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nc4_data_output.cpp @ 930

Last change on this file since 930 was 929, checked in by oabramkina, 8 years ago

Mesh connectivity:

Fixing a bug for UGRID in case meshes containing cells with different number of vertexes.

Function for determining face neighbors of a local domain added.

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: 111.1 KB

Rev	Line
[219]	1	#include "nc4_data_output.hpp"
	2
	3	#include <boost/lexical_cast.hpp>
[352]	4	#include "attribute_template.hpp"
	5	#include "group_template.hpp"
[219]	6
	7	#include "file.hpp"
	8	#include "calendar.hpp"
[278]	9	#include "context.hpp"
[300]	10	#include "context_server.hpp"
[498]	11	#include "netCdfException.hpp"
	12	#include "exception.hpp"
[219]	13
[335]	14	namespace xios
[219]	15	{
[878]	16	/// ////////////////////// Dfinitions ////////////////////// ///
[219]	17	CNc4DataOutput::CNc4DataOutput
	18	(const StdString & filename, bool exist)
	19	: SuperClass()
	20	, SuperClassWriter(filename, exist)
	21	, filename(filename)
	22	{
[879]	23	SuperClass::type = MULTI_FILE;
[219]	24	}
	25
	26	CNc4DataOutput::CNc4DataOutput
[878]	27	(const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
[924]	28	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
[219]	29	: SuperClass()
[878]	30	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
[379]	31	, comm_file(comm_file)
[219]	32	, filename(filename)
[335]	33	, isCollective(isCollective)
[219]	34	{
[879]	35	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
[219]	36	}
	37
	38	CNc4DataOutput::~CNc4DataOutput(void)
[879]	39	{ /* Ne rien faire de plus */ }
[219]	40
	41	///--------------------------------------------------------------
	42
	43	const StdString & CNc4DataOutput::getFileName(void) const
	44	{
	45	return (this->filename);
	46	}
	47
	48	//---------------------------------------------------------------
	49
[347]	50	void CNc4DataOutput::writeDomain_(CDomain* domain)
[219]	51	{
[881]	52	if (domain->type == CDomain::type_attr::unstructured)
	53	{
	54	if (SuperClassWriter::useCFConvention)
	55	writeUnstructuredDomain(domain) ;
	56	else
	57	writeUnstructuredDomainUgrid(domain) ;
	58	return ;
	59	}
[488]	60
[347]	61	CContext* context = CContext::getCurrent() ;
[300]	62	CContextServer* server=context->server ;
[488]	63
[219]	64	if (domain->IsWritten(this->filename)) return;
	65	domain->checkAttributes();
[488]	66
	67	if (domain->isEmpty())
[881]	68	if (SuperClass::type==MULTI_FILE) return;
[219]	69
	70	std::vector<StdString> dim0, dim1;
[772]	71	StdString domid = domain->getDomainOutputName();
[318]	72	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
[706]	73	if (isWrittenDomain(domid)) return ;
[774]	74	else setWrittenDomain(domid);
[449]	75
	76
	77	StdString dimXid, dimYid ;
[488]	78
[664]	79	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
[449]	80	switch (domain->type)
[433]	81	{
[449]	82	case CDomain::type_attr::curvilinear :
	83	dimXid = StdString("x").append(appendDomid);
	84	dimYid = StdString("y").append(appendDomid);
	85	break ;
[664]	86	case CDomain::type_attr::rectilinear :
[449]	87	dimXid = StdString("lon").append(appendDomid);
	88	dimYid = StdString("lat").append(appendDomid);
	89	break;
[488]	90	}
	91
[617]	92	StdString dimVertId = StdString("nvertex").append(appendDomid);
	93
[449]	94	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	95	string areaId = "area" + appendDomid;
[391]	96	/*
[300]	97	StdString lonid_loc = (server->intraCommSize > 1)
[318]	98	? StdString("lon").append(appendDomid).append("_local")
[278]	99	: lonid;
[300]	100	StdString latid_loc = (server->intraCommSize > 1)
[318]	101	? StdString("lat").append(appendDomid).append("_local")
[278]	102	: latid;
[391]	103	*/
[219]	104
[498]	105	try
[219]	106	{
[498]	107	switch (SuperClass::type)
	108	{
	109	case (MULTI_FILE) :
	110	{
	111	// if (domain->isEmpty()) return;
[488]	112
[498]	113	if (server->intraCommSize > 1)
	114	{
	115	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
	116	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
	117	}
[286]	118
[498]	119	switch (domain->type)
	120	{
	121	case CDomain::type_attr::curvilinear :
	122	dim0.push_back(dimYid); dim0.push_back(dimXid);
	123	lonid = StdString("nav_lon").append(appendDomid);
	124	latid = StdString("nav_lat").append(appendDomid);
	125	break ;
[664]	126	case CDomain::type_attr::rectilinear :
[498]	127	lonid = StdString("lon").append(appendDomid);
	128	latid = StdString("lat").append(appendDomid);
	129	dim0.push_back(dimYid);
	130	dim1.push_back(dimXid);
	131	break;
	132	}
[488]	133
[617]	134	bounds_lonid = StdString("bounds_lon").append(appendDomid);
	135	bounds_latid = StdString("bounds_lat").append(appendDomid);
	136
[616]	137	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
	138	SuperClassWriter::addDimension(dimYid, domain->zoom_nj_srv);
[488]	139
[617]	140	if (domain->hasBounds)
	141	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	142
[498]	143	if (server->intraCommSize > 1)
	144	{
[616]	145	this->writeLocalAttributes(domain->zoom_ibegin_srv,
	146	domain->zoom_ni_srv,
	147	domain->zoom_jbegin_srv,
	148	domain->zoom_nj_srv,
	149	appendDomid);
[488]	150
[628]	151	if (singleDomain)
	152	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
	153	domain->zoom_ibegin_srv,
	154	domain->zoom_ni_srv,
	155	domain->zoom_jbegin_srv,
	156	domain->zoom_nj_srv,
	157	domain->ni_glo,domain->nj_glo,
	158	server->intraCommRank,server->intraCommSize);
[449]	159	}
[488]	160
[665]	161	if (domain->hasLonLat)
[498]	162	{
[665]	163	switch (domain->type)
	164	{
	165	case CDomain::type_attr::curvilinear :
	166	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
	167	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
	168	break ;
	169	case CDomain::type_attr::rectilinear :
	170	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
	171	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
	172	break ;
	173	}
[488]	174
[665]	175	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	176	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
[219]	177
[665]	178	if (domain->hasBounds)
	179	{
	180	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	181	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
[617]	182
[665]	183	dim0.clear();
	184	dim0.push_back(dimYid);
	185	dim0.push_back(dimXid);
	186	dim0.push_back(dimVertId);
	187	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
	188	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
	189	}
[617]	190	}
	191
[498]	192	dim0.clear();
[616]	193	dim0.push_back(dimYid);
[498]	194	dim0.push_back(dimXid);
[219]	195
	196
[498]	197	// supress mask if (server->intraCommSize > 1)
	198	// supress mask {
	199	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
	200	// supress mask
	201	// supress mask this->writeMaskAttributes(maskid,
	202	// supress mask domain->data_dim.getValue()/*,
	203	// supress mask domain->data_ni.getValue(),
	204	// supress mask domain->data_nj.getValue(),
	205	// supress mask domain->data_ibegin.getValue(),
	206	// supress mask domain->data_jbegin.getValue()*/);
	207	// supress mask }
[488]	208
[498]	209	//SuperClassWriter::setDefaultValue(maskid, &dvm);
[219]	210
[611]	211	if (domain->hasArea)
	212	{
	213	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
[614]	214	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	215	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	216	}
	217
[498]	218	SuperClassWriter::definition_end();
[449]	219
[665]	220	if (domain->hasLonLat)
[498]	221	{
[665]	222	switch (domain->type)
	223	{
	224	case CDomain::type_attr::curvilinear :
	225	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
	226	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
	227	break;
	228	case CDomain::type_attr::rectilinear :
	229	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
	230	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
	231	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
	232	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
	233	break;
	234	}
[611]	235
[665]	236	if (domain->hasBounds)
	237	{
	238	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
	239	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
	240	}
[617]	241	}
	242
[611]	243	if (domain->hasArea)
	244	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
	245
[498]	246	SuperClassWriter::definition_start();
[219]	247
[498]	248	break;
	249	}
	250	case (ONE_FILE) :
	251	{
[631]	252	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
	253	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
[286]	254
[617]	255	if (domain->hasBounds)
	256	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	257
[665]	258	if (domain->hasLonLat)
[498]	259	{
[665]	260	switch (domain->type)
	261	{
	262	case CDomain::type_attr::curvilinear :
	263	dim0.push_back(dimYid); dim0.push_back(dimXid);
	264	lonid = StdString("nav_lon").append(appendDomid);
	265	latid = StdString("nav_lat").append(appendDomid);
	266	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
	267	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
	268	break;
[449]	269
[665]	270	case CDomain::type_attr::rectilinear :
	271	dim0.push_back(dimYid);
	272	dim1.push_back(dimXid);
	273	lonid = StdString("lon").append(appendDomid);
	274	latid = StdString("lat").append(appendDomid);
	275	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
	276	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim1);
	277	break;
	278	}
	279
	280	bounds_lonid = StdString("bounds_lon").append(appendDomid);
	281	bounds_latid = StdString("bounds_lat").append(appendDomid);
	282
	283	this->writeAxisAttributes
	284	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
	285	this->writeAxisAttributes
	286	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
	287
	288	if (domain->hasBounds)
	289	{
	290	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
	291	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
	292
	293	dim0.clear();
[498]	294	dim0.push_back(dimYid);
[665]	295	dim0.push_back(dimXid);
	296	dim0.push_back(dimVertId);
	297	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
	298	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
	299	}
[498]	300	}
[611]	301
	302	if (domain->hasArea)
	303	{
	304	dim0.clear();
	305	dim0.push_back(dimYid); dim0.push_back(dimXid);
	306	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
[614]	307	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	308	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	309	dim0.clear();
	310	}
	311
	312	SuperClassWriter::definition_end();
[286]	313
[498]	314	switch (domain->type)
[384]	315	{
[498]	316	case CDomain::type_attr::curvilinear :
[449]	317	{
[498]	318	std::vector<StdSize> start(2) ;
	319	std::vector<StdSize> count(2) ;
	320	if (domain->isEmpty())
	321	{
[611]	322	start[0]=0 ; start[1]=0 ;
[498]	323	count[0]=0 ; count[1]=0 ;
	324	}
	325	else
	326	{
[631]	327	start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	328	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
[498]	329	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
	330	}
[488]	331
[665]	332	if (domain->hasLonLat)
	333	{
	334	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
	335	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
	336	}
[498]	337	break;
	338	}
[664]	339	case CDomain::type_attr::rectilinear :
[449]	340	{
[665]	341	if (domain->hasLonLat)
[498]	342	{
[665]	343	std::vector<StdSize> start(1) ;
	344	std::vector<StdSize> count(1) ;
	345	if (domain->isEmpty())
	346	{
	347	start[0]=0 ;
	348	count[0]=0 ;
	349	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
	350	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
[449]	351
[665]	352	}
	353	else
	354	{
	355	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
	356	count[0]=domain->zoom_nj_srv ;
	357	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
	358	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
	359
	360	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	361	count[0]=domain->zoom_ni_srv ;
	362	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
	363	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
	364	}
[498]	365	}
	366	break;
[449]	367	}
[384]	368	}
[611]	369
[617]	370	if (domain->hasBounds)
	371	{
	372	std::vector<StdSize> start(3);
	373	std::vector<StdSize> count(3);
	374	if (domain->isEmpty())
	375	{
	376	start[2] = start[1] = start[0] = 0;
	377	count[2] = count[1] = count[0] = 0;
	378	}
	379	else
	380	{
	381	start[2] = 0;
[631]	382	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
	383	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
[617]	384	count[2] = domain->nvertex;
	385	count[1] = domain->zoom_ni_srv;
	386	count[0] = domain->zoom_nj_srv;
	387	}
[625]	388
[878]	389	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0, &start, &count);
	390	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0, &start, &count);
[617]	391	}
	392
[611]	393	if (domain->hasArea)
	394	{
	395	std::vector<StdSize> start(2);
	396	std::vector<StdSize> count(2);
	397
	398	if (domain->isEmpty())
	399	{
	400	start[0] = 0; start[1] = 0;
	401	count[0] = 0; count[1] = 0;
	402	}
	403	else
	404	{
[631]	405	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
	406	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
[611]	407	count[1] = domain->zoom_ni_srv;
	408	count[0] = domain->zoom_nj_srv;
	409	}
	410
	411	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
	412	}
	413
[498]	414	SuperClassWriter::definition_start();
	415	break;
	416	}
	417	default :
	418	ERROR("CNc4DataOutput::writeDomain(domain)",
	419	<< "[ type = " << SuperClass::type << "]"
	420	<< " not implemented yet !");
	421	}
[449]	422	}
[498]	423	catch (CNetCdfException& e)
	424	{
	425	StdString msg("On writing the domain : ");
	426	msg.append(domid); msg.append("\n");
	427	msg.append("In the context : ");
	428	msg.append(context->getId()); msg.append("\n");
	429	msg.append(e.what());
	430	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
	431	}
	432
[449]	433	domain->addRelFile(this->filename);
	434	}
	435
[879]	436	//--------------------------------------------------------------
[878]	437
[879]	438	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
	439	{
	440	CContext* context = CContext::getCurrent() ;
	441	CContextServer* server=context->server ;
[878]	442
[879]	443	if (domain->IsWritten(this->filename)) return;
	444	domain->checkAttributes();
	445	if (domain->isEmpty())
	446	if (SuperClass::type==MULTI_FILE) return ;
[878]	447
[879]	448	std::vector<StdString> dim0;
	449	StdString domid = domain->getDomainOutputName();
	450	StdString domainName = domain->name;
[924]	451	domain->assignMesh(domainName, domain->nvertex);
	452	//domain->mesh->createMesh(domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
	453	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
[878]	454
[879]	455	StdString node_x = domainName + "_node_x";
	456	StdString node_y = domainName + "_node_y";
[878]	457
[879]	458	StdString edge_x = domainName + "_edge_x";
	459	StdString edge_y = domainName + "_edge_y";
	460	StdString edge_nodes = domainName + "_edge_nodes";
[878]	461
[879]	462	StdString face_x = domainName + "_face_x";
	463	StdString face_y = domainName + "_face_y";
	464	StdString face_nodes = domainName + "_face_nodes";
[902]	465	StdString face_edges = domainName + "_face_edges";
	466	StdString edge_faces = domainName + "_edge_face_links";
	467	StdString face_faces = domainName + "_face_links";
[878]	468
[879]	469	StdString dimNode = "n" + domainName + "_node";
	470	StdString dimEdge = "n" + domainName + "_edge";
	471	StdString dimFace = "n" + domainName + "_face";
	472	StdString dimVertex = "n" + domainName + "_vertex";
	473	StdString dimTwo = "Two";
[878]	474
[879]	475	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
	476	if (!isWrittenDomain(domid))
	477	{
	478	dim0.clear();
	479	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
	480	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
[924]	481	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
	482	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
[879]	483	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
	484	}
[878]	485
[879]	486	try
	487	{
	488	switch (SuperClass::type)
	489	{
	490	case (ONE_FILE) :
	491	{
	492	// Adding nodes
	493	if (domain->nvertex == 1)
	494	{
	495	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	496	{
[902]	497	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
[879]	498	dim0.clear();
	499	dim0.push_back(dimNode);
	500	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
	501	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	502	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	503	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
	504	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
	505	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	506	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	507	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	508	}
	509	} // domain->nvertex == 1
[878]	510
[879]	511	// Adding edges and nodes, if nodes have not been defined previously
	512	if (domain->nvertex == 2)
	513	{
	514	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	515	{
[924]	516	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	517	dim0.clear();
	518	dim0.push_back(dimNode);
	519	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
	520	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	521	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	522	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
	523	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
	524	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	525	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	526	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	527	}
[924]	528	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
	529	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	530	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
	531	dim0.clear();
	532	dim0.push_back(dimEdge);
	533	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
	534	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
	535	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
	536	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
	537	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
	538	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
	539	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
	540	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	541	dim0.clear();
	542	dim0.push_back(dimEdge);
	543	dim0.push_back(dimTwo);
	544	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
	545	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	546	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	547	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
[879]	548	} // domain->nvertex == 2
[878]	549
[879]	550	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
	551	if (domain->nvertex > 2)
	552	{
	553	// Nodes
	554	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
	555	{
[924]	556	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
[879]	557	dim0.clear();
	558	dim0.push_back(dimNode);
	559	SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
	560	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
[924]	561	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
[879]	562	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
	563	SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
	564	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
[924]	565	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
[879]	566	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
	567	}
	568	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
	569	{
	570	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
	571	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
[924]	572	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
[879]	573	dim0.clear();
	574	dim0.push_back(dimEdge);
	575	SuperClassWriter::addVariable(edge_x, NC_FLOAT, dim0);
	576	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
[924]	577	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
[879]	578	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
	579	SuperClassWriter::addVariable(edge_y, NC_FLOAT, dim0);
	580	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
[924]	581	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
[879]	582	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
	583	dim0.clear();
	584	dim0.push_back(dimEdge);
	585	dim0.push_back(dimTwo);
	586	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
	587	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
	588	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
	589	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
	590	}
[924]	591	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
	592	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
	593	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
	594	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
	595	dim0.clear();
	596	dim0.push_back(dimFace);
	597	SuperClassWriter::addVariable(face_x, NC_FLOAT, dim0);
	598	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
	599	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
	600	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
	601	SuperClassWriter::addVariable(face_y, NC_FLOAT, dim0);
	602	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
	603	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
	604	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
	605	dim0.clear();
	606	dim0.push_back(dimFace);
	607	dim0.push_back(dimVertex);
	608	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
	609	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
	610	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
	611	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
	612	dim0.clear();
	613	dim0.push_back(dimFace);
	614	dim0.push_back(dimVertex);
	615	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
	616	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
	617	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
	618	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
[929]	619	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
[924]	620	dim0.clear();
	621	dim0.push_back(dimEdge);
	622	dim0.push_back(dimTwo);
	623	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
	624	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
	625	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
	626	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
	627	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
	628	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
	629	dim0.clear();
	630	dim0.push_back(dimFace);
	631	dim0.push_back(dimVertex);
	632	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
	633	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
	634	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
	635	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
[929]	636	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
[924]	637	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
	638	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
[879]	639	} // domain->nvertex > 2
[878]	640
[879]	641	SuperClassWriter::definition_end();
[878]	642
[924]	643	std::vector<StdSize> startEdges(1) ;
	644	std::vector<StdSize> countEdges(1) ;
	645	std::vector<StdSize> startNodes(1) ;
	646	std::vector<StdSize> countNodes(1) ;
	647	std::vector<StdSize> startFaces(1) ;
	648	std::vector<StdSize> countFaces(1) ;
	649	std::vector<StdSize> startEdgeNodes(2) ;
	650	std::vector<StdSize> countEdgeNodes(2) ;
	651	std::vector<StdSize> startEdgeFaces(2) ;
	652	std::vector<StdSize> countEdgeFaces(2) ;
	653	std::vector<StdSize> startFaceConctv(2) ;
	654	std::vector<StdSize> countFaceConctv(2) ;
[902]	655
[879]	656	if (!isWrittenDomain(domid))
	657	{
	658	if (domain->nvertex == 1)
	659	{
[924]	660	if (domain->isEmpty())
	661	{
	662	startNodes[0]=0 ;
	663	countNodes[0]=0 ;
	664	}
	665	else
	666	{
	667	startNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	668	countNodes[0] = domain->zoom_ni_srv ;
	669	}
	670
	671	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	672	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
[879]	673	}
	674	else if (domain->nvertex == 2)
[924]	675	{
	676	if (domain->isEmpty())
	677	{
	678	startEdges[0]=0 ;
	679	countEdges[0]=0 ;
	680	startNodes[0]=0 ;
	681	countNodes[0]=0 ;
	682	startEdgeNodes[0]=0;
	683	startEdgeNodes[1]=0;
	684	countEdgeNodes[0]=0;
	685	countEdgeNodes[1]=0;
	686
	687	}
	688	else
	689	{
	690	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	691	countEdges[0] = domain->zoom_ni_srv ;
	692	startNodes[0] = domain->mesh->node_start;
	693	countNodes[0] = domain->mesh->node_count;
	694	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	695	startEdgeNodes[1] = 0;
	696	countEdgeNodes[0] = domain->zoom_ni_srv;
	697	countEdgeNodes[1]= 2;
	698	}
	699	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	700	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	701	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	702	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	703	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	704	}
[879]	705	else
	706	{
[924]	707	if (domain->isEmpty())
	708	{
	709	startFaces[0] = 0 ;
	710	countFaces[0] = 0 ;
	711	startNodes[0] = 0;
	712	countNodes[0] = 0;
	713	startEdges[0] = 0;
	714	countEdges[0] = 0;
	715	startEdgeFaces[0] = 0;
	716	startEdgeFaces[1] = 0;
	717	countEdgeFaces[0] = 0;
	718	countEdgeFaces[1] = 0;
	719	startFaceConctv[0] = 0;
	720	startFaceConctv[1] = 0;
	721	countFaceConctv[0] = 0;
	722	countFaceConctv[1] = 0;
	723	}
	724	else
	725	{
	726	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	727	countFaces[0] = domain->zoom_ni_srv ;
	728	startNodes[0] = domain->mesh->node_start;
	729	countNodes[0] = domain->mesh->node_count;
	730	startEdges[0] = domain->mesh->edge_start;
	731	countEdges[0] = domain->mesh->edge_count;
	732	startEdgeNodes[0] = domain->mesh->edge_start;
	733	startEdgeNodes[1] = 0;
	734	countEdgeNodes[0] = domain->mesh->edge_count;
	735	countEdgeNodes[1]= 2;
	736	startEdgeFaces[0] = domain->mesh->edge_start;
	737	startEdgeFaces[1]= 0;
	738	countEdgeFaces[0] = domain->mesh->edge_count;
	739	countEdgeFaces[1]= 2;
	740	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	741	startFaceConctv[1] = 0;
	742	countFaceConctv[0] = domain->zoom_ni_srv;
	743	countFaceConctv[1] = domain->nvertex;
	744	}
	745	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
	746	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
	747	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	748	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	749	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
	750	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
	751	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
	752	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
	753	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
	754	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
	755	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
[879]	756	}
	757	setWrittenDomain(domid);
	758	} // !isWrittenDomain
	759	else
	760	{
	761	if (domain->nvertex == 2)
	762	{
[924]	763	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	764	countEdges[0] = domain->zoom_ni_srv ;
	765	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	766	startEdgeNodes[1] = 0;
	767	countEdgeNodes[0] = domain->zoom_ni_srv;
	768	countEdgeNodes[1]= 2;
	769	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	770	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	771	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
[879]	772	}
	773	if (domain->nvertex > 2)
	774	{
[924]	775
[879]	776	if (!domain->mesh->edgesAreWritten)
	777	{
[924]	778	startEdges[0] = domain->mesh->edge_start;
	779	countEdges[0] = domain->mesh->edge_count;
	780	startEdgeNodes[0] = domain->mesh->edge_start;
	781	startEdgeNodes[1] = 0;
	782	countEdgeNodes[0] = domain->mesh->edge_count;
	783	countEdgeNodes[1]= 2;
	784	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
	785	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
	786	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
[879]	787	}
[924]	788	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	789	countFaces[0] = domain->zoom_ni_srv;
	790	startEdgeFaces[0] = domain->mesh->edge_start;
	791	startEdgeFaces[1]= 0;
	792	countEdgeFaces[0] = domain->mesh->edge_count;
	793	countEdgeFaces[1]= 2;
	794	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	795	startFaceConctv[1] = 0;
	796	countFaceConctv[0] = domain->zoom_ni_srv;
	797	countFaceConctv[1]= domain->nvertex;
	798	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
	799	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
	800	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
	801	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
	802	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
	803	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
[879]	804	}
	805	}// isWrittenDomain
[878]	806
[879]	807	SuperClassWriter::definition_start();
[878]	808
[879]	809	break;
	810	} // ONE_FILE
[878]	811
[879]	812	case (MULTI_FILE) :
	813	{
	814	break;
	815	}
[878]	816
[879]	817	default :
	818	ERROR("CNc4DataOutput::writeDomain(domain)",
	819	<< "[ type = " << SuperClass::type << "]"
	820	<< " not implemented yet !");
	821	} // switch
	822	} // try
[878]	823
[879]	824	catch (CNetCdfException& e)
	825	{
	826	StdString msg("On writing the domain : ");
	827	msg.append(domid); msg.append("\n");
	828	msg.append("In the context : ");
	829	msg.append(context->getId()); msg.append("\n");
	830	msg.append(e.what());
[924]	831	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
[879]	832	}
[878]	833
[879]	834	domain->addRelFile(this->filename);
	835	}
[878]	836
[879]	837	//--------------------------------------------------------------
[878]	838
[879]	839	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
[449]	840	{
	841	CContext* context = CContext::getCurrent() ;
	842	CContextServer* server=context->server ;
[488]	843
[449]	844	if (domain->IsWritten(this->filename)) return;
	845	domain->checkAttributes();
[488]	846
	847	if (domain->isEmpty())
[449]	848	if (SuperClass::type==MULTI_FILE) return ;
	849
	850	std::vector<StdString> dim0, dim1;
[772]	851	StdString domid = domain->getDomainOutputName();
[705]	852	if (isWrittenDomain(domid)) return ;
[774]	853	else setWrittenDomain(domid);
[705]	854
[449]	855	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
	856
	857	StdString dimXid = StdString("cell").append(appendDomid);
	858	StdString dimVertId = StdString("nvertex").append(appendDomid);
[488]	859
[449]	860	string lonid,latid,bounds_lonid,bounds_latid ;
[611]	861	string areaId = "area" + appendDomid;
[449]	862
[498]	863	try
[449]	864	{
[498]	865	switch (SuperClass::type)
	866	{
	867	case (MULTI_FILE) :
	868	{
	869	dim0.push_back(dimXid);
[657]	870	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
[488]	871
[665]	872	lonid = StdString("lon").append(appendDomid);
	873	latid = StdString("lat").append(appendDomid);
[498]	874	bounds_lonid = StdString("bounds_lon").append(appendDomid);
	875	bounds_latid = StdString("bounds_lat").append(appendDomid);
[665]	876	if (domain->hasLonLat)
	877	{
	878	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
	879	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
	880	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	881	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	882	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	883	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
	884	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	885	}
[498]	886	dim0.clear();
	887	if (domain->hasBounds)
	888	{
	889	dim0.push_back(dimXid);
	890	dim0.push_back(dimVertId);
	891	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
	892	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
	893	}
	894
	895	dim0.clear();
[449]	896	dim0.push_back(dimXid);
[611]	897	if (domain->hasArea)
	898	{
	899	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
[614]	900	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	901	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	902	}
	903
[498]	904	SuperClassWriter::definition_end();
[449]	905
[665]	906	if (domain->hasLonLat)
[498]	907	{
[665]	908	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
	909	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
	910	if (domain->hasBounds)
	911	{
	912	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
	913	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
	914	}
[498]	915	}
[611]	916
	917	if (domain->hasArea)
	918	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
	919
[498]	920	SuperClassWriter::definition_start();
	921	break ;
	922	}
[488]	923
[498]	924	case (ONE_FILE) :
	925	{
	926	lonid = StdString("lon").append(appendDomid);
	927	latid = StdString("lat").append(appendDomid);
	928	bounds_lonid = StdString("bounds_lon").append(appendDomid);
	929	bounds_latid = StdString("bounds_lat").append(appendDomid);
	930	dim0.push_back(dimXid);
[705]	931	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
[665]	932	if (domain->hasLonLat)
	933	{
	934	SuperClassWriter::addVariable(latid, NC_FLOAT, dim0);
	935	SuperClassWriter::addVariable(lonid, NC_FLOAT, dim0);
	936
	937	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
	938	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
	939	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
	940	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
	941	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
	942	}
[498]	943	dim0.clear();
[449]	944
[498]	945	if (domain->hasBounds)
	946	{
	947	dim0.push_back(dimXid);
	948	dim0.push_back(dimVertId);
	949	SuperClassWriter::addVariable(bounds_lonid, NC_FLOAT, dim0);
	950	SuperClassWriter::addVariable(bounds_latid, NC_FLOAT, dim0);
	951	}
[488]	952
[611]	953	if (domain->hasArea)
	954	{
	955	dim0.clear();
	956	dim0.push_back(dimXid);
	957	SuperClassWriter::addVariable(areaId, NC_FLOAT, dim0);
[614]	958	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
[611]	959	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
	960	}
	961
[498]	962	SuperClassWriter::definition_end();
[488]	963
[498]	964	std::vector<StdSize> start(1), startBounds(2) ;
	965	std::vector<StdSize> count(1), countBounds(2) ;
	966	if (domain->isEmpty())
	967	{
	968	start[0]=0 ;
	969	count[0]=0 ;
	970	startBounds[1]=0 ;
	971	countBounds[1]=domain->nvertex ;
	972	startBounds[0]=0 ;
	973	countBounds[0]=0 ;
	974	}
	975	else
	976	{
[705]	977	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
	978	count[0]=domain->zoom_ni_srv ;
	979	startBounds[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
[498]	980	startBounds[1]=0 ;
[705]	981	countBounds[0]=domain->zoom_ni_srv ;
[498]	982	countBounds[1]=domain->nvertex ;
	983	}
[665]	984
	985	if (domain->hasLonLat)
[498]	986	{
[665]	987	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
	988	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
	989	if (domain->hasBounds)
	990	{
	991	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
	992	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0,&startBounds,&countBounds);
	993	}
[498]	994	}
[488]	995
[611]	996	if (domain->hasArea)
	997	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
[488]	998
[498]	999	SuperClassWriter::definition_start();
[488]	1000
[498]	1001	break;
	1002	}
	1003	default :
	1004	ERROR("CNc4DataOutput::writeDomain(domain)",
	1005	<< "[ type = " << SuperClass::type << "]"
	1006	<< " not implemented yet !");
	1007	}
[219]	1008	}
[498]	1009	catch (CNetCdfException& e)
	1010	{
	1011	StdString msg("On writing the domain : ");
	1012	msg.append(domid); msg.append("\n");
	1013	msg.append("In the context : ");
	1014	msg.append(context->getId()); msg.append("\n");
	1015	msg.append(e.what());
	1016	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
	1017	}
[219]	1018	domain->addRelFile(this->filename);
	1019	}
	1020	//--------------------------------------------------------------
	1021
[347]	1022	void CNc4DataOutput::writeAxis_(CAxis* axis)
[219]	1023	{
[609]	1024	if (axis->IsWritten(this->filename)) return;
	1025	axis->checkAttributes();
	1026	int zoom_size_srv = axis->zoom_size_srv;
	1027	int zoom_begin_srv = axis->zoom_begin_srv;
[633]	1028	int zoom_size = (MULTI_FILE == SuperClass::type) ? zoom_size_srv
[821]	1029	: axis->global_zoom_n;
[633]	1030	int zoom_begin = (MULTI_FILE == SuperClass::type) ? zoom_begin_srv
[623]	1031	: axis->global_zoom_begin;
[488]	1032
[633]	1033	if ((0 == zoom_size_srv) && (MULTI_FILE == SuperClass::type)) return;
[498]	1034
[609]	1035	std::vector<StdString> dims;
[772]	1036	StdString axisid = axis->getAxisOutputName();
[705]	1037	if (isWrittenAxis(axisid)) return ;
[774]	1038	else setWrittenAxis(axisid);
[705]	1039
[609]	1040	try
	1041	{
	1042	SuperClassWriter::addDimension(axisid, zoom_size);
[816]	1043	if (axis->hasValue)
	1044	{
	1045	dims.push_back(axisid);
	1046	SuperClassWriter::addVariable(axisid, NC_FLOAT, dims);
[219]	1047
[816]	1048	if (!axis->name.isEmpty())
	1049	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
[219]	1050
[816]	1051	if (!axis->standard_name.isEmpty())
	1052	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
[540]	1053
[816]	1054	if (!axis->long_name.isEmpty())
	1055	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
[219]	1056
[816]	1057	if (!axis->unit.isEmpty())
	1058	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
[219]	1059
[816]	1060	if (!axis->positive.isEmpty())
	1061	{
	1062	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
	1063	SuperClassWriter::addAttribute("positive",
	1064	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
	1065	&axisid);
	1066	}
[399]	1067
[816]	1068	StdString axisBoundsId = axisid + "_bounds";
	1069	if (!axis->bounds.isEmpty())
	1070	{
	1071	dims.push_back("axis_nbounds");
	1072	SuperClassWriter::addVariable(axisBoundsId, NC_FLOAT, dims);
	1073	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
	1074	}
[488]	1075
[816]	1076	SuperClassWriter::definition_end();
	1077
	1078	switch (SuperClass::type)
[633]	1079	{
[816]	1080	case MULTI_FILE:
	1081	{
	1082	CArray<double,1> axis_value(zoom_size_srv);
	1083	for (int i = 0; i < zoom_size_srv; i++) axis_value(i) = axis->value_srv(i);
	1084	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
[633]	1085
[816]	1086	if (!axis->bounds.isEmpty())
	1087	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0);
[488]	1088
[816]	1089	SuperClassWriter::definition_start();
[219]	1090
[816]	1091	break;
	1092	}
	1093	case ONE_FILE:
	1094	{
	1095	CArray<double,1> axis_value(zoom_size_srv);
	1096	axis_value = axis->value_srv;
[498]	1097
[816]	1098	std::vector<StdSize> start(1), startBounds(2) ;
	1099	std::vector<StdSize> count(1), countBounds(2) ;
	1100	start[0] = startBounds[0] = zoom_begin_srv-axis->global_zoom_begin;
	1101	count[0] = countBounds[0] = zoom_size_srv;
	1102	startBounds[1] = 0;
	1103	countBounds[1] = 2;
	1104	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
[633]	1105
[816]	1106	if (!axis->bounds.isEmpty())
	1107	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
[609]	1108
[816]	1109	SuperClassWriter::definition_start();
[609]	1110
[816]	1111	break;
	1112	}
	1113	default :
	1114	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
	1115	<< "[ type = " << SuperClass::type << "]"
	1116	<< " not implemented yet !");
[609]	1117	}
	1118	}
	1119	}
	1120	catch (CNetCdfException& e)
	1121	{
	1122	StdString msg("On writing the axis : ");
	1123	msg.append(axisid); msg.append("\n");
	1124	msg.append("In the context : ");
	1125	CContext* context = CContext::getCurrent() ;
	1126	msg.append(context->getId()); msg.append("\n");
	1127	msg.append(e.what());
	1128	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
	1129	}
	1130	axis->addRelFile(this->filename);
[391]	1131	}
[488]	1132
[887]	1133	void CNc4DataOutput::writeScalar_(CScalar* scalar)
	1134	{
	1135	if (scalar->IsWritten(this->filename)) return;
	1136	scalar->checkAttributes();
	1137	int scalarSize = 1;
	1138
	1139	StdString scalaId = scalar->getScalarOutputName();
	1140	if (isWrittenAxis(scalaId)) return ;
	1141	else setWrittenAxis(scalaId);
	1142
	1143	try
	1144	{
	1145	if (!scalar->value.isEmpty())
	1146	{
	1147	// dims.push_back(scalaId);
	1148	std::vector<StdString> dims;
	1149	SuperClassWriter::addVariable(scalaId, NC_FLOAT, dims);
	1150
	1151	if (!scalar->name.isEmpty())
	1152	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
	1153
	1154	if (!scalar->standard_name.isEmpty())
	1155	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
	1156
	1157	if (!scalar->long_name.isEmpty())
	1158	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
	1159
	1160	if (!scalar->unit.isEmpty())
	1161	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
	1162
	1163	SuperClassWriter::definition_end();
	1164
	1165	switch (SuperClass::type)
	1166	{
	1167	case MULTI_FILE:
	1168	{
	1169	CArray<double,1> scalarValue(scalarSize);
	1170	scalarValue(0) = scalar->value;
	1171	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
	1172	SuperClassWriter::definition_start();
	1173
	1174	break;
	1175	}
	1176	case ONE_FILE:
	1177	{
	1178	CArray<double,1> scalarValue(scalarSize);
	1179	scalarValue(0) = scalar->value;
	1180
	1181	std::vector<StdSize> start(1);
	1182	std::vector<StdSize> count(1);
	1183	start[0] = 0;
	1184	count[0] = 1;
	1185	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
	1186	SuperClassWriter::definition_start();
	1187
	1188	break;
	1189	}
	1190	default :
	1191	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
	1192	<< "[ type = " << SuperClass::type << "]"
	1193	<< " not implemented yet !");
	1194	}
	1195	}
	1196	}
	1197	catch (CNetCdfException& e)
	1198	{
	1199	StdString msg("On writing the scalar : ");
	1200	msg.append(scalaId); msg.append("\n");
	1201	msg.append("In the context : ");
	1202	CContext* context = CContext::getCurrent() ;
	1203	msg.append(context->getId()); msg.append("\n");
	1204	msg.append(e.what());
	1205	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
	1206	}
	1207	scalar->addRelFile(this->filename);
	1208	}
	1209
[676]	1210	//--------------------------------------------------------------
	1211
	1212	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
	1213	{
	1214	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
	1215
	1216	try
	1217	{
[887]	1218	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
[676]	1219	std::vector<StdString> domainList = grid->getDomainList();
	1220	std::vector<StdString> axisList = grid->getAxisList();
[887]	1221	std::vector<StdString> scalarList = grid->getScalarList();
	1222	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
[676]	1223
	1224	std::vector<StdString> dims;
	1225
	1226	if (grid->isCompressible())
	1227	{
	1228	StdString varId = grid->getId() + "_points";
	1229
	1230	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
	1231	SuperClassWriter::addDimension(varId, nbIndexes);
	1232
	1233	dims.push_back(varId);
	1234	SuperClassWriter::addVariable(varId, NC_INT, dims);
	1235
	1236	StdOStringStream compress;
	1237	for (int i = numElement - 1; i >= 0; --i)
	1238	{
[887]	1239	if (2 == axisDomainOrder(i))
[676]	1240	{
	1241	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
[772]	1242	StdString domId = domain->getDomainOutputName();
[676]	1243	StdString appendDomId = singleDomain ? "" : "_" + domId;
	1244
	1245	switch (domain->type)
	1246	{
	1247	case CDomain::type_attr::curvilinear:
	1248	compress << "y" << appendDomId << " x" << appendDomId;
	1249	break;
	1250	case CDomain::type_attr::rectilinear:
	1251	compress << "lat" << appendDomId << " lon" << appendDomId;
	1252	break;
	1253	case CDomain::type_attr::unstructured:
	1254	compress << "cell" << appendDomId;
	1255	break;
	1256	}
	1257	++idxDomain;
	1258	}
[887]	1259	else if (1 == axisDomainOrder(i))
[676]	1260	{
	1261	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
[772]	1262	compress << axis->getAxisOutputName();
[676]	1263	++idxAxis;
	1264	}
[887]	1265	else
	1266	{
	1267	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
	1268	compress << scalar->getScalarOutputName();
	1269	++idxScalar;
	1270	}
[676]	1271
	1272	if (i != 0) compress << ' ';
	1273	}
	1274	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
	1275
	1276	grid->computeCompressedIndex();
	1277
	1278	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
	1279	std::map<int, CArray<size_t, 1> >::const_iterator it;
	1280	for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
	1281	{
	1282	const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
	1283	for (int i = 0; i < it->second.numElements(); i++)
	1284	indexes(compressedIndexes(i)) = it->second(i);
	1285	}
	1286
	1287	switch (SuperClass::type)
	1288	{
	1289	case (MULTI_FILE):
	1290	{
	1291	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
	1292	break;
	1293	}
	1294	case (ONE_FILE):
	1295	{
	1296	if (grid->doGridHaveDataDistributed())
	1297	grid->getDistributionServer()->computeGlobalIndex(indexes);
	1298
	1299	std::vector<StdSize> start, count;
	1300	start.push_back(grid->getOffsetWrittenIndexes());
	1301	count.push_back(grid->getNumberWrittenIndexes());
	1302
	1303	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
	1304	break;
	1305	}
	1306	}
	1307	}
	1308	else
	1309	{
	1310	for (int i = 0; i < numElement; ++i)
	1311	{
	1312	StdString varId, compress;
	1313	CArray<int, 1> indexes;
	1314	bool isDistributed;
	1315	StdSize nbIndexes, totalNbIndexes, offset;
	1316	int firstGlobalIndex;
	1317
[887]	1318	if (2 == axisDomainOrder(i))
[676]	1319	{
	1320	CDomain* domain = CDomain::get(domainList[idxDomain]);
[774]	1321	StdString domId = domain->getDomainOutputName();
	1322
[676]	1323	if (!domain->isCompressible()
	1324	\|\| domain->type == CDomain::type_attr::unstructured
[774]	1325	\|\| domain->isWrittenCompressed(this->filename)
	1326	\|\| isWrittenCompressedDomain(domId))
[676]	1327	continue;
	1328
	1329	StdString appendDomId = singleDomain ? "" : "_" + domId;
	1330
	1331	varId = domId + "_points";
	1332	switch (domain->type)
	1333	{
	1334	case CDomain::type_attr::curvilinear:
	1335	compress = "y" + appendDomId + " x" + appendDomId;
	1336	break;
	1337	case CDomain::type_attr::rectilinear:
	1338	compress = "lat" + appendDomId + " lon" + appendDomId;
	1339	break;
	1340	}
	1341
	1342	const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
	1343	indexes.resize(indexesToWrite.size());
	1344	for (int n = 0; n < indexes.numElements(); ++n)
	1345	indexes(n) = indexesToWrite[n];
	1346
	1347	isDistributed = domain->isDistributed();
	1348	nbIndexes = domain->getNumberWrittenIndexes();
	1349	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
	1350	offset = domain->getOffsetWrittenIndexes();
	1351	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
	1352
	1353	domain->addRelFileCompressed(this->filename);
[774]	1354	setWrittenCompressedDomain(domId);
[676]	1355	++idxDomain;
	1356	}
[887]	1357	else if (1 == axisDomainOrder(i))
[676]	1358	{
	1359	CAxis* axis = CAxis::get(axisList[idxAxis]);
[774]	1360	StdString axisId = axis->getAxisOutputName();
	1361
	1362	if (!axis->isCompressible()
	1363	\|\| axis->isWrittenCompressed(this->filename)
	1364	\|\| isWrittenCompressedAxis(axisId))
[676]	1365	continue;
	1366
	1367	varId = axisId + "_points";
	1368	compress = axisId;
	1369
	1370	const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
	1371	indexes.resize(indexesToWrite.size());
	1372	for (int n = 0; n < indexes.numElements(); ++n)
	1373	indexes(n) = indexesToWrite[n];
	1374
	1375	isDistributed = axis->isDistributed();
	1376	nbIndexes = axis->getNumberWrittenIndexes();
	1377	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
	1378	offset = axis->getOffsetWrittenIndexes();
	1379	firstGlobalIndex = axis->begin;
	1380
	1381	axis->addRelFileCompressed(this->filename);
[774]	1382	setWrittenCompressedAxis(axisId);
[676]	1383	++idxAxis;
	1384	}
[887]	1385	else
	1386	{
	1387	}
[676]	1388
	1389	if (!varId.empty())
	1390	{
	1391	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
	1392
	1393	dims.clear();
	1394	dims.push_back(varId);
	1395	SuperClassWriter::addVariable(varId, NC_INT, dims);
	1396
	1397	SuperClassWriter::addAttribute("compress", compress, &varId);
	1398
	1399	switch (SuperClass::type)
	1400	{
	1401	case (MULTI_FILE):
	1402	{
	1403	indexes -= firstGlobalIndex;
	1404	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
	1405	break;
	1406	}
	1407	case (ONE_FILE):
	1408	{
	1409	std::vector<StdSize> start, count;
	1410	start.push_back(offset);
	1411	count.push_back(nbIndexes);
	1412
	1413	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
	1414	break;
	1415	}
	1416	}
	1417	}
	1418	}
	1419
	1420	if (!dims.empty())
	1421	grid->computeCompressedIndex();
	1422	}
	1423
	1424	grid->addRelFileCompressed(this->filename);
	1425	}
	1426	catch (CNetCdfException& e)
	1427	{
	1428	StdString msg("On writing compressed grid : ");
	1429	msg.append(grid->getId()); msg.append("\n");
	1430	msg.append("In the context : ");
	1431	CContext* context = CContext::getCurrent();
	1432	msg.append(context->getId()); msg.append("\n");
	1433	msg.append(e.what());
	1434	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
	1435	}
	1436	}
	1437
	1438	//--------------------------------------------------------------
	1439
[391]	1440	void CNc4DataOutput::writeTimeDimension_(void)
	1441	{
[498]	1442	try
	1443	{
[802]	1444	SuperClassWriter::addDimension(getTimeCounterName());
[498]	1445	}
	1446	catch (CNetCdfException& e)
	1447	{
[614]	1448	StdString msg("On writing time dimension : time_couter\n");
[498]	1449	msg.append("In the context : ");
	1450	CContext* context = CContext::getCurrent() ;
	1451	msg.append(context->getId()); msg.append("\n");
	1452	msg.append(e.what());
	1453	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
	1454	}
[391]	1455	}
[676]	1456
[219]	1457	//--------------------------------------------------------------
	1458
[347]	1459	void CNc4DataOutput::writeField_(CField* field)
[219]	1460	{
[347]	1461	CContext* context = CContext::getCurrent() ;
[300]	1462	CContextServer* server=context->server ;
	1463
[219]	1464	std::vector<StdString> dims, coodinates;
[347]	1465	CGrid* grid = field->grid;
[567]	1466	if (!grid->doGridHaveDataToWrite())
	1467	if (SuperClass::type==MULTI_FILE) return ;
[488]	1468
[887]	1469	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
	1470	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
[567]	1471	std::vector<StdString> domainList = grid->getDomainList();
	1472	std::vector<StdString> axisList = grid->getAxisList();
[887]	1473	std::vector<StdString> scalarList = grid->getScalarList();
[219]	1474
[802]	1475	StdString timeid = getTimeCounterName();
[567]	1476	StdString dimXid,dimYid;
	1477	std::deque<StdString> dimIdList, dimCoordList;
[611]	1478	bool hasArea = false;
	1479	StdString cellMeasures = "area:";
[676]	1480	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
[488]	1481
[567]	1482	for (int i = 0; i < numElement; ++i)
[434]	1483	{
[887]	1484	if (2 == axisDomainOrder(i))
[567]	1485	{
	1486	CDomain* domain = CDomain::get(domainList[idxDomain]);
[772]	1487	StdString domId = domain->getDomainOutputName();
[676]	1488	StdString appendDomId = singleDomain ? "" : "_" + domId ;
	1489
	1490	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
	1491	{
	1492	dimIdList.push_back(domId + "_points");
	1493	field->setUseCompressedOutput();
	1494	}
	1495
[567]	1496	switch (domain->type)
	1497	{
[676]	1498	case CDomain::type_attr::curvilinear:
	1499	if (!compressedOutput \|\| !domain->isCompressible())
	1500	{
	1501	dimXid = StdString("x").append(appendDomId);
	1502	dimIdList.push_back(dimXid);
	1503	dimYid = StdString("y").append(appendDomId);
	1504	dimIdList.push_back(dimYid);
	1505	}
	1506	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
	1507	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
[567]	1508	break ;
[676]	1509	case CDomain::type_attr::rectilinear:
	1510	if (!compressedOutput \|\| !domain->isCompressible())
	1511	{
	1512	dimXid = StdString("lon").append(appendDomId);
	1513	dimIdList.push_back(dimXid);
	1514	dimYid = StdString("lat").append(appendDomId);
	1515	dimIdList.push_back(dimYid);
	1516	}
[567]	1517	break ;
[676]	1518	case CDomain::type_attr::unstructured:
[878]	1519	{
[879]	1520	if (SuperClassWriter::useCFConvention)
	1521	{
	1522	dimXid = StdString("cell").append(appendDomId);
	1523	dimIdList.push_back(dimXid);
	1524	dimCoordList.push_back(StdString("lon").append(appendDomId));
	1525	dimCoordList.push_back(StdString("lat").append(appendDomId));
	1526	}
	1527	else
	1528	{
	1529	StdString domainName = domain->name;
	1530	if (domain->nvertex == 1)
	1531	{
	1532	dimXid = "n" + domainName + "_node";
	1533	dimIdList.push_back(dimXid);
	1534	dimCoordList.push_back(StdString(domainName + "_node_x"));
	1535	dimCoordList.push_back(StdString(domainName + "_node_y"));
	1536	}
	1537	else if (domain->nvertex == 2)
	1538	{
	1539	dimXid = "n" + domainName + "_edge";
	1540	dimIdList.push_back(dimXid);
	1541	dimCoordList.push_back(StdString(domainName + "_edge_x"));
	1542	dimCoordList.push_back(StdString(domainName + "_edge_y"));
	1543	}
	1544	else
	1545	{
	1546	dimXid = "n" + domainName + "_face";
	1547	dimIdList.push_back(dimXid);
	1548	dimCoordList.push_back(StdString(domainName + "_face_x"));
	1549	dimCoordList.push_back(StdString(domainName + "_face_y"));
	1550	}
	1551	} // ugrid convention
	1552	} // case unstructured domain
[676]	1553	}
[878]	1554
[676]	1555	if (domain->hasArea)
	1556	{
	1557	hasArea = true;
	1558	cellMeasures += " area" + appendDomId;
	1559	}
	1560	++idxDomain;
[567]	1561	}
[887]	1562	else if (1 == axisDomainOrder(i))
[567]	1563	{
	1564	CAxis* axis = CAxis::get(axisList[idxAxis]);
[772]	1565	StdString axisId = axis->getAxisOutputName();
[676]	1566
	1567	if (compressedOutput && axis->isCompressible())
	1568	{
	1569	dimIdList.push_back(axisId + "_points");
	1570	field->setUseCompressedOutput();
	1571	}
	1572	else
	1573	dimIdList.push_back(axisId);
	1574
	1575	dimCoordList.push_back(axisId);
	1576	++idxAxis;
[567]	1577	}
[887]	1578	else // scalar
	1579	{
	1580	/* Do nothing here */
	1581	}
[567]	1582	}
[488]	1583
	1584	/*
[300]	1585	StdString lonid_loc = (server->intraCommSize > 1)
[318]	1586	? StdString("lon").append(appendDomid).append("_local")
[278]	1587	: lonid;
[300]	1588	StdString latid_loc = (server->intraCommSize > 1)
[318]	1589	? StdString("lat").append(appendDomid).append("_local")
[278]	1590	: latid;
[391]	1591	*/
[770]	1592	StdString fieldid = field->getFieldOutputName();
[219]	1593
[464]	1594	nc_type type ;
	1595	if (field->prec.isEmpty()) type = NC_FLOAT ;
	1596	else
	1597	{
	1598	if (field->prec==2) type = NC_SHORT ;
	1599	else if (field->prec==4) type = NC_FLOAT ;
[488]	1600	else if (field->prec==8) type = NC_DOUBLE ;
[464]	1601	}
[488]	1602
[645]	1603	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
[488]	1604
[219]	1605	if (wtime)
	1606	{
[488]	1607
[449]	1608	//StdOStringStream oss;
	1609	// oss << "time_" << field->operation.getValue()
	1610	// << "_" << field->getRelFile()->output_freq.getValue();
[488]	1611	//oss
[645]	1612	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
	1613	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
[219]	1614	dims.push_back(timeid);
	1615	}
	1616
[676]	1617	if (compressedOutput && grid->isCompressible())
[219]	1618	{
[676]	1619	dims.push_back(grid->getId() + "_points");
	1620	field->setUseCompressedOutput();
[219]	1621	}
[676]	1622	else
	1623	{
	1624	while (!dimIdList.empty())
	1625	{
	1626	dims.push_back(dimIdList.back());
	1627	dimIdList.pop_back();
	1628	}
	1629	}
[219]	1630
[567]	1631	while (!dimCoordList.empty())
[219]	1632	{
[567]	1633	coodinates.push_back(dimCoordList.back());
	1634	dimCoordList.pop_back();
[219]	1635	}
	1636
[498]	1637	try
	1638	{
	1639	SuperClassWriter::addVariable(fieldid, type, dims);
[488]	1640
[498]	1641	if (!field->standard_name.isEmpty())
	1642	SuperClassWriter::addAttribute
	1643	("standard_name", field->standard_name.getValue(), &fieldid);
[219]	1644
[498]	1645	if (!field->long_name.isEmpty())
	1646	SuperClassWriter::addAttribute
	1647	("long_name", field->long_name.getValue(), &fieldid);
[219]	1648
[498]	1649	if (!field->unit.isEmpty())
	1650	SuperClassWriter::addAttribute
	1651	("units", field->unit.getValue(), &fieldid);
[463]	1652
[498]	1653	if (!field->valid_min.isEmpty())
	1654	SuperClassWriter::addAttribute
	1655	("valid_min", field->valid_min.getValue(), &fieldid);
[463]	1656
[498]	1657	if (!field->valid_max.isEmpty())
	1658	SuperClassWriter::addAttribute
	1659	("valid_max", field->valid_max.getValue(), &fieldid);
[464]	1660
[498]	1661	if (!field->scale_factor.isEmpty())
	1662	SuperClassWriter::addAttribute
	1663	("scale_factor", field->scale_factor.getValue(), &fieldid);
[464]	1664
[498]	1665	if (!field->add_offset.isEmpty())
	1666	SuperClassWriter::addAttribute
	1667	("add_offset", field->add_offset.getValue(), &fieldid);
[488]	1668
[498]	1669	SuperClassWriter::addAttribute
	1670	("online_operation", field->operation.getValue(), &fieldid);
[472]	1671
[498]	1672	// write child variables as attributes
[488]	1673
	1674
[498]	1675	vector<CVariable*> listVars = field->getAllVariables() ;
	1676	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
[472]	1677
[488]	1678
[498]	1679	if (wtime)
	1680	{
[614]	1681	CDuration freqOp = field->freq_op.getValue();
	1682	freqOp.solveTimeStep(*context->calendar);
	1683	StdString freqOpStr = freqOp.toStringUDUnits();
[612]	1684	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
[437]	1685
[614]	1686	CDuration freqOut = field->getRelFile()->output_freq.getValue();
	1687	freqOut.solveTimeStep(*context->calendar);
	1688	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
[612]	1689
[618]	1690	StdString cellMethods = "time: ";
[612]	1691	if (field->operation.getValue() == "instant") cellMethods += "point";
	1692	else if (field->operation.getValue() == "average") cellMethods += "mean";
	1693	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
	1694	else cellMethods += field->operation;
[614]	1695	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
	1696	cellMethods += " (interval: " + freqOpStr + ")";
[612]	1697	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
[498]	1698	}
[488]	1699
[611]	1700	if (hasArea)
	1701	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
	1702
[498]	1703	if (!field->default_value.isEmpty())
	1704	{
	1705	double default_value = field->default_value.getValue();
	1706	float fdefault_value = (float)default_value;
	1707	if (type == NC_DOUBLE)
	1708	SuperClassWriter::setDefaultValue(fieldid, &default_value);
	1709	else
	1710	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
	1711	}
	1712	else
[517]	1713	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
[219]	1714
[606]	1715	if (field->compression_level.isEmpty())
	1716	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
	1717	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
	1718
[878]	1719	{ // Ecriture des coordonnes
[488]	1720
[498]	1721	StdString coordstr; //boost::algorithm::join(coodinates, " ")
	1722	std::vector<StdString>::iterator
	1723	itc = coodinates.begin(), endc = coodinates.end();
[488]	1724
[498]	1725	for (; itc!= endc; itc++)
	1726	{
	1727	StdString & coord = *itc;
	1728	if (itc+1 != endc)
	1729	coordstr.append(coord).append(" ");
	1730	else coordstr.append(coord);
	1731	}
[219]	1732
[498]	1733	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
[219]	1734
[498]	1735	}
[219]	1736	}
[498]	1737	catch (CNetCdfException& e)
	1738	{
	1739	StdString msg("On writing field : ");
	1740	msg.append(fieldid); msg.append("\n");
	1741	msg.append("In the context : ");
	1742	msg.append(context->getId()); msg.append("\n");
	1743	msg.append(e.what());
	1744	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
	1745	}
[879]	1746	} // writeField_()
[219]	1747
	1748	//--------------------------------------------------------------
	1749
[347]	1750	void CNc4DataOutput::writeFile_ (CFile* file)
[219]	1751	{
[773]	1752	StdString filename = file->getFileOutputName();
[219]	1753	StdString description = (!file->description.isEmpty())
	1754	? file->description.getValue()
[335]	1755	: StdString("Created by xios");
[609]	1756
	1757	singleDomain = (file->nbDomains == 1);
	1758
[498]	1759	try
	1760	{
[879]	1761	if (SuperClassWriter::useCFConvention)
[878]	1762	this->writeFileAttributes(filename, description,
	1763	StdString("CF-1.5"),
	1764	StdString("An IPSL model"),
	1765	this->getTimeStamp());
	1766	else
	1767	this->writeFileAttributes(filename, description,
	1768	StdString("UGRID"),
	1769	StdString("An IPSL model"),
	1770	this->getTimeStamp());
[609]	1771
[878]	1772
[701]	1773	if (!appendMode)
	1774	SuperClassWriter::addDimension("axis_nbounds", 2);
[498]	1775	}
	1776	catch (CNetCdfException& e)
	1777	{
	1778	StdString msg("On writing file : ");
	1779	msg.append(filename); msg.append("\n");
	1780	msg.append("In the context : ");
	1781	CContext* context = CContext::getCurrent() ;
	1782	msg.append(context->getId()); msg.append("\n");
	1783	msg.append(e.what());
	1784	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
	1785	}
[219]	1786	}
[488]	1787
[472]	1788	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
	1789	{
[773]	1790	StdString name = var->getVariableOutputName();
[488]	1791
[498]	1792	try
	1793	{
[527]	1794	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	1795	addAttribute(name, var->getData<int>(), &fieldId);
	1796	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	1797	addAttribute(name, var->getData<short int>(), &fieldId);
	1798	else if (var->type.getValue() == CVariable::type_attr::t_float)
	1799	addAttribute(name, var->getData<float>(), &fieldId);
	1800	else if (var->type.getValue() == CVariable::type_attr::t_double)
	1801	addAttribute(name, var->getData<double>(), &fieldId);
	1802	else if (var->type.getValue() == CVariable::type_attr::t_string)
	1803	addAttribute(name, var->getData<string>(), &fieldId);
	1804	else
	1805	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
	1806	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	1807	}
	1808	catch (CNetCdfException& e)
	1809	{
	1810	StdString msg("On writing attributes of variable with name : ");
	1811	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
	1812	msg.append("In the context : ");
	1813	CContext* context = CContext::getCurrent() ;
	1814	msg.append(context->getId()); msg.append("\n");
	1815	msg.append(e.what());
	1816	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
	1817	}
[472]	1818	}
[488]	1819
[472]	1820	void CNc4DataOutput::writeAttribute_ (CVariable* var)
	1821	{
[773]	1822	StdString name = var->getVariableOutputName();
	1823
[498]	1824	try
	1825	{
[527]	1826	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
	1827	addAttribute(name, var->getData<int>());
	1828	else if (var->type.getValue() == CVariable::type_attr::t_int16)
	1829	addAttribute(name, var->getData<short int>());
	1830	else if (var->type.getValue() == CVariable::type_attr::t_float)
	1831	addAttribute(name, var->getData<float>());
	1832	else if (var->type.getValue() == CVariable::type_attr::t_double)
	1833	addAttribute(name, var->getData<double>());
	1834	else if (var->type.getValue() == CVariable::type_attr::t_string)
	1835	addAttribute(name, var->getData<string>());
	1836	else
	1837	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
	1838	<< "Unsupported variable of type " << var->type.getStringValue());
[498]	1839	}
	1840	catch (CNetCdfException& e)
	1841	{
	1842	StdString msg("On writing attributes of variable with name : ");
	1843	msg.append(name); msg.append("\n");
	1844	msg.append("In the context : ");
	1845	CContext* context = CContext::getCurrent() ;
	1846	msg.append(context->getId()); msg.append("\n");
	1847	msg.append(e.what());
	1848	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
	1849	}
[488]	1850	}
	1851
[321]	1852	void CNc4DataOutput::syncFile_ (void)
	1853	{
[498]	1854	try
	1855	{
	1856	SuperClassWriter::sync() ;
	1857	}
	1858	catch (CNetCdfException& e)
	1859	{
	1860	StdString msg("On synchronizing the write among processes");
	1861	msg.append("In the context : ");
	1862	CContext* context = CContext::getCurrent() ;
	1863	msg.append(context->getId()); msg.append("\n");
	1864	msg.append(e.what());
	1865	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	1866	}
[321]	1867	}
[219]	1868
[286]	1869	void CNc4DataOutput::closeFile_ (void)
	1870	{
[498]	1871	try
	1872	{
	1873	SuperClassWriter::close() ;
	1874	}
	1875	catch (CNetCdfException& e)
	1876	{
	1877	StdString msg("On closing file");
	1878	msg.append("In the context : ");
	1879	CContext* context = CContext::getCurrent() ;
	1880	msg.append(context->getId()); msg.append("\n");
	1881	msg.append(e.what());
	1882	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
	1883	}
	1884
[286]	1885	}
	1886
[219]	1887	//---------------------------------------------------------------
	1888
	1889	StdString CNc4DataOutput::getTimeStamp(void) const
	1890	{
	1891	const int buffer_size = 100;
	1892	time_t rawtime;
	1893	struct tm * timeinfo = NULL;
	1894	char buffer [buffer_size];
	1895
	1896	time ( &rawtime );
	1897	timeinfo = localtime ( &rawtime );
	1898	strftime (buffer, buffer_size, "%Y-%b-%d %H:%M:%S %Z", timeinfo);
	1899
	1900	return (StdString(buffer));
	1901	}
[488]	1902
[219]	1903	//---------------------------------------------------------------
[488]	1904
[347]	1905	void CNc4DataOutput::writeFieldData_ (CField* field)
[219]	1906	{
[707]	1907	CContext* context = CContext::getCurrent();
	1908	CContextServer* server = context->server;
	1909	CGrid* grid = field->grid;
[300]	1910
[707]	1911	if (!grid->doGridHaveDataToWrite())
	1912	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
[488]	1913
[770]	1914	StdString fieldid = field->getFieldOutputName();
[286]	1915
[707]	1916	StdOStringStream oss;
	1917	string timeAxisId;
	1918	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
	1919	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
[488]	1920
[802]	1921	StdString timeBoundId = getTimeCounterName() + "_bounds";
[449]	1922
[707]	1923	StdString timeAxisBoundId;
	1924	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
	1925	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
[488]	1926
[707]	1927	if (!field->wasWritten())
	1928	{
[757]	1929	if (appendMode && field->file->record_offset.isEmpty())
[707]	1930	{
	1931	field->resetNStep(getRecordFromTime(field->last_Write_srv) + 1);
	1932	}
[488]	1933
[707]	1934	field->setWritten();
	1935	}
[488]	1936
	1937
[707]	1938	CArray<double,1> time_data(1);
	1939	CArray<double,1> time_data_bound(2);
	1940	CArray<double,1> time_counter(1);
	1941	CArray<double,1> time_counter_bound(2);
	1942
	1943	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
	1944
[444]	1945	if (wtime)
	1946	{
[692]	1947	Time lastWrite = field->last_Write_srv;
	1948	Time lastLastWrite = field->lastlast_Write_srv;
	1949
[645]	1950	if (field->getOperationTimeType() == func::CFunctor::instant)
[692]	1951	time_data(0) = lastWrite;
	1952	else if (field->getOperationTimeType() == func::CFunctor::centered)
	1953	time_data(0) = (lastWrite + lastLastWrite) / 2;
[488]	1954
[645]	1955	if (field->getOperationTimeType() == func::CFunctor::instant)
[692]	1956	time_data_bound(0) = time_data_bound(1) = lastWrite;
[645]	1957	else if (field->getOperationTimeType() == func::CFunctor::centered)
[488]	1958	{
[692]	1959	time_data_bound(0) = lastLastWrite;
	1960	time_data_bound(1) = lastWrite;
[488]	1961	}
	1962
[692]	1963	if (field->file->time_counter == CFile::time_counter_attr::instant)
	1964	time_counter(0) = lastWrite;
	1965	else if (field->file->time_counter == CFile::time_counter_attr::centered)
	1966	time_counter(0) = (lastWrite + lastLastWrite) / 2;
	1967	else if (field->file->time_counter == CFile::time_counter_attr::record)
	1968	time_counter(0) = field->getNStep() - 1;
	1969
	1970
	1971	if (field->file->time_counter == CFile::time_counter_attr::instant)
	1972	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
	1973	else if (field->file->time_counter == CFile::time_counter_attr::centered)
	1974	{
	1975	time_counter_bound(0) = lastLastWrite;
	1976	time_counter_bound(1) = lastWrite;
	1977	}
	1978	else if (field->file->time_counter == CFile::time_counter_attr::record)
	1979	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
	1980	}
	1981
[707]	1982	bool isRoot = (server->intraCommRank == 0);
[488]	1983
[464]	1984	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
	1985	{
[707]	1986	double scaleFactor = 1.0;
	1987	double addOffset = 0.0;
	1988	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
	1989	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
	1990	field->scaleFactorAddOffset(scaleFactor, addOffset);
[464]	1991	}
[488]	1992
[498]	1993	try
[219]	1994	{
[676]	1995	size_t writtenSize;
	1996	if (field->getUseCompressedOutput())
	1997	writtenSize = grid->getNumberWrittenIndexes();
	1998	else
	1999	writtenSize = grid->getWrittenDataSize();
	2000
	2001	CArray<double,1> fieldData(writtenSize);
[567]	2002	if (!field->default_value.isEmpty()) fieldData = field->default_value;
[676]	2003
	2004	if (field->getUseCompressedOutput())
	2005	field->outputCompressedField(fieldData);
	2006	else
	2007	field->outputField(fieldData);
	2008
[707]	2009	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
[567]	2010
	2011	switch (SuperClass::type)
[498]	2012	{
[567]	2013	case (MULTI_FILE) :
	2014	{
[692]	2015	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
[567]	2016	if (wtime)
	2017	{
[692]	2018	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
	2019	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
	2020	if (field->file->time_counter != CFile::time_counter_attr::none)
	2021	{
[802]	2022	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
[692]	2023	if (field->file->time_counter != CFile::time_counter_attr::record)
	2024	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
	2025	}
[567]	2026	}
[707]	2027	break;
[567]	2028	}
	2029	case (ONE_FILE) :
	2030	{
[676]	2031	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
	2032	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
	2033	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
[464]	2034
[676]	2035	std::vector<StdSize> start, count;
[464]	2036
[676]	2037	if (field->getUseCompressedOutput())
	2038	{
	2039	if (grid->isCompressible())
	2040	{
	2041	start.push_back(grid->getOffsetWrittenIndexes());
	2042	count.push_back(grid->getNumberWrittenIndexes());
	2043	}
	2044	else
	2045	{
[887]	2046	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
[676]	2047	std::vector<StdString> domainList = grid->getDomainList();
	2048	std::vector<StdString> axisList = grid->getAxisList();
	2049	int numElement = axisDomainOrder.numElements();
	2050	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
	2051	int idx = nZoomBeginGlobal.size() - 1;
[464]	2052
[676]	2053	start.reserve(nZoomBeginGlobal.size());
	2054	count.reserve(nZoomBeginGlobal.size());
	2055
	2056
	2057	for (int i = numElement - 1; i >= 0; --i)
	2058	{
[887]	2059	if (2 == axisDomainOrder(i))
[676]	2060	{
	2061	CDomain* domain = CDomain::get(domainList[idxDomain]);
	2062
	2063	if (domain->isCompressible())
	2064	{
	2065	start.push_back(domain->getOffsetWrittenIndexes());
	2066	count.push_back(domain->getNumberWrittenIndexes());
[710]	2067	idx -= 2;
[676]	2068	}
	2069	else
	2070	{
[710]	2071	if ((domain->type) != CDomain::type_attr::unstructured)
	2072	{
	2073	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
	2074	count.push_back(nZoomSizeServer[idx]);
	2075	}
	2076	--idx;
[676]	2077	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
	2078	count.push_back(nZoomSizeServer[idx]);
[710]	2079	--idx;
[676]	2080	}
	2081	--idxDomain;
	2082	}
[887]	2083	else if (1 == axisDomainOrder(i))
[676]	2084	{
	2085	CAxis* axis = CAxis::get(axisList[idxAxis]);
	2086
	2087	if (axis->isCompressible())
	2088	{
	2089	start.push_back(axis->getOffsetWrittenIndexes());
	2090	count.push_back(axis->getNumberWrittenIndexes());
	2091	}
	2092	else
	2093	{
	2094	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
	2095	count.push_back(nZoomSizeServer[idx]);
	2096	}
	2097
	2098	--idxAxis;
	2099	--idx;
	2100	}
	2101	}
	2102	}
	2103	}
	2104	else
[498]	2105	{
[705]	2106
[887]	2107	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
[705]	2108	std::vector<StdString> domainList = grid->getDomainList();
	2109	std::vector<StdString> axisList = grid->getAxisList();
	2110	int numElement = axisDomainOrder.numElements();
	2111	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
	2112	int idx = nZoomBeginGlobal.size() - 1;
	2113
	2114	start.reserve(nZoomBeginGlobal.size());
	2115	count.reserve(nZoomBeginGlobal.size());
	2116
	2117	for (int i = numElement - 1; i >= 0; --i)
	2118	{
[887]	2119	if (2 == axisDomainOrder(i))
[705]	2120	{
	2121	CDomain* domain = CDomain::get(domainList[idxDomain]);
[710]	2122	if ((domain->type) != CDomain::type_attr::unstructured)
[705]	2123	{
	2124	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
	2125	count.push_back(nZoomSizeServer[idx]);
	2126	}
	2127	--idx ;
	2128	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
	2129	count.push_back(nZoomSizeServer[idx]);
	2130	--idx ;
	2131	--idxDomain;
	2132	}
[887]	2133	else if (1 == axisDomainOrder(i))
[705]	2134	{
	2135	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
	2136	count.push_back(nZoomSizeServer[idx]);
	2137	--idx;
[887]	2138	}
	2139	else
	2140	{
	2141	if (1 == axisDomainOrder.numElements())
	2142	{
	2143	start.push_back(0);
	2144	count.push_back(1);
	2145	}
	2146	--idx;
	2147	}
[705]	2148	}
[498]	2149	}
[488]	2150
[676]	2151	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
[586]	2152	if (wtime)
	2153	{
[692]	2154	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
	2155	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
	2156	if (field->file->time_counter != CFile::time_counter_attr::none)
	2157	{
[802]	2158	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
[692]	2159	if (field->file->time_counter != CFile::time_counter_attr::record)
	2160	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
	2161	}
[586]	2162	}
	2163
	2164	break;
[286]	2165	}
[567]	2166	}
[219]	2167	}
[498]	2168	catch (CNetCdfException& e)
	2169	{
	2170	StdString msg("On writing field data: ");
	2171	msg.append(fieldid); msg.append("\n");
	2172	msg.append("In the context : ");
	2173	msg.append(context->getId()); msg.append("\n");
	2174	msg.append(e.what());
	2175	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
	2176	}
[219]	2177	}
	2178
	2179	//---------------------------------------------------------------
	2180
	2181	void CNc4DataOutput::writeTimeAxis_
[347]	2182	(CField* field,
[343]	2183	const boost::shared_ptr<CCalendar> cal)
[219]	2184	{
	2185	StdOStringStream oss;
[488]	2186
[645]	2187	if (field->getOperationTimeType() == func::CFunctor::once) return ;
[488]	2188
[449]	2189	// oss << "time_" << field->operation.getValue()
	2190	// << "_" << field->getRelFile()->output_freq.getValue();
[488]	2191
[449]	2192	// StdString axisid = oss.str();
[645]	2193	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
	2194	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
[219]	2195
[488]	2196	StdString axisid("time_centered") ;
	2197	StdString axisBoundId("time_centered_bounds");
[802]	2198	StdString timeid(getTimeCounterName());
[614]	2199	StdString timeBoundId("axis_nbounds");
[488]	2200
[645]	2201	if (field->getOperationTimeType() == func::CFunctor::instant)
[488]	2202	{
	2203	axisid = "time_instant";
	2204	axisBoundId = "time_instant_bounds";
	2205	}
	2206
[498]	2207	try
[219]	2208	{
[498]	2209	// Adding time_instant or time_centered
	2210	std::vector<StdString> dims;
	2211	dims.push_back(timeid);
	2212	if (!SuperClassWriter::varExist(axisid))
	2213	{
	2214	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
[488]	2215
[498]	2216	CDate timeOrigin=cal->getTimeOrigin() ;
	2217	StdOStringStream oss2;
	2218	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
	2219	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
	2220	StdString strInitdate=oss2.str() ;
	2221	StdString strTimeOrigin=timeOrigin.toString() ;
	2222	this->writeTimeAxisAttributes
	2223	(axisid, cal->getType(),
	2224	StdString("seconds since ").append(strTimeOrigin),
	2225	strTimeOrigin, axisBoundId);
	2226	}
[219]	2227
[498]	2228	// Adding time_instant_bounds or time_centered_bounds variables
	2229	if (!SuperClassWriter::varExist(axisBoundId))
	2230	{
	2231	dims.clear() ;
	2232	dims.push_back(timeid);
	2233	dims.push_back(timeBoundId);
	2234	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2235	}
[488]	2236
[692]	2237	if (field->file->time_counter != CFile::time_counter_attr::none)
[498]	2238	{
[692]	2239	// Adding time_counter
[802]	2240	axisid = getTimeCounterName();
	2241	axisBoundId = getTimeCounterName() + "_bounds";
[692]	2242	dims.clear();
	2243	dims.push_back(timeid);
	2244	if (!SuperClassWriter::varExist(axisid))
	2245	{
	2246	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
	2247	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
[488]	2248
[692]	2249	if (field->file->time_counter != CFile::time_counter_attr::record)
	2250	{
	2251	CDate timeOrigin = cal->getTimeOrigin();
	2252	StdString strTimeOrigin = timeOrigin.toString();
[498]	2253
[692]	2254	this->writeTimeAxisAttributes(axisid, cal->getType(),
	2255	StdString("seconds since ").append(strTimeOrigin),
	2256	strTimeOrigin, axisBoundId);
	2257	}
	2258	}
	2259
	2260	// Adding time_counter_bound dimension
	2261	if (field->file->time_counter != CFile::time_counter_attr::record)
	2262	{
	2263	if (!SuperClassWriter::varExist(axisBoundId))
	2264	{
	2265	dims.clear();
	2266	dims.push_back(timeid);
	2267	dims.push_back(timeBoundId);
	2268	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
	2269	}
	2270	}
[498]	2271	}
[488]	2272	}
[498]	2273	catch (CNetCdfException& e)
[488]	2274	{
[498]	2275	StdString msg("On writing time axis data: ");
	2276	msg.append("In the context : ");
	2277	CContext* context = CContext::getCurrent() ;
	2278	msg.append(context->getId()); msg.append("\n");
	2279	msg.append(e.what());
	2280	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
	2281	const boost::shared_ptr<CCalendar> cal)", << msg);
[488]	2282	}
[219]	2283	}
	2284
	2285	//---------------------------------------------------------------
[488]	2286
[219]	2287	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
	2288	const StdString & calendar,
	2289	const StdString & units,
	2290	const StdString & time_origin,
[488]	2291	const StdString & time_bounds,
[219]	2292	const StdString & standard_name,
[613]	2293	const StdString & long_name)
[219]	2294	{
[498]	2295	try
	2296	{
	2297	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2298	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
	2299	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
	2300	SuperClassWriter::addAttribute("units", units , &axis_name);
	2301	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
	2302	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
	2303	}
	2304	catch (CNetCdfException& e)
	2305	{
	2306	StdString msg("On writing time axis Attribute: ");
	2307	msg.append("In the context : ");
	2308	CContext* context = CContext::getCurrent() ;
	2309	msg.append(context->getId()); msg.append("\n");
	2310	msg.append(e.what());
	2311	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
[613]	2312	const StdString & calendar,\
	2313	const StdString & units, \
	2314	const StdString & time_origin, \
	2315	const StdString & time_bounds, \
	2316	const StdString & standard_name, \
	2317	const StdString & long_name)", << msg);
[498]	2318	}
[219]	2319	}
[488]	2320
[219]	2321	//---------------------------------------------------------------
	2322
	2323	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
	2324	const StdString & axis,
	2325	const StdString & standard_name,
	2326	const StdString & long_name,
	2327	const StdString & units,
	2328	const StdString & nav_model)
	2329	{
[498]	2330	try
	2331	{
[613]	2332	if (!axis.empty())
	2333	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
	2334
[498]	2335	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
	2336	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
	2337	SuperClassWriter::addAttribute("units" , units , &axis_name);
	2338	SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
	2339	}
	2340	catch (CNetCdfException& e)
	2341	{
	2342	StdString msg("On writing Axis Attribute: ");
	2343	msg.append("In the context : ");
	2344	CContext* context = CContext::getCurrent() ;
	2345	msg.append(context->getId()); msg.append("\n");
	2346	msg.append(e.what());
	2347	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
[613]	2348	const StdString & axis, \
	2349	const StdString & standard_name, \
	2350	const StdString & long_name, \
	2351	const StdString & units, \
	2352	const StdString & nav_model)", << msg);
[498]	2353	}
[219]	2354	}
	2355
	2356	//---------------------------------------------------------------
[488]	2357
[219]	2358	void CNc4DataOutput::writeLocalAttributes
	2359	(int ibegin, int ni, int jbegin, int nj, StdString domid)
	2360	{
[498]	2361	try
	2362	{
[318]	2363	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
	2364	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
	2365	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
	2366	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
[498]	2367	}
	2368	catch (CNetCdfException& e)
	2369	{
	2370	StdString msg("On writing Local Attributes: ");
	2371	msg.append("In the context : ");
	2372	CContext* context = CContext::getCurrent() ;
	2373	msg.append(context->getId()); msg.append("\n");
	2374	msg.append(e.what());
	2375	ERROR("CNc4DataOutput::writeLocalAttributes \
	2376	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
	2377	}
	2378
[219]	2379	}
	2380
[628]	2381	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
	2382	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
[391]	2383	{
	2384	CArray<int,1> array(2) ;
	2385
[498]	2386	try
	2387	{
	2388	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
	2389	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
[629]	2390	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
[498]	2391	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
	2392	array=ni_glo,nj_glo ;
	2393	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
	2394	array=ni,nj ;
	2395	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
[819]	2396	array=ibegin+1,jbegin+1 ;
[498]	2397	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
[819]	2398	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
[498]	2399	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
	2400	array=0,0 ;
	2401	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
	2402	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
	2403	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
	2404	/*
	2405	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
	2406	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
	2407	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
	2408	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
	2409	*/
	2410	}
	2411	catch (CNetCdfException& e)
	2412	{
[628]	2413	StdString msg("On writing Local Attributes IOIPSL \n");
[498]	2414	msg.append("In the context : ");
	2415	CContext* context = CContext::getCurrent() ;
	2416	msg.append(context->getId()); msg.append("\n");
	2417	msg.append(e.what());
	2418	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
	2419	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
	2420	}
[391]	2421	}
[219]	2422	//---------------------------------------------------------------
	2423
	2424	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
	2425	const StdString & description,
	2426	const StdString & conventions,
	2427	const StdString & production,
	2428	const StdString & timeStamp)
	2429	{
[498]	2430	try
	2431	{
	2432	SuperClassWriter::addAttribute("name" , name);
	2433	SuperClassWriter::addAttribute("description", description);
[613]	2434	SuperClassWriter::addAttribute("title" , description);
	2435	SuperClassWriter::addAttribute("Conventions", conventions);
[498]	2436	SuperClassWriter::addAttribute("production" , production);
	2437	SuperClassWriter::addAttribute("timeStamp" , timeStamp);
	2438	}
	2439	catch (CNetCdfException& e)
	2440	{
	2441	StdString msg("On writing File Attributes \n ");
	2442	msg.append("In the context : ");
	2443	CContext* context = CContext::getCurrent() ;
	2444	msg.append(context->getId()); msg.append("\n");
	2445	msg.append(e.what());
	2446	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
	2447	const StdString & description, \
	2448	const StdString & conventions, \
	2449	const StdString & production, \
	2450	const StdString & timeStamp)", << msg);
	2451	}
[219]	2452	}
	2453
	2454	//---------------------------------------------------------------
	2455
	2456	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
	2457	int data_dim,
	2458	int data_ni,
	2459	int data_nj,
	2460	int data_ibegin,
	2461	int data_jbegin)
	2462	{
[498]	2463	try
	2464	{
	2465	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
	2466	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
	2467	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
	2468	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
	2469	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
	2470	}
	2471	catch (CNetCdfException& e)
	2472	{
	2473	StdString msg("On writing Mask Attributes \n ");
	2474	msg.append("In the context : ");
	2475	CContext* context = CContext::getCurrent() ;
	2476	msg.append(context->getId()); msg.append("\n");
	2477	msg.append(e.what());
	2478	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
	2479	int data_dim, \
	2480	int data_ni, \
	2481	int data_nj, \
	2482	int data_ibegin, \
	2483	int data_jbegin)", << msg);
	2484	}
[219]	2485	}
	2486
	2487	///--------------------------------------------------------------
	2488
[707]	2489	StdSize CNc4DataOutput::getRecordFromTime(Time time)
	2490	{
	2491	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
	2492	if (it == timeToRecordCache.end())
	2493	{
[802]	2494	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
[707]	2495	if (!SuperClassWriter::varExist(timeAxisBoundsId))
	2496	timeAxisBoundsId = "time_instant_bounds";
	2497
	2498	CArray<double,2> timeAxisBounds;
	2499	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
	2500
	2501	StdSize record = 0;
	2502	double dtime(time);
	2503	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
	2504	{
	2505	if (timeAxisBounds(1, n) < dtime)
	2506	{
	2507	record = n + 1;
	2508	break;
	2509	}
	2510	}
	2511	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
	2512	}
	2513	return it->second;
	2514	}
[774]	2515
	2516	///--------------------------------------------------------------
	2517
	2518	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
	2519	{
	2520	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
	2521	}
	2522
	2523	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
	2524	{
	2525	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
	2526	}
	2527
	2528	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
	2529	{
	2530	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
	2531	}
	2532
	2533	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
	2534	{
	2535	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
	2536	}
	2537
[887]	2538	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
	2539	{
	2540	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
	2541	}
	2542
[774]	2543	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
	2544	{
	2545	this->writtenDomains.insert(domainName);
	2546	}
	2547
	2548	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
	2549	{
	2550	this->writtenCompressedDomains.insert(domainName);
	2551	}
	2552
	2553	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
	2554	{
	2555	this->writtenAxis.insert(axisName);
	2556	}
	2557
	2558	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
	2559	{
	2560	this->writtenCompressedAxis.insert(axisName);
	2561	}
[887]	2562
	2563	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
	2564	{
	2565	this->writtenScalar.insert(scalarName);
	2566	}
[335]	2567	} // namespace xios

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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 930

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