;
	1387	count[0] = 1;
[1435]	1388	if (!scalar->value.isEmpty() && scalar->label.isEmpty())
[1430]	1389	{
[1435]	1390	scalarValue(0) = scalar->value;
	1391	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
	1392	}
	1393	if (!scalar->bounds.isEmpty() && scalar->label.isEmpty())
	1394	{
[1436]	1395	scalarBounds(0) = scalar->bounds(0);
	1396	scalarBounds(1) = scalar->bounds(1);
	1397	count[0] = 2;
	1398	SuperClassWriter::writeData(scalarBounds, boundsId, isCollective, 0, &start, &count);
[1430]	1399	}
[1435]	1400	if (!scalar->label.isEmpty())
	1401	{
	1402	scalarLabel(0) = scalar->label;
	1403	count[0] = stringArrayLen;
	1404	SuperClassWriter::writeData(scalarLabel, scalaId, isCollective, 0, &start, &count);
	1405	}
	1406
[887]	1407	SuperClassWriter::definition_start();
	1408
	1409	break;
	1410	}
	1411	default :
	1412	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
	1413	<< "[ type = " << SuperClass::type << "]"
	1414	<< " not implemented yet !");
	1415	}
	1416	}
	1417	}
	1418	catch (CNetCdfException& e)
	1419	{
	1420	StdString msg("On writing the scalar : ");
	1421	msg.append(scalaId); msg.append("\n");
	1422	msg.append("In the context : ");
	1423	CContext* context = CContext::getCurrent() ;
	1424	msg.append(context->getId()); msg.append("\n");
	1425	msg.append(e.what());
	1426	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
	1427	}
	1428	scalar->addRelFile(this->filename);
	1429	}
	1430
[676]	1431	//--------------------------------------------------------------
	1432
	1433	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
	1434	{
[1957]	1435	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
	1436
	1437	// NOTA : The cuurent algorithm to write compress elements of the grid
	1438	// will work pretting well when on server side you dont't get
	1439	// partial overlap on elements between differents participating process
	1440	// So the element must be totally distributed or non distributed
	1441	// If an element is partially overlaping betwwen process then the
	1442	// total compressed part will apear artificially greater than expected
	1443	// For the current implementation of writer which is decomposed only on
	1444	// one element, it will work as expected, but for future, it must be
	1445	// reconsidered again.
	1446	try
	1447	{
	1448	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1449	std::vector<StdString> domainList = grid->getDomainList();
	1450	std::vector<StdString> axisList = grid->getAxisList();
	1451	std::vector<StdString> scalarList = grid->getScalarList();
	1452	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
	1453	int commRank ;
	1454	MPI_Comm_rank(comm_file,&commRank) ;
[676]	1455
[1957]	1456	std::vector<StdString> dims;
[676]	1457
[1957]	1458	for (int i = 0; i < numElement; ++i)
	1459	{
	1460	StdString varId, compress;
	1461	CArray<size_t, 1> indexes;
	1462	bool isDistributed;
	1463	size_t nbIndexes, totalNbIndexes, offset;
	1464	size_t firstGlobalIndex;
	1465
	1466	if (2 == axisDomainOrder(i))
	1467	{
	1468	CDomain* domain = CDomain::get(domainList[idxDomain]);
	1469	StdString domId = domain->getDomainOutputName();
[676]	1470
[1957]	1471	if (!domain->isCompressible()
	1472	\|\| domain->type == CDomain::type_attr::unstructured
	1473	\|\| domain->isWrittenCompressed(this->filename)
	1474	\|\| isWrittenCompressedDomain(domId))
	1475	continue;
	1476
	1477	// unstructured grid seems not be taken into account why ?
[676]	1478
[1957]	1479	string lonName,latName ;
[676]	1480
[1957]	1481	if (domain->lon_name.isEmpty())
	1482	{
	1483	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
	1484	else lonName = "lon";
	1485	}
	1486	else lonName = domain->lon_name;
[676]	1487
[1957]	1488	if (domain->lat_name.isEmpty())
	1489	{
	1490	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
	1491	else latName = "lat";
	1492	}
	1493	else latName = domain->lat_name;
	1494
	1495	StdString appendDomId = singleDomain ? "" : "_" + domId;
[676]	1496
[1957]	1497	varId = domId + "_points";
	1498	compress = latName + appendDomId + " " + lonName + appendDomId;
	1499
[2267]	1500	shared_ptr<CLocalView> workflowView = domain->getLocalView(CElementView::WORKFLOW) ;
[1957]	1501	workflowView->getGlobalIndexView(indexes) ;
	1502	nbIndexes = workflowView->getSize() ;
	1503	isDistributed = domain->isDistributed();
	1504	if (isDistributed)
	1505	{
	1506	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	1507	if (commRank==0) offset=0 ;
	1508	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
	1509	}
	1510	else
	1511	{
	1512	offset=0 ;
	1513	totalNbIndexes = nbIndexes ;
	1514	}
[676]	1515
[2507]	1516	firstGlobalIndex = domain->ibeginValue_ + domain->jbeginValue_ * domain->ni_glo;
[676]	1517
[1957]	1518	domain->addRelFileCompressed(this->filename);
	1519	setWrittenCompressedDomain(domId);
	1520	++idxDomain;
	1521	}
	1522	else if (1 == axisDomainOrder(i))
	1523	{
	1524	CAxis* axis = CAxis::get(axisList[idxAxis]);
	1525	StdString axisId = axis->getAxisOutputName();
[676]	1526
[1957]	1527	if (!axis->isCompressible()
	1528	\|\| axis->isWrittenCompressed(this->filename)
	1529	\|\| isWrittenCompressedAxis(axisId))
	1530	continue;
[676]	1531
[1957]	1532	varId = axisId + "_points";
	1533	compress = axisId;
[676]	1534
[2267]	1535	shared_ptr<CLocalView> workflowView = axis->getLocalView(CElementView::WORKFLOW) ;
[1957]	1536	workflowView->getGlobalIndexView(indexes) ;
	1537	nbIndexes = workflowView->getSize() ;
	1538	isDistributed = axis->isDistributed();
	1539	if (isDistributed)
	1540	{
	1541	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	1542	if (commRank==0) offset=0 ;
	1543	MPI_Allreduce(&nbIndexes,&totalNbIndexes,1 , MPI_SIZE_T, MPI_SUM, comm_file) ;
	1544	}
	1545	else
	1546	{
	1547	offset=0 ;
	1548	totalNbIndexes = nbIndexes ;
	1549	}
	1550	firstGlobalIndex = axis->begin;
	1551
	1552	axis->addRelFileCompressed(this->filename);
	1553	setWrittenCompressedAxis(axisId);
	1554	++idxAxis;
	1555	}
	1556	else
	1557	{
	1558	//for scalar
	1559	}
[676]	1560
[1957]	1561	if (!varId.empty())
	1562	{
	1563	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
[774]	1564
[1957]	1565	dims.clear();
	1566	dims.push_back(varId);
	1567	SuperClassWriter::addVariable(varId, NC_UINT64, dims);
[676]	1568
[1957]	1569	SuperClassWriter::addAttribute("compress", compress, &varId);
[676]	1570
[1957]	1571	switch (SuperClass::type)
	1572	{
	1573	case (MULTI_FILE):
	1574	{
	1575	indexes -= firstGlobalIndex;
	1576	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
	1577	break;
	1578	}
	1579	case (ONE_FILE):
	1580	{
	1581	std::vector<StdSize> start, count;
	1582	start.push_back(offset);
	1583	count.push_back(nbIndexes);
[676]	1584
[1957]	1585	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
	1586	break;
	1587	}
	1588	}
[1144]	1589	}
[1957]	1590	}
[676]	1591
[1957]	1592	grid->addRelFileCompressed(this->filename);
	1593	}
	1594	catch (CNetCdfException& e)
	1595	{
	1596	StdString msg("On writing compressed grid : ");
	1597	msg.append(grid->getId()); msg.append("\n");
	1598	msg.append("In the context : ");
	1599	CContext* context = CContext::getCurrent();
	1600	msg.append(context->getId()); msg.append("\n");
	1601	msg.append(e.what());
	1602	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
	1603	}
	1604	}
[676]	1605
	1606	//--------------------------------------------------------------
	1607
[391]	1608	void CNc4DataOutput::writeTimeDimension_(void)
	1609	{
[498]	1610	try
	1611	{
[802]	1612	SuperClassWriter::addDimension(getTimeCounterName());
[498]	1613	}
	1614	catch (CNetCdfException& e)
	1615	{
[614]	1616	StdString msg("On writing time dimension : time_couter\n");
[498]	1617	msg.append("In the context : ");
	1618	CContext* context = CContext::getCurrent() ;
	1619	msg.append(context->getId()); msg.append("\n");
	1620	msg.append(e.what());
	1621	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
	1622	}
[391]	1623	}
[676]	1624
[219]	1625	//--------------------------------------------------------------
	1626
[347]	1627	void CNc4DataOutput::writeField_(CField* field)
[219]	1628	{
[1158]	1629	CContext* context = CContext::getCurrent() ;
[300]	1630
[1158]	1631	std::vector<StdString> dims, coodinates;
[1869]	1632	CGrid* grid = field->getGrid();
[1158]	1633	if (!grid->doGridHaveDataToWrite())
[567]	1634	if (SuperClass::type==MULTI_FILE) return ;
[488]	1635
[1158]	1636	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1637	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
	1638	std::vector<StdString> domainList = grid->getDomainList();
	1639	std::vector<StdString> axisList = grid->getAxisList();
	1640	std::vector<StdString> scalarList = grid->getScalarList();
[219]	1641
[1158]	1642	StdString timeid = getTimeCounterName();
	1643	StdString dimXid,dimYid;
	1644	std::deque<StdString> dimIdList, dimCoordList;
	1645	bool hasArea = false;
	1646	StdString cellMeasures = "area:";
	1647	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
[488]	1648
[1158]	1649	for (int i = 0; i < numElement; ++i)
	1650	{
	1651	if (2 == axisDomainOrder(i))
	1652	{
	1653	CDomain* domain = CDomain::get(domainList[idxDomain]);
	1654	StdString domId = domain->getDomainOutputName();
	1655	StdString appendDomId = singleDomain ? "" : "_" + domId ;
[1391]	1656	StdString lonName,latName ;
[1430]	1657	StdString dimIname,dimJname ;
[676]	1658
[1415]	1659	if (domain->lon_name.isEmpty())
	1660	{
	1661	if (domain->type==CDomain::type_attr::curvilinear) lonName = "nav_lon";
	1662	else lonName = "lon";
	1663	}
[1391]	1664	else lonName = domain->lon_name;
	1665
[1415]	1666	if (domain->lat_name.isEmpty())
	1667	{
	1668	if (domain->type==CDomain::type_attr::curvilinear) latName = "nav_lat";
	1669	else latName = "lat";
	1670	}
[1391]	1671	else latName = domain->lat_name;
[1430]	1672
	1673	if (domain->dim_i_name.isEmpty())
	1674	{
	1675	if (domain->type==CDomain::type_attr::curvilinear) dimIname = "x";
	1676	else if (domain->type==CDomain::type_attr::unstructured) dimIname = "cell";
	1677	else dimIname = lonName;
	1678	}
	1679	else dimIname = domain->dim_i_name;
	1680
	1681	if (domain->dim_j_name.isEmpty())
	1682	{
	1683	if (domain->type==CDomain::type_attr::curvilinear) dimJname = "y";
	1684	else dimJname = latName;
	1685	}
	1686	else dimJname = domain->dim_j_name;
[1391]	1687
[1158]	1688	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
	1689	{
	1690	dimIdList.push_back(domId + "_points");
	1691	field->setUseCompressedOutput();
	1692	}
[676]	1693
[1158]	1694	switch (domain->type)
[879]	1695	{
[1158]	1696	case CDomain::type_attr::curvilinear:
	1697	if (!compressedOutput \|\| !domain->isCompressible())
	1698	{
[1430]	1699	dimXid=dimIname+appendDomId;
	1700	dimYid=dimJname+appendDomId;
[1158]	1701	dimIdList.push_back(dimXid);
	1702	dimIdList.push_back(dimYid);
	1703	}
[1415]	1704	dimCoordList.push_back(lonName+appendDomId);
	1705	dimCoordList.push_back(latName+appendDomId);
[1158]	1706	break ;
	1707	case CDomain::type_attr::rectilinear:
	1708	if (!compressedOutput \|\| !domain->isCompressible())
	1709	{
[1430]	1710	dimXid = dimIname+appendDomId;
	1711	dimYid = dimJname+appendDomId;
[1158]	1712	dimIdList.push_back(dimXid);
	1713	dimIdList.push_back(dimYid);
	1714	}
[1430]	1715	if (lonName != dimIname) dimCoordList.push_back(lonName+appendDomId);
	1716	if (latName != dimJname) dimCoordList.push_back(latName+appendDomId);
	1717
[1158]	1718	break ;
	1719	case CDomain::type_attr::unstructured:
	1720	{
	1721	if (SuperClassWriter::useCFConvention)
	1722	{
[1430]	1723	dimXid = dimIname + appendDomId;
[1158]	1724	dimIdList.push_back(dimXid);
[1415]	1725	dimCoordList.push_back(lonName+appendDomId);
	1726	dimCoordList.push_back(latName+appendDomId);
[1158]	1727	}
	1728	else
	1729	{
	1730	StdString domainName = domain->name;
	1731	if (domain->nvertex == 1)
	1732	{
	1733	dimXid = "n" + domainName + "_node";
	1734	dimIdList.push_back(dimXid);
	1735	dimCoordList.push_back(StdString(domainName + "_node_x"));
	1736	dimCoordList.push_back(StdString(domainName + "_node_y"));
	1737	}
	1738	else if (domain->nvertex == 2)
	1739	{
	1740	dimXid = "n" + domainName + "_edge";
	1741	dimIdList.push_back(dimXid);
	1742	dimCoordList.push_back(StdString(domainName + "_edge_x"));
	1743	dimCoordList.push_back(StdString(domainName + "_edge_y"));
	1744	}
	1745	else
	1746	{
	1747	dimXid = "n" + domainName + "_face";
	1748	dimIdList.push_back(dimXid);
	1749	dimCoordList.push_back(StdString(domainName + "_face_x"));
	1750	dimCoordList.push_back(StdString(domainName + "_face_y"));
	1751	}
	1752	} // ugrid convention
	1753	} // case unstructured domain
[879]	1754	}
[1158]	1755
	1756	if (domain->hasArea)
[879]	1757	{
[1158]	1758	hasArea = true;
	1759	cellMeasures += " area" + appendDomId;
[879]	1760	}
[1158]	1761	++idxDomain;
	1762	}
	1763	else if (1 == axisDomainOrder(i))
	1764	{
	1765	CAxis* axis = CAxis::get(axisList[idxAxis]);
	1766	StdString axisId = axis->getAxisOutputName();
[1430]	1767	StdString axisDim;
[1158]	1768
[1430]	1769	if (axis->dim_name.isEmpty()) axisDim = axisId;
	1770	else axisDim=axis->dim_name.getValue();
	1771
[1158]	1772	if (compressedOutput && axis->isCompressible())
[879]	1773	{
[1430]	1774	dimIdList.push_back(axisDim + "_points");
[1158]	1775	field->setUseCompressedOutput();
[879]	1776	}
[1158]	1777	else
[1430]	1778	dimIdList.push_back(axisDim);
[878]	1779
[1430]	1780	if (axisDim != axisId) dimCoordList.push_back(axisId);
[1158]	1781	++idxAxis;
	1782	}
[1430]	1783	else
[1158]	1784	{
[1430]	1785	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
	1786	StdString scalarId = scalar->getScalarOutputName();
[1446]	1787	if (!scalar->value.isEmpty() \|\| !scalar->label.isEmpty())
	1788	dimCoordList.push_back(scalarId);
[1430]	1789	++idxScalar;
[1158]	1790	}
	1791	}
[488]	1792
[1158]	1793	StdString fieldid = field->getFieldOutputName();
[219]	1794
[1158]	1795	nc_type type ;
	1796	if (field->prec.isEmpty()) type = NC_FLOAT ;
	1797	else
	1798	{
	1799	if (field->prec==2) type = NC_SHORT ;
	1800	else if (field->prec==4) type = NC_FLOAT ;
	1801	else if (field->prec==8) type = NC_DOUBLE ;
	1802	}
[488]	1803
[1158]	1804	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
[488]	1805
[1158]	1806	if (wtime)
	1807	{
	1808	if (field->hasTimeInstant && hasTimeInstant) coodinates.push_back(string("time_instant"));
	1809	else if (field->hasTimeCentered && hasTimeCentered) coodinates.push_back(string("time_centered"));
	1810	dims.push_back(timeid);
	1811	}
[488]	1812
[1961]	1813	while (!dimIdList.empty())
[1158]	1814	{
[1961]	1815	dims.push_back(dimIdList.back());
	1816	dimIdList.pop_back();
[1158]	1817	}
[219]	1818
[1158]	1819	while (!dimCoordList.empty())
	1820	{
	1821	coodinates.push_back(dimCoordList.back());
	1822	dimCoordList.pop_back();
	1823	}
[219]	1824
[1158]	1825	try
	1826	{
[2481]	1827	SuperClassWriter::addVariable(fieldid, type, dims, false);
[2479]	1828	SuperClassWriter::addChunk(field, type, dims);
[488]	1829
[498]	1830	if (!field->standard_name.isEmpty())
	1831	SuperClassWriter::addAttribute
	1832	("standard_name", field->standard_name.getValue(), &fieldid);
[219]	1833
[498]	1834	if (!field->long_name.isEmpty())
	1835	SuperClassWriter::addAttribute
	1836	("long_name", field->long_name.getValue(), &fieldid);
[219]	1837
[498]	1838	if (!field->unit.isEmpty())
	1839	SuperClassWriter::addAttribute
	1840	("units", field->unit.getValue(), &fieldid);
[463]	1841
[1158]	1842	// Ugrid field attributes "mesh" and "location"
	1843	if (!SuperClassWriter::useCFConvention)
	1844	{
	1845	if (!domainList.empty())
	1846	{
	1847	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
	1848	StdString mesh = domain->name;
	1849	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
	1850	StdString location;
	1851	if (domain->nvertex == 1)
	1852	location = "node";
	1853	else if (domain->nvertex == 2)
	1854	location = "edge";
	1855	else if (domain->nvertex > 2)
	1856	location = "face";
	1857	SuperClassWriter::addAttribute("location", location, &fieldid);
	1858	}
	1859
	1860	}
	1861
	1862	if (!field->valid_min.isEmpty())
[498]	1863	SuperClassWriter::addAttribute
	1864	("valid_min", field->valid_min.getValue(), &fieldid);
[463]	1865
[498]	1866	if (!field->valid_max.isEmpty())
	1867	SuperClassWriter::addAttribute
	1868	("valid_max", field->valid_max.getValue(), &fieldid);
[464]	1869
[498]	1870	if (!field->scale_factor.isEmpty())
	1871	SuperClassWriter::addAttribute
	1872	("scale_factor", field->scale_factor.getValue(), &fieldid);
[464]	1873
[498]	1874	if (!field->add_offset.isEmpty())
	1875	SuperClassWriter::addAttribute
	1876	("add_offset", field->add_offset.getValue(), &fieldid);
[488]	1877
[498]	1878	SuperClassWriter::addAttribute
	1879	("online_operation", field->operation.getValue(), &fieldid);
[472]	1880
[498]	1881	// write child variables as attributes
[488]	1882
	1883
[1021]	1884	bool alreadyAddCellMethod = false;
	1885	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
	1886	if (!field->cell_methods.isEmpty())
	1887	{
[1158]	1888	StdString cellMethodString = field->cell_methods;
	1889	if (field->cell_methods_mode.isEmpty() \|\|
[1021]	1890	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
[1158]	1891	{
	1892	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
	1893	alreadyAddCellMethod = true;
	1894	}
	1895	else
	1896	{
	1897	switch (field->cell_methods_mode)
	1898	{
	1899	case (CField::cell_methods_mode_attr::prefix):
	1900	cellMethodsPrefix = cellMethodString;
	1901	cellMethodsPrefix += " ";
	1902	break;
	1903	case (CField::cell_methods_mode_attr::suffix):
	1904	cellMethodsSuffix = " ";
	1905	cellMethodsSuffix += cellMethodString;
	1906	break;
	1907	case (CField::cell_methods_mode_attr::none):
	1908	break;
	1909	default:
	1910	break;
	1911	}
	1912	}
[1021]	1913	}
[488]	1914
[1021]	1915
[498]	1916	if (wtime)
	1917	{
[614]	1918	CDuration freqOp = field->freq_op.getValue();
	1919	freqOp.solveTimeStep(*context->calendar);
	1920	StdString freqOpStr = freqOp.toStringUDUnits();
[612]	1921	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
[437]	1922
[614]	1923	CDuration freqOut = field->getRelFile()->output_freq.getValue();
	1924	freqOut.solveTimeStep(*context->calendar);
	1925	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
[612]	1926
[1021]	1927	StdString cellMethods(cellMethodsPrefix + "time: ");
[612]	1928	if (field->operation.getValue() == "instant") cellMethods += "point";
	1929	else if (field->operation.getValue() == "average") cellMethods += "mean";
	1930	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
	1931	else cellMethods += field->operation;
[614]	1932	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
	1933	cellMethods += " (interval: " + freqOpStr + ")";
[1021]	1934	cellMethods += cellMethodsSuffix;
	1935	if (!alreadyAddCellMethod)
	1936	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
[498]	1937	}
[488]	1938
[611]	1939	if (hasArea)
	1940	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
	1941
[498]	1942	if (!field->default_value.isEmpty())
	1943	{
[1424]	1944	double default_value = field->default_value.getValue();
	1945	if (type == NC_DOUBLE)
	1946	{
	1947	SuperClassWriter::setDefaultValue(fieldid, &default_value);
	1948	}
	1949	else if (type == NC_SHORT)
	1950	{
	1951	short sdefault_value = (short)default_value;
	1952	SuperClassWriter::setDefaultValue(fieldid, &sdefault_value);
	1953	}
	1954	else
	1955	{
	1956	float fdefault_value = (float)default_value;
	1957	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
	1958	}
[498]	1959	}
	1960	else
[517]	1961	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
[219]	1962
[606]	1963	if (field->compression_level.isEmpty())
[1872]	1964	field->compression_level = field->getRelFile()->compression_level.isEmpty() ? 0 : field->getRelFile()->compression_level;
[2577]	1965	if ( (field->compression_level.getValue()>0)&&(field->compression_type.isEmpty()) )
[2529]	1966	field->compression_type.setValue( "gzip" );
	1967	if (field->compression_type.isEmpty())
	1968	field->compression_type = "None";
	1969	if (field->compression_params.isEmpty())
	1970	field->compression_params.resize( 0 );
	1971	SuperClassWriter::setCompressionLevel(fieldid, field->compression_type, field->compression_level, field->compression_params);
[606]	1972
[878]	1973	{ // Ecriture des coordonnes
[488]	1974
[2629]	1975	StdString coordstr;
[498]	1976	std::vector<StdString>::iterator
	1977	itc = coodinates.begin(), endc = coodinates.end();
[488]	1978
[498]	1979	for (; itc!= endc; itc++)
	1980	{
	1981	StdString & coord = *itc;
	1982	if (itc+1 != endc)
	1983	coordstr.append(coord).append(" ");
	1984	else coordstr.append(coord);
	1985	}
[219]	1986
[498]	1987	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
[219]	1988
[498]	1989	}
[1222]	1990
	1991	vector<CVariable*> listVars = field->getAllVariables() ;
	1992	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
	1993
[219]	1994	}
[498]	1995	catch (CNetCdfException& e)
	1996	{
	1997	StdString msg("On writing field : ");
	1998	msg.append(fieldid); msg.append("\n");
	1999	msg.append("In the context : ");
	2000	msg.append(context->getId()); msg.append("\n");
	2001	msg.append(e.what());
	2002	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
	2003	}
[879]	2004	} // writeField_()
[219]	2005
	2006	//--------------------------------------------------------------
	2007
[347]	2008	void CNc4DataOutput::writeFile_ (CFile* file)
[219]	2009	{
[773]	2010	StdString filename = file->getFileOutputName();
[219]	2011	StdString description = (!file->description.isEmpty())
	2012	? file->description.getValue()
[335]	2013	: StdString("Created by xios");
[609]	2014
	2015	singleDomain = (file->nbDomains == 1);
	2016
[1158]	2017	StdString conv_str ;
	2018	if (file->convention_str.isEmpty())
	2019	{
	2020	if (SuperClassWriter::useCFConvention) conv_str="CF-1.6" ;
	2021	else conv_str="UGRID" ;
	2022	}
	2023	else conv_str=file->convention_str ;
	2024
[498]	2025	try
	2026	{
[1309]	2027	if (!appendMode) this->writeFileAttributes(filename, description,
	2028	conv_str,
	2029	StdString("An IPSL model"),
	2030	this->getTimeStamp());
[609]	2031
[701]	2032	if (!appendMode)
	2033	SuperClassWriter::addDimension("axis_nbounds", 2);
[498]	2034	}
	2035	catch (CNetCdfException& e)
	2036	{
	2037	StdString msg("On writing file : ");
	2038	msg.append(filename); msg.append("\n");
	2039	msg.append("In the context : ");
	2040	CContext* context = CContext::getCurrent() ;
	2041	msg.append(context->getId()); msg.append("\n");
	2042	msg.append(e.what());
	2043	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
	2044	}
[219]	2045	}
[488]	2046
[472]	2047	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
	2048	{
[773]	2049	StdString name = var->getVariableOutputName();
[488]	2050
[498]	2051	try
	2052	{
[527]	2053	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	2054	addAttribute(name, var->getData<int>(), &fieldId);
	2055	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	2056	addAttribute(name, var->getData<short int>(), &fieldId);
	2057	else if (var->type.getValue() == CVariable::type_attr::t_float)
	2058	addAttribute(name, var->getData<float>(), &fieldId);
	2059	else if (var->type.getValue() == CVariable::type_attr::t_double)
	2060	addAttribute(name, var->getData<double>(), &fieldId);
	2061	else if (var->type.getValue() == CVariable::type_attr::t_string)
	2062	addAttribute(name, var->getData<string>(), &fieldId);
	2063	else
	2064	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
	2065	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	2066	}
	2067	catch (CNetCdfException& e)
	2068	{
	2069	StdString msg("On writing attributes of variable with name : ");
	2070	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
	2071	msg.append("In the context : ");
	2072	CContext* context = CContext::getCurrent() ;
	2073	msg.append(context->getId()); msg.append("\n");
	2074	msg.append(e.what());
	2075	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
	2076	}
[472]	2077	}
[488]	2078
[472]	2079	void CNc4DataOutput::writeAttribute_ (CVariable* var)
	2080	{
[773]	2081	StdString name = var->getVariableOutputName();
	2082
[498]	2083	try
	2084	{
[527]	2085	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	2086	addAttribute(name, var->getData<int>());
	2087	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	2088	addAttribute(name, var->getData<short int>());
	2089	else if (var->type.getValue() == CVariable::type_attr::t_float)
	2090	addAttribute(name, var->getData<float>());
	2091	else if (var->type.getValue() == CVariable::type_attr::t_double)
	2092	addAttribute(name, var->getData<double>());
	2093	else if (var->type.getValue() == CVariable::type_attr::t_string)
	2094	addAttribute(name, var->getData<string>());
	2095	else
	2096	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
	2097	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	2098	}
	2099	catch (CNetCdfException& e)
	2100	{
	2101	StdString msg("On writing attributes of variable with name : ");
	2102	msg.append(name); msg.append("\n");
	2103	msg.append("In the context : ");
	2104	CContext* context = CContext::getCurrent() ;
	2105	msg.append(context->getId()); msg.append("\n");
	2106	msg.append(e.what());
	2107	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
	2108	}
[488]	2109	}
	2110
[321]	2111	void CNc4DataOutput::syncFile_ (void)
	2112	{
[498]	2113	try
	2114	{
	2115	SuperClassWriter::sync() ;
	2116	}
	2117	catch (CNetCdfException& e)
	2118	{
	2119	StdString msg("On synchronizing the write among processes");
	2120	msg.append("In the context : ");
	2121	CContext* context = CContext::getCurrent() ;
	2122	msg.append(context->getId()); msg.append("\n");
	2123	msg.append(e.what());
	2124	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	2125	}
[321]	2126	}
[219]	2127
[286]	2128	void CNc4DataOutput::closeFile_ (void)
	2129	{
[498]	2130	try
	2131	{
	2132	SuperClassWriter::close() ;
	2133	}
	2134	catch (CNetCdfException& e)
	2135	{
	2136	StdString msg("On closing file");
	2137	msg.append("In the context : ");
	2138	CContext* context = CContext::getCurrent() ;
	2139	msg.append(context->getId()); msg.append("\n");
	2140	msg.append(e.what());
	2141	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	2142	}
	2143
[286]	2144	}
	2145
[219]	2146	//---------------------------------------------------------------
	2147
	2148	StdString CNc4DataOutput::getTimeStamp(void) const
	2149	{
	2150	const int buffer_size = 100;
	2151	time_t rawtime;
	2152	struct tm * timeinfo = NULL;
	2153	char buffer [buffer_size];
[1158]	2154	StdString formatStr;
	2155	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
	2156	else formatStr=file->time_stamp_format;
[219]	2157
[1158]	2158	// time ( &rawtime );
	2159	// timeinfo = localtime ( &rawtime );
[219]	2160	time ( &rawtime );
[1158]	2161	timeinfo = gmtime ( &rawtime );
	2162	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
[219]	2163
	2164	return (StdString(buffer));
	2165	}
[488]	2166
[219]	2167	//---------------------------------------------------------------
[488]	2168
[1961]	2169	int CNc4DataOutput::writeFieldData_ (CField* field, const CArray<double,1>& data, const CDate& lastWrite,
	2170	const CDate& currentWrite, int nstep)
[219]	2171	{
[707]	2172	CContext* context = CContext::getCurrent();
[1869]	2173	CGrid* grid = field->getGrid();
[1961]	2174
	2175	if (nstep<1)
[1158]	2176	{
[1961]	2177	return nstep;
[1158]	2178	}
[952]	2179
[707]	2180	if (!grid->doGridHaveDataToWrite())
[1158]	2181	if (SuperClass::type == MULTI_FILE \|\| !isCollective)
	2182	{
[1961]	2183	return nstep;
[1158]	2184	}
[488]	2185
[770]	2186	StdString fieldid = field->getFieldOutputName();
[286]	2187
[707]	2188	StdOStringStream oss;
	2189	string timeAxisId;
[1158]	2190	if (field->hasTimeInstant) timeAxisId = "time_instant";
	2191	else if (field->hasTimeCentered) timeAxisId = "time_centered";
[488]	2192
[802]	2193	StdString timeBoundId = getTimeCounterName() + "_bounds";
[449]	2194
[707]	2195	StdString timeAxisBoundId;
[1158]	2196	if (field->hasTimeInstant) timeAxisBoundId = "time_instant_bounds";
	2197	else if (field->hasTimeCentered) timeAxisBoundId = "time_centered_bounds";
[488]	2198
[707]	2199	if (!field->wasWritten())
	2200	{
[1872]	2201	if (appendMode && field->getRelFile()->record_offset.isEmpty() &&
[1158]	2202	field->getOperationTimeType() != func::CFunctor::once)
[707]	2203	{
[1158]	2204	double factorUnit;
[1872]	2205	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
[1158]	2206	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
	2207	else factorUnit=1 ;
[1962]	2208	nstep = getRecordFromTime(currentWrite,factorUnit) + 1;
[707]	2209	}
[488]	2210
[707]	2211	field->setWritten();
	2212	}
[488]	2213
	2214
[707]	2215	CArray<double,1> time_data(1);
	2216	CArray<double,1> time_data_bound(2);
	2217	CArray<double,1> time_counter(1);
	2218	CArray<double,1> time_counter_bound(2);
	2219
	2220	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
[1158]	2221	bool wtimeCounter =false ;
	2222	bool wtimeData =false ;
	2223
[707]	2224
[444]	2225	if (wtime)
	2226	{
[1158]	2227
	2228	if (field->hasTimeInstant)
	2229	{
[2542]	2230	time_data(0) = time_data_bound(1) = (Time) currentWrite;
[1961]	2231	time_data_bound(0) = time_data_bound(1) = (Time) currentWrite;
[1158]	2232	if (timeCounterType==instant)
	2233	{
	2234	time_counter(0) = time_data(0);
	2235	time_counter_bound(0) = time_data_bound(0);
	2236	time_counter_bound(1) = time_data_bound(1);
	2237	wtimeCounter=true ;
	2238	}
	2239	if (hasTimeInstant) wtimeData=true ;
	2240	}
	2241	else if (field->hasTimeCentered)
[488]	2242	{
[1961]	2243	time_data(0) = ((Time)currentWrite + (Time)lastWrite) / 2;
	2244	time_data_bound(0) = (Time)lastWrite;
	2245	time_data_bound(1) = (Time)currentWrite;
[1158]	2246	if (timeCounterType==centered)
	2247	{
	2248	time_counter(0) = time_data(0) ;
	2249	time_counter_bound(0) = time_data_bound(0) ;
	2250	time_counter_bound(1) = time_data_bound(1) ;
	2251	wtimeCounter=true ;
	2252	}
	2253	if (hasTimeCentered) wtimeData=true ;
[488]	2254	}
	2255
[1158]	2256	if (timeCounterType==record)
	2257	{
[1961]	2258	time_counter(0) = nstep - 1;
	2259	time_counter_bound(0) = time_counter_bound(1) = nstep - 1;
[1158]	2260	wtimeCounter=true ;
	2261	}
[692]	2262
[1872]	2263	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days)
[692]	2264	{
[1158]	2265	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
	2266	time_data/=secByDay;
	2267	time_data_bound/=secByDay;
	2268	time_counter/=secByDay;
	2269	time_counter_bound/=secByDay;
[692]	2270	}
	2271	}
	2272
[1853]	2273	bool isRoot = (context->intraCommRank_ == 0);
[488]	2274
[498]	2275	try
[219]	2276	{
[567]	2277	switch (SuperClass::type)
[498]	2278	{
[567]	2279	case (MULTI_FILE) :
	2280	{
[2628]	2281	if (info.isActive(logProfile)) CTimer::get("Files : writing data").resume();
[2600]	2282	writeAndConvertData(field, data, nstep - 1);
[2628]	2283	if (info.isActive(logProfile)) CTimer::get("Files : writing data").suspend();
[567]	2284	if (wtime)
	2285	{
[2628]	2286	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").resume();
[1158]	2287	if ( wtimeData)
[692]	2288	{
[1961]	2289	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
	2290	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
[1158]	2291	}
	2292	if (wtimeCounter)
	2293	{
[1961]	2294	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
	2295	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
[692]	2296	}
[2628]	2297	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").suspend();
[567]	2298	}
[707]	2299	break;
[567]	2300	}
	2301	case (ONE_FILE) :
	2302	{
[464]	2303
[676]	2304	std::vector<StdSize> start, count;
[464]	2305
[676]	2306	if (field->getUseCompressedOutput())
	2307	{
[1957]	2308	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	2309	std::vector<StdString> domainList = grid->getDomainList();
	2310	std::vector<StdString> axisList = grid->getAxisList();
	2311	int numElement = axisDomainOrder.numElements();
	2312	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
	2313	int idx = domainList.size() * 2 + axisList.size() - 1;
	2314	int commRank ;
[464]	2315
[1957]	2316	MPI_Comm_rank(comm_file,&commRank) ;
[676]	2317
[1957]	2318	start.reserve(idx+1);
	2319	count.reserve(idx+1);
	2320
	2321	for (int i = numElement - 1; i >= 0; --i)
	2322	{
	2323	if (2 == axisDomainOrder(i))
[676]	2324	{
[1957]	2325	CDomain* domain = CDomain::get(domainList[idxDomain]);
	2326
	2327	if (domain->isCompressible())
[676]	2328	{
[1957]	2329	size_t offset ;
	2330	size_t nbIndexes = domain->getLocalView(CElementView::WORKFLOW)->getSize() ;
	2331	if (domain->isDistributed())
[676]	2332	{
[1957]	2333	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	2334	if (commRank==0) offset=0 ;
[676]	2335	}
[1957]	2336	else offset=0 ;
	2337
	2338	start.push_back(offset);
	2339	count.push_back(nbIndexes);
	2340	idx -= 2;
	2341	}
	2342	else
	2343	{
	2344	if ((domain->type) != CDomain::type_attr::unstructured)
[676]	2345	{
[2507]	2346	start.push_back(domain->jbeginValue_);
	2347	count.push_back(domain->njValue_);
[676]	2348	}
[1957]	2349	--idx;
[2507]	2350	start.push_back(domain->ibeginValue_);
	2351	count.push_back(domain->niValue_);
[1957]	2352	--idx;
[676]	2353	}
[1957]	2354	--idxDomain;
	2355	}
	2356	else if (1 == axisDomainOrder(i))
	2357	{
	2358	CAxis* axis = CAxis::get(axisList[idxAxis]);
	2359
	2360	if (axis->isCompressible())
[676]	2361	{
[1957]	2362	size_t offset ;
	2363	size_t nbIndexes = axis->getLocalView(CElementView::WORKFLOW)->getSize() ;
	2364	if (axis->isDistributed())
[676]	2365	{
[1957]	2366	MPI_Exscan(&nbIndexes, &offset, 1, MPI_SIZE_T, MPI_SUM, comm_file) ;
	2367	if (commRank==0) offset=0 ;
[676]	2368	}
[1957]	2369	else offset=0 ;
	2370
	2371	start.push_back(offset);
	2372	count.push_back(nbIndexes);
[676]	2373	}
[1957]	2374	else
	2375	{
	2376	start.push_back(axis->begin);
	2377	count.push_back(axis->n);
	2378	}
	2379	--idxAxis;
	2380	--idx;
[676]	2381	}
[1158]	2382	}
[1961]	2383	}
[676]	2384	else
[498]	2385	{
[887]	2386	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
[705]	2387	std::vector<StdString> domainList = grid->getDomainList();
	2388	std::vector<StdString> axisList = grid->getAxisList();
[2264]	2389	std::vector<StdString> scalarList = grid->getScalarList() ;
[705]	2390	int numElement = axisDomainOrder.numElements();
[2391]	2391	int idxDomain = domainList.size() - 1 ;
	2392	int idxAxis = axisList.size() - 1 ;
	2393	int idxScalar = scalarList.size() - 1 ;
[1553]	2394	int idx = domainList.size() * 2 + axisList.size() - 1;
[705]	2395
[1553]	2396	start.reserve(idx+1);
	2397	count.reserve(idx+1);
[705]	2398
	2399	for (int i = numElement - 1; i >= 0; --i)
	2400	{
[887]	2401	if (2 == axisDomainOrder(i))
[705]	2402	{
	2403	CDomain* domain = CDomain::get(domainList[idxDomain]);
[710]	2404	if ((domain->type) != CDomain::type_attr::unstructured)
[705]	2405	{
[2507]	2406	start.push_back(domain->jbeginValue_);
	2407	count.push_back(domain->njValue_);
[705]	2408	}
	2409	--idx ;
[1143]	2410
[2507]	2411	start.push_back(domain->ibeginValue_);
	2412	count.push_back(domain->niValue_);
[705]	2413	--idx ;
	2414	--idxDomain;
	2415	}
[887]	2416	else if (1 == axisDomainOrder(i))
[705]	2417	{
[1143]	2418	CAxis* axis = CAxis::get(axisList[idxAxis]);
[1559]	2419	start.push_back(axis->begin);
	2420	count.push_back(axis->n);
[705]	2421	--idx;
[1025]	2422	--idxAxis;
[887]	2423	}
	2424	else
	2425	{
[2391]	2426	if (idx ==-1)
[887]	2427	{
[2391]	2428	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
[887]	2429	start.push_back(0);
[2264]	2430	count.push_back(scalar->n);
[2391]	2431	idx-- ;
[887]	2432	}
[2391]	2433	else if (idx<-1)
	2434	{
	2435	CScalar* scalar = CScalar::get(scalarList[idxScalar]);
	2436	count.back()*=scalar->n;
	2437	idx-- ;
	2438	}
	2439	--idxScalar;
[887]	2440	}
[705]	2441	}
[498]	2442	}
[488]	2443
[1158]	2444
[2628]	2445	if (info.isActive(logProfile)) CTimer::get("Files : writing data").resume();
[2600]	2446	writeAndConvertData(field, data, nstep - 1, &start, &count);
[2628]	2447	if (info.isActive(logProfile)) CTimer::get("Files : writing data").suspend();
[1158]	2448
	2449	if (wtime)
	2450	{
[2628]	2451	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").resume();
[1158]	2452	if ( wtimeData)
[692]	2453	{
[1961]	2454	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, nstep - 1, isRoot);
	2455	SuperClassWriter::writeTimeAxisDataBounds(time_data_bound, timeAxisBoundId, isCollective, nstep - 1, isRoot);
[692]	2456	}
[1158]	2457	if (wtimeCounter)
	2458	{
[1961]	2459	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, nstep - 1,isRoot);
	2460	if (timeCounterType!=record) SuperClassWriter::writeTimeAxisDataBounds(time_counter_bound, timeBoundId, isCollective, nstep - 1, isRoot);
[586]	2461
[1158]	2462	}
[2628]	2463	if (info.isActive(logProfile)) CTimer::get("Files : writing time axis").suspend();
[1158]	2464	}
	2465
[586]	2466	break;
[286]	2467	}
[567]	2468	}
[1961]	2469	return nstep ;
[219]	2470	}
[498]	2471	catch (CNetCdfException& e)
	2472	{
	2473	StdString msg("On writing field data: ");
	2474	msg.append(fieldid); msg.append("\n");
	2475	msg.append("In the context : ");
	2476	msg.append(context->getId()); msg.append("\n");
	2477	msg.append(e.what());
[1130]	2478	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
[498]	2479	}
[219]	2480	}
	2481
[2600]	2482	void CNc4DataOutput::writeAndConvertData(CField* field, const CArray<double,1>& data, StdSize record, const std::vector<StdSize> start, const std::vector<StdSize> count)
	2483	{
	2484	StdString fieldid = field->getFieldOutputName();
	2485	nc_type type ;
	2486	if (field->prec.isEmpty()) type = NC_FLOAT ;
	2487	else
	2488	{
	2489	if (field->prec==2) type = NC_SHORT ;
	2490	else if (field->prec==4) type = NC_FLOAT ;
	2491	else if (field->prec==8) type = NC_DOUBLE ;
	2492	}
	2493
	2494	bool conversionByNetCDF = true; // default : conversion operated by NetCDF for now (legacy behaviour)
[2617]	2495	if (!field->conversion_by_netcdf.isEmpty())
[2600]	2496	{
[2617]	2497	// use conversion_by_netcdf = ".false." to bypass NetCDF conversion
[2600]	2498	// poor performances from NC_DOUBLE to NC_FLOAT with isgreater/isless in recent NetCDF available at TGCC
[2617]	2499	conversionByNetCDF = field->conversion_by_netcdf;
[2600]	2500	}
	2501	if ( ( type == NC_DOUBLE ) \|\| ( conversionByNetCDF ) )
	2502	{
	2503	SuperClassWriter::writeData(data, fieldid, isCollective, record, start, count);
	2504	}
	2505	else if ( type == NC_FLOAT )
	2506	{
	2507	CArray<float,1> f_data;
	2508	f_data.resize( data.numElements() );
	2509	for (int i = 0; i < data.numElements(); i++)
	2510	{
	2511	if (data(i) <= X_FLOAT_MAX \|\| data(i) >= X_FLOAT_MIN)
	2512	f_data(i) = data(i);
	2513	else if (data(i) > X_FLOAT_MAX)
	2514	f_data(i) = X_FLOAT_MAX;
	2515	else if (data(i) < X_FLOAT_MIN)
	2516	f_data(i) = X_FLOAT_MIN;
	2517	}
	2518	SuperClassWriter::writeData(f_data, fieldid, isCollective, record, start, count);
	2519	}
	2520	else if ( type == NC_SHORT )
	2521	{
	2522	CArray<short,1> s_data;
	2523	s_data.resize( data.numElements() );
	2524	for (int i = 0; i < data.numElements(); i++)
	2525	{
	2526	if (data(i) <= X_SHORT_MAX \|\| data(i) >= X_SHORT_MIN)
	2527	s_data(i) = data(i);
	2528	else if (data(i) > X_SHORT_MAX)
	2529	s_data(i) = X_SHORT_MAX;
	2530	else if (data(i) < X_SHORT_MIN)
	2531	s_data(i) = X_SHORT_MIN;
	2532	}
	2533	SuperClassWriter::writeData(s_data, fieldid, isCollective, record, start, count);
	2534	}
	2535	else
	2536	{
	2537	ERROR("CNc4DataOutput::writeAndConvertData(...)", << "Type conversion not managed for " << fieldid );
	2538	}
	2539
	2540	}
	2541
[219]	2542	//---------------------------------------------------------------
	2543
	2544	void CNc4DataOutput::writeTimeAxis_
[347]	2545	(CField* field,
[1542]	2546	const std::shared_ptr<CCalendar> cal)
[219]	2547	{
	2548	StdOStringStream oss;
[1158]	2549	bool createInstantAxis=false ;
	2550	bool createCenteredAxis=false ;
	2551	bool createTimeCounterAxis=false ;
	2552
[645]	2553	if (field->getOperationTimeType() == func::CFunctor::once) return ;
[488]	2554
	2555
[1158]	2556	StdString axisId ;
	2557	StdString axisBoundId;
[802]	2558	StdString timeid(getTimeCounterName());
[614]	2559	StdString timeBoundId("axis_nbounds");
[488]	2560
[1158]	2561	StdString strTimeUnits ;
[1872]	2562	if (!field->getRelFile()->time_units.isEmpty() && field->getRelFile()->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
[1158]	2563	else strTimeUnits="seconds since " ;
	2564
	2565	if (field->getOperationTimeType() == func::CFunctor::instant) field->hasTimeInstant = true;
	2566	if (field->getOperationTimeType() == func::CFunctor::centered) field->hasTimeCentered = true;
	2567
	2568
[1872]	2569	if (field->getRelFile()->time_counter.isEmpty())
[488]	2570	{
[1158]	2571	if (timeCounterType==none) createTimeCounterAxis=true ;
	2572	if (field->hasTimeCentered)
	2573	{
	2574	timeCounterType=centered ;
	2575	if (!hasTimeCentered) createCenteredAxis=true ;
	2576	}
	2577	if (field->hasTimeInstant)
	2578	{
	2579	if (timeCounterType==none) timeCounterType=instant ;
	2580	if (!hasTimeInstant) createInstantAxis=true ;
	2581	}
[488]	2582	}
[1872]	2583	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant)
[1158]	2584	{
	2585	if (field->hasTimeCentered)
	2586	{
	2587	if (!hasTimeCentered) createCenteredAxis=true ;
	2588	}
	2589	if (field->hasTimeInstant)
	2590	{
	2591	if (timeCounterType==none) createTimeCounterAxis=true ;
	2592	timeCounterType=instant ;
	2593	if (!hasTimeInstant) createInstantAxis=true ;
	2594	}
	2595	}
[1872]	2596	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered)
[1158]	2597	{
	2598	if (field->hasTimeCentered)
	2599	{
	2600	if (timeCounterType==none) createTimeCounterAxis=true ;
	2601	timeCounterType=centered ;
	2602	if (!hasTimeCentered) createCenteredAxis=true ;
	2603	}
	2604	if (field->hasTimeInstant)
	2605	{
	2606	if (!hasTimeInstant) createInstantAxis=true ;
	2607	}
	2608	}
[1872]	2609	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::instant_exclusive)
[1158]	2610	{
	2611	if (field->hasTimeCentered)
	2612	{
	2613	if (!hasTimeCentered) createCenteredAxis=true ;
	2614	}
	2615	if (field->hasTimeInstant)
	2616	{
	2617	if (timeCounterType==none) createTimeCounterAxis=true ;
	2618	timeCounterType=instant ;
	2619	}
	2620	}
[1872]	2621	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::centered_exclusive)
[1158]	2622	{
	2623	if (field->hasTimeCentered)
	2624	{
	2625	if (timeCounterType==none) createTimeCounterAxis=true ;
	2626	timeCounterType=centered ;
	2627	}
	2628	if (field->hasTimeInstant)
	2629	{
	2630	if (!hasTimeInstant) createInstantAxis=true ;
	2631	}
	2632	}
[1872]	2633	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::exclusive)
[1158]	2634	{
	2635	if (field->hasTimeCentered)
	2636	{
	2637	if (timeCounterType==none) createTimeCounterAxis=true ;
	2638	if (timeCounterType==instant) createInstantAxis=true ;
	2639	timeCounterType=centered ;
	2640	}
	2641	if (field->hasTimeInstant)
	2642	{
	2643	if (timeCounterType==none)
	2644	{
	2645	createTimeCounterAxis=true ;
	2646	timeCounterType=instant ;
	2647	}
	2648	if (timeCounterType==centered)
	2649	{
	2650	if (!hasTimeInstant) createInstantAxis=true ;
	2651	}
	2652	}
	2653	}
[1872]	2654	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::none)
[1158]	2655	{
	2656	if (field->hasTimeCentered)
	2657	{
	2658	if (!hasTimeCentered) createCenteredAxis=true ;
	2659	}
	2660	if (field->hasTimeInstant)
	2661	{
	2662	if (!hasTimeInstant) createInstantAxis=true ;
	2663	}
	2664	}
[1872]	2665	else if (field->getRelFile()->time_counter==CFile::time_counter_attr::record)
[1158]	2666	{
	2667	if (timeCounterType==none) createTimeCounterAxis=true ;
	2668	timeCounterType=record ;
	2669	if (field->hasTimeCentered)
	2670	{
	2671	if (!hasTimeCentered) createCenteredAxis=true ;
	2672	}
	2673	if (field->hasTimeInstant)
	2674	{
	2675	if (!hasTimeInstant) createInstantAxis=true ;
	2676	}
	2677	}
	2678
	2679	if (createInstantAxis)
	2680	{
	2681	axisId="time_instant" ;
	2682	axisBoundId="time_instant_bounds";
	2683	hasTimeInstant=true ;
	2684	}
[488]	2685
[1158]	2686	if (createCenteredAxis)
	2687	{
	2688	axisId="time_centered" ;
	2689	axisBoundId="time_centered_bounds";
	2690	hasTimeCentered=true ;
	2691	}
	2692
	2693
[498]	2694	try
[219]	2695	{
[1158]	2696	std::vector<StdString> dims;
	2697
	2698	if (createInstantAxis \|\| createCenteredAxis)
	2699	{
	2700	// Adding time_instant or time_centered
	2701	dims.push_back(timeid);
	2702	if (!SuperClassWriter::varExist(axisId))
	2703	{
	2704	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
[488]	2705
[1158]	2706	CDate timeOrigin=cal->getTimeOrigin() ;
	2707	StdOStringStream oss2;
	2708	StdString strInitdate=oss2.str() ;
	2709	StdString strTimeOrigin=timeOrigin.toString() ;
	2710	this->writeTimeAxisAttributes(axisId, cal->getType(),strTimeUnits+strTimeOrigin,
	2711	strTimeOrigin, axisBoundId);
	2712	}
[219]	2713
[1158]	2714	// Adding time_instant_bounds or time_centered_bounds variables
	2715	if (!SuperClassWriter::varExist(axisBoundId))
	2716	{
	2717	dims.clear() ;
	2718	dims.push_back(timeid);
	2719	dims.push_back(timeBoundId);
	2720	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2721	}
[498]	2722	}
[488]	2723
[1158]	2724	if (createTimeCounterAxis)
[498]	2725	{
[692]	2726	// Adding time_counter
[1158]	2727	axisId = getTimeCounterName();
[802]	2728	axisBoundId = getTimeCounterName() + "_bounds";
[692]	2729	dims.clear();
	2730	dims.push_back(timeid);
[1158]	2731	if (!SuperClassWriter::varExist(axisId))
[692]	2732	{
[1158]	2733	SuperClassWriter::addVariable(axisId, NC_DOUBLE, dims);
	2734	SuperClassWriter::addAttribute("axis", string("T"), &axisId);
[488]	2735
[1872]	2736	if (field->getRelFile()->time_counter.isEmpty() \|\|
	2737	(field->getRelFile()->time_counter != CFile::time_counter_attr::record))
[692]	2738	{
	2739	CDate timeOrigin = cal->getTimeOrigin();
	2740	StdString strTimeOrigin = timeOrigin.toString();
[498]	2741
[1158]	2742	this->writeTimeAxisAttributes(axisId, cal->getType(),
	2743	strTimeUnits+strTimeOrigin,
[692]	2744	strTimeOrigin, axisBoundId);
	2745	}
	2746	}
	2747
	2748	// Adding time_counter_bound dimension
[1872]	2749	if (field->getRelFile()->time_counter.isEmpty() \|\| (field->getRelFile()->time_counter != CFile::time_counter_attr::record))
[692]	2750	{
	2751	if (!SuperClassWriter::varExist(axisBoundId))
	2752	{
	2753	dims.clear();
	2754	dims.push_back(timeid);
	2755	dims.push_back(timeBoundId);
	2756	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2757	}
	2758	}
[498]	2759	}
[488]	2760	}
[498]	2761	catch (CNetCdfException& e)
[488]	2762	{
[498]	2763	StdString msg("On writing time axis data: ");
	2764	msg.append("In the context : ");
	2765	CContext* context = CContext::getCurrent() ;
	2766	msg.append(context->getId()); msg.append("\n");
	2767	msg.append(e.what());
	2768	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
[1542]	2769	const std::shared_ptr<CCalendar> cal)", << msg);
[488]	2770	}
[219]	2771	}
	2772
	2773	//---------------------------------------------------------------
[488]	2774
[219]	2775	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
	2776	const StdString & calendar,
	2777	const StdString & units,
	2778	const StdString & time_origin,
[488]	2779	const StdString & time_bounds,
[219]	2780	const StdString & standard_name,
[613]	2781	const StdString & long_name)
[219]	2782	{
[498]	2783	try
	2784	{
	2785	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2786	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
	2787	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
	2788	SuperClassWriter::addAttribute("units", units , &axis_name);
	2789	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
	2790	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
	2791	}
	2792	catch (CNetCdfException& e)
	2793	{
	2794	StdString msg("On writing time axis Attribute: ");
	2795	msg.append("In the context : ");
	2796	CContext* context = CContext::getCurrent() ;
	2797	msg.append(context->getId()); msg.append("\n");
	2798	msg.append(e.what());
	2799	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
[613]	2800	const StdString & calendar,\
	2801	const StdString & units, \
	2802	const StdString & time_origin, \
	2803	const StdString & time_bounds, \
	2804	const StdString & standard_name, \
	2805	const StdString & long_name)", << msg);
[498]	2806	}
[219]	2807	}
[488]	2808
[219]	2809	//---------------------------------------------------------------
	2810
	2811	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
	2812	const StdString & axis,
	2813	const StdString & standard_name,
	2814	const StdString & long_name,
	2815	const StdString & units,
	2816	const StdString & nav_model)
	2817	{
[498]	2818	try
	2819	{
[613]	2820	if (!axis.empty())
	2821	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
	2822
[498]	2823	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2824	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
	2825	SuperClassWriter::addAttribute("units" , units , &axis_name);
[973]	2826	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
[498]	2827	}
	2828	catch (CNetCdfException& e)
	2829	{
	2830	StdString msg("On writing Axis Attribute: ");
	2831	msg.append("In the context : ");
	2832	CContext* context = CContext::getCurrent() ;
	2833	msg.append(context->getId()); msg.append("\n");
	2834	msg.append(e.what());
	2835	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
[613]	2836	const StdString & axis, \
	2837	const StdString & standard_name, \
	2838	const StdString & long_name, \
	2839	const StdString & units, \
	2840	const StdString & nav_model)", << msg);
[498]	2841	}
[219]	2842	}
	2843
	2844	//---------------------------------------------------------------
[488]	2845
[219]	2846	void CNc4DataOutput::writeLocalAttributes
	2847	(int ibegin, int ni, int jbegin, int nj, StdString domid)
	2848	{
[498]	2849	try
	2850	{
[318]	2851	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
	2852	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
	2853	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
	2854	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
[498]	2855	}
	2856	catch (CNetCdfException& e)
	2857	{
	2858	StdString msg("On writing Local Attributes: ");
	2859	msg.append("In the context : ");
	2860	CContext* context = CContext::getCurrent() ;
	2861	msg.append(context->getId()); msg.append("\n");
	2862	msg.append(e.what());
	2863	ERROR("CNc4DataOutput::writeLocalAttributes \
	2864	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
	2865	}
	2866
[219]	2867	}
	2868
[628]	2869	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
	2870	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
[391]	2871	{
	2872	CArray<int,1> array(2) ;
	2873
[498]	2874	try
	2875	{
	2876	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
	2877	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
[629]	2878	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
[498]	2879	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
	2880	array=ni_glo,nj_glo ;
	2881	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
	2882	array=ni,nj ;
	2883	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
[819]	2884	array=ibegin+1,jbegin+1 ;
[498]	2885	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
[819]	2886	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
[498]	2887	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
	2888	array=0,0 ;
	2889	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
	2890	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
	2891	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
	2892	/*
	2893	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
	2894	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
	2895	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
	2896	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
	2897	*/
	2898	}
	2899	catch (CNetCdfException& e)
	2900	{
[628]	2901	StdString msg("On writing Local Attributes IOIPSL \n");
[498]	2902	msg.append("In the context : ");
	2903	CContext* context = CContext::getCurrent() ;
	2904	msg.append(context->getId()); msg.append("\n");
	2905	msg.append(e.what());
	2906	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
	2907	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
	2908	}
[391]	2909	}
[219]	2910	//---------------------------------------------------------------
	2911
	2912	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
	2913	const StdString & description,
	2914	const StdString & conventions,
	2915	const StdString & production,
	2916	const StdString & timeStamp)
	2917	{
[498]	2918	try
	2919	{
	2920	SuperClassWriter::addAttribute("name" , name);
	2921	SuperClassWriter::addAttribute("description", description);
[613]	2922	SuperClassWriter::addAttribute("title" , description);
	2923	SuperClassWriter::addAttribute("Conventions", conventions);
[1158]	2924	// SuperClassWriter::addAttribute("production" , production);
	2925
	2926	StdString timeStampStr ;
	2927	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
	2928	else timeStampStr=file->time_stamp_name ;
	2929	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
	2930
	2931	StdString uuidName ;
	2932	if (file->uuid_name.isEmpty()) uuidName="uuid" ;
	2933	else uuidName=file->uuid_name ;
	2934
	2935	if (file->uuid_format.isEmpty()) SuperClassWriter::addAttribute(uuidName, getUuidStr());
	2936	else SuperClassWriter::addAttribute(uuidName, getUuidStr(file->uuid_format));
	2937
[498]	2938	}
	2939	catch (CNetCdfException& e)
	2940	{
	2941	StdString msg("On writing File Attributes \n ");
	2942	msg.append("In the context : ");
	2943	CContext* context = CContext::getCurrent() ;
	2944	msg.append(context->getId()); msg.append("\n");
	2945	msg.append(e.what());
	2946	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
	2947	const StdString & description, \
	2948	const StdString & conventions, \
	2949	const StdString & production, \
	2950	const StdString & timeStamp)", << msg);
	2951	}
[219]	2952	}
	2953
	2954	//---------------------------------------------------------------
	2955
	2956	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
	2957	int data_dim,
	2958	int data_ni,
	2959	int data_nj,
	2960	int data_ibegin,
	2961	int data_jbegin)
	2962	{
[498]	2963	try
	2964	{
	2965	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
	2966	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
	2967	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
	2968	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
	2969	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
	2970	}
	2971	catch (CNetCdfException& e)
	2972	{
	2973	StdString msg("On writing Mask Attributes \n ");
	2974	msg.append("In the context : ");
	2975	CContext* context = CContext::getCurrent() ;
	2976	msg.append(context->getId()); msg.append("\n");
	2977	msg.append(e.what());
	2978	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
	2979	int data_dim, \
	2980	int data_ni, \
	2981	int data_nj, \
	2982	int data_ibegin, \
	2983	int data_jbegin)", << msg);
	2984	}
[219]	2985	}
	2986
	2987	///--------------------------------------------------------------
	2988
[1158]	2989	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
[707]	2990	{
	2991	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
	2992	if (it == timeToRecordCache.end())
	2993	{
[802]	2994	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
[1158]	2995	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_centered_bounds";
	2996	if (!SuperClassWriter::varExist(timeAxisBoundsId)) timeAxisBoundsId = "time_instant_bounds";
[707]	2997
	2998	CArray<double,2> timeAxisBounds;
[1158]	2999	std::vector<StdSize> dimSize(SuperClassWriter::getDimensions(timeAxisBoundsId)) ;
	3000
[707]	3001	StdSize record = 0;
	3002	double dtime(time);
[1158]	3003	for (int n = dimSize[0] - 1; n >= 0; n--)
[707]	3004	{
[1158]	3005	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective, n);
	3006	timeAxisBounds*=factorUnit ;
	3007	if (timeAxisBounds(1, 0) < dtime)
[707]	3008	{
	3009	record = n + 1;
	3010	break;
	3011	}
	3012	}
	3013	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
	3014	}
	3015	return it->second;
	3016	}
[774]	3017
	3018	///--------------------------------------------------------------
	3019
	3020	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
	3021	{
	3022	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
	3023	}
	3024
	3025	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
	3026	{
	3027	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
	3028	}
	3029
	3030	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
	3031	{
	3032	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
	3033	}
	3034
	3035	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
	3036	{
	3037	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
	3038	}
	3039
[887]	3040	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
	3041	{
	3042	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
	3043	}
	3044
[774]	3045	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
	3046	{
	3047	this->writtenDomains.insert(domainName);
	3048	}
	3049
	3050	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
	3051	{
	3052	this->writtenCompressedDomains.insert(domainName);
	3053	}
	3054
	3055	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
	3056	{
	3057	this->writtenAxis.insert(axisName);
	3058	}
	3059
	3060	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
	3061	{
	3062	this->writtenCompressedAxis.insert(axisName);
	3063	}
[887]	3064
	3065	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
	3066	{
	3067	this->writtenScalar.insert(scalarName);
	3068	}
[335]	3069	} // namespace xios

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

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