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source: issm/trunk-jpl/src/m/classes/model.m@ 25996

Last change on this file since 25996 was 25996, checked in by bulthuis, 4 years ago
NEW: add new class sampling to model for stochastic sampling capability
File size: 72.9 KB

Rev	Line
[8926]	1	%MODEL class definition
	2	%
	3	% Usage:
	4	% md = model(varargin)
	5
	6	classdef model
[13692]	7	properties (SetAccess=public) %Model fields
	8	% {{{
	9	%Careful here: no other class should be used as default value this is a bug of matlab
	10	mesh = 0;
	11	mask = 0;
[9778]	12
[13692]	13	geometry = 0;
	14	constants = 0;
[19527]	15	smb = 0;
[13692]	16	basalforcings = 0;
	17	materials = 0;
[16160]	18	damage = 0;
[13692]	19	friction = 0;
	20	flowequation = 0;
	21	timestepping = 0;
	22	initialization = 0;
	23	rifts = 0;
[24469]	24	dsl = 0;
[25118]	25	solidearth = 0;
[9778]	26
[13692]	27	debug = 0;
	28	verbose = 0;
	29	settings = 0;
[14621]	30	toolkits = 0;
[13692]	31	cluster = 0;
[9778]	32
[13692]	33	balancethickness = 0;
[17757]	34	stressbalance = 0;
[13692]	35	groundingline = 0;
	36	hydrology = 0;
[17757]	37	masstransport = 0;
[13692]	38	thermal = 0;
	39	steadystate = 0;
	40	transient = 0;
[25996]	41	levelset = 0;
[18757]	42	calving = 0;
[23652]	43	frontalforcings = 0;
[25996]	44	love = 0;
	45	gia = 0;
[21260]	46	esa = 0;
[25996]	47	sampling = 0;
[22958]	48
[13692]	49	autodiff = 0;
	50	inversion = 0;
	51	qmu = 0;
[22955]	52	amr = 0;
[13692]	53	results = 0;
[16388]	54	outputdefinition = 0;
[13692]	55	radaroverlay = 0;
	56	miscellaneous = 0;
	57	private = 0;
[9778]	58
[13692]	59	%}}}
	60	end
	61	methods (Static)
	62	function md = loadobj(md) % {{{
	63	% This function is directly called by matlab when a model object is
	64	% loaded. If the input is a struct it is an old version of model and
	65	% old fields must be recovered (make sure they are in the deprecated
	66	% model properties)
[8926]	67
[13692]	68	if verLessThan('matlab','7.9'),
	69	disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
	70	disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
[8952]	71
[13692]	72	% This is a Matlab bug: all the fields of md have their default value
	73	% Example of error message:
	74	% Warning: Error loading an object of class 'model':
	75	% Undefined function or method 'exist' for input arguments of type 'cell'
	76	%
	77	% This has been fixed in MATLAB 7.9 (R2009b) and later versions
	78	end
[8952]	79
[13692]	80	if isstruct(md)
	81	disp('Recovering model object from a previous version');
	82	md = structtomodel(model,md);
	83	end
[13239]	84
[13692]	85	%2012 August 4th
	86	if isa(md.materials,'materials'),
	87	disp('Recovering old materials');
	88	if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
[13718]	89	md.materials=matice(md.materials);
	90	else
[13692]	91	md.materials=matdamageice(md.materials);
	92	end
	93	end
[14559]	94	%2013 April 12
[15771]	95	if numel(md.stressbalance.loadingforce==1)
	96	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]	97	end
[14618]	98	%2013 April 17
	99	if isa(md.hydrology,'hydrology'),
	100	disp('Recovering old hydrology class');
	101	md.hydrology=hydrologyshreve(md.materials);
	102	end
[16356]	103	%2013 October 9
	104	if ~isa(md.damage,'damage'),
	105	md.damage=damage();
	106	md.damage.D=zeros(md.mesh.numberofvertices,1);
	107	md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
	108	end
[16822]	109	%2013 November 18
	110	if ~isa(md.outputdefinition,'outputdefinition'),
	111	md.outputdefinition=outputdefinition();
	112	end
[17558]	113	%2014 March 26th
	114	if isa(md.mesh,'mesh'),
[17566]	115	disp('Recovering old mesh class');
	116	if isprop(md.mesh,'dimension'),
	117	if md.mesh.dimension==2,
	118	md.mesh=mesh2d(md.mesh);
	119	else
	120	md.mesh=mesh3dprisms(md.mesh);
	121	end
[17558]	122	else
[17566]	123	md.mesh=mesh2dvertical(md.mesh);
[17558]	124	end
	125	end
[18775]	126	%2014 November 12
[21702]	127	if isa(md.calving,'double'); md.calving=calving(); end
[21260]	128	%2016 October 11
[21702]	129	if isa(md.esa,'double'); md.esa=esa(); end
[21545]	130	%2017 February 10th
[23434]	131	if isa(md.settings,'settings'), %this 'isa' verification: 2018 October 24th
	132	if md.settings.solver_residue_threshold==0,
	133	md.settings.solver_residue_threshold = 1e-6;
	134	end
[21545]	135	end
[21667]	136	%2017 April 10th
[25066]	137	if isa(md.gia,'gia'), md.gia=giamme(); end
[21702]	138	%2017 May 4th
	139	if isa(md.amr,'double'); md.amr=amr(); end
[22019]	140	%2017 Aug 29th
[22040]	141	if isa(md.love,'double'); md.love=fourierlove(); end
[22194]	142	%2017 Oct 26th
	143	if isa(md.calving,'calvingdev')
	144	disp('Warning: calvingdev is now calvingvonmises');
	145	md.calving=calvingvonmises(md.calving);
	146	end
[22955]	147	%2017 Dec 21st (needs to be here)
	148	if isempty(md.settings)
	149	disp('Warning: md.settings had to be reset, make sure to adjust md.settings.output_frequency and other fields');
	150	md.settings = issmsettings();
	151	end
[23503]	152	%2018 Dec 1st
	153	if md.settings.sb_coupling_frequency==0
	154	md.settings.sb_coupling_frequency=1;
	155	end
[23652]	156	%2019 Jan..
	157	if isa(md.frontalforcings,'double');
[24476]	158	if(isprop('meltingrate',md.calving) & ~isnan(md.calving.meltingrate))
[23652]	159	disp('Warning: md.calving.meltingrate is now in md.frontalforcings');
	160	end
	161	md.frontalforcings=frontalforcings(md.calving);
	162	end
[23758]	163	%2019 Feb 26
	164	if isa(md.settings.results_on_nodes,'double')
	165	if md.settings.results_on_nodes == 0
	166	md.settings.results_on_nodes = {};
	167	else
	168	md.settings.results_on_nodes = {'all'};
	169	end
	170	end
[23814]	171	%2019 Mar 28
[23984]	172	if isa(md.smb,'SMBcomponents') \| isa(md.smb,'SMBmeltcomponents') \| isa(md.smb,'SMBforcing') \| isa(md.smb,'SMBgemb')
	173	if isa(md.smb.isclimatology,'double')
	174	if prod(size(md.smb.isclimatology)) ~= 1
	175	md.smb.isclimatology = 0;
	176	end
[23814]	177	end
	178	end
[24474]	179	%2019 Dec 16
[24510]	180	if isa(md.dsl,'double') \| isempty(md.dsl.compute_fingerprints)
[24474]	181	md.dsl=dsl();
	182	end
[24738]	183	%2020 April 24
	184	if isa(md.smb,'SMBgemb')
	185	if isa(md.smb.isconstrainsurfaceT,'double')
	186	if prod(size(md.smb.isconstrainsurfaceT)) ~= 1
	187	md.smb.isconstrainsurfaceT = 0;
	188	end
	189	end
[25996]	190	end
	191	%2021 February 17
	192	if isa(md.sampling,'double'); md.sampling=sampling(); end
[13692]	193	end% }}}
	194	end
	195	methods
	196	function md = model(varargin) % {{{
[8926]	197
[13692]	198	switch nargin
	199	case 0
[25767]	200	md=setdefaultparameters(md,'earth');
[13692]	201	otherwise
[25767]	202	options=pairoptions(varargin{:});
	203	planet=getfieldvalue(options,'planet','earth');
	204	md=setdefaultparameters(md,planet);
[13692]	205	end
[25758]	206
[13692]	207	end
	208	%}}}
[25767]	209	function md = setdefaultparameters(md,planet) % {{{
	210
	211	%initialize subclasses
	212	md.mesh = mesh2d();
	213	md.mask = mask();
	214	md.constants = constants();
	215	md.geometry = geometry();
	216	md.initialization = initialization();
	217	md.smb = SMBforcing();
	218	md.basalforcings = basalforcings();
	219	md.friction = friction();
	220	md.rifts = rifts();
	221	md.solidearth = solidearth(planet);
	222	md.dsl = dsl();
	223	md.timestepping = timestepping();
	224	md.groundingline = groundingline();
	225	md.materials = matice();
	226	md.damage = damage();
	227	md.flowequation = flowequation();
	228	md.debug = debug();
	229	md.verbose = verbose();
	230	md.settings = issmsettings();
	231	md.toolkits = toolkits();
	232	md.cluster = generic();
	233	md.balancethickness = balancethickness();
	234	md.stressbalance = stressbalance();
	235	md.hydrology = hydrologyshreve();
	236	md.masstransport = masstransport();
	237	md.thermal = thermal();
	238	md.steadystate = steadystate();
	239	md.transient = transient();
	240	md.levelset = levelset();
	241	md.calving = calving();
	242	md.frontalforcings = frontalforcings();
	243	md.gia = giamme();
	244	md.love = fourierlove();
	245	md.esa = esa();
[25996]	246	md.sampling = sampling();
[25767]	247	md.autodiff = autodiff();
	248	md.inversion = inversion();
	249	md.qmu = qmu();
	250	md.amr = amr();
	251	md.radaroverlay = radaroverlay();
	252	md.results = struct();
	253	md.outputdefinition = outputdefinition();
	254	md.miscellaneous = miscellaneous();
	255	md.private = private();
	256	end
	257	%}}}
[13692]	258	function md = checkmessage(md,string) % {{{
	259	if(nargout~=1) error('wrong usage, model must be an output'); end
	260	disp(['model not consistent: ' string]);
	261	md.private.isconsistent=false;
	262	end
	263	%}}}
	264	function md = collapse(md)% {{{
	265	%COLLAPSE - collapses a 3d mesh into a 2d mesh
	266	%
	267	% This routine collapses a 3d model into a 2d model
[25499]	268	% and collapses all the fields of the 3d model by
[13692]	269	% taking their depth-averaged values
	270	%
	271	% Usage:
	272	% md=collapse(md)
	273	%
	274	% See also: EXTRUDE, MODELEXTRACT
[13005]	275
[13692]	276	%Check that the model is really a 3d model
[17687]	277	if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]	278	error('collapse error message: only 3d mesh can be collapsed')
	279	end
[13005]	280
[17724]	281	%Start with changing all the fields from the 3d mesh
[13005]	282
[21827]	283	%dealing with the friction law
[13692]	284	%drag is limited to nodes that are on the bedrock.
[18775]	285	if isa(md.friction,'friction'),
	286	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	287	md.friction.p=project2d(md,md.friction.p,1);
	288	md.friction.q=project2d(md,md.friction.q,1);
[21819]	289	elseif isa(md.friction,'frictioncoulomb'),
	290	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	291	md.friction.coefficientcoulomb=project2d(md,md.friction.coefficientcoulomb,1);
	292	md.friction.p=project2d(md,md.friction.p,1);
	293	md.friction.q=project2d(md,md.friction.q,1);
[18775]	294	elseif isa(md.friction,'frictionhydro'),
	295	md.friction.q=project2d(md,md.friction.q,1);
	296	md.friction.C=project2d(md,md.friction.C,1);
	297	md.friction.As=project2d(md,md.friction.As,1);
[18798]	298	md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
[18775]	299	elseif isa(md.friction,'frictionwaterlayer'),
	300	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	301	md.friction.p=project2d(md,md.friction.p,1);
	302	md.friction.q=project2d(md,md.friction.q,1);
	303	md.friction.water_layer=project2d(md,md.friction.water_layer,1);
	304	elseif isa(md.friction,'frictionweertman'),
	305	md.friction.C=project2d(md,md.friction.C,1);
	306	md.friction.m=project2d(md,md.friction.m,1);
[19720]	307	elseif isa(md.friction,'frictionweertmantemp'),
	308	md.friction.C=project2d(md,md.friction.C,1);
	309	md.friction.m=project2d(md,md.friction.m,1);
[25943]	310	elseif isa(md.friction,'frictionjosh'),
	311	md.friction.coefficient=project2d(md,md.friction.coefficient,1);
	312	md.friction.pressure_adjusted_temperature=project2d(md,md.friction.pressure_adjusted_temperature,1);
[19720]	313	else
	314	disp('friction type not supported');
[21827]	315	end
[13005]	316
[13692]	317	%observations
[25499]	318	if ~isnan(md.inversion.vx_obs),
	319	md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers);
	320	end
	321	if ~isnan(md.inversion.vy_obs),
	322	md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers);
	323	end
	324	if ~isnan(md.inversion.vel_obs),
	325	md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers);
	326	end
	327	if ~isnan(md.inversion.thickness_obs),
	328	md.inversion.thickness_obs=project2d(md,md.inversion.thickness_obs,md.mesh.numberoflayers);
	329	end
	330	if ~isnan(md.inversion.cost_functions_coefficients),
	331	md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers);
	332	end
	333	if numel(md.inversion.min_parameters)>1,
	334	md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers);
	335	end
	336	if numel(md.inversion.max_parameters)>1,
	337	md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers);
	338	end
[19527]	339	if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
	340	md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
	341	elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
	342	md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
[25499]	343	end
[13005]	344
[13692]	345	%results
[25499]	346	if ~isnan(md.initialization.vx),
	347	md.initialization.vx=DepthAverage(md,md.initialization.vx);
	348	end
	349	if ~isnan(md.initialization.vy),
	350	md.initialization.vy=DepthAverage(md,md.initialization.vy);
	351	end
	352	if ~isnan(md.initialization.vz),
	353	md.initialization.vz=DepthAverage(md,md.initialization.vz);
	354	end
	355	if ~isnan(md.initialization.vel),
	356	md.initialization.vel=DepthAverage(md,md.initialization.vel);
	357	end
	358	if ~isnan(md.initialization.temperature),
	359	md.initialization.temperature=DepthAverage(md,md.initialization.temperature);
	360	end
	361	if ~isnan(md.initialization.pressure),
	362	md.initialization.pressure=project2d(md,md.initialization.pressure,1);
	363	end
	364	if ~isnan(md.initialization.sediment_head),
	365	md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);
	366	end
	367	if ~isnan(md.initialization.epl_head),
	368	md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);
	369	end
	370	if ~isnan(md.initialization.epl_thickness),
	371	md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);
	372	end
	373	if ~isnan(md.initialization.waterfraction),
	374	md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);
	375	end
	376	if ~isnan(md.initialization.watercolumn),
	377	md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);
	378	end
	379
[21530]	380	%giaivins
[25074]	381	if isa(md.gia,'giaivins'),
	382	if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
	383	if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
	384	end
[15021]	385
[13692]	386	%elementstype
	387	if ~isnan(md.flowequation.element_equation)
	388	md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
	389	md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]	390	md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
	391	md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
	392	md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[25499]	393	end
[13005]	394
[13692]	395	%boundary conditions
[15771]	396	md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
	397	md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
	398	md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
	399	md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
	400	md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[25499]	401	if numel(md.masstransport.spcthickness)>1,
	402	md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
	403	end
	404	if numel(md.damage.spcdamage)>1,
	405	md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers);
	406	end
	407	if numel(md.levelset.spclevelset)>1,
	408	md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers);
	409	end
[13692]	410	md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]	411
[18506]	412	% Hydrologydc variables
	413	if isa(md.hydrology,'hydrologydc');
	414	md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
	415	md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
	416	md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
	417	md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
	418	if(md.hydrology.isefficientlayer==1)
	419	md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
[21808]	420	end
	421	end
[18506]	422
[13692]	423	%materials
	424	md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
	425	md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]	426
	427	%damage:
[17940]	428	if md.damage.isdamage,
	429	md.damage.D=DepthAverage(md,md.damage.D);
	430	end
[13005]	431
[13692]	432	%special for thermal modeling:
[18378]	433	if ~isnan(md.basalforcings.groundedice_melting_rate),
	434	md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
	435	end
[21417]	436	if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
[18378]	437	md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
	438	end
[13692]	439	md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]	440
[21417]	441	if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
	442	md.calving.coeff=project2d(md,md.calving.coeff,1);
	443	end
[23652]	444	if isprop(md.frontalforcings,'meltingrate') & ~isnan(md.frontalforcings.meltingrate),
	445	md.frontalforcings.meltingrate=project2d(md,md.frontalforcings.meltingrate,1);
[21417]	446	end
	447
[13692]	448	%update of connectivity matrix
	449	md.mesh.average_vertex_connectivity=25;
[13005]	450
[13692]	451	%Collapse the mesh
	452	nodes2d=md.mesh.numberofvertices2d;
	453	elements2d=md.mesh.numberofelements2d;
[13005]	454
[13692]	455	%parameters
	456	md.geometry.surface=project2d(md,md.geometry.surface,1);
	457	md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]	458	md.geometry.base=project2d(md,md.geometry.base,1);
[18480]	459	if ~isnan(md.geometry.bed),
	460	md.geometry.bed=project2d(md,md.geometry.bed,1);
	461	end
[24861]	462	if ~isnan(md.mask.ocean_levelset),
	463	md.mask.ocean_levelset=project2d(md,md.mask.ocean_levelset,1);
[18378]	464	end
	465	if ~isnan(md.mask.ice_levelset),
	466	md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
	467	end
[13005]	468
[22955]	469	%lat long
[25499]	470	if numel(md.mesh.lat)==md.mesh.numberofvertices,
	471	md.mesh.lat=project2d(md,md.mesh.lat,1);
	472	end
	473	if numel(md.mesh.long)==md.mesh.numberofvertices,
	474	md.mesh.long=project2d(md,md.mesh.long,1);
	475	end
[22955]	476
[21808]	477	%outputdefinitions
	478	for i=1:length(md.outputdefinition.definitions)
	479	if isobject(md.outputdefinition.definitions{i})
	480	%get subfields
[25758]	481	solutionsubfields=fields(md.outputdefinition.definitions{i});
[21808]	482	for j=1:length(solutionsubfields),
	483	field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
	484	if length(field)==md.mesh.numberofvertices \| length(field)==md.mesh.numberofelements,
	485	md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
	486	end
	487	end
	488	end
	489	end
	490
[25499]	491	%Initialize the 2d mesh
[17724]	492	mesh=mesh2d();
	493	mesh.x=md.mesh.x2d;
	494	mesh.y=md.mesh.y2d;
	495	mesh.numberofvertices=md.mesh.numberofvertices2d;
	496	mesh.numberofelements=md.mesh.numberofelements2d;
	497	mesh.elements=md.mesh.elements2d;
[25499]	498	if numel(md.mesh.lat)==md.mesh.numberofvertices,
	499	mesh.lat=project2d(md,md.mesh.lat,1);
	500	end
	501	if numel(md.mesh.long)==md.mesh.numberofvertices,
	502	mesh.long=project2d(md,md.mesh.long,1);
	503	end
[21499]	504	mesh.epsg=md.mesh.epsg;
[25499]	505	if numel(md.mesh.scale_factor)==md.mesh.numberofvertices,
	506	mesh.scale_factor=project2d(md,md.mesh.scale_factor,1);
	507	end
	508	if ~isnan(md.mesh.vertexonboundary),
	509	mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
	510	end
	511	if ~isnan(md.mesh.elementconnectivity),
	512	mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
	513	end
[17724]	514	md.mesh=mesh;
[18738]	515	md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
	516	md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
[19955]	517	md.mesh.segments=contourenvelope(md.mesh);
[13005]	518
[13692]	519	end % }}}
[22955]	520	function md2 = extract(md,area,varargin) % {{{
[13692]	521	%extract - extract a model according to an Argus contour or flag list
	522	%
	523	% This routine extracts a submodel from a bigger model with respect to a given contour
	524	% md must be followed by the corresponding exp file or flags list
	525	% It can either be a domain file (argus type, .exp extension), or an array of element flags.
	526	% If user wants every element outside the domain to be
[15564]	527	% extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]	528	% an empty string '' will be considered as an empty domain
	529	% a string 'all' will be considered as the entire domain
	530	%
	531	% Usage:
	532	% md2=extract(md,area);
	533	%
	534	% Examples:
	535	% md2=extract(md,'Domain.exp');
	536	%
	537	% See also: EXTRUDE, COLLAPSE
[13005]	538
[13692]	539	%copy model
	540	md1=md;
[13005]	541
[22955]	542	%recover optoins:
	543	options=pairoptions(varargin{:});
	544
[13692]	545	%some checks
[22955]	546	if ((nargin<2) \| (nargout~=1)),
[13692]	547	help extract
	548	error('extract error message: bad usage');
	549	end
[13005]	550
[13692]	551	%get elements that are inside area
	552	flag_elem=FlagElements(md1,area);
	553	if ~any(flag_elem),
	554	error('extracted model is empty');
	555	end
[13005]	556
[13692]	557	%kick out all elements with 3 dirichlets
[22955]	558	if getfieldvalue(options,'spccheck',1)
	559	spc_elem=find(~flag_elem);
	560	spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
	561	flag=ones(md1.mesh.numberofvertices,1);
	562	flag(spc_node)=0;
	563	pos=find(sum(flag(md1.mesh.elements),2)==0);
	564	flag_elem(pos)=0;
	565	end
[13005]	566
[13692]	567	%extracted elements and nodes lists
	568	pos_elem=find(flag_elem);
	569	pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]	570
[13692]	571	%keep track of some fields
	572	numberofvertices1=md1.mesh.numberofvertices;
	573	numberofelements1=md1.mesh.numberofelements;
	574	numberofvertices2=length(pos_node);
	575	numberofelements2=length(pos_elem);
	576	flag_node=zeros(numberofvertices1,1);
	577	flag_node(pos_node)=1;
[13005]	578
[13692]	579	%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
	580	Pelem=zeros(numberofelements1,1);
	581	Pelem(pos_elem)=[1:numberofelements2]';
	582	Pnode=zeros(numberofvertices1,1);
	583	Pnode(pos_node)=[1:numberofvertices2]';
[13005]	584
[13857]	585	%renumber the elements (some nodes won't exist anymore)
[13692]	586	elements_1=md1.mesh.elements;
	587	elements_2=elements_1(pos_elem,:);
	588	elements_2(:,1)=Pnode(elements_2(:,1));
	589	elements_2(:,2)=Pnode(elements_2(:,2));
	590	elements_2(:,3)=Pnode(elements_2(:,3));
[17558]	591	if isa(md1.mesh,'mesh3dprisms'),
[13692]	592	elements_2(:,4)=Pnode(elements_2(:,4));
	593	elements_2(:,5)=Pnode(elements_2(:,5));
	594	elements_2(:,6)=Pnode(elements_2(:,6));
	595	end
[13005]	596
[13857]	597	%OK, now create the new model!
[13005]	598
[13857]	599	%take every field from model
[13692]	600	md2=md1;
[13005]	601
[13692]	602	%automatically modify fields
[13005]	603
[13692]	604	%loop over model fields
[25758]	605	model_fields=fields(md1);
[13692]	606	for i=1:length(model_fields),
	607	%get field
	608	field=md1.(model_fields{i});
	609	fieldsize=size(field);
	610	if isobject(field), %recursive call
[25758]	611	object_fields=fields(md1.(model_fields{i}));
[13692]	612	for j=1:length(object_fields),
	613	%get field
	614	field=md1.(model_fields{i}).(object_fields{j});
	615	fieldsize=size(field);
	616	%size = number of nodes * n
	617	if fieldsize(1)==numberofvertices1
	618	md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
	619	elseif (fieldsize(1)==numberofvertices1+1)
	620	md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]	621	%size = number of elements * n
[13692]	622	elseif fieldsize(1)==numberofelements1
	623	md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
[21428]	624	elseif (fieldsize(1)==numberofelements1+1)
	625	md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
[13692]	626	end
	627	end
	628	else
	629	%size = number of nodes * n
	630	if fieldsize(1)==numberofvertices1
	631	md2.(model_fields{i})=field(pos_node,:);
	632	elseif (fieldsize(1)==numberofvertices1+1)
	633	md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]	634	%size = number of elements * n
[13692]	635	elseif fieldsize(1)==numberofelements1
	636	md2.(model_fields{i})=field(pos_elem,:);
[21428]	637	elseif (fieldsize(1)==numberofelements1+1)
	638	md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
[13692]	639	end
	640	end
	641	end
[13005]	642
[13692]	643	%modify some specific fields
[13005]	644
[13692]	645	%Mesh
	646	md2.mesh.numberofelements=numberofelements2;
	647	md2.mesh.numberofvertices=numberofvertices2;
	648	md2.mesh.elements=elements_2;
[13005]	649
[13692]	650	%mesh.uppervertex mesh.lowervertex
[17558]	651	if isa(md1.mesh,'mesh3dprisms'),
[13692]	652	md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
	653	pos=find(~isnan(md2.mesh.uppervertex));
	654	md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]	655
[13692]	656	md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
	657	pos=find(~isnan(md2.mesh.lowervertex));
	658	md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]	659
[13692]	660	md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
	661	pos=find(~isnan(md2.mesh.upperelements));
	662	md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]	663
[13692]	664	md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
	665	pos=find(~isnan(md2.mesh.lowerelements));
	666	md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
	667	end
[13005]	668
[13692]	669	%Initial 2d mesh
[17558]	670	if isa(md1.mesh,'mesh3dprisms'),
[13692]	671	flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
	672	pos_elem_2d=find(flag_elem_2d);
	673	flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
	674	pos_node_2d=find(flag_node_2d);
[13005]	675
[13692]	676	md2.mesh.numberofelements2d=length(pos_elem_2d);
	677	md2.mesh.numberofvertices2d=length(pos_node_2d);
	678	md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
	679	md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
	680	md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
	681	md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]	682
[13692]	683	md2.mesh.x2d=md1.mesh.x(pos_node_2d);
	684	md2.mesh.y2d=md1.mesh.y(pos_node_2d);
	685	end
[13005]	686
[13692]	687	%Edges
[17686]	688	if(dimension(md.mesh)==2),
[17563]	689	if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
	690	%renumber first two columns
	691	pos=find(md2.mesh.edges(:,4)~=-1);
	692	md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
	693	md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
	694	md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
	695	md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
	696	%remove edges when the 2 vertices are not in the domain.
	697	md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
	698	%Replace all zeros by -1 in the last two columns
	699	pos=find(md2.mesh.edges(:,3)==0);
	700	md2.mesh.edges(pos,3)=-1;
	701	pos=find(md2.mesh.edges(:,4)==0);
	702	md2.mesh.edges(pos,4)=-1;
	703	%Invert -1 on the third column with last column (Also invert first two columns!!)
	704	pos=find(md2.mesh.edges(:,3)==-1);
	705	md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
	706	md2.mesh.edges(pos,4)=-1;
	707	values=md2.mesh.edges(pos,2);
	708	md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
	709	md2.mesh.edges(pos,1)=values;
	710	%Finally remove edges that do not belong to any element
	711	pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
	712	md2.mesh.edges(pos,:)=[];
	713	end
[13692]	714	end
[13005]	715
[13692]	716	%Penalties
[15771]	717	if ~isnan(md2.stressbalance.vertex_pairing),
	718	for i=1:size(md1.stressbalance.vertex_pairing,1);
	719	md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]	720	end
[15771]	721	md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]	722	end
[15767]	723	if ~isnan(md2.masstransport.vertex_pairing),
	724	for i=1:size(md1.masstransport.vertex_pairing,1);
	725	md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]	726	end
[15767]	727	md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]	728	end
[13005]	729
[13692]	730	%recreate segments
[20322]	731	if isa(md1.mesh,'mesh2d') \| isa(md1.mesh','mesh3dsurface'),
[13692]	732	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	733	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
[19957]	734	md2.mesh.segments=contourenvelope(md2.mesh);
[25499]	735	md2.mesh.vertexonboundary=zeros(numberofvertices2,1);
	736	md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
[13692]	737	else
	738	%First do the connectivity for the contourenvelope in 2d
	739	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
	740	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[19957]	741	segments=contourenvelope(md2.mesh);
[25499]	742	md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1);
	743	md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]	744	md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
	745	%Then do it for 3d as usual
	746	md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
	747	md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
	748	end
[13005]	749
[13692]	750	%Boundary conditions: Dirichlets on new boundary
	751	%Catch the elements that have not been extracted
	752	orphans_elem=find(~flag_elem);
	753	orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
	754	%Figure out which node are on the boundary between md2 and md1
	755	nodestoflag1=intersect(orphans_node,pos_node);
	756	nodestoflag2=Pnode(nodestoflag1);
[23771]	757	if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>1 & numel(md1.stressbalance.spcvz)>1,
[13692]	758	if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]	759	md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
	760	md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]	761	else
[15771]	762	md2.stressbalance.spcvx(nodestoflag2)=NaN;
	763	md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]	764	disp(' ')
	765	disp('!! extract warning: spc values should be checked !!')
	766	disp(' ')
	767	end
	768	%put 0 for vz
[15771]	769	md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]	770	end
	771	if ~isnan(md1.thermal.spctemperature),
	772	md2.thermal.spctemperature(nodestoflag2,1)=1;
	773	end
[13005]	774
[13692]	775	%Results fields
	776	if isstruct(md1.results),
	777	md2.results=struct();
[25758]	778	solutionfields=fields(md1.results);
[13692]	779	for i=1:length(solutionfields),
[14230]	780	if isstruct(md1.results.(solutionfields{i}))
	781	%get subfields
[24134]	782	% loop over time steps
	783	for p=1:length(md1.results.(solutionfields{i}))
	784	current = md1.results.(solutionfields{i})(p);
[25758]	785	solutionsubfields=fields(current);
[24134]	786	for j=1:length(solutionsubfields),
	787	field=md1.results.(solutionfields{i})(p).(solutionsubfields{j});
[14230]	788	if length(field)==numberofvertices1,
[24134]	789	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_node);
[14230]	790	elseif length(field)==numberofelements1,
[24134]	791	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field(pos_elem);
[14230]	792	else
[24134]	793	md2.results.(solutionfields{i})(p).(solutionsubfields{j})=field;
[14230]	794	end
[24134]	795	end
[14230]	796	end
	797	else
	798	field=md1.results.(solutionfields{i});
[13692]	799	if length(field)==numberofvertices1,
[14230]	800	md2.results.(solutionfields{i})=field(pos_node);
[13692]	801	elseif length(field)==numberofelements1,
[14230]	802	md2.results.(solutionfields{i})=field(pos_elem);
[13692]	803	else
[14230]	804	md2.results.(solutionfields{i})=field;
[13692]	805	end
	806	end
	807	end
	808	end
[13005]	809
[21808]	810	%OutputDefinitions fields
	811	for i=1:length(md1.outputdefinition.definitions),
	812	if isobject(md1.outputdefinition.definitions{i})
	813	%get subfields
[25758]	814	solutionsubfields=fields(md1.outputdefinition.definitions{i});
[21808]	815	for j=1:length(solutionsubfields),
	816	field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
	817	if length(field)==numberofvertices1,
	818	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
	819	elseif length(field)==numberofelements1,
	820	md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
	821	end
	822	end
	823	end
	824	end
	825
[13692]	826	%Keep track of pos_node and pos_elem
	827	md2.mesh.extractedvertices=pos_node;
	828	md2.mesh.extractedelements=pos_elem;
	829	end % }}}
	830	function md = extrude(md,varargin) % {{{
	831	%EXTRUDE - vertically extrude a 2d mesh
	832	%
	833	% vertically extrude a 2d mesh and create corresponding 3d mesh.
	834	% The vertical distribution can:
	835	% - follow a polynomial law
	836	% - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
	837	% - be discribed by a list of coefficients (between 0 and 1)
	838	%
	839	%
	840	% Usage:
	841	% md=extrude(md,numlayers,extrusionexponent);
	842	% md=extrude(md,numlayers,lowerexponent,upperexponent);
	843	% md=extrude(md,listofcoefficients);
	844	%
	845	% Example:
[18216]	846	% md=extrude(md,15,1.3);
	847	% md=extrude(md,15,1.3,1.2);
[13692]	848	% md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
	849	%
	850	% See also: MODELEXTRACT, COLLAPSE
[13005]	851
[13692]	852	%some checks on list of arguments
	853	if ((nargin>4) \| (nargin<2) \| (nargout~=1)),
	854	help extrude;
	855	error('extrude error message');
	856	end
[24511]	857	if numel(md.geometry.base)~=md.mesh.numberofvertices \|\| numel(md.geometry.surface)~=md.mesh.numberofvertices
	858	error('model has not been parameterized yet: base and/or surface not set');
	859	end
[13005]	860
[13692]	861	%Extrude the mesh
	862	if nargin==2, %list of coefficients
	863	clist=varargin{1};
	864	if any(clist<0) \| any(clist>1),
	865	error('extrusioncoefficients must be between 0 and 1');
	866	end
	867	extrusionlist=sort(unique([clist(:);0;1]));
	868	numlayers=length(extrusionlist);
	869	elseif nargin==3, %one polynomial law
	870	if varargin{2}<=0,
	871	help extrude;
	872	error('extrusionexponent must be >=0');
	873	end
	874	numlayers=varargin{1};
	875	extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
	876	elseif nargin==4, %two polynomial laws
	877	numlayers=varargin{1};
	878	lowerexp=varargin{2};
	879	upperexp=varargin{3};
[13005]	880
[13692]	881	if varargin{2}<=0 \| varargin{3}<=0,
	882	help extrude;
	883	error('lower and upper extrusionexponents must be >=0');
	884	end
[13005]	885
[13692]	886	lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
	887	upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
	888	extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]	889
[13692]	890	end
[13005]	891
[13692]	892	if numlayers<2,
	893	error('number of layers should be at least 2');
	894	end
[17686]	895	if strcmp(md.mesh.domaintype(),'3D')
[13692]	896	error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
	897	end
[13005]	898
[13692]	899	%Initialize with the 2d mesh
[17558]	900	mesh2d = md.mesh;
	901	md.mesh=mesh3dprisms();
	902	md.mesh.x = mesh2d.x;
	903	md.mesh.y = mesh2d.y;
	904	md.mesh.elements = mesh2d.elements;
	905	md.mesh.numberofelements = mesh2d.numberofelements;
	906	md.mesh.numberofvertices = mesh2d.numberofvertices;
	907
	908	md.mesh.lat = mesh2d.lat;
	909	md.mesh.long = mesh2d.long;
[18558]	910	md.mesh.epsg = mesh2d.epsg;
[22324]	911	md.mesh.scale_factor = mesh2d.scale_factor;
[17558]	912
	913	md.mesh.vertexonboundary = mesh2d.vertexonboundary;
	914	md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
	915	md.mesh.elementconnectivity = mesh2d.elementconnectivity;
	916	md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
	917
	918	md.mesh.extractedvertices = mesh2d.extractedvertices;
	919	md.mesh.extractedelements = mesh2d.extractedelements;
	920
[13692]	921	x3d=[];
	922	y3d=[];
	923	z3d=[]; %the lower node is on the bed
	924	thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]	925	bed3d=md.geometry.base;
[13005]	926
[13692]	927	%Create the new layers
	928	for i=1:numlayers,
	929	x3d=[x3d; md.mesh.x];
	930	y3d=[y3d; md.mesh.y];
	931	%nodes are distributed between bed and surface accordingly to the given exponent
	932	z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
	933	end
	934	number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	935
[13692]	936	%Extrude elements
	937	elements3d=[];
	938	for i=1:numlayers-1,
	939	elements3d=[elements3d;[md.mesh.elements+(i-1)md.mesh.numberofvertices md.mesh.elements+imd.mesh.numberofvertices]]; %Create the elements of the 3d mesh for the non extruded part
	940	end
	941	number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]	942
[13692]	943	%Keep a trace of lower and upper nodes
[17590]	944	lowervertex=NaN*ones(number_nodes3d,1);
	945	uppervertex=NaN*ones(number_nodes3d,1);
	946	lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
	947	uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
	948	md.mesh.lowervertex=lowervertex;
	949	md.mesh.uppervertex=uppervertex;
[13005]	950
[13692]	951	%same for lower and upper elements
[17590]	952	lowerelements=NaN*ones(number_el3d,1);
	953	upperelements=NaN*ones(number_el3d,1);
	954	lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
	955	upperelements(1:(numlayers-2)md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)md.mesh.numberofelements;
	956	md.mesh.lowerelements=lowerelements;
	957	md.mesh.upperelements=upperelements;
[13005]	958
[13692]	959	%Save old mesh
	960	md.mesh.x2d=md.mesh.x;
	961	md.mesh.y2d=md.mesh.y;
	962	md.mesh.elements2d=md.mesh.elements;
	963	md.mesh.numberofelements2d=md.mesh.numberofelements;
	964	md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]	965
[13692]	966	%Build global 3d mesh
	967	md.mesh.elements=elements3d;
	968	md.mesh.x=x3d;
	969	md.mesh.y=y3d;
	970	md.mesh.z=z3d;
	971	md.mesh.numberofelements=number_el3d;
	972	md.mesh.numberofvertices=number_nodes3d;
	973	md.mesh.numberoflayers=numlayers;
[13005]	974
[13692]	975	%Ok, now deal with the other fields from the 2d mesh:
[13005]	976
[19048]	977	%bedinfo and surface info
	978	md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
	979	md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
	980	md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
	981
[13692]	982	%lat long
	983	md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
	984	md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[22324]	985	md.mesh.scale_factor=project3d(md,'vector',md.mesh.scale_factor,'type','node');
[13005]	986
[19048]	987	md.geometry=extrude(md.geometry,md);
	988	md.friction = extrude(md.friction,md);
	989	md.inversion = extrude(md.inversion,md);
[19527]	990	md.smb = extrude(md.smb,md);
[19048]	991	md.initialization = extrude(md.initialization,md);
[13005]	992
[19050]	993	md.flowequation=md.flowequation.extrude(md);
[19048]	994	md.stressbalance=extrude(md.stressbalance,md);
[19050]	995	md.thermal=md.thermal.extrude(md);
	996	md.masstransport=md.masstransport.extrude(md);
[20460]	997	md.levelset=extrude(md.levelset,md);
[19048]	998	md.calving=extrude(md.calving,md);
[23652]	999	md.frontalforcings=extrude(md.frontalforcings,md);
[19048]	1000	md.hydrology = extrude(md.hydrology,md);
[25118]	1001	md.solidearth = extrude(md.solidearth,md);
[24469]	1002	md.dsl = extrude(md.dsl,md);
[13005]	1003
[13692]	1004	%connectivity
[17991]	1005	if ~isnan(md.mesh.elementconnectivity)
	1006	md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
	1007	md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
	1008	for i=2:numlayers-1,
	1009	md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)...
	1010	=md.mesh.elementconnectivity((i-1)md.mesh.numberofelements2d+1:(i)md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
	1011	end
	1012	md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]	1013	end
[13005]	1014
[19048]	1015	md.materials=extrude(md.materials,md);
	1016	md.damage=extrude(md.damage,md);
	1017	md.mask=extrude(md.mask,md);
	1018	md.qmu=extrude(md.qmu,md);
	1019	md.basalforcings=extrude(md.basalforcings,md);
[21808]	1020	md.outputdefinition=extrude(md.outputdefinition,md);
[13005]	1021
[13692]	1022	%increase connectivity if less than 25:
	1023	if md.mesh.average_vertex_connectivity<=25,
	1024	md.mesh.average_vertex_connectivity=100;
	1025	end
[13005]	1026	end % }}}
[13692]	1027	function md = structtomodel(md,structmd) % {{{
[8952]	1028
[13692]	1029	if ~isstruct(structmd) error('input model is not a structure'); end
[8952]	1030
[13692]	1031	%loaded model is a struct, initialize output and recover all fields
	1032	md = structtoobj(model,structmd);
[8952]	1033
[13692]	1034	%Old field now classes
	1035	if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
	1036	if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]	1037
[13692]	1038	%Field name change
	1039	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	1040	if isfield(structmd,'p'), md.friction.p=structmd.p; end
	1041	if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]	1042	if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]	1043	if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]	1044	if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[19527]	1045	if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
[13692]	1046	if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
	1047	if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
	1048	if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
	1049	if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]	1050	if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]	1051	if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
	1052	if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
	1053	if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]	1054	if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]	1055	if isfield(structmd,'g'), md.constants.g=structmd.g; end
	1056	if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
[19527]	1057	if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
[18068]	1058	if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]	1059	if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
	1060	if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
	1061	if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
	1062	if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
	1063	if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
	1064	if isfield(structmd,'riftproperties'), %old implementation
	1065	md.rifts=rifts();
	1066	md.rifts.riftproperties=structmd.riftproperties;
	1067	md.rifts.riftstruct=structmd.rifts;
	1068	md.rifts.riftproperties=structmd.riftinfo;
	1069	end
	1070	if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
	1071	if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
	1072	if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
	1073	if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
	1074	if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
	1075	if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
	1076	if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
	1077	if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
	1078	if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
	1079	if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
	1080	if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
	1081	if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
	1082	if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
	1083	if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
	1084	if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
	1085	if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
	1086	if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
	1087	if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
	1088	if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
	1089	if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
	1090	if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
	1091	if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]	1092	if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
	1093	if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
	1094	if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
	1095	if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
	1096	if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]	1097	if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
	1098	if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
	1099	if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
	1100	if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]	1101	if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]	1102	if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
	1103	if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
	1104	if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]	1105	if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
	1106	if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]	1107	if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
	1108	if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
	1109	if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
	1110	if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]	1111	if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]	1112	if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]	1113	if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
	1114	if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
	1115	if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
	1116	if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
	1117	if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
	1118	if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
	1119	if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
	1120	if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
	1121	if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
	1122	if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
	1123	if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
	1124	if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
	1125	if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
	1126	if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
	1127	if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
	1128	if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
	1129	if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
	1130	if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
	1131	if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
	1132	if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]	1133	if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]	1134	if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]	1135	if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]	1136	if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
	1137	if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
	1138	if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
	1139	if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
	1140	if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
	1141	if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
	1142	if isfield(structmd,'long'), md.mesh.long=structmd.long; end
[22324]	1143	if isfield(structmd,'scale_factor'), md.mesh.scale_factor=structmd.scale_factor; end
[13692]	1144	if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
	1145	if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
	1146	if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
	1147	if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
	1148	if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
	1149	if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
	1150	if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
	1151	if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
	1152	if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
	1153	if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
	1154	if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
	1155	if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
	1156	if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
	1157	if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
	1158	if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
	1159	if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]	1160	if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]	1161	if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
	1162	if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
	1163	if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
	1164	if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]	1165	if isfield(structmd,'edges'),
	1166	md.mesh.edges=structmd.edges;
	1167	md.mesh.edges(isnan(md.mesh.edges))=-1;
	1168	end
[13692]	1169	if isfield(structmd,'y'), md.mesh.y=structmd.y; end
	1170	if isfield(structmd,'x'), md.mesh.x=structmd.x; end
	1171	if isfield(structmd,'z'), md.mesh.z=structmd.z; end
[15771]	1172	if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]	1173	if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
	1174	if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]	1175
[13692]	1176	if isnumeric(md.verbose),
	1177	md.verbose=verbose;
	1178	end
[15768]	1179
[13692]	1180	if isfield(structmd,'spcvelocity'),
[15771]	1181	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1182	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1183	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1184	pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
	1185	pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
	1186	pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]	1187	end
	1188	if isfield(structmd,'spcvx'),
[15771]	1189	md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
	1190	pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]	1191	end
	1192	if isfield(structmd,'spcvy'),
[15771]	1193	md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
	1194	pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]	1195	end
	1196	if isfield(structmd,'spcvz'),
[15771]	1197	md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
	1198	pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]	1199	end
[14620]	1200	if isfield(structmd,'pressureload'),
	1201	if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]	1202	pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
	1203	pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
	1204	pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]	1205	end
[13692]	1206	end
	1207	if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
	1208	pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
	1209	pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
	1210	pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
	1211	pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
	1212	pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
	1213	pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
	1214	pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
	1215	pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
	1216	end
	1217	if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
	1218	pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
	1219	pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
	1220	pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
	1221	pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
	1222	pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
	1223	pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
	1224	pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
	1225	pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
	1226	end
	1227	if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
	1228	if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
	1229	if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
	1230	if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
	1231	end
	1232	if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
	1233	if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]	1234	if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]	1235	if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
	1236	end
	1237	if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
	1238	if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
	1239	if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
	1240	if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
	1241	end
	1242	if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
	1243	pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
	1244	pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
	1245	pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
	1246	pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
	1247	pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
	1248	pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
	1249	pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
	1250	pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
	1251	pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
	1252	end
[11659]	1253
[13692]	1254	if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
	1255	md.thermal.stabilization=2;
[15767]	1256	md.masstransport.stabilization=1;
[13692]	1257	md.balancethickness.stabilization=1;
	1258	end
[15767]	1259	if isnumeric(md.masstransport.hydrostatic_adjustment)
	1260	if md.masstransport.hydrostatic_adjustment==269,
	1261	md.masstransport.hydrostatic_adjustment='Incremental';
[13692]	1262	else
[15767]	1263	md.masstransport.hydrostatic_adjustment='Absolute';
[13692]	1264	end
	1265	end
[8952]	1266
[13692]	1267	%New fields
[19124]	1268	if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1269	md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
	1270	md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
	1271	end
[19124]	1272	if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
[13692]	1273	md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
	1274	md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
	1275	end
	1276	if ~isfield(structmd,'diagnostic_ref');
[15771]	1277	md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]	1278	end
[14529]	1279	if ~isfield(structmd,'loadingforce');
[15771]	1280	md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]	1281	end
[15768]	1282
	1283	%2013 August 9
	1284	if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
	1285	disp('Recovering old prognostic class');
	1286	md.masstransport=masstransport(structmd.prognostic);
	1287	end
[15771]	1288	%2013 August 9
[15775]	1289	if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') \|\| isa(structmd.diagnostic,'stressbalance')),
[15771]	1290	disp('Recovering old diagnostic class');
[15775]	1291	md.stressbalance=stressbalance(structmd.diagnostic);
[15771]	1292	end
[19642]	1293	%2014 January 9th
[21148]	1294	if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
[19642]	1295	disp('Recovering old surfaceforcings class');
	1296	mass_balance=structmd.surfaceforcings.mass_balance;
	1297	md.smb=SMB();
	1298	md.smb.mass_balance=mass_balance;
	1299	end
	1300	%2015 September 10
[21148]	1301	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
[19642]	1302	disp('Recovering old SMB class');
	1303	md.smb=SMBforcing(structmd.surfaceforcings);
	1304	end
[21148]	1305	if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
	1306	disp('Recovering old SMBhenning class');
	1307	md.smb=SMBhenning(structmd.surfaceforcings);
	1308	end
[25119]	1309	if isfield(structmd,'slr'),
	1310	disp('Recovering old slr class');
[25828]	1311	if isfield(structmd.slr,'sealevel'),
	1312	md.solidearth.sealevel=structmd.slr.sealevel;
	1313	end
[25119]	1314	md.solidearth.planetradius=structmd.slr.planetradius;
	1315	md.solidearth.requested_outputs=structmd.slr.requested_outputs;
	1316	md.solidearth.transitions=structmd.slr.transitions;
	1317
	1318	md.solidearth.transitions=structmd.slr.transitions;
	1319	md.solidearth.settings.reltol=structmd.slr.reltol;
	1320	md.solidearth.settings.abstol=structmd.slr.abstol;
	1321	md.solidearth.settings.maxiter=structmd.slr.maxiter;
	1322	md.solidearth.settings.rigid=structmd.slr.rigid;
	1323	md.solidearth.settings.elastic=structmd.slr.elastic;
	1324	md.solidearth.settings.rotation=structmd.slr.rotation;
	1325	md.solidearth.settings.runfrequency=structmd.slr.geodetic_run_frequency;
	1326	md.solidearth.settings.computesealevelchange=structmd.slr.geodetic;
	1327	md.solidearth.settings.degacc=structmd.slr.degacc;
	1328	md.solidearth.settings.horiz=structmd.slr.horiz;
	1329	md.solidearth.settings.ocean_area_scaling=structmd.slr.ocean_area_scaling;
	1330
	1331	md.solidearth.surfaceload.icethicknesschange=structmd.slr.deltathickness;
	1332	md.solidearth.surfaceload.waterheightchange=structmd.slr.hydro_rate;
	1333
[25162]	1334	md.solidearth.lovenumbers.h=structmd.slr.love_h;
	1335	md.solidearth.lovenumbers.k=structmd.slr.love_k;
	1336	md.solidearth.lovenumbers.l=structmd.slr.love_l;
	1337	md.solidearth.lovenumbers.th=structmd.slr.tide_love_h;
	1338	md.solidearth.lovenumbers.tk=structmd.slr.tide_love_k;
	1339	md.solidearth.lovenumbers.tk2secular=structmd.slr.fluid_love;
[25119]	1340
	1341	md.solidearth.rotational.equatorialmoi=structmd.slr.equatorial_moi;
	1342	md.solidearth.rotational.polarmoi=structmd.slr.polar_moi;
	1343	md.solidearth.rotational.angularvelocity=structmd.slr.angular_velocity;
	1344	end
[13692]	1345	end% }}}
[17483]	1346	function md = tetras(md,varargin) % {{{
	1347	%TETRAS - split 3d prismatic mesh into 3 tetrahedrons
	1348	%
	1349	% Usage:
	1350	% md=tetra(md)
	1351
	1352	if ~isa(md.mesh,'mesh3dprisms')
	1353	error('mesh is not a 3d prismatic mesh');
	1354	end
	1355
	1356	%Initialize tetra mesh
	1357	md.mesh=mesh3dtetras(md.mesh);
	1358
[17754]	1359	%Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
	1360	steiner = 0;
	1361	nbv = md.mesh.numberofvertices;
	1362	nbt = 3*md.mesh.numberofelements;
	1363	elements = zeros(nbt,4);
	1364	for i=1:md.mesh.numberofelements
	1365	v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
	1366	v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
	1367	if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1368	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1369	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1370	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1371	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1372	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1373	elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
	1374	elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
	1375	elements(end+1,:) = [v2 v3 v5 v7];
	1376	elements(end+1,:) = [v3 v5 v6 v7];
	1377	elements(end+1,:) = [v1 v3 v6 v7];
	1378	elements(end+1,:) = [v1 v4 v6 v7];
	1379	elements(end+1,:) = [v4 v5 v6 v7];
	1380	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1381	elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
	1382	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1383	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1384	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1385	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1386	elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
	1387	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1388	elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1389	elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
	1390	elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
	1391	elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]	1392	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]	1393	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1394	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1395	elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
	1396	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1397	elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
	1398	elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
	1399	elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
	1400	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1401	elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
	1402	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1403	elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
	1404	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
	1405	elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
	1406	elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
	1407	elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
	1408	elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
	1409	steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
	1410	md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
	1411	md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
	1412	md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
	1413	elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
	1414	elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
	1415	elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
	1416	elements(end+1,:) = [v2 v5 v6 v7];
	1417	elements(end+1,:) = [v2 v3 v6 v7];
	1418	elements(end+1,:) = [v3 v4 v6 v7];
	1419	elements(end+1,:) = [v1 v3 v4 v7];
	1420	elements(end+1,:) = [v4 v5 v6 v7];
	1421	else
	1422	error('Case not supported'); %not supposed to happen!
	1423	end
[17774]	1424	%Reorder elements to make sure they are direct
	1425	for j=1:3
	1426	element = elements(3*(i-1)+j,:);
	1427	matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
	1428	if det(matrix)>0,
	1429	elements(3*(i-1)+j,1)=element(2);
	1430	elements(3*(i-1)+j,2)=element(1);
	1431	end
	1432	end
[17754]	1433	end
	1434	%%Split in 3 tetras
	1435	%subelement1 = [1 2 3 5];
	1436	%subelement2 = [4 6 5 1];
	1437	%subelement3 = [5 6 3 1];
	1438	%elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]	1439	if steiner==0,
	1440	disp('No Steiner point required to split prismatic mesh into tets');
	1441	else
	1442	disp([num2str(steiner) ' Steiner points had to be included'])
	1443	error('Steiner point not supported yet');
	1444	end
[17754]	1445
[17483]	1446	pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
	1447
	1448	md.mesh.elements=elements;
	1449	md.mesh.numberofelements=size(elements,1);
	1450
	1451	%p and q (same deal, except for element that are on the bedrock: )
[17774]	1452	if ~isnan(md.friction.p),
	1453	md.friction.p=md.friction.p(pos_elements);
	1454	md.friction.q=md.friction.q(pos_elements);
	1455	end
[17483]	1456
	1457	%elementstype
	1458	if ~isnan(md.flowequation.element_equation)
	1459	oldelements_type=md.flowequation.element_equation;
	1460	md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
	1461	end
	1462
	1463	%connectivity
	1464	md.mesh.elementconnectivity=NaN;
	1465
	1466	%materials
[17774]	1467	if ~isnan(md.materials.rheology_n),
	1468	md.materials.rheology_n=md.materials.rheology_n(pos_elements);
	1469	end
[17483]	1470
	1471	%increase connectivity if less than 25:
	1472	if md.mesh.average_vertex_connectivity<=25,
	1473	md.mesh.average_vertex_connectivity=100;
	1474	end
	1475	end % }}}
[19040]	1476	function disp(self) % {{{
	1477	disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
	1478	disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
	1479	disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
	1480	disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
[19527]	1481	disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
[19040]	1482	disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
	1483	disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
	1484	disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
	1485	disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
	1486	disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
	1487	disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
	1488	disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
	1489	disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
[25118]	1490	disp(sprintf('%19s: %-22s -- %s','solidearth' ,['[1x1 ' class(self.solidearth) ']'],'solidearth inputs and settings'));
[24469]	1491	disp(sprintf('%19s: %-22s -- %s','dsl' ,['[1x1 ' class(self.dsl) ']'],'dynamic sea-level '));
[19040]	1492	disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
	1493	disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
	1494	disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
	1495	disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
[25988]	1496	disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of CPUs...)'));
[19040]	1497	disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
	1498	disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
	1499	disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
	1500	disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
	1501	disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
	1502	disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
	1503	disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
[25988]	1504	disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parHwoameters for transient solution'));
[21544]	1505	disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
[19040]	1506	disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
[23652]	1507	disp(sprintf('%19s: %-22s -- %s','frontalforcings' ,['[1x1 ' class(self.frontalforcings) ']'],'parameters for frontalforcings'));
[22955]	1508	disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
[21260]	1509	disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
[22955]	1510	disp(sprintf('%19s: %-22s -- %s','love' ,['[1x1 ' class(self.love) ']'],'parameters for love solution'));
[25996]	1511	disp(sprintf('%19s: %-22s -- %s','sampling' ,['[1x1 ' class(self.sampling) ']'],'parameters for stochastic sampler'));
[19040]	1512	disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
	1513	disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
[25988]	1514	disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'Dakota properties'));
[21674]	1515	disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
[19040]	1516	disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
	1517	disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
	1518	disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
	1519	disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
[13692]	1520	end % }}}
[19040]	1521	function memory(self) % {{{
[15106]	1522
[14611]	1523	disp(sprintf('\nMemory imprint:\n'));
[14307]	1524
[14603]	1525	fields=properties('model');
	1526	mem=0;
[15106]	1527
[14603]	1528	for i=1:length(fields),
[19040]	1529	field=self.(fields{i});
[14603]	1530	s=whos('field');
	1531	mem=mem+s.bytes/1e6;
[14611]	1532	disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]	1533	end
[14603]	1534	disp(sprintf('%19s--%10s','--------------','--------------'));
	1535	disp(sprintf('%19s: %g Mb','Total',mem));
[14307]	1536	end % }}}
[19040]	1537	function netcdf(self,filename) % {{{
[14603]	1538	%NETCDF - save model as netcdf
	1539	%
	1540	% Usage:
	1541	% netcdf(md,filename)
	1542	%
	1543	% Example:
	1544	% netcdf(md,'model.nc');
	1545
	1546	disp('Saving model as NetCDF');
	1547	%1. Create NetCDF file
	1548	ncid=netcdf.create(filename,'CLOBBER');
	1549	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[19040]	1550	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
[14603]	1551	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
	1552	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
	1553
[14611]	1554	%Preallocate variable id, needed to write variables in netcdf file
[14631]	1555	var_id=zeros(1000,1);%preallocate
[14609]	1556
	1557	for step=1:2,
	1558	counter=0;
[19040]	1559	[var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
[14609]	1560	if step==1, netcdf.endDef(ncid); end
[14603]	1561	end
[14611]	1562
[14631]	1563	if counter>1000,
	1564	warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]	1565	end
	1566
	1567	netcdf.close(ncid)
[14603]	1568	end % }}}
[19040]	1569	function xylim(self) % {{{
[14405]	1570
[19040]	1571	xlim([min(self.mesh.x) max(self.mesh.x)]);
	1572	ylim([min(self.mesh.y) max(self.mesh.y)])
[14405]	1573	end % }}}
[15316]	1574	function md=upload(md) % {{{
	1575	%the goal of this routine is to upload the model onto a server, and to empty it.
	1576	%So first, save the model with a unique name and upload the file to the server:
	1577	random_part=fix(rand(1)*10000);
	1578	id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
	1579	eval(['save ' id ' md']);
	1580
	1581	%Now, upload the file:
	1582	issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
	1583
	1584	%Now, empty this model of everything except settings, and record name of file we just uploaded!
	1585	settings_back=md.settings;
	1586	md=model();
	1587	md.settings=settings_back;
	1588	md.settings.upload_filename=id;
	1589
	1590	%get locally rid of file that was uploaded
	1591	eval(['delete ' id]);
	1592
	1593	end % }}}
	1594	function md=download(md) % {{{
[15643]	1595
[15316]	1596	%the goal of this routine is to download the internals of the current model from a server, because
	1597	%this model is empty, except for the settings which tell us where to go and find this model!
[15643]	1598
[15316]	1599	%Download the file:
	1600	issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
	1601
	1602	name=md.settings.upload_filename;
	1603
	1604	%Now, load this model:
	1605	md=loadmodel(md.settings.upload_filename);
	1606
	1607	%get locally rid of file that was downloaded
	1608	eval(['delete ' name]);
	1609
	1610	end % }}}
[22955]	1611	function savemodeljs(md,modelname,websiteroot,varargin) % {{{
	1612
[19879]	1613	%the goal of this routine is to save the model as a javascript array that can be included in any html
	1614	%file:
	1615
[22955]	1616	options=pairoptions(varargin{:});
	1617	optimization=getfieldvalue(options,'optimize',0);
	1618
	1619
[19879]	1620	%disp:
[19894]	1621	disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
[19879]	1622
	1623	%open file for writing and declare the model:
[19894]	1624	fid=fopen([websiteroot '/js/' modelname '.js'],'w');
[19879]	1625	fprintf(fid,'var %s=new model();\n',modelname);
	1626
	1627	%now go through all the classes and fwrite all the corresponding fields:
	1628
	1629	fields=properties('model');
	1630	for i=1:length(fields),
	1631	field=fields{i};
	1632
	1633	%Some properties do not need to be saved
[19894]	1634	if ismember(field,{'results','cluster' }),
[19879]	1635	continue;
	1636	end
	1637
[22955]	1638	%some optimization:
	1639	if optimization==1,
	1640	%optimize for plotting only:
	1641	if ~ismember(field,{'geometry','mesh','mask'}),
	1642	continue;
	1643	end
	1644	end
	1645
[19879]	1646	%Check that current field is an object
	1647	if ~isobject(md.(field))
	1648	error(['field ''' char(field) ''' is not an object']);
	1649	end
	1650
	1651	%savemodeljs for current object
	1652	%disp(['javascript saving ' field '...']);
	1653	savemodeljs(md.(field),fid,modelname);
	1654	end
	1655
	1656	%done, close file:
	1657	fclose(fid);
	1658	end
[13692]	1659	end
[8926]	1660	end

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